6mer Seed Toxicity in Viral microRNAs

Murmann, Andrea E.; Bartom, Elizabeth T.; Schipma, Matthew J.; Vilker, Jacob; Chen, Siquan; Peter, Marcus E.

doi:10.1016/j.isci.2019.11.031

Cited by 17 publications

(28 citation statements)

References 83 publications

(75 reference statements)

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“…The genes downregulated in the siGGGGGC transfected cells, were enriched in a reference set of recently defined survival genes (10) (Fig. 3A), similar to the activity we reported for the two tumor suppressive miRNAs miR-34a-5p and miR-15/16-3p and their matching 6mer seed containing siRNAs (12,14). A gene ontology analysis suggested that the form of cell death induced by siGGGGGC, siGGCAGU (the miR-34a-5p 6mer seed), and even the chemotherapeutic drug carboplatin were very similar with shared GO terms we had previously reported to characterize DISE (10,12,23).…”

Section: Sigggggc Is Highly Toxic To Multiple Cancer Cells and Prefersupporting

confidence: 82%

“…This suggested that while in the context of si/shRNAs that are designed to selectively silence single genes DISE could be viewed as an off-target effect, in the context of the biological function of miRNAs, this activity should be considered an on-target activity. In agreement with this interpretation, are findings that established major tumor suppressive miRNA families such as miR-34/449-5p and miR-15/16-5p kill cancer cells largely through 6mer Seed Tox by targeting hundreds of survival genes (12,14,15). si/shRNAs with a toxic 6mer seed can be used to treat cancer in mice.…”

supporting

confidence: 56%

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Identification of the toxic 6mer seed consensus in human cancer cells

Patel

Bartom

Paudel

et al. 2020

Preprint

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Abstract6mer seed toxicity is a novel anti-cancer mechanism that kills cancer cells by triggering death induced by survival gene elimination (DISE). It is based on si- or shRNAs with a specific G-rich nucleotide composition in position 2-7 of their guide strand. An arrayed screen of 4096 6mer seeds on two human and two mouse cell lines identified a consensus GGGGGC as the most toxic seed. After testing two more cell lines, one human and one mouse, we found that the GGGGGC seed while also toxic to murine cells, is more toxic to human cells, suggesting that the evolution to use of Gs as part of the toxic seeds is still slowly evolving, with Gs more common in the human toxic seeds. While new RNA Seq and bioinformatics analyses suggest that the GGGGGC seed is toxic to cancer cells by targeting GCCCCC seed matches in the 3’ UTR of a set of genes critical for cell survival, we now directly confirm this by identifying a number of genes targeted by this seed. Furthermore, by using a luciferase reporter fused to the 3’ UTR of these genes we confirm direct and specific on-targeting of GCCCCC seed matches. Targeting is strongly attenuated after mutating the GCCCCC seed matches in these 3’ UTRs. Our data confirm that an siRNA containing the GGGGGC seed kills cancer cells through its miRNA like activity and points at artificial miRNAs, si- or shRNAs containing this seed as a potential new cancer therapeutics.

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Section: Sigggggc Is Highly Toxic To Multiple Cancer Cells and Prefersupporting

confidence: 82%

supporting

confidence: 56%

Identification of the toxic 6mer seed consensus in human cancer cells

Patel

Bartom

Paudel

et al. 2020

Preprint

Self Cite

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“…5E). In this analysis in which we applied a paired Student’s T test in three out of 4 patients, the most abundant upregulated miRNA was miR-15b-5p which can kill cancer cells in part through 6mer Seed Tox (27), and the most abundant downregulated nontoxic miRNA was again miR-125b-5p. Analysis of all patient tumor pairs suggests that the differences seen between primary tumors and matched recurrences in this rare patient population are due to intrinsic changes in the tumor cells.…”

Section: Resultsmentioning

confidence: 99%

“…In human cells, we recently identified the seed consensus GGGGGC (targeting the seed match GCCCCC in a miRNA like fashion) as the most toxic seed sequence across three cell lines (19). Toxic 6mer seeds are found in tumor-suppressive miRNAs, including the prototypical tumor suppressive miRNA families, miR-34/449-5p and miR-15/16-5p (21, 22), and we and others have shown that 6mer seed toxicity (6mer Seed Tox) can be developed for cancer treatment (17, 23). When we treated xenografted OC with siRNAs containing toxic seeds, normal tissues were unaffected (17).…”

Section: Introductionmentioning

confidence: 99%

The balance between toxic versus nontoxic microRNAs determines platinum sensitivity in ovarian cancer

Patel

Wang

Bartom

et al. 2021

Preprint

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Development of platinum (Pt) resistance is a major barrier to curing ovarian cancer (OC). 6mer seed toxicity is a novel cancer killing mechanism mediated by tumor suppressive miRNAs with a toxic 6mer seed sequence (positions 2-7) through the RNA-induced silencing complex (RISC). The most toxic 6mer seeds are G-rich and kill cells by targeting the 3′ untranslated region of genes critical for cell survival. We now show that treatment of OC cells with Pt leads to an increase in RISC-bound miRNAs carrying toxic 6mer seeds and a decrease in miRNAs with nontoxic seeds. Pt-resistant cells did not exhibit this Pt induced toxicity shift but retained sensitivity to death mediated by siRNAs carrying toxic 6mer seeds. Analysis of RISC-bound miRNAs in OC patients revealed that miRNA 6mer seed toxicity ratios were predictive of treatment outcomes. Our results suggest that 6mer seed toxicity can be exploited to treat patients with Pt-resistant OC.

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“…The microRNA (miRNA) is non-coding single-stranded RNA molecules with the lengths of approximately 22 nucleotides and regulate gene expression at the posttranscriptional level [ [6] , [7] , [8] ]. The miRNA can regulate many types of cancers [ [9] , [10] , [11] , [12] ] and can be proto-oncogenes or tumour suppressor genes that are closely associated with many diseases [ 9 , 10 , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] ].…”

Section: Introductionmentioning

confidence: 99%