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Takemoto Y, Ito D, Komori S, Kishimoto Y, Yamada S, Hashizume A, Katsuno M, Nakatochi M. Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs. BMC Bioinformatics 2024; 25:221. [PMID: 38902629 PMCID: PMC11188187 DOI: 10.1186/s12859-024-05840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Extracellular vesicle-derived (EV)-miRNAs have potential to serve as biomarkers for the diagnosis of various diseases. miRNA microarrays are widely used to quantify circulating EV-miRNA levels, and the preprocessing of miRNA microarray data is critical for analytical accuracy and reliability. Thus, although microarray data have been used in various studies, the effects of preprocessing have not been studied for Toray's 3D-Gene chip, a widely used measurement method. We aimed to evaluate batch effect, missing value imputation accuracy, and the influence of preprocessing on measured values in 18 different preprocessing pipelines for EV-miRNA microarray data from two cohorts with amyotrophic lateral sclerosis using 3D-Gene technology. RESULTS Eighteen different pipelines with different types and orders of missing value completion and normalization were used to preprocess the 3D-Gene microarray EV-miRNA data. Notable results were suppressed in the batch effects in all pipelines using the batch effect correction method ComBat. Furthermore, pipelines utilizing missForest for missing value imputation showed high agreement with measured values. In contrast, imputation using constant values for missing data exhibited low agreement. CONCLUSIONS This study highlights the importance of selecting the appropriate preprocessing strategy for EV-miRNA microarray data when using 3D-Gene technology. These findings emphasize the importance of validating preprocessing approaches, particularly in the context of batch effect correction and missing value imputation, for reliably analyzing data in biomarker discovery and disease research.
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Affiliation(s)
- Yuto Takemoto
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan
| | - Daisuke Ito
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shota Komori
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Kishimoto
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shinichiro Yamada
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Atsushi Hashizume
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan.
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Zhou L, Liu X, Wu T, Liu Q, Jing M, Li H, Xu N, Tang H. Identification of survival related key genes and long-term survival specific differentially expressed genes related key miRNA network of primary glioblastoma. Heliyon 2024; 10:e28439. [PMID: 38601561 PMCID: PMC11004527 DOI: 10.1016/j.heliyon.2024.e28439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Primary glioblastoma(pGBM) is the most malignant tumor of the central nervous system. Radiotherapy, chemotherapy and surgical treatment have little effect on the survival of pGBM patients. The prognosis is often poorly once the tumor recurs. It is urgent to develop new therapies for patients. In recent years, studies have been clarified that miRNA have a powerful regulating effect on the genes. However, the main group of miRNAs in regulating long-term survival specific related genes of pGBM is still unclear. Given that the survival period of most glioma patients is relatively short, studying long-term survival patients with pGBM is of great value for this disease. Our study aim to identify key miRNAs with long-term survival related genes present in pGBM and uncover their potential mechanisms. The gene expression profiles of GSE53733, GSE15824, GSE30563, GSE50161 were obtained from the Gene Expression Omnibus database. Firstly, samples were divided into 3 groups according to its survival time and each group compare to the normal control group. Then we obtained differential expression genes (DEGs) with a long-term survival specific (LTSDEGs) and a short-term survival specific DEGs (STSDEGs). Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted with LTSDEGs and STSDEGs together. Moreover, we used the UALCAN database to verify LTSDEGs and STSDEGs, and obtained long-term verified survival specific DEGs(LTVSDEGs) and short-term verified survival specific DEGs(STVSDEGs). Finally, we established the predicted key miRNAs-LTVSDEGs interaction network. The protein expressions of the top 4 LTVSDEGs were verified in the HPA database with immunohistochemical staining. In total, we found 260 genes changed in LTSDEGs and 822 genes changed in STSDEGs. GO and KEGG results shown that the major changes are focused on tumor metabolism. 9 LTVSDEGs and 18 STVSDEGs were verified in UALCAN database. As for protein expression verification in top 4 LTVSDEGs, ZNF630, BLVRB and RPA3 were verified, while TPBG was not detected. We obtained 59 key miRNA from the predicted key miRNAs-LTVSDEGs interaction network. 25 key miRNAs were verified using GSE90603. Finally, we constructed the key miRNAs-LTVSDEGs network using a Sankey diagram, including 25 miRNAs and 7 LTVSDEGs. In conclusion, our study shows that there is a close relationship between metabolic changes and survival in pGBM. Besides, we established a key miRNAs-LTVSDEGs network for pGBM, which could be the key path in prolonging the life of pGBM patients.
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Affiliation(s)
- Lingqi Zhou
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
- Guangzhou Key Laboratory of Child Neurodevelopment, Guangzhou, 510623, China
- Institute Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
| | - Xuemei Liu
- Department of Gynecology, Shunde Hospital,Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, 528308, China
| | - Tong Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
| | - Qundi Liu
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Meilian Jing
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Huahan Li
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Ning Xu
- Department of Clinical Laboratory, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518111, China
| | - Hai Tang
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
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Chen Z, Wang Q, Liu J, Wang W, Yuan W, Liu Y, Sun Z, Wang C. Effects of extracellular vesicle-derived noncoding RNAs on pre-metastatic niche and tumor progression. Genes Dis 2024; 11:176-188. [PMID: 37588211 PMCID: PMC10425748 DOI: 10.1016/j.gendis.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 01/20/2023] Open
Abstract
A pre-metastatic niche (PMN) is a protective microenvironment that facilitates the colonization of disseminating tumor cells in future metastatic organs. Extracellular vesicles (EVs) play a role in intercellular communication by delivering cargoes, such as noncoding RNAs (ncRNAs). The pivotal role of extracellular vesicle-derived noncoding RNAs (EV-ncRNAs) in the PMN has attracted increasing attention. In this review, we summarized the effects of EV-ncRNAs on the PMN in terms of immunosuppression, vascular permeability and angiogenesis, inflammation, metabolic reprogramming, and fibroblast alterations. In particular, we provided a comprehensive overview of the effects of EV-ncRNAs on the PMN in different cancers. Finally, we discussed the promising clinical applications of EV-ncRNAs, including their potential as diagnostic and prognostic markers and therapeutic targets.
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Affiliation(s)
- Zhuang Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Wenkang Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yang Liu
- Department of Radiotherapy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chengzeng Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
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Formation of pre-metastatic niches induced by tumor extracellular vesicles in lung metastasis. Pharmacol Res 2023; 188:106669. [PMID: 36681367 DOI: 10.1016/j.phrs.2023.106669] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
There are a number of malignant tumors that metastasize into the lung as one of their most common sites of dissemination. The successful infiltration of tumor cells into distant organs is the result of the cooperation between tumor cells and distant host cells. When tumor cells have not yet reached distant organs, in situ tumor cells secrete extracellular vesicles (EVs) carrying important biological information. In recent years, scholars have found that tumor cells-derived EVs act as the bridge between orthotopic tumors and secondary metastases by promoting the formation of a pre-metastatic niche (PMN), which plays a key role in awakening dormant circulating tumor cells and promoting tumor cell colonization. This review provides an overview of multiple routes and mechanisms underlying PMN formation induced by EVs and summaries study findings that underline a potential role of EVs in the intervention of lung PMN, both as a target or a carrier for drug design. In this review, the underlying mechanisms of EVs in lung PMN formation are highlighted as well as potential applications to lung metastasis diagnosis and treatment.
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Cen S, Cai M, Wang Y, Lu X, Chen Z, Chen H, Fang Y, Wu C, Qiu S, Liu Z. Aberrant lncRNA–mRNA expression profile and function networks during the adipogenesis of mesenchymal stem cells from patients with ankylosing spondylitis. Front Genet 2022; 13:991875. [PMID: 36246583 PMCID: PMC9563993 DOI: 10.3389/fgene.2022.991875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: We have already demonstrated that mesenchymal stem cells from patients with ankylosing spondylitis (ASMSCs) exhibited greater adipogenic differentiation potential than those from healthy donors (HDMSCs). Here, we further investigated the expression profile of long noncoding RNA (lncRNA) and mRNA, aiming to explore the underlying mechanism of abnormal adipogenic differentiation in ASMSCs.Methods: HDMSCs and ASMSCs were separately isolated and induced with adipogenic differentiation medium for 10 days. Thereafter, lncRNAs and mRNAs that were differentially expressed (DE) between HDMSCs and ASMSCs were identified via high-throughput sequencing and confirmed by quantitative real-time PCR (qRT–PCR) assays. Then, the DE genes were annotated and enriched by GO analysis. In addition, protein interaction network was constructed to evaluate the interactions between DE mRNAs and to find hub nodes and study cliques. Besides, co-expression network analysis was carried out to assess the co-expressions between DE mRNA and DE lncRNAs, and competing endogenous RNA (ceRNA) network analysis were conducted to predict the relationships among lncRNAs, mRNAs and miRNAs. The signaling pathways based on the DE genes and the predicted DE genes were enriched by KEGG analysis.Results: A total of 263 DE lncRNAs and 1376 DE mRNAs were found during adipogenesis in ASMSCs. qRT–PCR indicated that the expression of the top 20 mRNAs and the top 10 lncRNAs was consistent with the high-throughput sequencing data. Several lncRNAs (NR_125386.1, NR_046473.1 and NR_038937.1) and their target genes (SPN and OR1AIP2), together with the significantly co-expressed pairs of DE lncRNAs and DE mRNAs (SLC38A5-ENST00000429588.1, TMEM61-ENST00000400755.3 and C5orf46-ENST00000512300.1), were closely related to the enhanced adipogenesis of ASMSCs by modulating the PPAR signaling pathway.Conclusion: Our study analyzed the expression profiles of DE lncRNAs and DE mRNAs during adipogenesis in ASMSCs and HDMSCs. Several DE lncRNAs, DE mRNAs and signaling pathways that probably participate in the aberrant adipogenesis of ASMSCs were selected for future study. These results will likely provide potential targets for our intervention on fat metaplasia and subsequent new bone formation in patients with AS in the future.
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Affiliation(s)
- Shuizhong Cen
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxi Cai
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yihan Wang
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiuyi Lu
- Department of Dermatology, The Fourth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhipeng Chen
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haobo Chen
- Department of Orthopedics, People’s Hospital of Taishan, Jiangmen, China
| | - Yingdong Fang
- Department of Orthopedics, People’s Hospital of Taishan, Jiangmen, China
| | - Changping Wu
- Department of Orthopedics, People’s Hospital of Taishan, Jiangmen, China
| | - Sujun Qiu
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Sujun Qiu, ; Zhenhua Liu,
| | - Zhenhua Liu
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Sujun Qiu, ; Zhenhua Liu,
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Lucotti S, Kenific CM, Zhang H, Lyden D. Extracellular vesicles and particles impact the systemic landscape of cancer. EMBO J 2022; 41:e109288. [PMID: 36052513 PMCID: PMC9475536 DOI: 10.15252/embj.2021109288] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/16/2022] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
Intercellular cross talk between cancer cells and stromal and immune cells is essential for tumor progression and metastasis. Extracellular vesicles and particles (EVPs) are a heterogeneous class of secreted messengers that carry bioactive molecules and that have been shown to be crucial for this cell-cell communication. Here, we highlight the multifaceted roles of EVPs in cancer. Functionally, transfer of EVP cargo between cells influences tumor cell growth and invasion, alters immune cell composition and function, and contributes to stromal cell activation. These EVP-mediated changes impact local tumor progression, foster cultivation of pre-metastatic niches at distant organ-specific sites, and mediate systemic effects of cancer. Furthermore, we discuss how exploiting the highly selective enrichment of molecules within EVPs has profound implications for advancing diagnostic and prognostic biomarker development and for improving therapy delivery in cancer patients. Altogether, these investigations into the role of EVPs in cancer have led to discoveries that hold great promise for improving cancer patient care and outcome.
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Affiliation(s)
- Serena Lucotti
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Candia M Kenific
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Haiying Zhang
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
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Cucchiari D, Tubita V, Rovira J, Ramirez-Bajo MJ, Banon-Maneus E, Lazo-Rodriguez M, Hierro-Garcia N, Borràs FE, Ventura-Aguiar P, Piñeiro GJ, Martorell J, Peri L, Musquera M, Hertig A, Oppenheimer F, Campistol JM, Diekmann F, Revuelta I. B Cell-Derived Extracellular Vesicles Reveal Residual B Cell Activity in Kidney Graft Recipients Undergoing Pre-Transplant Desensitization. Front Med (Lausanne) 2021; 8:781239. [PMID: 34977082 PMCID: PMC8716735 DOI: 10.3389/fmed.2021.781239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Living-donor kidney transplant (LDKT) recipients undergoing desensitization for Human Leukocyte Antigen (HLA)-incompatibility have a high risk of developing antibody-mediated rejection (ABMR). The purpose of the study is to evaluate if residual B cell activity after desensitization could be estimated by the presence of circulating B cell-derived extracellular vesicles (BEVs).Methods: BEVs were isolated by Sepharose-based size exclusion chromatography and defined as CD19+ and HLA-II+ extracellular vesicles. We analyzed stored serum samples from positive crossmatch LDKT recipients before and after desensitization at first post-transplant biopsy and at 12-month protocol biopsy (n = 11). Control groups were formed by hypersensitized patients who were not submitted to desensitization (n = 10) and by low-risk recipients (n = 9). A prospective validation cohort of 11 patients also included the analysis of B cells subpopulations in recipients' blood and lymph nodes recovered upon graft implantation, along with BEVs analysis before and after desensitization.Results: We found out that CD19+ and HLA-II+BEVs dropped significantly after desensitization and relapse in patients who later developed ABMR was evident. We validated these findings in a proof-of-concept prospective cohort of 6 patients who received the same desensitization protocol and also in a control group of 5 LDKT recipients. In these patients, B cell subpopulations were also studied in recipients' blood and lymph nodes that were recovered before the graft implantation. We confirmed the significant drop in BEVs after desensitization and that this paralleled the reduction in CD19+cells in lymph nodes, while in peripheral blood B cells, this change was almost undetectable.Conclusions: BEVs reflected B cell residual activity after desensitization and this could be a valid surrogate of humoral alloreactivity in this setting.
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Affiliation(s)
- David Cucchiari
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- *Correspondence: Ignacio Revuelta
| | - Valeria Tubita
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jordi Rovira
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Maria J. Ramirez-Bajo
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Elisenda Banon-Maneus
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Marta Lazo-Rodriguez
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Natalia Hierro-Garcia
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Francesc E. Borràs
- Red de Investigación Renal (REDINREN), Madrid, Spain
- REMAR-IVECAT Group, “Germans Trias i Pujol” Health Science Research Institute, Badalona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Pedro Ventura-Aguiar
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
| | - Gastón J. Piñeiro
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
| | | | - Lluís Peri
- Department of Urology, Hospital Clínic, Barcelona, Spain
| | | | | | - Federico Oppenheimer
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Josep M. Campistol
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Fritz Diekmann
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Ignacio Revuelta
- Department of Nephrology and Kidney Transplantation, Hospital Clínic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
- David Cucchiari
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Chang YC, Chan MH, Li CH, Fang CY, Hsiao M, Chen CL. Exosomal Components and Modulators in Colorectal Cancer: Novel Diagnosis and Prognosis Biomarkers. Biomedicines 2021; 9:biomedicines9080931. [PMID: 34440135 PMCID: PMC8391321 DOI: 10.3390/biomedicines9080931] [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: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
The relatively high incidence and mortality rates for colorectal carcinoma (CRC) make it a formidable malignant tumor. Comprehensive strategies have been applied to predict patient survival and diagnosis. Various clinical regimens have also been developed to improve the therapeutic outcome. Extracellular vesicles (EVs) are recently proposed cellular structures that can be produced by natural or artificial methods and have been extensively studied. In addition to their innate functions, EVs can be manipulated to be drug carriers and exert many biological functions. The composition of EVs, their intravesicular components, and the surrounding tumor microenvironment are closely related to the development of colorectal cancer. Determining the expression profiles of exocytosis samples and using them as indicators for selecting effective combination therapy is an indispensable direction for EV study and should be regarded as a novel prediction platform in addition to cancer stage, prognosis, and other clinical assessments. In this review, we summarize the function, regulation, and application of EVs in the colon cancer research field. We provide an update on and discuss potential values for clinical applications of EVs. Moreover, we illustrate the specific markers, mediators, and genetic alterations of EVs in colorectal carcinogenesis. Furthermore, we outline the vital markers present in the EVs and discuss their plausible uses in colon cancer patient therapy in combination with the currently used clinical strategies. The development and application of these EVs will significantly improve the accuracy of diagnosis, lead to more precise prognoses, and may lead to the improved treatment of colorectal cancer.
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Affiliation(s)
- Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Science, National Yang-Ming University, Taipei 112, Taiwan;
- Department of Biomedical Imaging and Radiological Science, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ming-Hsien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
| | - Chien-Hsiu Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
| | - Chih-Yeu Fang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: (M.H.); (C.-L.C.); Tel.: +886-2-2787-1243 (M.H.); +886-2-2736-1661 (ext. 3139) (C.-L.C.); Fax: +886-2-2789-9931 (M.H.)
| | - Chi-Long Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Pathology, Taipei Medical University Hospital, Taipei 110, Taiwan
- Correspondence: (M.H.); (C.-L.C.); Tel.: +886-2-2787-1243 (M.H.); +886-2-2736-1661 (ext. 3139) (C.-L.C.); Fax: +886-2-2789-9931 (M.H.)
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Caner V, Cetin GO, Hacioglu S, Baris IC, Tepeli E, Turk NS, Bagci G, Yararbas K, Cagliyan G. The miRNA content of circulating exosomes in DLBCL patients and in vitro influence of DLBCL-derived exosomes on miRNA expression of healthy B cells from peripheral blood. Cancer Biomark 2021; 32:519-529. [PMID: 34275894 DOI: 10.3233/cbm-210110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Due to the heterogeneous nature of Diffuse Large B-cell Lymphoma (DLBCL), the mechanisms underlying tumor development and progression have not yet been fully elucidated. OBJECTIVE This study aimed to compare the characteristics of plasma exosomes of DLBCL patients and healthy individuals and to evaluate the exosomal interactions between DLBCL cell lines and normal B-cells. METHODS Exosome isolation was performed using an ultracentrifugation-based protocol from plasma of 20 patients with DLBCL and 20 controls. The expression of miRNAs from exosome samples was analyzed using a miRNA expression microarray. The presence of exosome-mediated communication between the lymphoma cells and normal B-cells was determined by the co-culture model. RESULTS A significant increase in plasma exosome concentrations of DLBCL patients was observed. There was also a significant decrease in the expression of 33 miRNAs in plasma exosomes of DLBCL patients. It was determined that normal B-cells internalize DLBCL-derived exosomes and then miRNA expression differences observed in normal B-cells are specific to lymphoma-subtypes. CONCLUSIONS MiR-3960, miR-6089 and miR-939-5p can be used as the miRNA signature in DLBCL diagnosis. We suppose that the exosomes changed the molecular signature of the target cells depending on the genomic characterization of the lymphoma cells they have originated.
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Affiliation(s)
- Vildan Caner
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Gokhan Ozan Cetin
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Sibel Hacioglu
- Department of Hematology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Ikbal Cansu Baris
- Department of Medical Biology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Emre Tepeli
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Nilay Sen Turk
- Department of Medical Pathology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Gulseren Bagci
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Kanay Yararbas
- Department of Medical Genetics, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Gulsum Cagliyan
- Department of Hematology, School of Medicine, Pamukkale University, Denizli, Turkey
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10
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LINC00689 participates in proliferation, chemoresistance and metastasis via miR-31-5p/YAP/β-catenin axis in colorectal cancer. Exp Cell Res 2020; 395:112176. [PMID: 32682784 DOI: 10.1016/j.yexcr.2020.112176] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
As a kind of high-incidence malignant tumors in the digestive tract, colorectal cancer (CRC) has extremely morbidity and mortality in the population. LncRNAs have been proved to regulate the proliferation, chemoresistance and metastasis of tumors including CRC. LINC00689 and miR-31-5p in CRC were found misregulated in CRC by TCGA analysis. However, the mechanism of LINC00689 and miR-31-5p in regulating CRC remains unknown. The expression levels of LINC00689, miR-31-5p and LATS2 in CRC tissues and cell lines were examined by qRT-PCR assay. Cell proliferation, metastasis (including invasion and migration) were quantified by MTT assay, colony formation and Transwell assay, respectively. Western blotting assay was then performed to verify the levels of YAP/β-catenin and metastasis-related proteins. Dual-luciferase reporter assay and RIP assay were performed to evaluate the interaction between LINC00689 (LATS2) and miR-31-5p. Moreover, the function of LINC00689 and miR-31-5p were confirmed by CRC xenograft in nude mice. LINC00689 was decreased while miR-31-5p was increased in CRC. The overexpression of LINC00689 or the knockdown of miR-31-5p inhibited cell proliferation, chemoresistance and metastasis of CRC cells. Meanwhile, the up-regulated LATS2 suppressed the activity of YAP/β-catenin pathway to repress CRC occurrence. Silencing LATS2 reversed the inhibition effects of overexpression of LINC00689 or knockdown of miR-31-5p on proliferation, chemoresistance and metastasis of CRC cells. LINC00689 indeed acted as a miR-31-5p sponge to inhibit CRC proliferation, chemoresistance and metastasis through up-regulating LATS2 and repressing YAP/β-catenin signaling pathway.
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11
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Extracellular Vesicles in Cell Biology and Medicine. Sci Rep 2020; 10:8667. [PMID: 32439963 PMCID: PMC7242379 DOI: 10.1038/s41598-020-65826-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
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12
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Cui G, Yuan A, Li Z, Goll R, Florholmen J. ST2 and regulatory T cells in the colorectal adenoma/carcinoma microenvironment: implications for diseases progression and prognosis. Sci Rep 2020; 10:5892. [PMID: 32246094 PMCID: PMC7125220 DOI: 10.1038/s41598-020-62502-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
ST2 (also known as IL1RL1) is the critical functional receptor for interleukin (IL)-33 in stimulating regulatory T cell (Treg) expansion and function in physiological and pathological conditions. We examined the correlation between ST2 cell expression and FoxP3 positive Tregs in both colorectal adenoma and cancer (CRC) microenvironment by real-time PCR, immunohistochemistry (IHC) and double immunofluorescences. The clinicopathological and prognostic significance of cellular ST2-positive cells and FoxP3-positive Tregs in patients with adenoma and CRC were evaluated. Real-time PCR results revealed increased expression levels of ST2 and FoxP3 mRNAs in both adenoma and CRC tissues as compared with control tissues. IHC analysis confirmed increased densities of ST2-positive cells in both the adenoma/CRC epithelium and stroma, which show a close positive linear association with the densities of FoxP3-positive Tregs in respective compartments. Pathological feature analysis showed that densities of ST2-positive cells in the tumor stroma were notably associated with degree of dysplastic grading in patients with adenoma, and disease stages and lymph node metastasis in patients with CRC. Kaplan-Meier survival curves suggested that CRC patients with high densities of ST2-positive cells in the stroma tend to have a shorter overall survival. We therefore concluded that increased densities of ST2-postive cells relate to Treg accumulation within the adenoma/CRC microenvironment, suggesting the IL-33/ST2 pathway as a potential contributor for immunosuppressive milieu formation that impact disease stage and prognosis in patients with CRC.
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Affiliation(s)
- Guanglin Cui
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Henan, China. .,Faculty of Health Science, Nord University at Campus Levanger, Levanger, Norway.
| | - Aping Yuan
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Henan, China
| | - Zhenfeng Li
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Henan, China
| | - Rasmus Goll
- Department of Gastroenterology & Nutrition, University Hospital of North Norway, Tromsø, University of Tromsø, Tromsø, Norway
| | - Jon Florholmen
- Department of Gastroenterology & Nutrition, University Hospital of North Norway, Tromsø, University of Tromsø, Tromsø, Norway
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13
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Mannavola F, D’Oronzo S, Cives M, Stucci LS, Ranieri G, Silvestris F, Tucci M. Extracellular Vesicles and Epigenetic Modifications Are Hallmarks of Melanoma Progression. Int J Mol Sci 2019; 21:E52. [PMID: 31861757 PMCID: PMC6981648 DOI: 10.3390/ijms21010052] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
Cutaneous melanoma shows a high metastatic potential based on its ability to overcome the immune system's control. The mechanisms activated for these functions vary extremely and are also represented by the production of a number of extracellular vesicles including exosomes. Other vesicles showing a potential role in the melanoma progression include oncosomes and melanosomes and the majority of them mediate tumor processes including angiogenesis, immune regulation, and modifications of the micro-environment. Moreover, a number of epigenetic modifications have been described in melanoma and abundant production of altered microRNAs (mi-RNAs), non-coding RNAs, histones, and abnormal DNA methylation have been associated with different phases of melanoma progression. In addition, exosomes, miRNAs, and other molecular factors have been used as potential biomarkers reflecting disease evolution while others have been suggested to be potential druggable molecules for therapeutic application.
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Affiliation(s)
- Francesco Mannavola
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
| | - Stella D’Oronzo
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
- National Cancer Research Center, Istituto Tumori ‘Giovanni Paolo II’, 70121 Bari, Italy;
| | - Mauro Cives
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
| | - Luigia Stefania Stucci
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
| | - Girolamo Ranieri
- National Cancer Research Center, Istituto Tumori ‘Giovanni Paolo II’, 70121 Bari, Italy;
| | - Franco Silvestris
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
| | - Marco Tucci
- Department of Biomedical Sciences and Clinical Oncology, University of Bari, ‘Aldo Moro’, 70121 Bari, Italy; (F.M.); (S.D.); (M.C.); (L.S.S.); (F.S.)
- National Cancer Research Center, Istituto Tumori ‘Giovanni Paolo II’, 70121 Bari, Italy;
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