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.
Proteomics. 2024 Jun;24(11):e2300058. doi: 10.1002/pmic.202300058. Epub 2024 Mar 12.
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.
先前，我们曾报道过人类原发性（SW480）和转移性（SW620）结直肠（CRC）细胞释放三类膜包裹的细胞外囊泡（EVs）：中体残余物（MBRs）、外泌体（Exos）和微颗粒（MPs）。我们曾报道过 MBRs 在蛋白质水平上具有分子上的差异。为了更深入地了解 MBRs、Exos 和 MPs 及其在 CRC 中的新兴作用，我们首次使用下一代 RNA 测序技术对这三种 EV 类别的转录组和长非编码 RNA 测序分析以及融合基因进行了全面分析，并在此报告。差异转录表达分析显示，MBRs 与 Exos 和 MPs 相比具有独特的转录组谱，富含线粒体转录物、lncRNA/假基因转录物，这些转录物被预测与核糖核蛋白复合物、剪接体和 RNA/应激颗粒蛋白结合。这项研究的一个显著发现是，与 Exos、MPs 和源自其亲本细胞的细胞裂解物相比，MBRs 中几个融合基因的富集程度更高，例如 MSH2（编码 DNA 错配修复蛋白 MSH2 的基因）。这表明 EV-液体活检可能有用于癌症检测的靶标。重要的是，从 SW480（EGFR）和 SW620（MET 和 MACCA1）细胞系衍生的 EV 类中发现的与癌症进展相关的转录物的表达反映了它们的亲本细胞类型。我们的研究报告了 MBRs（包括 Exos 和 MPs）内的 RNA 和融合基因组成，这些组成可能会对 EV 在癌症进展和检测中的功能产生影响，并使用 EV 为候选癌症生物标志物的 RNA/融合基因。
