A pH-activatable DNA origami nanostructure with geometrically patterned CD95 ligands reverses symptoms in a mouse model of rheumatoid arthritis without apparent side effects.

While assembling the figures, incorrect loading controls were used to compose the anti-miR-182 panel (shown at the right in Fig. 2A) and the "GIC-16" Western blot panel in Figure 4C and Supplemental Figure S8B.For Figure 2A, the Hsp70 loading control from the miR-182 panel was mistakenly duplicated.Similarly, for Figure 4C and Supplemental Figure S8B, the loading control from the "GIC-20" panel was mistakenly duplicated and used as a loading control for the "GIC-16" panel.We now show the correctly assembled subpanels.Importantly, the revised loading controls show equal loading across the respective sample groups.Therefore, the findings and conclusions from these two experiments remain unchanged, as do the overarching conclusions of our study.

Alzheimer’s disease (AD) is characterized by progressive neurodegeneration, but the specific events that cause cell death remain poorly understood. Death Induced by Survival gene Elimination (DISE) is a cell death mechanism mediated by short (s) RNAs acting through the RNA-induced silencing complex (RISC). DISE is thus a form of RNA interference, in which G-rich 6mer seed sequences in the sRNAs (position 2-7) target hundreds of C-rich 6mer seed matches in genes essential for cell survival, resulting in the activation of cell death pathways. Here, using Argonaute precipitation and RNAseq (Ago-RP-Seq), we analyze RISC-bound sRNAs to quantify 6mer seed toxicity in several model systems. In mouse AD models and aging brain, in induced pluripotent stem cell-derived neurons from AD patients, and in cells exposed to Aβ42 oligomers, RISC-bound sRNAs show a shift to more toxic 6mer seeds compared to controls. In contrast, in brains of “SuperAgers”, humans over age 80 who have superior memory performance, RISC-bound sRNAs are shifted to more nontoxic 6mer seeds. Cells depleted of nontoxic sRNAs are sensitized to Aβ42-induced cell death, and reintroducing nontoxic RNAs is protective. Altogether, the correlation between DISE and Aβ42 toxicity suggests that increasing the levels of nontoxic miRNAs in the brain or blocking the activity of toxic RISC-bound sRNAs could ameliorate neurodegeneration.

Several mechanisms by which initial HIV infection is cytotoxic to infected cells have been reported and involve various forms of cell death. Characterizing the mechanisms underlying the long-term survival of certain T cells that become persistent provirus reservoirs is critical to developing a cure.

Supplementary Figure S1. Sequencing of HGSOC reveals conserved mutational signatures and TP53 mutations. Supplementary Figure S2. Distribution of mutations and mutational signatures in HGSOC. Supplementary Figure S3. Genomic instability is a core feature of ovarian cancer that frequently involves DNA-damage repair genes. Supplementary Figure S4. Annotated dendrograms of HGSOC metastatic trajectories. Supplementary Figure S5. Ex vivo model of metastasis to the fallopian tube. Supplementary Figure S6. In vitro model of HGSOC-fallopian tube adhesion.

<p>Contains the analysis of all published papers on the role of miRNAs in OC. Please disregard last two pages. Had to be added for the references to format correctly in Endnote.</p>

PDF file - 71K, Detailed description of methods.

PDF file - 198K, Analysis of microRNA array and gene array data.

CD95/Fas ligand (CD95L) induces apoptosis through protein binding to the CD95 receptor. However, CD95L mRNA also induces toxicity in the absence of CD95 through induction of DISE (Death Induced by Survival Gene Elimination), a form of cell death mediated by RNA interference (RNAi). We now report that CD95L mRNA processing generates a short (s)RNA nearly identical to shL3, a commercial CD95L-targeting shRNA that led to the discovery of DISE. Neither of the miRNA biogenesis proteins Drosha nor Dicer are required for this processing. Interestingly, CD95L toxicity depends on the core component of the RISC, Ago2, in some cell lines, but not in others. In the HCT116 colon cancer cell line, Ago 1–4 appear to function redundantly in RNAi. In fact, Ago 1/2/3 knockout cells retain sensitivity to CD95L mRNA toxicity. Toxicity was only blocked by mutation of all in-frame start codons in the CD95L ORF. Dying cells exhibited an enrichment of RISC bound (R)-sRNAs with toxic 6mer seed sequences, while expression of the non-toxic CD95L mutant enriched for loading of R-sRNAs with nontoxic 6mer seeds. However, CD95L is not the only source of these R-sRNAs. We find that CD95L mRNA may induce DISE directly and indirectly, and that alternate mechanisms may underlie CD95L mRNA processing and toxicity.

TP53 mutations in the patient cohort.

Despite the multiple advances in therapy, cancer remains one of the most common causes of death globally. It is a systemic disease affecting people of all ages, originates at the level of single cells, which upon acquisition of mutations become neo-plastically transformed. Cell division is the biggest risk factor for accumulation of mutations [1], explaining why all multicellular organisms which evolved about 2 billion years ago, are prone to cancer. Given the recent achievements in cancer treatment with immune checkpoint blockade therapies, one could argue that multicellular organisms developed the immune system as a mechanism to eradicate cancerous cells [2]. However, the immune system arose relatively recent, ~500 million years ago [3]. Moreover, studies have shown that cancer cells can become resistant to the anticancer activity of both the innate and the adaptive immune system [4, 5]. Therefore, the immune system while important, is likely not the most vital machinery that emerged in multicellular organisms to prevent cancer formation; we believe that there must be other more effective and archaic anti-cancer mechanisms that are conserved during evolution. Of note, RNA interference (RNAi) is a highly conserved biological mechanism for silencing gene expression. While RNAi likely emerged as a defense tool against viruses and other foreign nucleic acids, it has also evolved to have other activities in the cells [6]. Our research has identified a new evolutionarily conserved RNAi-based form of cell death that targets essential survival genes, Death Induced by Survival gene Elimination (DISE) [7, 8]. DISE is effective against all cancers we tested. DISE was discovered through our work on CD95 and its ligand, CD95L, where we found that more than 80% of 26 different short interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) derived from the two genes, killed multiple cancer cell lines via simultaneous activation of multiple cell death pathways; and we were unable to find a way to inhibit this form of cell death [9]. We subsequently reported that CD95L is enriched in sequences that when converted to sRNAs are toxic to cells. In fact, we found that CD95L is processed into short RNAs (sRNAs) that are loaded into the RNA induced silencing complex (RISC) and kill cells through DISE [10, 11]. Later, we determined that all these toxic sRNAs did not kill cells by acting like typical siRNAs i.e., by silencing genes through complete complementarity to a section of the mRNA, but by working in a microRNA (miRNA)-like fashion i.e. using just a seed sequence and predominantly targeting the 3′UTR [12]. In fact, the shortest seed of 6 nucleotides was sufficient to have toxicity. The most toxic 6mer seeds were then identified in large arrayed screens testing all possible 4096 6mer seeds embedded in a 19 double stranded short RNA (sRNA) in three human and three mouse cancer cell lines [12, 13]. We assessed the toxicity of positions 2–7 in the guide strand of the sRNA by blocking the loading of the passenger strand via two 2′-O-methylation of its positions 1 and 2 [14]. We found that the most toxic seeds were all G-rich and they targeted C-rich sequences in the 3′UTRs of essential survival genes. The rules of “6mer seed toxicity” were universal and independent of cancer type or species. When put into the context of the coevolution of the ~2300 known human miRNAs with the 3′UTRs of genes, especially survival genes [12, 15], it became clear that we discovered a death mechanism based on miRNAs selectively targeting survival genes. Consequently, we found that some of the seeds of major tumor suppressive and death inducing miRNAs

Supplementary Table 2 from Identification of Let-7–Regulated Oncofetal Genes

<p>Legends for Tables S3-S5</p>

Newick trees and cophenetic correlation coefficients.

Supplementary Figures 1-4 from Loss of E-Cadherin Promotes Ovarian Cancer Metastasis via α₅-Integrin, which Is a Therapeutic Target

Abstract MicroRNAs (miRNA) are small RNA molecules of ∼20 to 22 nucleotides that reduce expression of proteins through mRNA degradation and/or translational silencing. Each known miRNA has a large number of predicted targets. Members of the let-7/miR-98 family of miRNAs are up-regulated at the end of embryonic development. Let-7 is often down-regulated early during cancer development, suggesting that let-7–regulated oncofetal genes (LOG) may become reexpressed in cancer cells. Using comparative bioinformatics, we have identified 12 conserved LOGs that include HMGA2 and IMP-1/CRD-BP. IMP-1 has growth-promoting activities through stabilization of c-myc mRNA. We experimentally confirmed that IMP-1 is a direct let-7 target that promotes cell growth and motility of tumor cells, and we confirmed by proteomics analysis that IMP-1 and HMGA2 are major miRNA targets. Our data suggest that a substantial part of the growth inhibitory activities of let-7 comes from suppressing the expression of IMP-1. LOGs could be novel therapeutic targets and potential biomarkers for cancer treatment. [Cancer Res 2008;68(8):2587–91]

Supplementary Methods, Figures 1-3, Table 1 from Identification of Let-7–Regulated Oncofetal Genes

<p>All Suppl. Figures</p>

<p>Lists the most abundant miRNAs that are differentially expressed between Pt-R and Pt-S patients.</p>