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Zheng T, Zheng Z, Zhou H, Guo Y, Li S. The multifaceted roles of COL4A4 in lung adenocarcinoma: An integrated bioinformatics and experimental study. Comput Biol Med 2024; 170:107896. [PMID: 38217972 DOI: 10.1016/j.compbiomed.2023.107896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Abnormal expression of collagen IV subunits has been reported in cancers, but the significance is not clear. No study has reported the significance of COL4A4 in lung adenocarcinoma (LUAD). METHODS COL4A4 expression data, single-cell sequencing data and clinical data were downloaded from public databases. A range of bioinformatics and experimental methods were adopted to analyze the association of COL4A4 expression with clinical parameters, tumor microenvironment (TME), drug resistance and immunotherapy response, and to investigate the roles and underlying mechanism of COL4A4 in LUAD. RESULTS COL4A4 is differentially expressed in most of cancers analyzed, being associated with prognosis, tumor stemness, immune checkpoint gene expression and TME parameters. In LUAD, COL4A4 expression is down-regulated and associated with various TME parameters, response to immunotherapy and drug resistance. LUAD patients with lower COL4A4 have worse prognosis. Knockdown of COL4A4 significantly inhibited the expression of cell-cycle associated genes, and the expression and activation of signaling pathways including JAK/STAT3, p38, and ERK pathways, and induced quiescence in LUAD cells. Besides, it significantly induced the expression of a range of bioactive molecule genes that have been shown to have critical roles in TME remodeling and immune regulation. CONCLUSIONS COL4A4 is implicated in the pathogenesis of cancers including LUAD. Its function may be multifaceted. It can modulate the activity of LUAD cells, TME remodeling and tumor stemness, thus affecting the pathological process of LUAD. COL4A4 may be a prognostic molecular marker and a potential therapeutic target.
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Affiliation(s)
- Tiaozhan Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Zhiwen Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Hanxi Zhou
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Yiqing Guo
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Shikang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China.
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Amin S, Massoumi H, Tewari D, Roy A, Chaudhuri M, Jazayerli C, Krishan A, Singh M, Soleimani M, Karaca EE, Mirzaei A, Guaiquil VH, Rosenblatt MI, Djalilian AR, Jalilian E. Cell Type-Specific Extracellular Vesicles and Their Impact on Health and Disease. Int J Mol Sci 2024; 25:2730. [PMID: 38473976 PMCID: PMC10931654 DOI: 10.3390/ijms25052730] [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: 01/31/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Extracellular vesicles (EVs), a diverse group of cell-derived exocytosed particles, are pivotal in mediating intercellular communication due to their ability to selectively transfer biomolecules to specific cell types. EVs, composed of proteins, nucleic acids, and lipids, are taken up by cells to affect a variety of signaling cascades. Research in the field has primarily focused on stem cell-derived EVs, with a particular focus on mesenchymal stem cells, for their potential therapeutic benefits. Recently, tissue-specific EVs or cell type-specific extracellular vesicles (CTS-EVs), have garnered attention for their unique biogenesis and molecular composition because they enable highly targeted cell-specific communication. Various studies have outlined the roles that CTS-EVs play in the signaling for physiological function and the maintenance of homeostasis, including immune modulation, tissue regeneration, and organ development. These properties are also exploited for disease propagation, such as in cancer, neurological disorders, infectious diseases, autoimmune conditions, and more. The insights gained from analyzing CTS-EVs in different biological roles not only enhance our understanding of intercellular signaling and disease pathogenesis but also open new avenues for innovative diagnostic biomarkers and therapeutic targets for a wide spectrum of medical conditions. This review comprehensively outlines the current understanding of CTS-EV origins, function within normal physiology, and implications in diseased states.
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Affiliation(s)
- Sohil Amin
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Hamed Massoumi
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Deepshikha Tewari
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Arnab Roy
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Madhurima Chaudhuri
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Cedra Jazayerli
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Abhi Krishan
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Mannat Singh
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Mohammad Soleimani
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Emine E. Karaca
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
- Department of Ophthalmology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara 06800, Turkey
| | - Arash Mirzaei
- Department of Ophthalmology, University of Medical Sciences, Farabi Eye Hospital, Tehran 13366 16351, Iran;
| | - Victor H. Guaiquil
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Mark I. Rosenblatt
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Ali R. Djalilian
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
| | - Elmira Jalilian
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL 60612, USA; (S.A.); (H.M.); (D.T.); (A.R.); (M.C.); (C.J.); (A.K.); (M.S.); (M.S.); (E.E.K.); (V.H.G.); (M.I.R.); (E.J.)
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Saviana M, Romano G, McElroy J, Nigita G, Distefano R, Toft R, Calore F, Le P, Morales DDV, Atmajoana S, Deppen S, Wang K, Lee LJ, Acunzo M, Nana-Sinkam P. A plasma miRNA-based classifier for small cell lung cancer diagnosis. Front Oncol 2023; 13:1255527. [PMID: 37869089 PMCID: PMC10585112 DOI: 10.3389/fonc.2023.1255527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based classifier to assist in SCLC diagnoses. Methods We profiled deregulated circulating cell-free miRNAs in the plasma of SCLC patients. We tested selected miRNAs on a training cohort and created a classifier by integrating miRNA expression and patients' clinical data. Finally, we applied the classifier on a validation dataset. Results We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group. Discussion This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.
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Affiliation(s)
- Michela Saviana
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Giulia Romano
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Joseph McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH, United States
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Robin Toft
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Patricia Le
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Daniel Del Valle Morales
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah Atmajoana
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Stephen Deppen
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Kai Wang
- Institute for System Biology, Seattle, WA, United States
| | - L. James Lee
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Mario Acunzo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
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Saviana M, Le P, Micalo L, Del Valle-Morales D, Romano G, Acunzo M, Li H, Nana-Sinkam P. Crosstalk between miRNAs and DNA Methylation in Cancer. Genes (Basel) 2023; 14:genes14051075. [PMID: 37239435 DOI: 10.3390/genes14051075] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
miRNAs are some of the most well-characterized regulators of gene expression. Integral to several physiological processes, their aberrant expression often drives the pathogenesis of both benign and malignant diseases. Similarly, DNA methylation represents an epigenetic modification influencing transcription and playing a critical role in silencing numerous genes. The silencing of tumor suppressor genes through DNA methylation has been reported in many types of cancer and is associated with tumor development and progression. A growing body of literature has described the crosstalk between DNA methylation and miRNAs as an additional layer in the regulation of gene expression. Methylation in miRNA promoter regions inhibits its transcription, while miRNAs can target transcripts and subsequently regulate the proteins responsible for DNA methylation. Such relationships between miRNA and DNA methylation serve an important regulatory role in several tumor types and highlight a novel avenue for potential therapeutic targets. In this review, we discuss the crosstalk between DNA methylation and miRNA expression in the pathogenesis of cancer and describe how miRNAs influence DNA methylation and, conversely, how methylation impacts the expression of miRNAs. Finally, we address how these epigenetic modifications may be leveraged as biomarkers in cancer.
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Affiliation(s)
- Michela Saviana
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Patricia Le
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Lavender Micalo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Daniel Del Valle-Morales
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Giulia Romano
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Mario Acunzo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Howard Li
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
| | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
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Kim SY, Ha SM, Kim DU, Park J, Park S, Hyun KA, Jung HI. Modularized dynamic cell culture platform for efficient production of extracellular vesicles and sequential analysis. LAB ON A CHIP 2023; 23:1852-1864. [PMID: 36825402 DOI: 10.1039/d2lc01129h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Extracellular vesicles (EVs) are nanometer-sized particles naturally secreted by cells for intercellular communication that encapsulate bioactive cargo, such as proteins and RNA, with a lipid bilayer. Tumor cell-derived EVs (tdEVs) are particularly promising biomarkers for cancer research because their contents reflect the cell of origin. In most studies, tdEVs have been obtained from cancer cells cultured under static conditions, thus lacking the ability to recapitulate the microenvironment of cells in vivo. Recent developments in perfusable cell culture systems have allowed oxygen and a nutrient gradient to mimic the physiological and cellular microenvironment. However, as these systems are perfused by circulating the culture medium within the unified structure, independently harvesting cells and EVs at each time point for analysis presents a limitation. In this study, a modularized cell culture system is designed for the perfusion and real-time collection of EVs. The system consists of three detachable chambers, one each for fresh medium, cell culture, and EV collection. The fresh medium flows from the medium chamber to the culture chamber at a flow rate controlled by the hydraulic pressure injected with a syringe pump. When the culture medium containing EVs exceeds a certain volume within the chamber, it overflows into the collection chamber to harvest EVs. The compact and modularized chambers are highly interoperable with conventional cell culture modalities used in the laboratory, thus enabling various EV-based assays.
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Affiliation(s)
- Seo Yeon Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Seong Min Ha
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Dong-Uk Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Junhyun Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea
| | - Kyung-A Hyun
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Hyo-Il Jung
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea
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Zhao Y, Yu L, Wang L, Wu Y, Chen H, Wang Q, Wu Y. Current status of and progress in the treatment of malignant pleural effusion of lung cancer. Front Oncol 2023; 12:961440. [PMID: 36818672 PMCID: PMC9933866 DOI: 10.3389/fonc.2022.961440] [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: 06/04/2022] [Accepted: 12/30/2022] [Indexed: 01/22/2023] Open
Abstract
Malignant pleural effusion (MPE) is a common complication in the late stage of malignant tumors. The appearance of MPE indicates that the primary tumor has spread to the pleura or progressed to an advanced stage. The survival time of the patients will be significantly shortened, with a median survival of only a few months. There are a variety of traditional treatments, and their advantages and disadvantages are relatively clear. There are still many problems that cannot be solved by traditional methods in clinical work. The most common one is intrapleural perfusion therapy with chemotherapy drugs, but it has a large side effect of chemotherapy. At present, with the development of medical technology, there are a variety of treatment methods, and many innovative, significant and valuable treatment methods have emerged, which also bring hope for the treatment of refractory and recurrent MPE patients. Several clinical trials had confirmed that drug-carrying microparticles has less adverse reactions and obvious curative effect. However, there is still a long way to go to completely control and cure MPE, and the organic combination of clinical work and scientific research results is needed to bring dawn to refractory MPE patients.
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Affiliation(s)
| | | | | | | | | | | | - Yufeng Wu
- *Correspondence: Qiming Wang, ; Yufeng Wu,
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Yao X, Liao B, Chen F, Liu L, Wu K, Hao Y, Li Y, Wang Y, Fan R, Yin J, Liu L, Guo Y. Comparison of proteomic landscape of extracellular vesicles in pleural effusions isolated by three strategies. Front Bioeng Biotechnol 2023; 11:1108952. [PMID: 37122867 PMCID: PMC10130534 DOI: 10.3389/fbioe.2023.1108952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Extracellular vesicles (EVs) derived from pleural effusion (PE) is emerging as disease biomarkers. However, the methods for isolation of EVs from PE (pEVs) were rarely studied. In our study, three methods for isolating pEVs of lung cancer patients were compared, including ultracentrifugation (UC), a combination of UC and size exclusion chromatography (UC-SEC) and a combination of UC and density gradient ultracentrifugation (UC-DGU). The subpopulation of pEVs was identified by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), Western blotting (WB) and nano-flow cytometry (nFCM). Additionally, the proteomic landscape of pEVs was analyzed by Label-free proteomics. The results showed that, compared with UC and UC-DGU, the UC-SEC method separated pEVs with the highest purity. In the proteomic analysis, on average, 1595 proteins were identified in the pEVs isolated by UC-SEC, much more than pEVs isolated by UC (1222) or UC-DGU (807). Furthermore, approximately 90% of identified proteins in each method were found in the EVs public database ExoCarta. Consistent with this, GO annotation indicated that the core proteins identified in each method were mainly enriched in "extracellular exosome." Many of the top 100 proteins with high expression in each method were suggested as protein markers to validate the presence of EVs in the MISEV2018 guidelines. In addition, combined with lung tissue-specific proteins and vesicular membrane proteins, we screened out and validated several novel protein markers (CD11C, HLA DPA1 and HLA DRB1), which were enriched in pEVs rather than in plasma EVs. In conclusion, our study shows that the method of UC-SEC could significantly improve the purity of EVs and the performance of mass spectrometry-based proteomic profiling in analyzing pEVs. The exosomal proteins CD11C, HLA DPA1 and HLA DRB1 may act as potential markers of pEVs. The proteomic analysis of pEVs provides important information and new ideas for studying diseases complicated with PE.
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Affiliation(s)
- Xue Yao
- School of Medicine, Southwest Jiaotong University, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, China
| | - Baixue Liao
- School of Medicine, Southwest Jiaotong University, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, China
| | - Feng Chen
- Department of Respiratory, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Lüye Liu
- Medical Research Center, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Kaiwen Wu
- School of Medicine, Southwest Jiaotong University, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, China
| | - Yaying Hao
- Medical Research Center, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Yanping Li
- Department of Respiratory, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Yuebin Wang
- Department of Respiratory, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Ruiling Fan
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Jun Yin
- Department of Respiratory, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Lei Liu
- Medical Research Center, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- *Correspondence: Lei Liu, ; Yuanbiao Guo,
| | - Yuanbiao Guo
- Medical Research Center, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- *Correspondence: Lei Liu, ; Yuanbiao Guo,
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8
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Fu X, Liu H, Fan Y, Yuan J. Extracellular vesicle-mediated transfer of lncRNA CLDN10-AS1 aggravates low-density lipoprotein-induced vascular endothelial injury. Physiol Genomics 2022; 54:471-485. [PMID: 36250558 DOI: 10.1152/physiolgenomics.00094.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Oxidized low-density lipoprotein (ox-LDL) stimulation impairs the oxidation-reduction equilibrium in vascular endothelial cells (VECs) and contributes to atherosclerosis (AS). This study probed the mechanisms of extracellular vesicle (EV)-mediated transfer of lncRNA CLDN10 antisense RNA 1 (CLDN10-AS1) in ox-LDL-induced VEC injury. Initially, VEC injury models were established by treating human umbilical vein endothelial cells (HUVECs) with ox-LDL. EVs were isolated from HUVECs (HUVECs-EVs) and identified. CLDN10-AS1, microRNA (miR)-186, and Yin Yang 1 (YY1) expressions in ox-LDL-treated HUVECs and EVs derived from these cells (ox-EVs) were measured. HUVECs were incubated with EVs, after which the cell viability, apoptosis, and concentrations of proinflammatory cytokines and oxidative stress markers were measured. We discovered that CLDN10-AS1 and YY1 were upregulated in ox-LDL-treated HUVECs, whereas miR-186 was downregulated. ox-EVs treatment elevated CLDN10-AS1 expression in HUVECs and ox-EVs overexpressing CLDN10-AS1 promoted VEC injury. Besides, CLDN10-AS1 is competitively bound to miR-186 and promoted YY1 expression. Rescue experiments revealed that miR-186 overexpression or YY1 suppression partially reversed the roles of ox-EVs overexpressing CLDN10-AS1 in ox-LDL-induced VEC injury. Lastly, clinical serum samples were collected for verification. Overall, CLDN10-AS1 carried by HUVECs-EVs into HUVECs competitively bound to miR-186 to elevate YY1 expression, thereby aggravating ox-LDL-induced VEC injury.
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Affiliation(s)
- Xiaoyang Fu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China.,People's Hospital of Zhengzhou University, Zhengzhou, China.,Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Heng Liu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yulong Fan
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ji Yuan
- Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China.,Department of Anaesthesia, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Anaesthesia, Central China Fuwai Hospital, Zhengzhou, China
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9
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Shojaee S, Romano G, Sanchez TM, Yermakhanova G, Saviana M, Le P, Nigita G, Calore F, Guthrie R, Hess K, Kang L, Swift-Scanlan T, Graham JT, Rahman NM, Nana-Sinkam PS, Acunzo M. Extracellular Vesicle MicroRNA in Malignant Pleural Effusion. Genes (Basel) 2022; 13:2159. [PMID: 36421832 PMCID: PMC9691121 DOI: 10.3390/genes13112159] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 10/24/2023] Open
Abstract
Lung and breast cancer are the two most common causes of malignant pleural effusion (MPE). MPE diagnosis plays a crucial role in determining staging and therapeutic interventions in these cancers. However, our understanding of the pathogenesis and progression of MPE at the molecular level is limited. Extracellular Vesicles (EVs) and their contents, including microRNAs (miRNAs), can be isolated from all bodily fluids, including pleural fluid. This study aims to compare EV-miRNA patterns of expression in MPE caused by breast (BA-MPE) and lung (LA-MPE) adenocarcinomas compared to the control group of heart-failure-induced effusions (HF-PE). We conducted an analysis of 24 pleural fluid samples (8 LA-MPE, 8 BA-MPE, and 8 HF-PE). Using NanoString technology, we profiled miRNAs within EVs isolated from 12 cases. Bioinformatic analysis demonstrated differential expression of miR-1246 in the MPE group vs. HF-PE group and miR-150-5p and miR-1246 in the BA-MPE vs. LA-MPE group, respectively. This difference was demonstrated and validated in an independent cohort using real-time PCR (RT-PCR). miRNA-1246 demonstrated 4-fold increased expression (OR: 3.87, 95% CI: 0.43, 35) in the MPE vs. HF-PE group, resulting in an area under the curve of 0.80 (95% CI: 0.60, 0.99). The highest accuracy for differentiating MPE vs. HF-PE was seen with a combination of miRNAs compared to each miRNA alone. Consistent with prior studies, this study demonstrates dysregulation of specific EV-based miRNAs in breast and lung cancer; pleural fluid provides direct access for the analysis of these EV-miRNAs as biomarkers and potential targets and may provide insight into the underlying pathogenesis of tumor progression. These findings should be explored in large prospective studies.
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Affiliation(s)
- Samira Shojaee
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Giulia Romano
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Trinidad M. Sanchez
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Gulmira Yermakhanova
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Michela Saviana
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Patricia Le
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Rachel Guthrie
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Kathryn Hess
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Le Kang
- Virginia Commonwealth University Health System, Department of Biostatistics, Richmond, VA 23298, USA
| | | | - Jacob T. Graham
- Virginia Commonwealth University School of Nursing, Richmond, VA 23298, USA
| | - Najib M. Rahman
- Oxford Respiratory Trials Unit, University of Oxford, Oxford NIHR Biomedical Research Centre, Oxford and Chinese Academy of Medical Sciences Oxford Institute, Oxford OX3 7LE, UK
| | - Patrick S. Nana-Sinkam
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Mario Acunzo
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
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10
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Proteomic Analysis of Lung Cancer Types—A Pilot Study. Cancers (Basel) 2022; 14:cancers14112629. [PMID: 35681609 PMCID: PMC9179298 DOI: 10.3390/cancers14112629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the leading cause of tumor-related mortality, therefore significant effort is directed towards understanding molecular alterations occurring at the origin of the disease to improve current treatment options. The aim of our pilot-scale study was to carry out a detailed proteomic analysis of formalin-fixed paraffin-embedded tissue sections from patients with small cell or non-small cell lung cancer (adenocarcinoma, squamous cell carcinoma, and large cell carcinoma). Tissue surface digestion was performed on relatively small cancerous and tumor-adjacent normal regions and differentially expressed proteins were identified using label-free quantitative mass spectrometry and subsequent statistical analysis. Principal component analysis clearly distinguished cancerous and cancer adjacent normal samples, while the four lung cancer types investigated had distinct molecular profiles and gene set enrichment analysis revealed specific dysregulated biological processes as well. Furthermore, proteins with altered expression unique to a specific lung cancer type were identified and could be the targets of future studies.
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Aramini B, Masciale V, Arienti C, Dominici M, Stella F, Martinelli G, Fabbri F. Cancer Stem Cells (CSCs), Circulating Tumor Cells (CTCs) and Their Interplay with Cancer Associated Fibroblasts (CAFs): A New World of Targets and Treatments. Cancers (Basel) 2022; 14:cancers14102408. [PMID: 35626011 PMCID: PMC9139858 DOI: 10.3390/cancers14102408] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The world of small molecules in solid tumors as cancer stem cells (CSCs), circulating tumor cells (CTCs) and cancer-associated fibroblasts (CAFs) continues to be under-debated, but not of minor interest in recent decades. One of the main problems in regard to cancer is the development of tumor recurrence, even in the early stages, in addition to drug resistance and, consequently, ineffective or an incomplete response against the tumor. The findings behind this resistance are probably justified by the presence of small molecules such as CSCs, CTCs and CAFs connected with the tumor microenvironment, which may influence the aggressiveness and the metastatic process. The mechanisms, connections, and molecular pathways behind them are still unknown. Our review would like to represent an important step forward to highlight the roles of these molecules and the possible connections among them. Abstract The importance of defining new molecules to fight cancer is of significant interest to the scientific community. In particular, it has been shown that cancer stem cells (CSCs) are a small subpopulation of cells within tumors with capabilities of self-renewal, differentiation, and tumorigenicity; on the other side, circulating tumor cells (CTCs) seem to split away from the primary tumor and appear in the circulatory system as singular units or clusters. It is becoming more and more important to discover new biomarkers related to these populations of cells in combination to define the network among them and the tumor microenvironment. In particular, cancer-associated fibroblasts (CAFs) are a key component of the tumor microenvironment with different functions, including matrix deposition and remodeling, extensive reciprocal signaling interactions with cancer cells and crosstalk with immunity. The settings of new markers and the definition of the molecular connections may present new avenues, not only for fighting cancer but also for the definition of more tailored therapies.
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Affiliation(s)
- Beatrice Aramini
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, 47121 Forlì, Italy;
- Correspondence:
| | - Valentina Masciale
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41122 Modena, Italy; (V.M.); (M.D.)
| | - Chiara Arienti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.A.); (G.M.); (F.F.)
| | - Massimo Dominici
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41122 Modena, Italy; (V.M.); (M.D.)
| | - Franco Stella
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, 47121 Forlì, Italy;
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.A.); (G.M.); (F.F.)
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.A.); (G.M.); (F.F.)
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