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Supplemental Tables S1-2, Figures S1-2 from Breast Cancer–Specific miR Signature Unique to Extracellular Vesicles Includes “microRNA-like” tRNA Fragments

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posted on 2023-04-03, 17:11 authored by Nicole Guzman, Kitty Agarwal, Dilip Asthagiri, Lianbo Yu, Motoyasu Saji, Matthew D. Ringel, Michael E. Paulaitis

Supplemental Tables S1-2, Figures S1-2. Table S1. NanoString nCounterTM assay measurements of miRNA copy numbers/cell detected in MCF7 and MCF10A cells at 72 hrs of serum deprivation and in EVs derived from MCF7 and MCF10A cells over 72 hrs of serum deprivation. Table S2. qRT-PCR assay measurements of miRNA copy numbers/cell detected in MCF7 and MCF10A cells at 72 hrs of serum deprivation and in EVs secreted from MCF7 and MCF10A cells over 72 hrs of serum deprivation. Figure S1. Total cellular RNA concentration (top panel) and changes in miR-21 expression levels (middle panel) and changes in miR-1274a and miR-1274b expression levels (bottom panel) for MCF10A cells (open symbols) and MCF7 cells (filled symbols) as a function of time in response to serum deprivation at 0 hrs. Figure S2. Sequence alignments for miRNA pairs depicting positions that share identical nucleotides.

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ARTICLE ABSTRACT

Extracellular vesicles (EV), including exosomes and shed vesicles, have been implicated in intercellular communication; however, their biomarker potential is less clear. Therefore, EVs derived from MCF7 and MCF10A cells were analyzed to identify unique miRNA (miR) profiles that distinguish their origin. One characteristic common to the miR profiles of MCF7 EVs and their parent cells is the high abundance of miR-21, let-7a, miR-100, and miR-125b, and low levels of miR-205. A second characteristic is the high abundance of “miRNA-like” tRNA fragments, which is unique to the MCF7 EVs, and is not found in comparing the cellular profiles. In addition, correlations were examined in the MCF7 cellular expression levels of these five miRs and two tRNA-derived miRNAs, miR-720 and miR-1274b, and compared with the correlations in MCF7 EV levels. Interestingly, correlations in the cellular expression of miR-125b, miR-100, and let-7a are mirrored in the EVs. In contrast, correlations in tRNA-derived miRNA levels are found only in the EVs. The findings suggest that EV miR clusters can be defined based on functional miR interactions related to correlated cellular expression levels or physical miR interactions, for example, aggregation due to comparable binding affinities to common targets.Implications: These results point to using high levels of tRNA-derived small RNA fragments in combination with known miR signatures of tumors to distinguish tumor-derived EVs in circulation from EVs derived from other cell sources. Such biomarkers would be unique to the EVs where high abundances of tRNA fragments are amplified with respect to their cellular levels. Mol Cancer Res; 13(5); 891–901. ©2015 AACR.

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