A safe ride in extracellular vesicles – small RNA trafficking between plant hosts and pathogens

Abstract For studying cellular communications ex-vivo, a two-dimensional (2D) cell culture model is currently used as the “gold standard”. 2D culture models are also widely used in the study of RNA expression profiles from tumor cells secreted extracellular vesicles (EVs) for tumor biomarker discovery. Although the 2D culture system is simple and easily accessible, the culture environment is unable to represent in vivo extracellular matrix (ECM) microenvironment. Our study observed that 2D- culture derived EVs showed significantly different profiles in terms of secretion dynamics and essential signaling molecular contents (RNAs and DNAs), when compared to the three-dimensional (3D) culture derived EVs. By performing small RNA next-generation sequencing (NGS) analysis of cervical cancer cells and their EVs compared with cervical cancer patient plasma EV-derived small RNAs, we observed that 3D- culture derived EV small RNAs differ from their parent cell small RNA profile which may indicate a specific sorting process. Most importantly, the 3D- culture derived EV small RNA profile exhibited a much higher similarity (~96%) to in vivo circulating EVs derived from cervical cancer patient plasma. However, 2D- culture derived EV small RNA profile correlated better with only their parent cells cultured in 2D. On the other hand, DNA sequencing analysis suggests that culture and growth conditions do not affect the genomic information carried by EV secretion. This work also suggests that tackling EV molecular alterations secreted into interstitial fluids can provide an alternative, non-invasive approach for investigating 3D tissue behaviors at the molecular precision. This work could serve as a foundation for building precise models employed in mimicking in vivo tissue system with EVs as the molecular indicators or transporters. Such models could be used for investigating tumor biomarkers, drug screening, and understanding tumor progression and metastasis.

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Characterization of the small RNA content of Trypanosoma cruzi extracellular vesicles

Molecular and Biochemical Parasitology ◽

10.1016/j.molbiopara.2014.02.004 ◽

2014 ◽

Vol 193 (2) ◽

pp. 71-74 ◽

Cited By ~ 41

Author(s):

Ethel Bayer-Santos ◽

Fábio Mitsuo Lima ◽

Jeronimo Conceição Ruiz ◽

Igor C. Almeida ◽

José Franco da Silveira

Keyword(s):

Trypanosoma Cruzi ◽

Extracellular Vesicles ◽

Small Rna ◽

Rna Content

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Relationships of Alzheimer’s disease and apolipoprotein E genotypes with small RNA and protein cargo of brain tissue extracellular vesicles

10.1101/2020.12.12.20247890 ◽

2020 ◽

Author(s):

Yiyao Huang ◽

Tom A. P. Driedonks ◽

Lesley Cheng ◽

Andrey Turchinovich ◽

Harinda Rajapaksha ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Extracellular Vesicles ◽

Small Rna ◽

Apoe Genotype ◽

Tau Proteins ◽

Small Rna Sequencing ◽

Health Crisis ◽

Metabolic Functions ◽

Apolipoprotein E Genotypes

ABSTRACTAlzheimer’s disease (AD) is a public health crisis that grows as populations age. Hallmarks of this neurodegenerative disease include aggregation of beta-amyloid peptides and hyperphosphorylated tau proteins in the brain. Variants of the APOE gene are the greatest known risk factors for sporadic AD. As emerging players in AD pathophysiology, extracellular vesicles (EVs) contain proteins, lipids, and RNAs and are involved in disposal of cellular toxins and intercellular communication. AD-related changes in the molecular composition of EVs may contribute to pathophysiology and lend insights into disease mechanisms. We recently adapted a method for separation of brain-derived EVs (bdEVs) from post-mortem tissues. Using this method, we isolated bdEVs from AD patients with different APOE genotypes (n=23) and controls (n=7). bdEVs were counted, sized, and subjected to parallel small RNA sequencing and proteomic analysis. Numerous bdEV-associated RNAs and proteins correlated with AD pathology and APOE genotype. Some of the identified entities have been implicated previously in important AD-related pathways, including amyloid processing, neurodegeneration, and metabolic functions. These findings provide further evidence that bdEVs and their molecular cargo modulate development and progression of AD.

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exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer

10.1101/2020.09.28.20190009 ◽

2020 ◽

Author(s):

Navneet Dogra ◽

Mehmet Eren Ahsen ◽

Edgar Gonzalez Kozlova ◽

Tzu-yi Chen ◽

kimaada allette ◽

...

Keyword(s):

Prostate Cancer ◽

Differential Expression ◽

Extracellular Vesicles ◽

Small Rna ◽

Tumor Tissue ◽

Biomarker Discovery ◽

De Novo ◽

Culture Media ◽

Tumor Resection ◽

Small Rna Sequencing

Circulating extracellular vesicles (EVs) present in the bodily fluids of patients with cancer may provide non-invasive access to the tumor tissue. Yet, the transcriptomic lineage of tumor-derived EVs before and after tumor-resection remains poorly understood. Here, we established 60 total small RNA-sequencing profiles from 17 aggressive prostate cancer (PCa) patients tumor and adjacent normal tissue, and EVs isolated from urine, serum, and cancer cell culture media. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate tissue leads to differential expression of reactive oxygen species (ROS), P53 pathways, inflammatory/cytokines, oncogenes, and tumor suppressor genes in the EV nanosatellites. Furthermore, we provide a set of novel EV-specific RNA signature, which are present in cancer but are nonexistent in post-resection patients with undetectable cancer. Finally, using a de novo RNAseq assembly followed by characterization of the small RNA landscape, we found novel small RNA clusters (smRCs) in the EVs, which reside in the unannotated regions. Novel smRCs were orthogonally validated for their differential expression in the biomarker discovery cohort using RT-qPCR. We demonstrate that circulating tumor EVs provide a glimpse of the tumor tissue biology, resolving a major bottleneck in the current liquid biopsy efforts. Secretory vesicles appear to be playing a key role in non-canonical Wnt signaling and miRNA pathways, similar to the circulating tumor cells (CTCs), hence, we propose that such vesicles be called circulating tumor extracellular vesicles (CTEVs).

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Small RNA-seq analysis of extracellular vesicles from porcine uterine flushing fluids during peri-implantation

Gene ◽

10.1016/j.gene.2020.145117 ◽

2021 ◽

Vol 766 ◽

pp. 145117

Author(s):

Renwu Hua ◽

Yueying Wang ◽

Weisi Lian ◽

Wenchao Li ◽

Yu Xi ◽

...

Keyword(s):

Extracellular Vesicles ◽

Small Rna ◽

Rna Seq ◽

Uterine Flushing

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Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles

Scientific Reports ◽

10.1038/srep25486 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 53

Author(s):

Raphatphorn Navakanitworakul ◽

Wei-Ting Hung ◽

Sumedha Gunewardena ◽

John S. Davis ◽

Wilaiwan Chotigeat ◽

...

Keyword(s):

Extracellular Vesicles ◽

Small Rna ◽

Follicular Fluid ◽

Antral Follicles ◽

Rna Content

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Driving the Next Generation: Paternal Lifetime Experiences Transmitted via Extracellular Vesicles and Their Small RNA Cargo

Biological Psychiatry ◽

10.1016/j.biopsych.2018.09.007 ◽

2019 ◽

Vol 85 (2) ◽

pp. 164-171 ◽

Cited By ~ 21

Author(s):

Christopher P. Morgan ◽

Jennifer C Chan ◽

Tracy L. Bale

Keyword(s):

Extracellular Vesicles ◽

Small Rna ◽

Next Generation

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Gene Expression Changes Induced byTrypanosoma cruziShed Microvesicles in Mammalian Host Cells: Relevance of tRNA-Derived Halves

BioMed Research International ◽

10.1155/2014/305239 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 52

Author(s):

Maria R. Garcia-Silva ◽

Florencia Cabrera-Cabrera ◽

Roberta Ferreira Cura das Neves ◽

Thaís Souto-Padrón ◽

Wanderley de Souza ◽

...

Keyword(s):

Gene Expression ◽

Host Cell ◽

Extracellular Vesicles ◽

Small Rna ◽

Hela Cells ◽

Small Rnas ◽

Host Cells ◽

Mammalian Host ◽

Large Set ◽

Rna Pathways

At present, noncoding small RNAs are recognized as key players in novel forms of posttranscriptional gene regulation in most eukaryotes. However, canonical small RNA pathways seem to be lost or excessively simplified in some unicellular organisms includingTrypanosoma cruziwhich lack functional RNAi pathways. Recently, we reported the presence of alternate small RNA pathways inT. cruzimainly represented by homogeneous populations of tRNA- and rRNA-derived small RNAs, which are secreted to the extracellular medium included in extracellular vesicles. Extracellular vesicle cargo could be delivered to other parasites and to mammalian susceptible cells promoting metacyclogenesis and conferring susceptibility to infection, respectively. Here we analyzed the changes in gene expression of host HeLa cells induced by extracellular vesicles fromT. cruzi. As assessed by microarray assays a large set of genes in HeLa cells were differentially expressed upon incorporation ofT. cruzi-derived extracellular vesicles. The elicited response modified mainly host cell cytoskeleton, extracellular matrix, and immune responses pathways. Some genes were also modified by the most abundant tRNA-derived small RNAs included in extracellular vesicles. These data suggest that microvesicles secreted byT. cruzicould be relevant players in early events of theT. cruzihost cell interplay.

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