|
1
|
Suwakulsiri W, Xu R, Rai A, Chen M, Shafiq A, Greening DW, Simpson RJ. Transcriptomic analysis and fusion gene identifications of midbody remnants released from colorectal cancer cells reveals they are molecularly distinct from exosomes and microparticles. Proteomics 2024; 24:e2300058. [PMID: 38470197 DOI: 10.1002/pmic.202300058] [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: 10/01/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Previously, we reported that human primary (SW480) and metastatic (SW620) colorectal (CRC) cells release three classes of membrane-encapsulated extracellular vesicles (EVs); midbody remnants (MBRs), exosomes (Exos), and microparticles (MPs). We reported that MBRs were molecularly distinct at the protein level. To gain further biochemical insights into MBRs, Exos, and MPs and their emerging role in CRC, we performed, and report here, for the first time, a comprehensive transcriptome and long noncoding RNA sequencing analysis and fusion gene identification of these three EV classes using the next-generation RNA sequencing technique. Differential transcript expression analysis revealed that MBRs have a distinct transcriptomic profile compared to Exos and MPs with a high enrichment of mitochondrial transcripts lncRNA/pseudogene transcripts that are predicted to bind to ribonucleoprotein complexes, spliceosome, and RNA/stress granule proteins. A salient finding from this study is a high enrichment of several fusion genes in MBRs compared to Exos, MPs, and cell lysates from their parental cells such as MSH2 (gene encoded DNA mismatch repair protein MSH2). This suggests potential EV-liquid biopsy targets for cancer detection. Importantly, the expression of cancer progression-related transcripts found in EV classes derived from SW480 (EGFR) and SW620 (MET and MACCA1) cell lines reflects their parental cell types. Our study is the report of RNA and fusion gene compositions within MBRs (including Exos and MPs) that could have an impact on EV functionality in cancer progression and detection using EV-based RNA/ fusion gene candidates for cancer biomarkers.
Collapse
Affiliation(s)
- Wittaya Suwakulsiri
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, New South Wales, Australia
| | - Rong Xu
- Nanobiotechnology Laboratory, Australia Centre for Blood Diseases, Centre Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Maoshan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Adnan Shafiq
- Department of Cell & Developmental Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard J Simpson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| |
Collapse
|
|
2
|
Eichhorn T, Weiss R, Huber S, Ebeyer-Masotta M, Mostageer M, Emprechtinger R, Knabl L, Knabl L, Würzner R, Weber V. Expression of Tissue Factor and Platelet/Leukocyte Markers on Extracellular Vesicles Reflect Platelet-Leukocyte Interaction in Severe COVID-19. Int J Mol Sci 2023; 24:16886. [PMID: 38069209 PMCID: PMC10707108 DOI: 10.3390/ijms242316886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Severe COVID-19 is frequently associated with thromboembolic complications. Increased platelet activation and platelet-leukocyte aggregate formation can amplify thrombotic responses by inducing tissue factor (TF) expression on leukocytes. Here, we characterized TF-positive extracellular vesicles (EVs) and their cellular origin in 12 patients suffering from severe COVID-19 (time course, 134 samples overall) and 25 healthy controls. EVs exposing phosphatidylserine (PS) were characterized by flow cytometry. Their cellular origin was determined by staining with anti-CD41, anti-CD45, anti-CD235a, and anti-CD105 as platelet, leukocyte, red blood cell, and endothelial markers. We further investigated the association of EVs with TF, platelet factor 4 (PF4), C-reactive protein (CRP), and high mobility group box-1 protein (HMGB-1). COVID-19 patients showed higher levels of PS-exposing EVs compared to controls. The majority of these EVs originated from platelets. A higher amount of EVs in patient samples was associated with CRP, HMGB-1, PF4, and TF as compared to EVs from healthy donors. In COVID-19 samples, 16.5% of all CD41+ EVs displayed the leukocyte marker CD45, and 55.5% of all EV aggregates (CD41+CD45+) co-expressed TF, which reflects the interaction of platelets and leukocytes in COVID-19 on an EV level.
Collapse
Affiliation(s)
- Tanja Eichhorn
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, 3500 Krems, Austria; (R.W.); (M.E.-M.); (M.M.); (V.W.)
| | - René Weiss
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, 3500 Krems, Austria; (R.W.); (M.E.-M.); (M.M.); (V.W.)
| | - Silke Huber
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (S.H.); (R.W.)
| | - Marie Ebeyer-Masotta
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, 3500 Krems, Austria; (R.W.); (M.E.-M.); (M.M.); (V.W.)
| | - Marwa Mostageer
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, 3500 Krems, Austria; (R.W.); (M.E.-M.); (M.M.); (V.W.)
| | - Robert Emprechtinger
- Faculty of Health and Medicine, University for Continuing Education Krems, 3500 Krems, Austria;
| | - Ludwig Knabl
- Department of Internal Medicine, Hospital St. Vinzenz, 6511 Zams, Austria;
| | | | - Reinhard Würzner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (S.H.); (R.W.)
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, 3500 Krems, Austria; (R.W.); (M.E.-M.); (M.M.); (V.W.)
| |
Collapse
|