No abstract

MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of messenger RNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA-target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute-miRNA complexes and all sequences ≤12 nucleotides in length. This approach revealed noncanonical target sites specific to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.

Nanomedicines have enormous potential to improve the precision of cancer therapy, yet our ability to efficiently home these materials to regions of disease in vivo remains very limited. Inspired by the ability for communication to improve targeting in biological systems, such inflammatory cell recruitment to sites of disease, we construct systems where synthetic biological and nanotechnological components communicate to amplify disease targeting in vivo. These systems are composed of ‘Signalling’ modules (nanoparticles or engineered proteins) that target tumours and then locally active the coagulation cascade to broadcast tumour location to clot-targeted ‘Receiving’ nanoparticles in circulation that carry a diagnostic or therapeutic cargo, thereby amplifying their delivery. We show that communicating nanoparticle systems can be composed from multiple types of Signalling and Receiving modules, can transmit information via multiple molecular pathways in coagulation, can operate autonomously, and can target over 40-fold higher doses of chemotherapeutics to tumours than non-communicating controls.

Mesoporous silica nanoparticles (MSNPs) have garnered a great deal of attention as potential carriers for therapeutic payloads. However, achieving triggered drug release from MSNPs in vivo has been challenging. Here, we describe the synthesis of stimulus-responsive polymer-coated MSNPs and the loading of therapeutics into both the core and shell domains. We characterize MSNP drug-eluting properties in vitro and demonstrate that the polymer-coated MSNPs release doxorubicin in response to proteases present at a tumor site in vivo, resulting in cellular apoptosis. These results demonstrate the utility of polymer-coated nanoparticles in specifically delivering an antitumor payload.

Polycrystalline graphene sensors easily obtained through chemical vapor deposition (CVD) have been developed for chemical sensing. We show that linear defects or continuous lines of point defects on these sensors result in significantly higher sensitivity than that of pristine graphene and carbon nanotube film sensors. Further sensitivity enhancement is obtained by cutting the graphene into ribbons of width comparable to the linear defect dimensions (micrometers).

doi: bioRxiv preprint poly(A)-tail lengths for mRNAs corresponding to thousands of individual genes showed that tails from mRNAs of essentially every gene shortened over time in the cytoplasm (Figure 1C-D). Correspondence Between mRNA Half-life and Deadenylation RateAfter 2 h of labeling, a broad range of mean tail lengths was observed, as mean tail lengths for mRNAs of some genes approached their steady-state values, whereas those for others still resembled their initial values (Figure 1C). These different rates of approach to steady-state tail lengths presumably at least partly reflected differences in mRNA degradation rates, as short-lived mRNAs were expected to reach their steady-state abundance and poly(A)-tail length more rapidly than were long-lived mRNAs.To determine these degradation rates, we fit the yield of PAL-seq tags obtained for each gene at each time interval (normalizing to the spike-in controls) to the exponential function describing the approach to steady state, while also fitting a global offset to account for a delay between the time that 5EU was added and the time that labeled mRNAs appeared in the cytoplasm. This offset ranged from 27-36 min, depending on the experiment, a range consistent with single-gene measurements of the time required for mRNA transcription, processing, and export (Shav-Tal et al., 2004; Mor et al., 2010). Our half-life values (Table S1) correlated well with those previously reported for mRNAs of 3T3 cells growing in similar conditions (Schwanhäusser et al., S3A; R s = 0.68-0.77), although our absolute values were substantially shorter (Figure S3B-D, median 2.1 h for mRNAs of the 3T3 cell line 2, as opposed to 9 h for previously reported values). This difference was attributable to potential divergence in . 2011) (Figure

With noncommunicable diseases (NCDs) now constituting the majority of global mortality, there is a growing need for low-cost, noninvasive methods to diagnose and treat this class of diseases, especially in resource-limited settings. Molecular biomarkers combined with low-cost point-of-care assays constitute a potential solution for diagnosing NCDs, but the dearth of naturally occurring, predictive markers limits this approach. Here, we describe the design of exogenous agents that serve as synthetic biomarkers for NCDs by producing urinary signals that can be quantified by a companion paper test. These synthetic biomarkers are composed of nanoparticles conjugated to ligand-encoded reporters via protease-sensitive peptide substrates. Upon delivery, the nanoparticles passively target diseased sites, such as solid tumors or blood clots, where up-regulated proteases cleave the peptide substrates and release reporters that are cleared into urine. The reporters are engineered for detection by sandwich immunoassays, and we demonstrate their quantification directly from unmodified urine; furthermore, capture antibody specificity allows the probes to be multiplexed in vivo and quantified simultaneously by ELISA or paper lateral flow assay (LFA). We tailor synthetic biomarkers specific to colorectal cancer, a representative solid tumor, and thrombosis, a common cardiovascular disorder, and demonstrate urinary detection of these diseases in mouse models by paper diagnostic. Together, the LFA and injectable synthetic biomarkers, which could be tailored for multiple diseases, form a generalized diagnostic platform for NCDs that can be applied in almost any setting without expensive equipment or trained medical personnel.protease nanosensor | urine biomarker | image-free diagnostic | engineered disease reporter | global health

MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of mRNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA-target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute-miRNA complexes and all ≤12-nucleotide sequences. This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.