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Chen H, Fang Y, Dai S, Jiang K, Shen L, Zhao J, Huang K, Zhou X, Ding K. Characterization and proteomic analysis of plasma-derived small extracellular vesicles in locally advanced rectal cancer patients. Cell Oncol (Dordr) 2024; 47:1995-2009. [PMID: 39162991 DOI: 10.1007/s13402-024-00983-1] [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] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Neoadjuvant chemoradiotherapy (nCRT) stands as a pivotal therapeutic approach for locally advanced rectal cancer (LARC), yet the absence of a reliable biomarker to forecast its efficacy remains a challenge. Thus, this study aimed to assess whether the proteomic compositions of small extracellular vesicles (sEVs) might offer predictive insights into nCRT response among patients with LARC, while also delving into the proteomic alterations within sEVs post nCRT. METHODS Plasma samples were obtained from LARC patients both pre- and post-nCRT. Plasma-derived sEVs were isolated utilizing the TIO2-based method, followed by LC-MS/MS-based proteomic analysis. Subsequently, pathway enrichment analysis was performed to the Differentially Expressed Proteins (DEPs). Additionally, ROC curves were generated to evaluate the predictive potential of sEV proteins in determining nCRT response. Public databases were interrogated to identify sEV protein-associated genes that are correlated with the response to nCRT in LARC. RESULTS A total of 16 patients were enrolled. Among them, 8 patients achieved a pathological complete response (good responders, GR), while the remaining 8 did not achieve a complete response (poor responders, PR). Our analysis of pretreatment plasma-derived sEVs revealed 67 significantly up-regulated DEPs and 9 significantly down-regulated DEPs. Notably, PROC (AUC: 0.922), F7 (AUC: 0.953) and AZU1 (AUC: 0.906) demonstrated high AUC values and significant differences (P value < 0.05) in discriminating between GR and PR patients. Furthermore, a signature consisting of 5 sEV protein-associated genes (S100A6, ENO1, MIF, PRDX6 and MYL6) was capable of predicting the response to nCRT, yielding an AUC of 0.621(95% CI: 0.454-0.788). Besides, this 5-sEV protein-associated gene signature enabled stratification of patients into low- and high-risk group, with the low-risk group demonstrating a longer overall survival in the testing set (P = 0.048). Moreover, our investigation identified 11 significantly up-regulated DEPs and 31 significantly down-regulated DEPs when comparing pre- and post-nCRT proteomic profiles. GO analysis unveiled enrichment in the regulation of phospholipase A2 activity. CONCLUSIONS Differential expression of sEV proteins distinguishes between GR and PR patients and holds promise as predictive markers for nCRT response and prognosis in patients with LARC. Furthermore, our findings highlight substantial alterations in sEV protein composition following nCRT.
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Affiliation(s)
- Haiyan Chen
- Department of Radiation Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China.
- Anhui Hospital of the Second Affiliated Hospital, Zhejiang University School of Medicine, Bengbu, 233000, China.
| | - Yimin Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siqi Dai
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kai Jiang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li Shen
- Department of Radiation Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Zhao
- Department of Radiation Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China
- Anhui Hospital of the Second Affiliated Hospital, Zhejiang University School of Medicine, Bengbu, 233000, China
| | - Kanghua Huang
- Department of Radiation Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaofeng Zhou
- Department of Radiation Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for CANCER, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China.
- Department of Colorectal Surgery (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Ghazi B, Harmak Z, Rghioui M, Kone AS, El Ghanmi A, Badou A. Decoding the secret of extracellular vesicles in the immune tumor microenvironment of the glioblastoma: on the border of kingdoms. Front Immunol 2024; 15:1423232. [PMID: 39267734 PMCID: PMC11390556 DOI: 10.3389/fimmu.2024.1423232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024] Open
Abstract
Over the last decades, extracellular vesicles (EVs) have become increasingly popular for their roles in various pathologies, including cancer and neurological and immunological disorders. EVs have been considered for a long time as a means for normal cells to get rid of molecules it no longer needs. It is now well established that EVs play their biological roles also following uptake or by the interaction of EV surface proteins with cellular receptors and membranes. In this review, we summarize the current status of EV production and secretion in glioblastoma, the most aggressive type of glioma associated with high mortality. The main purpose is to shed light on the EVs as a universal mediator of interkingdom and intrakingdom communication in the context of tumor microenvironment heterogeneity. We focus on the immunomodulatory EV functions in glioblastoma-immune cross-talk to enhance immune escape and reprogram tumor-infiltrating immune cells. We critically examine the evidence that GBM-, immune cell-, and microbiome-derived EVs impact local tumor microenvironment and host immune responses, and can enter the circulatory system to disseminate and drive premetastatic niche formation in distant organs. Taking into account the current state of the art in intratumoral microbiome studies, we discuss the emerging role of bacterial EV in glioblastoma and its response to current and future therapies including immunotherapies.
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Affiliation(s)
- Bouchra Ghazi
- Immunopathology-Immunotherapy-Immunomonitoring Laboratory, Faculty of Medicine, Mohammed VI University of Sciences and Health, Casablanca, Morocco
- Mohammed VI International University Hospital, Bouskoura, Morocco
| | - Zakia Harmak
- Immuno-genetics and Human Pathology Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Mounir Rghioui
- Immunopathology-Immunotherapy-Immunomonitoring Laboratory, Faculty of Medicine, Mohammed VI University of Sciences and Health, Casablanca, Morocco
- Mohammed VI International University Hospital, Bouskoura, Morocco
| | - Abdou-Samad Kone
- Immuno-genetics and Human Pathology Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Adil El Ghanmi
- Immunopathology-Immunotherapy-Immunomonitoring Laboratory, Faculty of Medicine, Mohammed VI University of Sciences and Health, Casablanca, Morocco
- Mohammed VI International University Hospital, Bouskoura, Morocco
| | - Abdallah Badou
- Immuno-genetics and Human Pathology Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, Morocco
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Wang L, Li F, Wang L, Wu B, Du M, Xing H, Pan S. Exosomes Derived from Bone Marrow Mesenchymal Stem Cells Alleviate Rheumatoid Arthritis Symptoms via Shuttling Proteins. J Proteome Res 2024; 23:1298-1312. [PMID: 38500415 DOI: 10.1021/acs.jproteome.3c00697] [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: 03/20/2024]
Abstract
Our prior investigations have evidenced that bone marrow mesenchymal stem cell (BMSC) therapy can significantly improve the outcomes of rheumatoid arthritis (RA). This study aims to conduct a comprehensive analysis of the proteomics between BMSCs and BMSCs-Exos, and to further elucidate the potential therapeutic effect of BMSCs-Exos on RA, so as to establish a theoretical framework for the prevention and therapy of BMSCs-Exos on RA. The 4D label-free LC-MS/MS technique was used for comparative proteomic analysis of BMSCs and BMSCs-Exos. Collagen-induced arthritis (CIA) rat model was used to investigate the therapeutic effect of BMSCs-Exos on RA. Our results showed that some homology and differences were observed between BMSCs and BMSCs-Exos proteins, among which proteins highly enriched in BMSCs-Exos were related to extracellular matrix and extracellular adhesion. BMSCs-Exos can be taken up by chondrocytes, promoting cell proliferation and migration. In vivo results revealed that BMSCs-Exos significantly improved the clinical symptoms of RA, showing a certain repair effect on the injury of articular cartilage. In short, our study revealed, for the first time, that BMSCs-Exos possess remarkable efficacy in alleviating RA symptoms, probably through shuttling proteins related to cell adhesion and tissue repair ability in CIA rats, suggesting that BMSCs-Exos carrying expressed proteins may become a useful biomaterial for RA treatment.
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Affiliation(s)
- Lijun Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Fei Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Liting Wang
- Department of Rehabilitation, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250011, China
| | - Bingxing Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman ,Washington 99163, United States
| | - Hua Xing
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Shifeng Pan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
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Lee YJ, Chae S, Choi D. Monitoring of single extracellular vesicle heterogeneity in cancer progression and therapy. Front Oncol 2023; 13:1256585. [PMID: 37823055 PMCID: PMC10562638 DOI: 10.3389/fonc.2023.1256585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
Cancer cells actively release lipid bilayer extracellular vesicles (EVs) that affect their microenvironment, favoring their progression and response to extracellular stress. These EVs contain dynamically regulating molecular cargos (proteins and nucleic acids) selected from their parental cells, representing the active biological functionality for cancer progression. These EVs are heterogeneous according to their size and molecular composition and are usually defined based on their biogenetic mechanisms, such as exosomes and ectosomes. Recent single EV detection technologies, such as nano-flow cytometry, have revealed the dynamically regulated molecular diversity within bulk EVs, indicating complex EV heterogeneity beyond classical biogenetic-based EV subtypes. EVs can be changed by internal oncogenic transformation or external stress such as chemotherapy. Among the altered combinations of EV subtypes, only a specific set of EVs represents functional molecular cargo, enabling cancer progression and immune modulation in the tumor microenvironment through their altered targeting efficiency and specificity. This review covers the heterogeneity of EVs discovered by emerging single EV analysis technologies, which reveal the complex distribution of EVs affected by oncogenic transformation and chemotherapy. Encouragingly, these unique molecular signatures in individual EVs indicate the status of their parental cancer cells. Thus, precise molecular profiling of circulating single EVs would open new areas for in-depth monitoring of the cancer microenvironment and shed new light on non-invasive diagnostic approaches using liquid biopsy.
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Affiliation(s)
| | | | - Dongsic Choi
- Department of Biochemistry, College of Medicine, Soonchunhyang University, Cheonan, Chungcheongnam, Republic of Korea
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5
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Parra-Aguilar TJ, Sarmiento-López LG, Santana O, Olivares JE, Pascual-Morales E, Jiménez-Jiménez S, Quero-Hostos A, Palacios-Martínez J, Chávez-Martínez AI, Cárdenas L. TETRASPANIN 8-1 from Phaseolus vulgaris plays a key role during mutualistic interactions. FRONTIERS IN PLANT SCIENCE 2023; 14:1152493. [PMID: 37465390 PMCID: PMC10352089 DOI: 10.3389/fpls.2023.1152493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi and rhizobia form two of the most important plant-microbe associations for the assimilation of phosphorus (P) and nitrogen (N). Symbiont-derived signals are able to coordinate the infection process by triggering multiple responses in the plant root, such as calcium influxes and oscillations, increased reactive oxygen species (ROS), cytoskeletal rearrangements and altered gene expression. An examination was made of the role of tetraspanins, which are transmembrane proteins that self-organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking, and ROS generation. In plant cells, tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, plasmodesmata and hormonal regulation. Some plant tetraspanins, such as Arabidopsis thaliana TETRASPANIN 8 and TETRASPANIN 9 (AtTET8 and AtTET9) are associated with exosomes during inter-kingdom communication. In this study, a homolog of AtTET8, PvTET8-1, in common bean (Phaseolus vulgaris L. var. Negro Jamapa) was examined in roots during interactions with Rhizobium tropici and Rhizophagus irregularis. The promoter of PvTET8-1 contained several cis-acting regulatory DNA elements potentially related to mutualistic interactions, and PvTET8-1 was transcriptionally activated during AM fungal and rhizobial associations. Silencing it decreased the size and number of nodules, nitrogen fixation, and mycorrhizal arbuscule formation, whereas overexpressing it increased the size and number of nodules, and mycorrhizal arbuscule formation but decreased nitrogen fixation. PvTET8-1 appears to be an important element in both of these mutualistic interactions, perhaps through its interaction with NADPH oxidase and the generation of ROS during the infection processes.
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Affiliation(s)
- Thelma J. Parra-Aguilar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis G. Sarmiento-López
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Sinaloa-Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan Elías Olivares
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Pascual-Morales
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Saul Jiménez-Jiménez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Andrea Quero-Hostos
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Janet Palacios-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ana I. Chávez-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Ganesan H, Nandy SK, Banerjee A, Pathak S, Zhang H, Sun XF. RNA-Interference-Mediated miR-122-Based Gene Regulation in Colon Cancer, a Structural In Silico Analysis. Int J Mol Sci 2022; 23:ijms232315257. [PMID: 36499586 PMCID: PMC9739210 DOI: 10.3390/ijms232315257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The role of microRNA 122 (miR-122) in colorectal cancer (CRC) has not been widely investigated. In the current study, we aimed to identify the prominent gene and protein interactors of miR122 in CRC. Based on their binding affinity, these targets were chosen as candidate genes for the creation of miR122-mRNA duplexes. Following this, we examined the miRNA-mediated silencing mechanism using the gene-silencing complex protein Argonaute (AGO). Public databases, STRING, and GeneMANIA were utilized to identify major proteins and genes interacting with miR-122. DAVID, PANTHER, UniProt, FunRich, miRwalk, and KEGG were used for functional annotation, pathway enrichment, binding affinity analysis, and expression of genes in different stages of cancer. Three-dimensional duplexes of hub genes and miR-122 were created using the RNA composer, followed by molecular interaction analysis using molecular docking with the AGO protein. We analyzed, classified, and scrutinized 93 miR-122 interactors using various bioinformatic approaches. A total of 14 hub genes were categorized as major interactors of miR-122. The study confirmed the role of various experimentally documented miR-122 interactors such as MTDH (Q86UE4), AKT1 (P31749), PTPN1 (P18031), MYC (P01106), GSK3B (P49841), RHOA (P61586), and PIK3CG (P48736) and put forth several novel interactors, with AKT3 (Q9Y243), NCOR2 (Q9Y618), PIK3R2 (O00459), SMAD4 (P61586), and TGFBR1 (P36897). Double-stranded RNA duplexes of the strongest interactors were found to exhibit higher binding affinity with AGO. In conclusions, the study has explored the role of miR-122 in CRC and has identified a closely related group of genes influencing the prognosis of CRC in multiple ways. Further, these genes prove to be targets of gene silencing through RNA interference and might serve as effective therapeutic targets in understanding and treating CRC.
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Affiliation(s)
- Harsha Ganesan
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Suman K. Nandy
- BioNEST Bioincubator Facility, North-Eastern Hill University, Tura Campus, Chasingre, Tura 793022, Meghalaya, India
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Correspondence: (S.P.); (X.-F.S.)
| | - Hong Zhang
- School of Medical Sciences, Faculty of Medicine and Health, Orebro University, 702 81 Örebro, Sweden
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Correspondence: (S.P.); (X.-F.S.)
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Kong J, Ha D, Lee J, Kim I, Park M, Im SH, Shin K, Kim S. Network-based machine learning approach to predict immunotherapy response in cancer patients. Nat Commun 2022; 13:3703. [PMID: 35764641 PMCID: PMC9240063 DOI: 10.1038/s41467-022-31535-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have substantially improved the survival of cancer patients over the past several years. However, only a minority of patients respond to ICI treatment (~30% in solid tumors), and current ICI-response-associated biomarkers often fail to predict the ICI treatment response. Here, we present a machine learning (ML) framework that leverages network-based analyses to identify ICI treatment biomarkers (NetBio) that can make robust predictions. We curate more than 700 ICI-treated patient samples with clinical outcomes and transcriptomic data, and observe that NetBio-based predictions accurately predict ICI treatment responses in three different cancer types-melanoma, gastric cancer, and bladder cancer. Moreover, the NetBio-based prediction is superior to predictions based on other conventional ICI treatment biomarkers, such as ICI targets or tumor microenvironment-associated markers. This work presents a network-based method to effectively select immunotherapy-response-associated biomarkers that can make robust ML-based predictions for precision oncology.
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Affiliation(s)
- JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Juhun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, 37666, Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- ImmunoBiome Inc., Pohang, 37666, Korea
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea
| | - Kunyoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea.
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea.
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Chen Z, Yuan R, Hu S, Yuan W, Sun Z. Roles of the Exosomes Derived From Myeloid-Derived Suppressor Cells in Tumor Immunity and Cancer Progression. Front Immunol 2022; 13:817942. [PMID: 35154134 PMCID: PMC8829028 DOI: 10.3389/fimmu.2022.817942] [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: 11/18/2021] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Tumor immunity is involved in malignant tumor progression. Myeloid-derived suppressor cells (MDSCs) play an irreplaceable role in tumor immunity. MDSCs are composed of immature myeloid cells and exhibit obvious immunomodulatory functions. Exosomes released by MDSCs (MDSCs-Exos) have similar effects to parental MDSCs in regulating tumor immunity. In this review, we provided a comprehensive description of the characteristics, functions and mechanisms of exosomes. We analyzed the immunosuppressive, angiogenesis and metastatic effects of MDSCs-Exos in different tumors through multiple perspectives. Immunotherapy targeting MDSCs-Exos has demonstrated great potential in cancers and non-cancerous diseases.
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Affiliation(s)
- Zhuang Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rui Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shengyun Hu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Park J, Kim NE, Yoon H, Shin CM, Kim N, Lee DH, Park JY, Choi CH, Kim JG, Kim YK, Shin TS, Yang J, Park YS. Fecal Microbiota and Gut Microbe-Derived Extracellular Vesicles in Colorectal Cancer. Front Oncol 2021; 11:650026. [PMID: 34595105 PMCID: PMC8477046 DOI: 10.3389/fonc.2021.650026] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022] Open
Abstract
The human microbiota comprises trillions of microbes, and the relationship between cancer and microbiota is very complex. The impact of fecal microbiota alterations on colorectal cancer (CRC) pathogenesis is emerging. This study analyzed changes in the microbial composition in CRC subjects with both fecal microbiota and gut microbe-derived extracellular vesicles (EVs). From August 2017 to August 2018, 70 CRC patients and 158 control subjects were enrolled in the study. Metagenomic profiling of fecal microbiota and gut microbe-derived EVs in stool was performed using 16S ribosomal DNA sequencing. Relative abundance, evenness, and diversity in both the gut microbiota and gut microbe-derived EVs were analyzed. Additionally, microbial composition changes according to the stage and location of CRC were analyzed. Microbial composition was significantly changed in CRC subjects compared to control subjects, with evenness and diversity significantly lower in the fecal microbiota of CRC subjects. Gut microbe-derived EVs of stool demonstrated significant differences in the microbial composition, evenness, and diversity in CRC subjects compared to the control subjects. Additionally, microbial composition, evenness, and diversity significantly changed in late CRC subjects compared to early CRC subjects with both fecal microbiota and gut microbe-derived EVs. Alistipes-derived EVs could be novel biomarkers for diagnosing CRC and predicting CRC stages. Ruminococcus 2-derived EVs significantly decreased in distal CRC subjects than in proximal CRC subjects. Gut microbe-derived EVs in CRC had a distinct microbial composition compared to the controls. Profiling of microbe-derived EVs may offer a novel biomarker for detecting and predicting CRC prognosis.
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Affiliation(s)
- Jihye Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam-Eun Kim
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Hyuk Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jae Yong Park
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Chang Hwan Choi
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Jae Gyu Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Yoon-Keun Kim
- R&D Center, Institute of MD Healthcare Inc., Seoul, South Korea
| | - Tae-Seop Shin
- R&D Center, Institute of MD Healthcare Inc., Seoul, South Korea
| | - Jinho Yang
- R&D Center, Institute of MD Healthcare Inc., Seoul, South Korea
| | - Young Soo Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
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10
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Gurunathan S, Kang MH, Qasim M, Khan K, Kim JH. Biogenesis, Membrane Trafficking, Functions, and Next Generation Nanotherapeutics Medicine of Extracellular Vesicles. Int J Nanomedicine 2021; 16:3357-3383. [PMID: 34040369 PMCID: PMC8140893 DOI: 10.2147/ijn.s310357] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/25/2021] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of membrane-limited vesicles and multi-signal messengers loaded with biomolecules. Exosomes and ectosomes are two different types of EVs generated by all cell types. Their formation depends on local microdomains assembled in endocytic membranes for exosomes and in the plasma membrane for ectosomes. Further, EV release is a fundamental process required for intercellular communication in both normal physiology and pathological conditions to transmit/exchange bioactive molecules to recipient cells and the extracellular environment. The unique structure and composition of EVs enable them to serve as natural nanocarriers, and their physicochemical properties and biological functions can be used to develop next-generation nano and precision medicine. Knowledge of the cellular processes that govern EVs biology and membrane trafficking is essential for their clinical applications. However, in this rapidly expanding field, much remains unknown regarding EV origin, biogenesis, cargo sorting, and secretion, as well as EV-based theranostic platform generation. Hence, we present a comprehensive overview of the recent advances in biogenesis, membrane trafficking, and functions of EVs, highlighting the impact of nanoparticles and oxidative stress on EVs biogenesis and release and finally emphasizing the role of EVs as nanotherapeutic agents.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Min-Hee Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Muhammad Qasim
- Center of Bioengineering and Nanomedicine, Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Khalid Khan
- Science and Technology KPK, Peshawar, Pakistan
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
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11
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The Mystery of Red Blood Cells Extracellular Vesicles in Sleep Apnea with Metabolic Dysfunction. Int J Mol Sci 2021; 22:ijms22094301. [PMID: 33919065 PMCID: PMC8122484 DOI: 10.3390/ijms22094301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Sleep is very important for overall health and quality of life, while sleep disorder has been associated with several human diseases, namely cardiovascular, metabolic, cognitive, and cancer-related alterations. Obstructive sleep apnea (OSA) is the most common respiratory sleep-disordered breathing, which is caused by the recurrent collapse of the upper airway during sleep. OSA has emerged as a major public health problem and increasing evidence suggests that untreated OSA can lead to the development of various diseases including neurodegenerative diseases. In addition, OSA may lead to decreased blood oxygenation and fragmentation of the sleep cycle. The formation of free radicals or reactive oxygen species (ROS) can emerge and react with nitric oxide (NO) to produce peroxynitrite, thereby diminishing the bioavailability of NO. Hypoxia, the hallmark of OSA, refers to a decline of tissue oxygen saturation and affects several types of cells, playing cell-to-cell communication a vital role in the outcome of this interplay. Red blood cells (RBCs) are considered transporters of oxygen and nutrients to the tissues, and these RBCs are important interorgan communication systems with additional functions, including participation in the control of systemic NO metabolism, redox regulation, blood rheology, and viscosity. RBCs have been shown to induce endothelial dysfunction and increase cardiac injury. The mechanistic links between changes of RBC functional properties and cardiovascular are largely unknown. Extracellular vesicles (EVs) are secreted by most cell types and released in biological fluids both under physiological and pathological conditions. EVs are involved in intercellular communication by transferring complex cargoes including proteins, lipids, and nucleic acids from donor cells to recipient cells. Advancing our knowledge about mechanisms of RBC-EVs formation and their pathophysiological relevance may help to shed light on circulating EVs and to translate their application to clinical practice. We will focus on the potential use of RBC-EVs as valuable diagnostic and prognostic biomarkers and state-specific cargoes, and possibilities as therapeutic vehicles for drug and gene delivery. The use of RBC-EVs as a precision medicine for the diagnosis and treatment of the patient with sleep disorder will improve the prognosis and the quality of life in patients with cardiovascular disease (CVD).
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12
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Martínez‐Greene JA, Hernández‐Ortega K, Quiroz‐Baez R, Resendis‐Antonio O, Pichardo‐Casas I, Sinclair DA, Budnik B, Hidalgo‐Miranda A, Uribe‐Querol E, Ramos‐Godínez MDP, Martínez‐Martínez E. Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer-based precipitation and size exclusion chromatography. J Extracell Vesicles 2021; 10:e12087. [PMID: 33936570 PMCID: PMC8077108 DOI: 10.1002/jev2.12087] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
The molecular characterization of extracellular vesicles (EVs) has revealed a great heterogeneity in their composition at a cellular and tissue level. Current isolation methods fail to efficiently separate EV subtypes for proteomic and functional analysis. The aim of this study was to develop a reproducible and scalable isolation workflow to increase the yield and purity of EV preparations. Through a combination of polymer-based precipitation and size exclusion chromatography (Pre-SEC), we analyzed two subsets of EVs based on their CD9, CD63 and CD81 content and elution time. EVs were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blot assays. To evaluate differences in protein composition between the early- and late-eluting EV fractions, we performed a quantitative proteomic analysis of MDA-MB-468-derived EVs. We identified 286 exclusive proteins in early-eluting fractions and 148 proteins with a differential concentration between early- and late-eluting fractions. A density gradient analysis further revealed EV heterogeneity within each analyzed subgroup. Through a systems biology approach, we found significant interactions among proteins contained in the EVs which suggest the existence of functional clusters related to specific biological processes. The workflow presented here allows the study of EV subtypes within a single cell type and contributes to standardizing the EV isolation for functional studies.
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Affiliation(s)
- Juan A. Martínez‐Greene
- Laboratory of Cell Communication & Extracellular VesiclesInstituto Nacional de Medicina GenómicaMexico CityMexico
| | - Karina Hernández‐Ortega
- Departamento de BiologíaFacultad de QuímicaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Ricardo Quiroz‐Baez
- Departamento de Investigación BásicaInstituto Nacional de GeriatríaMexico CityMexico
| | - Osbaldo Resendis‐Antonio
- Human Systems Biology LaboratoryInstituto Nacional de Medicina GenómicaMexico CityMexico
- Coordinación de la Investigación Científica‐Red de Apoyo a la InvestigaciónUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Israel Pichardo‐Casas
- Department of GeneticsPaul F. Glenn Labs for the Biology of AgingHarvard Medical SchoolBostonMassachusettsUSA
| | - David A. Sinclair
- Department of GeneticsPaul F. Glenn Labs for the Biology of AgingHarvard Medical SchoolBostonMassachusettsUSA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource LaboratoryDivision of ScienceHarvard UniversityCambridgeMassachusettsUSA
| | | | - Eileen Uribe‐Querol
- Laboratorio de Biología del DesarrolloDivisión de Estudios de Posgrado e InvestigaciónFacultad de OdontologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | | | - Eduardo Martínez‐Martínez
- Laboratory of Cell Communication & Extracellular VesiclesInstituto Nacional de Medicina GenómicaMexico CityMexico
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13
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Gurunathan S, Kang MH, Kim JH. A Comprehensive Review on Factors Influences Biogenesis, Functions, Therapeutic and Clinical Implications of Exosomes. Int J Nanomedicine 2021; 16:1281-1312. [PMID: 33628021 PMCID: PMC7898217 DOI: 10.2147/ijn.s291956] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/16/2021] [Indexed: 12/12/2022] Open
Abstract
Exosomes are nanoscale-sized membrane vesicles secreted by almost all cell types into the extracellular environment upon fusion of multivesicular bodies and plasma membrane. Biogenesis of exosomes is a protein quality control mechanism, and once released, exosomes transmit signals to other cells. The applications of exosomes have increased immensely in biomedical fields owing to their cell-specific cargos that facilitate intercellular communications with neighboring cells through the transfer of biologically active compounds. The diverse constituents of exosomes reflect their cell of origin and their detection in biological fluids represents a diagnostic marker for various diseases. Exosome research is expanding rapidly due to the potential for clinical application to therapeutics and diagnosis. However, several aspects of exosome biology remain elusive. To discover the use of exosomes in the biomedical applications, we must better understand the basic molecular mechanisms underlying their biogenesis and function. In this comprehensive review, we describe factors involved in exosomes biogenesis and the role of exosomes in intercellular signaling and cell-cell communications, immune responses, cellular homeostasis, autophagy, and infectious diseases. In addition, we discuss the role of exosomes as diagnostic markers, and their therapeutic and clinical implications. Furthermore, we addressed the challenges and outstanding developments in exosome research, and discuss future perspectives.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Min-Hee Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
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14
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Kong J, Lee H, Kim D, Han SK, Ha D, Shin K, Kim S. Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients. Nat Commun 2020; 11:5485. [PMID: 33127883 PMCID: PMC7599252 DOI: 10.1038/s41467-020-19313-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer patient classification using predictive biomarkers for anti-cancer drug responses is essential for improving therapeutic outcomes. However, current machine-learning-based predictions of drug response often fail to identify robust translational biomarkers from preclinical models. Here, we present a machine-learning framework to identify robust drug biomarkers by taking advantage of network-based analyses using pharmacogenomic data derived from three-dimensional organoid culture models. The biomarkers identified by our approach accurately predict the drug responses of 114 colorectal cancer patients treated with 5-fluorouracil and 77 bladder cancer patients treated with cisplatin. We further confirm our biomarkers using external transcriptomic datasets of drug-sensitive and -resistant isogenic cancer cell lines. Finally, concordance analysis between the transcriptomic biomarkers and independent somatic mutation-based biomarkers further validate our method. This work presents a method to predict cancer patient drug responses using pharmacogenomic data derived from organoid models by combining the application of gene modules and network-based approaches.
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Affiliation(s)
- JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Heetak Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Kunyoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea.
- Institute of Convergence Science, Yonsei University, Seoul, 120-749, Korea.
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea.
- Institute of Convergence Science, Yonsei University, Seoul, 120-749, Korea.
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15
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Choi D, Go G, Kim DK, Lee J, Park SM, Di Vizio D, Gho YS. Quantitative proteomic analysis of trypsin-treated extracellular vesicles to identify the real-vesicular proteins. J Extracell Vesicles 2020; 9:1757209. [PMID: 32489530 PMCID: PMC7241501 DOI: 10.1080/20013078.2020.1757209] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/23/2020] [Accepted: 04/10/2020] [Indexed: 01/06/2023] Open
Abstract
Extracellular vesicles (EVs) are nano-sized vesicles surrounded by a lipid bilayer and released into the extracellular milieu by most of cells. Although various EV isolation methods have been established, most of the current methods isolate EVs with contaminated non-vesicular proteins. By applying the label-free quantitative proteomic analyses of human colon cancer cell SW480-derived EVs, we identified trypsin-sensitive and trypsin-resistant vesicular proteins. Further systems biology and protein-protein interaction network analyses based on their cellular localization, we classified the trypsin-sensitive and trypsin-resistant vesicular proteins into two subgroups: 363 candidate real-vesicular proteins and 151 contaminated non-vesicular proteins. Moreover, the protein interaction network analyses showed that candidate real-vesicular proteins are mainly derived from plasma membrane (46.8%), cytosol (36.6%), cytoskeleton (8.0%) and extracellular region (2.5%). On the other hand, most of the contaminated non-vesicular proteins derived from nucleus, Golgi apparatus, endoplasmic reticulum and mitochondria. In addition, ribosomal protein complexes and T-complex proteins were classified as the contaminated non-vesicular proteins. Taken together, our trypsin-digested proteomic approach on EVs is an important advance to identify the real-vesicular proteins that could help to understand EV biogenesis and protein cargo-sorting mechanism during EV release, to identify more reliable EV diagnostic marker proteins, and to decode pathophysiological roles of EVs.
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Affiliation(s)
- Dongsic Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Research Institute of the McGill University Health Centre, Glen Site, McGill University, Montreal, Canada
| | - Gyeongyun Go
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dae-Kyum Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jaewook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seon-Min Park
- Pohang Center for Evaluation of Biomaterials, Pohang, Republic of Korea
| | - Dolores Di Vizio
- Department of Surgery, Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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16
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Aguilar-Rojas A, Castellanos-Castro S, Matondo M, Gianetto QG, Varet H, Sismeiro O, Legendre R, Fernandes J, Hardy D, Coppée JY, Olivo-Marin JC, Guillen N. Insights into amebiasis using a human 3D-intestinal model. Cell Microbiol 2020; 22:e13203. [PMID: 32175652 DOI: 10.1111/cmi.13203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/27/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022]
Abstract
Entamoeba histolytica is the causative agent of amebiasis, an infectious disease targeting the intestine and the liver in humans. Two types of intestinal infection are caused by this parasite: silent infection, which occurs in the majority of cases, and invasive disease, which affects 10% of infected persons. To understand the intestinal pathogenic process, several in vitro models, such as cell cultures, human tissue explants or human intestine xenografts in mice, have been employed. Nevertheless, our knowledge on the early steps of amebic intestinal infection and the molecules involved during human-parasite interaction is scarce, in part due to limitations in the experimental settings. In the present work, we took advantage of tissue engineering approaches to build a three-dimensional (3D)-intestinal model that is able to replicate the general characteristics of the human colon. This system consists of an epithelial layer that develops tight and adherens junctions, a mucus layer and a lamina propria-like compartment made up of collagen containing macrophages and fibroblast. By means of microscopy imaging, omics assays and the evaluation of immune responses, we show a very dynamic interaction between E. histolytica and the 3D-intestinal model. Our data highlight the importance of several virulence markers occurring in patients or in experimental models, but they also demonstrate the involvement of under described molecules and regulatory factors in the amoebic invasive process.
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Affiliation(s)
- Arturo Aguilar-Rojas
- Institut Pasteur, Bioimage Analysis Unit, Paris, France.,Instituto Mexicano del Seguro Social, Unidad de Investigación Médica en Medicina Reproductiva, Ciudad de México, Mexico
| | - Silvia Castellanos-Castro
- Institut Pasteur, Bioimage Analysis Unit, Paris, France.,Universidad Autónoma de la Ciudad de México, Colegio de Ciencias y Humanidades, Ciudad de México, Mexico
| | - Mariette Matondo
- Institut Pasteur, Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), Centrede Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), Centrede Ressources et Recherches Technologiques (C2RT), Paris, France.,Institut Pasteur, Plate-forme Transcriptome et EpiGenome, Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome et EpiGenome, Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France.,Institut Pasteur, Hub Bioinformatique et Biostatistique, Département de Biologie Computationnelle (USR3756 IP CNRS), Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et EpiGenome, Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Rachel Legendre
- Institut Pasteur, Plate-forme Transcriptome et EpiGenome, Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France.,Institut Pasteur, Hub Bioinformatique et Biostatistique, Département de Biologie Computationnelle (USR3756 IP CNRS), Paris, France
| | - Julien Fernandes
- Institut Pasteur, UTechSPBI, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - David Hardy
- Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et EpiGenome, Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | | | - Nancy Guillen
- Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Paris, France
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17
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A Review on the Function and Regulation of ARHGDIB/RhoGDI2 Expression Including the Hypothetical Role of ARHGDIB/RhoGDI2 Autoantibodies in Kidney Transplantation. Transplant Direct 2020; 6:e548. [PMID: 32548242 PMCID: PMC7213606 DOI: 10.1097/txd.0000000000000993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022] Open
Abstract
Challenging and still unsolved problems in kidney transplantation are risk stratification and the treatment of humoral rejection. Antibody-mediated rejection is an important cause of early and chronic rejection. The impact of donor-specific HLA antibodies on antibody-mediated rejection–causing graft damage is well known, but the clinical relevance of non-HLA antibodies remains unclear. Recently, in 2 independent studies, a new correlation was found between the presence of non-HLA anti-Rho guanosine diphosphate dissociation inhibitor 2 (ARHGDIB) antibodies and increased graft failure. RhoGDI2, another name for ARHGDIB, is a negative regulator of the Rho guanosine triphosphate (RhoGTP)ases RhoA, Rac1m, and Cdc42, whose main function is regulating the actin network in a variety of cells. RhoGDI2 is mainly expressed intracellularly, and some expression is observed on the cell surface. Currently, there is no mechanism known to explain this correlation. Additionally, the reason why the antibodies are produced is unknown. In this review, we will address these questions, provide an overview of other diseases in which these antibodies are prevalent, and describe the physiological role of RhoGDI2 itself. If the mechanism and impact of RhoGDI2 antibodies in kidney graft failure are known, improved risk stratification can be provided to decrease the rate of donor kidney graft failure.
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18
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Leidal AM, Debnath J. Unraveling the mechanisms that specify molecules for secretion in extracellular vesicles. Methods 2020; 177:15-26. [PMID: 31978536 DOI: 10.1016/j.ymeth.2020.01.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are small membrane-bound organelles naturally released from cells and potentially function as vehicles of intercellular communication. Cells release numerous sub-species of EVs, including exosomes and microvesicles, which are formed via distinct cellular pathways and molecular machineries and contain specific proteins, RNAs and lipids. Accumulating evidence indicates that the repertoire of molecules packaged into EVs is shaped by both the physiological state of the cell and the EV biogenesis pathway involved. Although these observations intimate that precisely regulated pathways sort molecules into EVs, the underlying molecular mechanisms that direct molecules for secretion remain poorly defined. Recently, with the advancement of mass spectrometry, next-generation sequencing techniques and molecular biology tools, several mechanisms contributing to EV cargo selection are beginning to be unraveled. This review examines strategies employed to reveal how specific proteins, RNAs and lipids are directed for secretion via EVs.
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Affiliation(s)
- Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
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19
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Li C, Zhou Y, Liu J, Su X, Qin H, Huang S, Huang X, Zhou N. Potential Markers from Serum-Purified Exosomes for Detecting Oral Squamous Cell Carcinoma Metastasis. Cancer Epidemiol Biomarkers Prev 2019; 28:1668-1681. [DOI: 10.1158/1055-9965.epi-18-1122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/27/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022] Open
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20
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Special issue on the role of extracellular vesicles in human diseases. Exp Mol Med 2019; 51:1-2. [PMID: 30872575 PMCID: PMC6418171 DOI: 10.1038/s12276-019-0208-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/18/2022] Open
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21
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α2-HS Glycoprotein in Plasma Extracellular Vesicles Inhibits the Osteogenic Differentiation of Human Mesenchymal Stromal Cells In Vitro. Stem Cells Int 2019; 2019:7246479. [PMID: 30881463 PMCID: PMC6383392 DOI: 10.1155/2019/7246479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/16/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Extracellular vesicles (Evs) contain diverse functional proteins, mRNAs, miRNAs, and DNA fragments, are secreted by various types of cells, and play important roles in cellular communication. Here, we show for the first time that plasma Evs inhibited the osteogenic differentiation of mesenchymal stromal cells (MSCs) in vitro and the level of inhibition was positively correlated with the plasma Evs concentration. Plasma Evs downregulated the expression of markers such as osteocalcin (OCN), Runt-related transcription factor 2 (Runx2), and Osterix at mRNA levels required for osteogenic differentiation and reduced pSmad1/5/8 levels in MSCs. Furthermore, pSmad1/5/8 levels increased and MSCs underwent normal osteogenic differentiation after Evs-derived α2-HS glycoprotein (AHSG) function was inhibited with an anti-AHSG neutralizing antibody. However, the levels of pERK1/2, active β-catenin, and HES1 were not significantly altered. Therefore, we propose that as essential components of the extracellular microenvironment of MSCs, plasma Evs are taken up by MSCs and subsequently repress osteogenic differentiation through an AHSG-mediated decrease in pSmad1/5/8 levels. Our work identifies plasma Evs as novel regulators of MSC osteogenic differentiation.
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22
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Choi D, Spinelli C, Montermini L, Rak J. Oncogenic Regulation of Extracellular Vesicle Proteome and Heterogeneity. Proteomics 2019; 19:e1800169. [PMID: 30561828 DOI: 10.1002/pmic.201800169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Indexed: 12/12/2022]
Abstract
Mutational and epigenetic driver events profoundly alter intercellular communication pathways in cancer. This effect includes deregulated release, molecular composition, and biological activity of extracellular vesicles (EVs), membranous cellular fragments ranging from a few microns to less than 100 nm in diameter and filled with bioactive molecular cargo (proteins, lipids, and nucleic acids). While EVs are usually classified on the basis of their physical properties and biogenetic mechanisms, recent analyses of their proteome suggest a larger than expected molecular diversity, a notion that is also supported by multicolour nano-flow cytometry and other emerging technology platforms designed to analyze single EVs. Both protein composition and EV diversity are markedly altered by oncogenic transformation, epithelial to mesenchymal transition, and differentiation of cancer stem cells. Interestingly, only a subset of EVs released from mutant cells may carry oncogenic proteins (e.g., EGFRvIII), hence, these EVs are often referred to as "oncosomes". Indeed, oncogenic transformation alters the repertoire of EV-associated proteins, increases the presence of pro-invasive cargo, and alters the composition of distinct EV populations. Molecular profiling of single EVs may reveal a more intricate effect of transforming events on the architecture of EV populations in cancer and shed new light on their biological role and diagnostic utility.
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Affiliation(s)
- Dongsic Choi
- Research Institute, Health Centre, Glen Site, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Cristiana Spinelli
- Research Institute, Health Centre, Glen Site, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Laura Montermini
- Research Institute, Health Centre, Glen Site, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Janusz Rak
- Research Institute, Health Centre, Glen Site, McGill University, Montreal, Quebec, H4A 3J1, Canada
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23
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Jimenez-Jimenez S, Hashimoto K, Santana O, Aguirre J, Kuchitsu K, Cárdenas L. Emerging roles of tetraspanins in plant inter-cellular and inter-kingdom communication. PLANT SIGNALING & BEHAVIOR 2019; 14:e1581559. [PMID: 30829110 PMCID: PMC6512927 DOI: 10.1080/15592324.2019.1581559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Inter-cellular and inter-kingdom signaling systems of various levels of complexity regulate pathogenic and mutualistic interactions between bacteria, parasites, and fungi and animal and plant hosts. Inter-kingdom interactions between mutualistic bacteria such as rhizobia and legumes during nodulation and between fungi and plants during mycorrhizal associations, are characterized by the extensive exchange of molecular signals, which allow nitrogen and phosphate assimilation, respectively. A novel aspect of this signaling exchange is the existence of specific structures, the exosomes, that carry important molecules that shape the plant-pathogen interactions. Exosomes contain a wide array of molecules, such as lipids, proteins, messenger RNA, and microRNAs, that play important roles in cell-to-cell communication in animal and plant cells by affecting gene expression and other physiological activity in distant cells within the same organism (e.g., during cancer metastases and neuron injuries). In plant cells, it has been recently reported that exosomes go beyond organism boundaries and inhibit a pathogenic interaction in plants. Plant produce and send exosomes loaded with specific small miRNA which inhibit the pathogen infection, but the pathogen can also produce exosomes carrying pro-pathogenic proteins and microRNAs. Therefore, exosomes are the important bridge regulating the signal exchange. Exosomes are small membrane-bound vesicles derived from multivesicular bodies (MVBs), which carries selected cargos from the cytoplasm (protein, lipids, and microRNAs) and under certain circumstances, they fuse with the plasma membrane, releasing the small vesicles as cargo-carrying exosomes into the extracellular space during intercellular and inter-kingdom communication. Animal and plant proteomic studies have demonstrated that tetraspanin proteins are an integral part of exosome membranes, positioning tetraspanins as essential components for endosome organization, with key roles in membrane fusion, cell trafficking, and membrane recognition. We discuss the similarities and differences between animal tetraspanins and plant tetraspanins formed during plant-microbe interactions and their potential role in mutualistic communication.
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Affiliation(s)
- Saul Jimenez-Jimenez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jesús Aguirre
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
- CONTACT Luis Cárdenas Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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24
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Xie Y, Gao Y, Zhang L, Chen Y, Ge W, Tang P. Involvement of serum-derived exosomes of elderly patients with bone loss in failure of bone remodeling via alteration of exosomal bone-related proteins. Aging Cell 2018; 17:e12758. [PMID: 29603567 PMCID: PMC5946082 DOI: 10.1111/acel.12758] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 12/31/2022] Open
Abstract
Exosomes are secreted into the blood by various types of cells. These extracellular vesicles are involved in the contribution of exosomal proteins to osteoblastic or osteoclastic regulatory networks during the failure of bone remodeling, which results in age-related bone loss. However, the molecular changes in serum-derived exosomes (SDEs) from aged patients with low bone density and their functions in bone remodeling remain to be fully elucidated. We present a quantitative proteomics analysis of exosomes purified from the serum of the elderly patients with osteoporosis/osteopenia and normal volunteers; these data are available via Proteome Xchange with the identifier PXD006463. Overall, 1,371 proteins were identified with an overlap of 1,160 Gene IDs among the ExoCarta proteins. Bioinformatics analysis and in vitro studies suggested that protein changes in SDEs of osteoporosis patients are not only involved in suppressing the integrin-mediated mechanosensation and activation of osteoblastic cells, but also trigger the differentiation and resorption of osteoclasts. In contrast, the main changes in SDEs of osteopenia patients facilitated both activation of osteoclasts and formation of new bone mass, which could result in a compensatory elevation in bone remodeling. While the SDEs from aged normal volunteers might play a protective role in bone health through facilitating adhesion of bone cells and suppressing aging-associated oxidative stress. This information will be helpful in elucidating the pathophysiological functions of SDEs and aid in the development of senile osteoporosis diagnostics and therapeutics.
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Affiliation(s)
- Yong Xie
- Department of Orthopedics; Chinese PLA General Hospital; Beijing China
| | - Yanpan Gao
- State Key Laboratory of Medical Molecular Biology; Department of Immunology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Licheng Zhang
- Department of Orthopedics; Chinese PLA General Hospital; Beijing China
| | - Yanyu Chen
- State Key Laboratory of Medical Molecular Biology; Department of Immunology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Wei Ge
- State Key Laboratory of Medical Molecular Biology; Department of Immunology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Peifu Tang
- Department of Orthopedics; Chinese PLA General Hospital; Beijing China
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25
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Shao H, Im H, Castro CM, Breakefield X, Weissleder R, Lee H. New Technologies for Analysis of Extracellular Vesicles. Chem Rev 2018; 118:1917-1950. [PMID: 29384376 PMCID: PMC6029891 DOI: 10.1021/acs.chemrev.7b00534] [Citation(s) in RCA: 1123] [Impact Index Per Article: 160.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Extracellular vesicles (EVs) are diverse, nanoscale membrane vesicles actively released by cells. Similar-sized vesicles can be further classified (e.g., exosomes, microvesicles) based on their biogenesis, size, and biophysical properties. Although initially thought to be cellular debris, and thus under-appreciated, EVs are now increasingly recognized as important vehicles of intercellular communication and circulating biomarkers for disease diagnoses and prognosis. Despite their clinical potential, the lack of sensitive preparatory and analytical technologies for EVs poses a barrier to clinical translation. New analytical platforms including molecular ones are thus actively being developed to address these challenges. Recent advances in the field are expected to have far-reaching impact in both basic and translational studies. This article aims to present a comprehensive and critical overview of emerging analytical technologies for EV detection and their clinical applications.
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Affiliation(s)
- Huilin Shao
- Departments of Biomedical Engineering and Surgery, National University of Singapore
- Biomedical Institute for Global Health Research and Technology, National University of Singapore
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital
- Department of Radiology, Massachusetts General Hospital
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General Hospital
- Department of Medicine, Massachusetts General Hospital
| | - Xandra Breakefield
- Department of Radiology, Massachusetts General Hospital
- Department of Neurology, Massachusetts General Hospital
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital
- Department of Radiology, Massachusetts General Hospital
- Department of Systems Biology, Harvard Medical School
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital
- Department of Radiology, Massachusetts General Hospital
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26
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Zöller M. Janus-Faced Myeloid-Derived Suppressor Cell Exosomes for the Good and the Bad in Cancer and Autoimmune Disease. Front Immunol 2018; 9:137. [PMID: 29456536 PMCID: PMC5801414 DOI: 10.3389/fimmu.2018.00137] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells originally described to hamper immune responses in chronic infections. Meanwhile, they are known to be a major obstacle in cancer immunotherapy. On the other hand, MDSC can interfere with allogeneic transplant rejection and may dampen autoreactive T cell activity. Whether MDSC-Exosomes (Exo) can cope with the dangerous and potentially therapeutic activities of MDSC is not yet fully explored. After introducing MDSC and Exo, it will be discussed, whether a blockade of MDSC-Exo could foster the efficacy of immunotherapy in cancer and mitigate tumor progression supporting activities of MDSC. It also will be outlined, whether application of native or tailored MDSC-Exo might prohibit autoimmune disease progression. These considerations are based on the steadily increasing knowledge on Exo composition, their capacity to distribute throughout the organism combined with selectivity of targeting, and the ease to tailor Exo and includes open questions that answers will facilitate optimizing protocols for a MDSC-Exo blockade in cancer as well as for strengthening their therapeutic efficacy in autoimmune disease.
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Affiliation(s)
- Margot Zöller
- Tumor Cell Biology, University Hospital of Surgery, University of Heidelberg, Heidelberg, Germany
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27
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Wang Z, Zhao K, Hackert T, Zöller M. CD44/CD44v6 a Reliable Companion in Cancer-Initiating Cell Maintenance and Tumor Progression. Front Cell Dev Biol 2018; 6:97. [PMID: 30211160 PMCID: PMC6122270 DOI: 10.3389/fcell.2018.00097] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022] Open
Abstract
Metastasis is the leading cause of cancer death, tumor progression proceeding through emigration from the primary tumor, gaining access to the circulation, leaving the circulation, settling in distant organs and growing in the foreign environment. The capacity of a tumor to metastasize relies on a small subpopulation of cells in the primary tumor, so called cancer-initiating cells (CIC). CIC are characterized by sets of markers, mostly membrane anchored adhesion molecules, CD44v6 being the most frequently recovered marker. Knockdown and knockout models accompanied by loss of tumor progression despite unaltered primary tumor growth unraveled that these markers are indispensable for CIC. The unexpected contribution of marker molecules to CIC-related activities prompted research on underlying molecular mechanisms. This review outlines the contribution of CD44, particularly CD44v6 to CIC activities. A first focus is given to the impact of CD44/CD44v6 to inherent CIC features, including the crosstalk with the niche, apoptosis-resistance, and epithelial mesenchymal transition. Following the steps of the metastatic cascade, we report on supporting activities of CD44/CD44v6 in migration and invasion. These CD44/CD44v6 activities rely on the association with membrane-integrated and cytosolic signaling molecules and proteases and transcriptional regulation. They are not restricted to, but most pronounced in CIC and are tightly regulated by feedback loops. Finally, we discuss on the engagement of CD44/CD44v6 in exosome biogenesis, loading and delivery. exosomes being the main acteurs in the long-distance crosstalk of CIC with the host. In brief, by supporting the communication with the niche and promoting apoptosis resistance CD44/CD44v6 plays an important role in CIC maintenance. The multifaceted interplay between CD44/CD44v6, signal transducing molecules and proteases facilitates the metastasizing tumor cell journey through the body. By its engagement in exosome biogenesis CD44/CD44v6 contributes to disseminated tumor cell settlement and growth in distant organs. Thus, CD44/CD44v6 likely is the most central CIC biomarker.
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Affiliation(s)
- Zhe Wang
- Department of Oncology, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong, China
| | - Kun Zhao
- Pancreas Section, University Hospital of Surgery, Heidelberg, Germany
| | - Thilo Hackert
- Pancreas Section, University Hospital of Surgery, Heidelberg, Germany
| | - Margot Zöller
- Pancreas Section, University Hospital of Surgery, Heidelberg, Germany
- *Correspondence: Margot Zöller
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28
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Barteneva NS, Baiken Y, Fasler-Kan E, Alibek K, Wang S, Maltsev N, Ponomarev ED, Sautbayeva Z, Kauanova S, Moore A, Beglinger C, Vorobjev IA. Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: On the border of Kingdoms. Biochim Biophys Acta Rev Cancer 2017; 1868:372-393. [DOI: 10.1016/j.bbcan.2017.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 12/16/2022]
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29
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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30
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Gho YS, Lee C. Emergent properties of extracellular vesicles: a holistic approach to decode the complexity of intercellular communication networks. MOLECULAR BIOSYSTEMS 2017; 13:1291-1296. [DOI: 10.1039/c7mb00146k] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Holistic approaches to decode emergent properties of extracellular vesicles either at a single vesicle level or at a systems level.
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Affiliation(s)
- Yong Song Gho
- Department of Life Sciences
- Pohang University of Science and Technology
- Pohang
- Republic of Korea
| | - Changjin Lee
- Department of Life Sciences
- Pohang University of Science and Technology
- Pohang
- Republic of Korea
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31
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D'Avino C, Palmieri D, Braddom A, Zanesi N, James C, Cole S, Salvatore F, Croce CM, De Lorenzo C. A novel fully human anti-NCL immunoRNase for triple-negative breast cancer therapy. Oncotarget 2016; 7:87016-87030. [PMID: 27894092 PMCID: PMC5349967 DOI: 10.18632/oncotarget.13522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/10/2016] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the most common cancer in women worldwide. A new promising anti-cancer therapy involves the use of monoclonal antibodies specific for target tumor-associated antigens (TAAs). A TAA of interest for immunotherapy of Triple Negative Breast Cancer (TNBC) is nucleolin (NCL), a multifunctional protein, selectively expressed on the surface of cancer cells, which regulates the biogenesis of specific microRNAs (miRNAs) involved in tumor development and drug-resistance. We previously isolated a novel human anti-NCL scFv, called 4LB5, that is endowed with selective anti-tumor effects. Here we report the construction and characterization of a novel immunoRNase constituted by 4LB5 and a human pancreatic RNase (HP-RNase) called "4LB5-HP-RNase". This immunoRNase retains both the enzymatic activity of human pancreatic RNase and the specific binding of the parental scFv to a panel of surface NCL-positive breast cancer cells. Notably, 4LB5-HP-RNase dramatically and selectively reduced the viability and proliferation of NCL-positive tumor cells in vitro and in vivo. Specifically, it induced apoptosis and reduced the levels of the tumorigenic miRNAs miR-21, -221 and -222. Thus, this novel immunoagent could be a valuable tool for the treatment of TNBC patients ineligible for currently available targeted treatments.
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Affiliation(s)
- Chiara D'Avino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- Ceinge Advanced Biotechnology S.C.ar.l., 80145 Naples, Italy
| | - Dario Palmieri
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Ashley Braddom
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Nicola Zanesi
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Cindy James
- Department of Mass Spectroscopy and Proteomics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Sara Cole
- Campus Microscopy and Imaging Facility, The Ohio State University, Columbus, 43210 Ohio, USA
| | | | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Claudia De Lorenzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- Ceinge Advanced Biotechnology S.C.ar.l., 80145 Naples, Italy
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32
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Xie Y, Chen Y, Zhang L, Ge W, Tang P. The roles of bone-derived exosomes and exosomal microRNAs in regulating bone remodelling. J Cell Mol Med 2016; 21:1033-1041. [PMID: 27878944 PMCID: PMC5387131 DOI: 10.1111/jcmm.13039] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
Pathological destructive bone diseases are primarily caused by the failure of a lifelong self-renewal process of the skeletal system called bone remodelling. The mechanisms underlying this process include enhanced osteoclast activity and decreased generation of the osteoblast lineage. Intercellular interaction and crosstalk among these cell types are crucial for the maintenance of bone remodelling, either through the secretion of growth factors or direct cell-cell physical engagement. Recent studies have revealed that exosomes derived from bone cells, including osteoclasts, osteoblasts and their precursors, play pivotal roles on bone remodelling by transferring biologically active molecules to target cells, especially in the processes of osteoclast and osteoblast differentiation. Here, we review the contents of bone-derived exosomes and their functions in the regulatory processes of differentiation and communication of osteoclasts and osteoblasts. In addition, we highlight the characteristics of microRNAs of bone-derived exosomes involved in the regulation of bone remodelling, as well as the potential clinical applications of bone-derived exosomes in bone remodelling disorders.
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Affiliation(s)
- Yong Xie
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, China
| | - Yanyu Chen
- National Key Laboratory of Medical Molecular Biology and Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Licheng Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, China
| | - Wei Ge
- National Key Laboratory of Medical Molecular Biology and Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Peifu Tang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, China
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33
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Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W. Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics. Int J Cancer 2016; 140:900-913. [PMID: 27813080 DOI: 10.1002/ijc.30496] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/26/2016] [Indexed: 12/11/2022]
Abstract
Tumor cells of colorectal cancer (CRC) release exosomes into the circulation. These exosomes can mediate communication between cells and affect various tumor-related processes in their target cells. We present a quantitative proteomics analysis of the exosomes purified from serum of patients with CRC and normal volunteers; data are available via ProteomeXchange with identifier PXD003875. We identified 918 proteins with an overlap of 725 Gene IDs in the Exocarta proteins list. Compared with the serum-purified exosomes (SPEs) of normal volunteers, we found 36 proteins upregulated and 22 proteins downregulated in the SPEs of CRC patients. Bioinformatics analysis revealed that upregulated proteins are involved in processes that modulate the pretumorigenic microenvironment for metastasis. In contrast, differentially expressed proteins (DEPs) that play critical roles in tumor growth and cell survival were principally downregulated. Our study demonstrates that SPEs of CRC patients play a pivotal role in promoting the tumor invasiveness, but have minimal influence on putative alterations in tumor survival or proliferation. According to bioinformatics analysis, we speculate that the protein contents of exosomes might be associated with whether they are involved in premetastatic niche establishment or growth and survival of metastatic tumor cells. This information will be helpful in elucidating the pathophysiological functions of tumor-derived exosomes, and aid in the development of CRC diagnostics and therapeutics.
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Affiliation(s)
- Yanyu Chen
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Yong Xie
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Lai Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Shaohua Zhan
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Yi Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Yanpan Gao
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Bin Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Wei Ge
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
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34
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Lässer C, Shelke GV, Yeri A, Kim DK, Crescitelli R, Raimondo S, Sjöstrand M, Gho YS, Van Keuren Jensen K, Lötvall J. Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing. RNA Biol 2016; 14:58-72. [PMID: 27791479 PMCID: PMC5270547 DOI: 10.1080/15476286.2016.1249092] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analyzed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the 2 exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
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Affiliation(s)
- Cecilia Lässer
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden
| | - Ganesh Vilas Shelke
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden
| | | | - Dae-Kyum Kim
- c Department of Life Sciences , Pohang University of Science and Technology , Pohang , Gyeongbuk , Republic of Korea
| | - Rossella Crescitelli
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden
| | - Stefania Raimondo
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden.,d Department of Biopathology, and Medical Biotechnologies , Section of Biology and Genetics, Università di Palermo , Palermo , Italy
| | - Margareta Sjöstrand
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden
| | - Yong Song Gho
- c Department of Life Sciences , Pohang University of Science and Technology , Pohang , Gyeongbuk , Republic of Korea
| | | | - Jan Lötvall
- a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden
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Gomzikova MO, Rizvanov AA. Current Trends in Regenerative Medicine: From Cell to Cell-Free Therapy. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-016-0348-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
Cancer diagnosis and therapy is steadily improving. Still, diagnosis is frequently late and diagnosis and follow-up procedures mostly are time-consuming and expensive. Searching for tumor-derived exosomes (TEX) in body fluids may provide an alternative, minimally invasive, yet highly reliable diagnostic tool. Beyond this, there is strong evidence that TEX could become a potent therapeutics. Exosomes, small vesicles delivered by many cells of the organism, are found in all body fluids. Exosomes are characterized by lipid composition, common and donor cell specific proteins, mRNA, small non-coding RNA including miRNA and DNA. Particularly the protein and miRNA markers received much attention as they may allow for highly specific diagnosis and can provide hints toward tumor aggressiveness and progression, where exosome-based diagnosis and follow-up is greatly facilitated by the recovery of exosomes in body fluids, particularly the peripheral blood. Beyond this, exosomes are the most important intercellular communicators that modulate, instruct, and reprogram their surrounding as well as distant organs. In concern about TEX this includes message transfer from tumor cells toward the tumor stroma, the premetastatic niche, the hematopoietic system and, last but not least, the instruction of non-cancer stem cells by cancer-initiating cells (CIC). Taking this into account, it becomes obvious that "tailored" exosomes offer themselves as potent therapeutic delivery system. In brief, during the last 4-5 years there is an ever-increasing, overwhelming interest in exosome research. This boom appears fully justified provided the content of the exosomes becomes most thoroughly analyzed and their mode of intercellular interaction can be unraveled in detail as this knowledge will open new doors toward cancer diagnosis and therapy including immunotherapy and CIC reprogramming.
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Affiliation(s)
- Margot Zöller
- Tumor Cell Biology, University Hospital of Surgery, im Neuenheimer Feld 365, 69120, Heidelberg, Germany.
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Heiler S, Wang Z, Zöller M. Pancreatic cancer stem cell markers and exosomes - the incentive push. World J Gastroenterol 2016; 22:5971-6007. [PMID: 27468191 PMCID: PMC4948278 DOI: 10.3748/wjg.v22.i26.5971] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/03/2016] [Accepted: 06/28/2016] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PaCa) has the highest death rate and incidence is increasing. Poor prognosis is due to late diagnosis and early metastatic spread, which is ascribed to a minor population of so called cancer stem cells (CSC) within the mass of the primary tumor. CSC are defined by biological features, which they share with adult stem cells like longevity, rare cell division, the capacity for self renewal, differentiation, drug resistance and the requirement for a niche. CSC can also be identified by sets of markers, which for pancreatic CSC (Pa-CSC) include CD44v6, c-Met, Tspan8, alpha6beta4, CXCR4, CD133, EpCAM and claudin7. The functional relevance of CSC markers is still disputed. We hypothesize that Pa-CSC markers play a decisive role in tumor progression. This is fostered by the location in glycolipid-enriched membrane domains, which function as signaling platform and support connectivity of the individual Pa-CSC markers. Outside-in signaling supports apoptosis resistance, stem cell gene expression and tumor suppressor gene repression as well as miRNA transcription and silencing. Pa-CSC markers also contribute to motility and invasiveness. By ligand binding host cells are triggered towards creating a milieu supporting Pa-CSC maintenance. Furthermore, CSC markers contribute to the generation, loading and delivery of exosomes, whereby CSC gain the capacity for a cell-cell contact independent crosstalk with the host and neighboring non-CSC. This allows Pa-CSC exosomes (TEX) to reprogram neighboring non-CSC towards epithelial mesenchymal transition and to stimulate host cells towards preparing a niche for metastasizing tumor cells. Finally, TEX communicate with the matrix to support tumor cell motility, invasion and homing. We will discuss the possibility that CSC markers are the initial trigger for these processes and what is the special contribution of CSC-TEX.
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Erb U, Zöller M. Progress and potential of exosome analysis for early pancreatic cancer detection. Expert Rev Mol Diagn 2016; 16:757-67. [PMID: 27206554 DOI: 10.1080/14737159.2016.1187563] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Pancreatic cancer (PaCa) is the most deadly malignancy, due to late diagnosis prohibiting surgery. Thus, strong efforts are taken improving early diagnosis via biomarkers recovered in the serum of PaCa patients. AREAS COVERED One promising option are PaCa-derived exosomes in patients' sera. Exosomes, small vesicles delivered by live cells and recovered in all body fluids, are a powerful diagnostic tool due to relative stability and composition covering the whole range of cancer-related biomarkers including proteins, metabolites, DNA, DNA modifications, coding and noncoding RNA. We discuss the mechanisms accounting for the condensed packaging of biomarkers, refer to studies using PaCa serum-exosomes for diagnosis. Based on an extensive literature search, we outline questions that answers may help establishing a serum-exosome-based screening for early PaCa detection. Expert commentary: Improved proteomic and genomic characterization and progress in the biogenesis of exosomes will allow for optimized and unified screening panels for PaCa diagnosis via TEX in body fluids.
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Affiliation(s)
- Ulrike Erb
- a Department of Tumor Cell Biology , University Hospital of Surgery , Heidelberg , Germany
| | - Margot Zöller
- a Department of Tumor Cell Biology , University Hospital of Surgery , Heidelberg , Germany
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Knol JC, de Reus I, Schelfhorst T, Beekhof R, de Wit M, Piersma SR, Pham TV, Smit EF, Verheul HM, Jiménez CR. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics. EUPA OPEN PROTEOMICS 2016; 11:11-15. [PMID: 29900106 PMCID: PMC5988555 DOI: 10.1016/j.euprot.2016.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 01/14/2023]
Abstract
Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since EVs are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, they represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation are laborious, time-consuming, and require high inputs. Ghosh and co-workers recently described an isolation method utilizing Heat Shock Protein (HSP)-binding peptide Vn96 to aggregate HSP-decorated EVs, which can be performed at small 'miniprep' scale. Based on microscopic, immunoblot, and RNA sequencing analyses this method compared well with ultracentrifugation-mediated EV isolation, but a detailed proteomic comparison was lacking. Therefore, we compared both methods using label-free proteomics of replicate EV isolations from HT-29 cell-conditioned medium. Despite a 30-fold different scale (ultracentrifugation: 60 ml/Vn96-mediated aggregation: 2 ml) both methods yielded comparable numbers of identified proteins (3115/3085), with similar reproducibility of identification (72.5%/75.5%) and spectral count-based quantification (average CV: 31%/27%). EV fractions obtained with either method contained established EV markers and proteins linked to vesicle-related gene ontologies. Thus, Vn96 peptide-mediated aggregation is an advantageous, simple and rapid approach for EV isolation from small biological samples, enabling high-throughput analysis in a biomarker discovery setting.
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Affiliation(s)
- Jaco C. Knol
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Inge de Reus
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Tim Schelfhorst
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Robin Beekhof
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Egbert F. Smit
- Department of Pulmonary Diseases, VU University Medical Center, The Netherlands
| | - Henk M.W. Verheul
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
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Lunavat TR, Cheng L, Kim DK, Bhadury J, Jang SC, Lässer C, Sharples RA, López MD, Nilsson J, Gho YS, Hill AF, Lötvall J. Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells--Evidence of unique microRNA cargos. RNA Biol 2016; 12:810-23. [PMID: 26176991 PMCID: PMC4615768 DOI: 10.1080/15476286.2015.1056975] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
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Affiliation(s)
- Taral R Lunavat
- a Krefting Research Center ; Institute of Medicine; University of Gothenburg ; Gothenburg , Sweden
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Kim YS, Choi JP, Kim MH, Park HK, Yang S, Kim YS, Kim TB, Cho YS, Oh YM, Jee YK, Lee SD, Kim YK. IgG Sensitization to Extracellular Vesicles in Indoor Dust Is Closely Associated With the Prevalence of Non-Eosinophilic Asthma, COPD, and Lung Cancer. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2016; 8:198-205. [PMID: 26922929 PMCID: PMC4773207 DOI: 10.4168/aair.2016.8.3.198] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/13/2015] [Accepted: 07/09/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Recent experimental evidence shows that extracellular vesicles (EVs) in indoor dust induce neurtrophilic pulmonary inflammation, which is a characteristic pathology in patients with severe asthma and chronic obstructive pulmonary disease (COPD). In addition, COPD is known to be an important risk factor for lung cancer, irrespective of cigarette smoking. Here, we evaluated whether sensitization to indoor dust EVs is a risk for the development of asthma, COPD, or lung cancer. METHODS Serum IgG antibodies against dust EVs were measured in 90 healthy control subjects, 294 asthmatics, 242 COPD patients, and 325 lung cancer patients. Serum anti-dust EV IgG titers were considered high if they exceeded a 95 percentile value of the control subjects. Age-, gender-, and cigarette smoke-adjusted multiple logistic regression analyses were performed to determine odds ratios (ORs) for asthma, COPD, and lung cancer patients vs the control subjects. RESULTS In total, 4.4%, 13.6%, 29.3%, and 54.9% of the control, asthma, COPD, and lung cancer groups, respectively, had high serum anti-dust EV IgG titers. Adjusted multiple logistic regression revealed that sensitization to dust EVs (high serum anti-dust EV IgG titer) was an independent risk factor for asthma (adjusted OR, 3.3; 95% confidence interval [CI], 1.1-10.0), COPD (adjusted OR, 8.0; 95% CI, 2.0-32.5) and lung cancer (adjusted OR, 38.7; 95% CI, 10.4-144.3). CONCLUSIONS IgG sensitization to indoor dust EVs appears to be a major risk for the development of asthma, COPD, and lung cancer.
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Affiliation(s)
- You Sun Kim
- Asan Institute for Life Science and University of Ulsan College of Medicine, Seoul, Korea
| | - Jun Pyo Choi
- Institute of Convergence Medicine, Ewha Womans University Medical Center and Ewha Womans University School of Medicine, Seoul, Korea
| | - Min Hye Kim
- Institute of Convergence Medicine, Ewha Womans University Medical Center and Ewha Womans University School of Medicine, Seoul, Korea
| | - Han Ki Park
- Institute of Convergence Medicine, Ewha Womans University Medical Center and Ewha Womans University School of Medicine, Seoul, Korea
| | - Sejung Yang
- Institute of Convergence Medicine, Ewha Womans University Medical Center and Ewha Womans University School of Medicine, Seoul, Korea
| | - Youn Seup Kim
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Korea
| | - Tae Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, Seoul, Korea
| | - You Sook Cho
- Department of Allergy and Clinical Immunology, Asan Medical Center, Seoul, Korea
| | - Yeon Mok Oh
- Department of Pulmonary and Critical Care Medicine, and Clinical Research Center for Chronic Obstructive Airway Disease, Asan Medical Center, Seoul, Korea.
| | - Young Koo Jee
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Korea. ykjee@dku,edu
| | - Sang Do Lee
- Department of Pulmonary and Critical Care Medicine, and Clinical Research Center for Chronic Obstructive Airway Disease, Asan Medical Center, Seoul, Korea
| | - Yoon Keun Kim
- Institute of Convergence Medicine, Ewha Womans University Medical Center and Ewha Womans University School of Medicine, Seoul, Korea.
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Green TM, Santos MF, Barsky SH, Rappa G, Lorico A. Analogies Between Cancer-Derived Extracellular Vesicles and Enveloped Viruses with an Emphasis on Human Breast Cancer. CURRENT PATHOBIOLOGY REPORTS 2016; 4:169-179. [PMID: 32226654 PMCID: PMC7099913 DOI: 10.1007/s40139-016-0116-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Purpose of Review Cancer cells utilize extracellular vesicles (EVs) as a means of transferring oncogenic proteins and nucleic acids to other cells to enhance the growth and spread of the tumor. There is an unexpected amount of similarities between these small, membrane-bound particles and enveloped virions, including protein content, physical characteristics (i.e., size and morphology), and mechanisms of entry and exit into target cells. Recent Findings This review describes the attributes shared by both cancer-derived EVs, with an emphasis on breast cancer-derived EVs, and enveloped viral particles and discusses the methods by which virions can utilize the EV pathway as a means of transferring viral material and oncogenes to host cells. Additionally, the possible links between human papilloma virus and its influence on the miRNA content of breast cancer-derived EVs are examined. Summary The rapidly growing field of EVs is allowing investigators from different disciplines to enter uncharted territory. The study of the emerging similarities between cancer-derived EVs and enveloped virions may lead to novel important scientific discoveries.
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Affiliation(s)
- Toni M Green
- Department of Pathology and Laboratory Medicine, College of Medicine, Roseman University of Health Sciences and The Roseman Comprehensive Community Cancer Center, Las Vegas, NV 89135 USA
| | - Mark F Santos
- Department of Pathology and Laboratory Medicine, College of Medicine, Roseman University of Health Sciences and The Roseman Comprehensive Community Cancer Center, Las Vegas, NV 89135 USA
| | - Sanford H Barsky
- Department of Pathology and Laboratory Medicine, College of Medicine, Roseman University of Health Sciences and The Roseman Comprehensive Community Cancer Center, Las Vegas, NV 89135 USA
| | - Germana Rappa
- Department of Pathology and Laboratory Medicine, College of Medicine, Roseman University of Health Sciences and The Roseman Comprehensive Community Cancer Center, Las Vegas, NV 89135 USA
| | - Aurelio Lorico
- Department of Pathology and Laboratory Medicine, College of Medicine, Roseman University of Health Sciences and The Roseman Comprehensive Community Cancer Center, Las Vegas, NV 89135 USA
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Quesenberry PJ, Aliotta J, Camussi G, Abdel-Mageed AB, Wen S, Goldberg L, Zhang HG, Tetta C, Franklin J, Coffey RJ, Danielson K, Subramanya V, Ghiran I, Das S, Chen CC, Pusic KM, Pusic AD, Chatterjee D, Kraig RP, Balaj L, Dooner M. Potential functional applications of extracellular vesicles: a report by the NIH Common Fund Extracellular RNA Communication Consortium. J Extracell Vesicles 2015; 4:27575. [PMID: 26320942 PMCID: PMC4553260 DOI: 10.3402/jev.v4.27575] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 12/13/2022] Open
Abstract
The NIH Extracellular RNA Communication Program's initiative on clinical utility of extracellular RNAs and therapeutic agents and developing scalable technologies is reviewed here. Background information and details of the projects are presented. The work has focused on modulation of target cell fate by extracellular vesicles (EVs) and RNA. Work on plant-derived vesicles is of intense interest, and non-mammalian sources of vesicles may represent a very promising source for different therapeutic approaches. Retro-viral-like particles are intriguing. Clearly, EVs share pathways with the assembly machinery of several other viruses, including human endogenous retrovirals (HERVs), and this convergence may explain the observation of viral-like particles containing viral proteins and nucleic acid in EVs. Dramatic effect on regeneration of damaged bone marrow, renal, pulmonary and cardiovascular tissue is demonstrated and discussed. These studies show restoration of injured cell function and the importance of heterogeneity of different vesicle populations. The potential for neural regeneration is explored, and the capacity to promote and reverse neoplasia by EV exposure is described. The tremendous clinical potential of EVs underlies many of these projects, and the importance of regulatory issues and the necessity of general manufacturing production (GMP) studies for eventual clinical trials are emphasized. Clinical trials are already being pursued and should expand dramatically in the near future.
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Affiliation(s)
- Peter J Quesenberry
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA;
| | - Jason Aliotta
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, Torino, Italy
| | - Asim B Abdel-Mageed
- Department of Urology, Tulane University School of Medicine, New Orleans, LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sicheng Wen
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Laura Goldberg
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Huang-Ge Zhang
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Ciro Tetta
- Department of Medical Sciences, University of Turin, Torino, Italy
| | - Jeffrey Franklin
- Department of Molecular Biology, Vanderbilt University, Nashville, TN, USA
| | - Robert J Coffey
- Department of Molecular Biology, Vanderbilt University, Nashville, TN, USA
| | - Kirsty Danielson
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Vinita Subramanya
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ionita Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Saumya Das
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Clark C Chen
- Department of Surgery, Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, CA, USA
| | - Kae M Pusic
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Aya D Pusic
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Devasis Chatterjee
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Richard P Kraig
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Leonora Balaj
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Mark Dooner
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, RI, USA
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Stec M, Baj-Krzyworzeka M, Baran J, Węglarczyk K, Zembala M, Barbasz J, Szczepanik A, Zembala M. Isolation and characterization of circulating micro(nano)vesicles in the plasma of colorectal cancer patients and their interactions with tumor cells. Oncol Rep 2015; 34:2768-75. [PMID: 26324403 DOI: 10.3892/or.2015.4228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/14/2015] [Indexed: 11/06/2022] Open
Abstract
Micro(nano)vesicles (MV) are regarded as important messengers in cell-to-cell communication. There is also evidence for their pivotal role in cancer progression. Circulating MV are of different body cells origin, including tumor cell‑derived MV (TMV) in cancer patients. Determination of circulating TMV is of importance because of their potential diagnostic and therapeutic applications. In the present study, an analysis of circulating MV in colorectal cancer (CRC) patients was undertaken. Plasma from healthy donors was used as the control. In order to define MV characteristics, two plasma fractions: obtained by sequential centrifugation at 15,000 x g (MV15) and 50,000 x g (MV50) were used for analysis. The two fractions possessed a large range of sizes: 70(80)-1,300(1,400) nm and the most common particles with sizes 70-90 nm, both in patients and controls. Atomic force microscopy images of MV50 revealed a heterogeneous population of particles with different shapes and sizes. MV15 contained an increased level of CD41+ and CD61+ particles, suggesting their platelet origin. No difference between patients and controls was observed. A more precise analysis of MV50 showed the increased level of particles expressing EGFR (HER-1/Erb B1), HER-2/neu and Mucin1 (MUC1), suggesting their tumor origin. The total level of MV50‑expressing EGFR, HER-2/neu and MUC1 was enhanced in CRC patients. MV50 both of patients and controls attached to a colon cancer cell line (SW480) and to isolated blood monocytes at 2 h and were engulfed at 24 h. This uptake showed the lack of specificity. Thus, apart from the direct delivery of MV to the tumor site by plasma, monocytes carrying MV may also be involved in their transportation. Taken together, the presented data indicate that MV15 contain mainly platelet‑derived particles, while MV50 from CRC patients are enriched in TMV. Interaction of MV with cancer cells may pin-point their role in communication between tumor cells, resulting in molecular cargo exchange between them.
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Affiliation(s)
- Małgorzata Stec
- Department of Clinical Immunology and Transplantation, Jagiellonian University Medical College, Cracow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology and Transplantation, Jagiellonian University Medical College, Cracow, Poland
| | - Jarosław Baran
- Department of Clinical Immunology and Transplantation, Jagiellonian University Medical College, Cracow, Poland
| | - Kazimierz Węglarczyk
- Department of Clinical Immunology and Transplantation, Jagiellonian University Medical College, Cracow, Poland
| | - Maria Zembala
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Cracow, Poland
| | - Jakub Barbasz
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Cracow, Poland
| | - Antoni Szczepanik
- First Department of General and Gastrointestinal Surgery, Jagiellonian University Medical College, Cracow, Poland
| | - Marek Zembala
- Department of Clinical Immunology and Transplantation, Jagiellonian University Medical College, Cracow, Poland
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Choi DS, Kim DK, Kim YK, Gho YS. Proteomics of extracellular vesicles: Exosomes and ectosomes. MASS SPECTROMETRY REVIEWS 2015; 34:474-90. [PMID: 24421117 DOI: 10.1002/mas.21420] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 05/24/2023]
Abstract
Almost all bacteria, archaea, and eukaryotic cells shed extracellular vesicles either constitutively or in a regulated manner. These nanosized membrane vesicles are spherical, bilayered proteolipids that harbor specific subsets of proteins, DNAs, RNAs, and lipids. Recent research has facilitated conceptual advancements in this emerging field that indicate that extracellular vesicles act as intercellular communicasomes by transferring signals to their target cell via surface ligands and delivering receptors and functional molecules. Recent progress in mass spectrometry-based proteomic analyses of mammalian extracellular vesicles derived from diverse cell types and body fluids has resulted in the identification of several thousand vesicular proteins that provide us with essential clues to the molecular mechanisms involved in vesicle cargo sorting and biogenesis. Furthermore, cell-type- or disease-specific vesicular proteins help us to understand the pathophysiological functions of extracellular vesicles and contribute to the discovery of diagnostic and therapeutic target proteins. This review focuses on the high-throughput mass spectrometry-based proteomic analyses of mammalian extracellular vesicles (i.e., exosomes and ectosomes), EVpedia (a free web-based integrated database of high-throughput data for systematic analyses of extracellular vesicles; http://evpedia.info), and the intravesicular protein-protein interaction network analyses of mammalian extracellular vesicles. The goal of this article is to encourage further studies to construct a comprehensive proteome database for extracellular vesicles that will help us to not only decode the biogenesis and cargo-sorting mechanisms during vesicle formation but also elucidate the pathophysiological roles of these complex extracellular organelles.
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Affiliation(s)
- Dong-Sic Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dae-Kyum Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yoon-Keun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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Yoon YJ, Kim OY, Gho YS. Extracellular vesicles as emerging intercellular communicasomes. BMB Rep 2015; 47:531-9. [PMID: 25104400 PMCID: PMC4261509 DOI: 10.5483/bmbrep.2014.47.10.164] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 12/21/2022] Open
Abstract
All living cells release extracellular vesicles having pleiotropic functions in intercellular communication. Mammalian extracellular vesicles, also known as exosomes and microvesicles, are spherical bilayered proteolipids composed of various bioactive molecules, including RNAs, DNAs, proteins, and lipids. Extracellular vesicles directly and indirectly control a diverse range of biological processes by transferring membrane proteins, signaling molecules, mRNAs, and miRNAs, and activating receptors of recipient cells. The active interaction of extracellular vesicles with other cells regulates various physiological and pathological conditions, including cancer, infectious diseases, and neurodegenerative disorders. Recent developments in high-throughput proteomics, transcriptomics, and lipidomics tools have provided ample data on the common and specific components of various types of extracellular vesicles. These studies may contribute to the understanding of the molecular mechanism involved in vesicular cargo sorting and the biogenesis of extracellular vesicles, and, further, to the identification of disease-specific biomarkers. This review focuses on the components, functions, and therapeutic and diagnostic potential of extracellular vesicles under various pathophysiological conditions.
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Affiliation(s)
- Yae Jin Yoon
- Department of Life Sciences, Pohang University of Science and Technology; Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Oh Youn Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
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Bellingham SA, Guo B, Hill AF. The secret life of extracellular vesicles in metal homeostasis and neurodegeneration. Biol Cell 2015; 107:389-418. [PMID: 26032945 DOI: 10.1111/boc.201500030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/27/2015] [Indexed: 12/21/2022]
Abstract
Biologically active metals such as copper, zinc and iron are fundamental for sustaining life in different organisms with the regulation of cellular metal homeostasis tightly controlled through proteins that coordinate metal uptake, efflux and detoxification. Many of the proteins involved in either uptake or efflux of metals are localised and function on the plasma membrane, traffic between intracellular compartments depending upon the cellular metal environment and can undergo recycling via the endosomal pathway. The biogenesis of exosomes also occurs within the endosomal system, with several major neurodegenerative disease proteins shown to be released in association with these vesicles, including the amyloid-β (Aβ) peptide in Alzheimer's disease and the infectious prion protein involved in Prion diseases. Aβ peptide and the prion protein also bind biologically active metals and are postulated to play important roles in metal homeostasis. In this review, we will discuss the role of extracellular vesicles in Alzheimer's and Prion diseases and explore their potential contribution to metal homeostasis.
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Affiliation(s)
- Shayne A Bellingham
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC, Australia
| | - Belinda Guo
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC, Australia
| | - Andrew F Hill
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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Kim JH, Lee J, Park J, Gho YS. Gram-negative and Gram-positive bacterial extracellular vesicles. Semin Cell Dev Biol 2015; 40:97-104. [PMID: 25704309 DOI: 10.1016/j.semcdb.2015.02.006] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/06/2015] [Accepted: 02/12/2015] [Indexed: 01/26/2023]
Abstract
Like mammalian cells, Gram-negative and Gram-positive bacteria release nano-sized membrane vesicles into the extracellular environment either in a constitutive manner or in a regulated manner. These bacterial extracellular vesicles are spherical bilayered proteolipids enriched with bioactive proteins, lipids, nucleic acids, and virulence factors. Recent progress in this field supports the critical pathophysiological functions of these vesicles in both bacteria-bacteria and bacteria-host interactions. This review provides an overview of the current understanding on Gram-negative and Gram-positive bacterial extracellular vesicles, especially regarding the biogenesis, components, and functions in poly-species communities. We hope that this review will stimulate additional research in this emerging field of bacterial extracellular vesicles and contribute to the development of extracellular vesicle-based diagnostic tools and effective vaccines against pathogenic Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Ji Hyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Jaewook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Jaesung Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea.
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Kim DK, Lee J, Simpson RJ, Lötvall J, Gho YS. EVpedia: A community web resource for prokaryotic and eukaryotic extracellular vesicles research. Semin Cell Dev Biol 2015; 40:4-7. [PMID: 25704310 DOI: 10.1016/j.semcdb.2015.02.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/06/2015] [Accepted: 02/12/2015] [Indexed: 12/31/2022]
Abstract
For cell-to-cell communication, all living cells including archaea, bacteria, and eukaryotes secrete nano-sized membrane vesicles into the extracellular space. These extracellular vesicles harbor specific subsets of proteins, mRNAs, miRNAs, lipids, and metabolites that represent their cellular status. These vesicle-specific cargos are considered as novel diagnostic biomarkers as well as therapeutic targets. With the advancement in high-throughput technologies on multiomics studies and improvements in bioinformatics approaches, a huge number of vesicular proteins, mRNAs, miRNAs, lipids, and metabolites have been identified, and our understanding of these complex extracellular organelles has considerably increased during these past years. In this review, we highlight EVpedia (http://evpedia.info), a community web portal for systematic analyses of prokaryotic and eukaryotic extracellular vesicles research.
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Affiliation(s)
- Dae-Kyum Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Jaewook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Richard J Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jan Lötvall
- Krefting Research Centre, Department of Internal Medicine, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
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50
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Jang SC, Kim SR, Yoon YJ, Park KS, Kim JH, Lee J, Kim OY, Choi EJ, Kim DK, Choi DS, Kim YK, Park J, Di Vizio D, Gho YS. In vivo kinetic biodistribution of nano-sized outer membrane vesicles derived from bacteria. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:456-461. [PMID: 25196673 DOI: 10.1002/smll.201401803] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Evaluation of kinetic distribution and behaviors of nanoparticles in vivo provides crucial clues into their roles in living organisms. Extracellular vesicles are evolutionary conserved nanoparticles, known to play important biological functions in intercellular, inter-species, and inter-kingdom communication. In this study, the first kinetic analysis of the biodistribution of outer membrane vesicles (OMVs)-bacterial extracellular vesicles-with immune-modulatory functions is performed. OMVs, injected intraperitoneally, spread to the whole mouse body and accumulate in the liver, lung, spleen, and kidney within 3 h of administration. As an early systemic inflammation response, increased levels of TNF-α and IL-6 are observed in serum and bronchoalveolar lavage fluid. In addition, the number of leukocytes and platelets in the blood is decreased. OMVs and cytokine concentrations, as well as body temperature are gradually decreased 6 h after OMV injection, in concomitance with the formation of eye exudates, and of an increase in ICAM-1 levels in the lung. Following OMV elimination, most of the inflammatory signs are reverted, 12 h post-injection. However, leukocytes in bronchoalveolar lavage fluid are increased as a late reaction. Taken together, these results suggest that OMVs are effective mediators of long distance communication in vivo.
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Affiliation(s)
- Su Chul Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
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