PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value

Abstract

Only recently, microRNAs (miRNAs) were found to exist in traceable and distinctive amounts in the human circulatory system, bringing forth the intriguing possibility of using them as minimally invasive biomarkers. miRNAs are short non-coding RNAs that act as potent post-transcriptional regulators of gene expression. Extensive studies in cancer and other disease landscapes investigate the protective/pathogenic functions of dysregulated miRNAs, as well as their biomarker potential. A specialized resource amassing experimentally verified, circulating miRNA biomarkers does not exist. We queried the existing literature to identify articles assessing diagnostic/prognostic roles of miRNAs in blood, serum, or plasma samples. Articles were scrutinized in order to exclude instances lacking sufficient experimental documentation or employing no biomarker assessment methods. We incorporated information from more than 200 biomedical articles, annotating crucial meta-information including cohort sizes, inclusion-exclusion criteria, disease/healthy confirmation methods and quantification details. miRNAs and diseases were systematically characterized using reference resources. Our circulating miRNA biomarker collection is provided as an online database, plasmiR. It consists of 1021 entries regarding 251 miRNAs and 112 diseases. More than half of plasmiR’s entries refer to cancerous and neoplastic conditions, 183 of them (32%) describing prognostic associations. plasmiR facilitates smart queries, emphasizing visualization and exploratory modes for all researchers.

Modulation of the Cellular microRNA Landscape: Contribution to the Protective Effects of High-Density Lipoproteins (HDL)

“…However, only HDL increased the expression of hsa-miR-21-5p and hsa-miR-7977, and reduced levels of hsa-miR-16-5p, hsa-miR-130a-3p and hsa-miR-191-5p, while a miR-21-5p mimic replicated HDL repression of SMAD7 and STAT3 in 1.1B4 cells [ 184 ]. Notably, except for hsa-miR-130a-3p and hsa-miR-7977, the other sequences regulated by HDL are found in serum or plasma, but are not reported in HDL (DIANA PlasmiR, accessed 20 July 2023) [ 187 ].…”

DIANA-microT 2023: including predicted targets of virally encoded miRNAs

“…Causal associations of miRNAs against diseases were retrieved from HMDD 3.2 ( 31 ). Circulating miRNA biomarker information was derived from plasmiR ( 32 ). For each miRNA, the number of HMDD or plasmiR entries supporting the association or biomarker capacity respectively was tallied and utilized to create miRNA disease clouds, implementing active hyperlinks towards these external resources.…”

“…We integrated miRNA abundance estimates regarding 60 tissues and 210 cell-lines derived from the miRNA Tissue Expression Database, DIANA-miTED ( 27 ) and gene expression for 99 human and mouse contexts from the Genotype-Tissue Expression project (GTEx) ( 28 ), The Cancer Genome Atlas (TCGA) ( 29 ) and the reference mouse publication by Sollner et al ( 30 ), to make possible the incorporation of abundance information in returned interactions. Finally, human miRNAs are annotated regarding their causal associations with diseases from HMDD resource ( 31 ), as well as with their capacity to function as circulating miRNA biomarkers, from plasmiR ( 32 ). The DIANA-microT 2023 webserver interface has been upgraded, and useful filtering and query functionalities have been set up to facilitate browsing through the enhanced content.…”

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

“…The potential for participation in cancer-associated processes decreases in a set of LINC00667 , LINC00668 > LINC00470 > LINC01926 , LINC01544 , LINC01909 , depending on the number of functional terms. Further, using the PlasmiR database [ 41 ], we additionally searched records on the diagnostic value of 17 microRNAs interacting with these lincRNAs (excluding LINC01909 ) in plasma and serum blood samples ( Table S12 ). Since lincRNAs act as molecular sponges for microRNAs [ 42 ], tissue-specific accumulation of lincRNAs may indirectly influence microRNA content in tissues and, hence, secretion to the biological fluids.…”

“…Figure S7: Panoramic view of characteristics of lincRNAs of human chromosome 18 (clustering and visualization). Supporting information include references [ 21 , 32 , 37 , 38 , 39 , 40 , 41 , 51 , 55 , 62 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 ].…”