Lipid nanoparticles (LNPs) have proven to be an effective delivery system for RNA therapeutics. The chemical composition of LNPs determines their functional delivery efficiency and targeting properties, which vary between in vitro and in vivo contexts. Here, we have systematically characterized and compared 25 novel C14120-based LNP formulations for mRNA delivery in vitro and assessed in vivo mRNA expression and biodistribution using deep sequencing of DNA barcodes in a pooled LNP-mRNA library. In vitro experiments showed correlations of lipid composition with particle size and mRNA transfection efficiency in 4 different cell lines of distinct tissue and species origin. In vivo experiments employed a pooled LNP delivery of luciferase mRNA in combination with a multiplexed barcode system and identified LNP compositions with organ-specific targeting properties. Individual validation of three selected LNP candidates based on mRNA expression analysis confirmed high specificity for the lung-targeting candidate, lower specificity for the liver-targeting candidate, and inconclusive results for the spleen-targeting candidate. These findings identify LNP formulations with promising potential for in vitro and in vivo organ-targeted delivery.

Survival is highly variable in amyotrophic lateral sclerosis (ALS), complicating prognosis and clinical trial design. Despite advances in biomarker development, accessible prognostic tools are limited. Small non-coding (snc) RNAs are a recently discovered biomarker class showing differential regulation across neurodegenerative diseases, including ALS. Here, we explored changes in sncRNAs over time in ALS. We performed small RNA sequencing in a discovery cohort of 116 longitudinal serum samples from ALS 40 patients collected at 3-to 4-month intervals and identified tRNA-derived stress-induced RNA (tiRNA) tDR-1:34-Gly-GCC as the top sncRNA to increase over time. The finding was validated using TaqMan PCR and replicated in an independent cohort of 35 patients. Both univariate and joint model analyses showed that higher tDR-1:34-Gly-GCC levels correlated with shorter survival. Given that the translation of mRNAs and stress-induced translation inhibition are dysregulated in ALS and linked to familial ALS genes, combined with these findings, serum tDR-1:34-Gly-GCC tiRNA levels hold potential as a prognostic biomarker and outcome measure in clinical trials.

OBJECTIVE:Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with variable site of onset, disease progression rates and survival times. Early-stage ALS characteristics are shared with other conditions, posing diagnostic challenges and resulting in diagnosis delays. We investigated tRNA-derived small RNAs (tsRNAs) and microRNAs (miRNAs) which are stable and abundantly expressed small non-coding RNAs (sncRNAs) as potential diagnostic serum biomarkers, comparing them to healthy controls and ALS mimics, and gained pathophysiological insights from dysregulated sncRNAs. METHODS:We analyzed small RNA-seq data from 158 patients with ALS, 60 healthy controls and 39 patients with neurological conditions that mimic ALS to identify differentially expressed sncRNAs. A classifier was built to evaluate their diagnostic potential, followed by hierarchical clustering to identify ALS molecular subtypes. Finally, we performed gene ontology and pathway analysis to identify pathways disrupted within subtypes. RESULTS:We identified several dysregulated tsRNAs and miRNAs and assessed their diagnostic potential using an extreme gradient boosting (XGBoost) classifier. Our models achieved an accuracy of 87.16% and 82.23% in classifying patients with ALS from healthy controls and ALS mimics, respectively. We identified four sncRNA expression-based ALS molecular subtypes with one C9orf72 enriched cluster. Further analysis of identified differentially expressed sncRNAs showed their involvement in neuronal pathways. CONCLUSION:Our study identified potential sncRNA-based diagnostic serum biomarkers and associated molecular subtypes which can be further studied to match clinical parameters and develop subtype specific biomarkers and therapeutic strategies for ALS.

Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease with no effective treatments, in part caused by variations in progression and the absence of biomarkers. Mice carrying the SOD1G93A transgene with different genetic backgrounds show variable disease rates, reflecting the diversity of patients. While extensive research has been done on the involvement of the central nervous system, the role of skeletal muscle remains underexplored. We examined the impact of angiogenin, including its RNase activity, in skeletal muscles of ALS mouse models and in biopsies from ALS patients. Elevated levels of angiogenin were found in slowly progressing mice but not in rapidly progressing mice, correlating with increased muscle regeneration and vascularisation. In patients, higher levels of angiogenin in skeletal muscles correlated with milder disease. Mechanistically, angiogenin promotes muscle regeneration and vascularisation through satellite cell-endothelial interactions during myogenesis and angiogenesis. Furthermore, specific angiogenin-derived tiRNAs were upregulated in slowly progressing mice, suggesting their role in mediating the effects of angiogenin. These findings highlight angiogenin and its tiRNAs as potential prognostic markers and therapeutic targets for ALS, offering avenues for patient stratification and interventions to mitigate disease progression by promoting muscle regeneration.

Circular RNAs (circRNAs) constitute a group of RNAs defined by a covalent bond between the 5' and 3' end formed by a unique back-splicing event. Most circRNAs are composed of more than one exon, which are spliced together in a linear fashion. This protocol describes methods to sequence full-length circRNA across the back-splicing junction, allowing unambiguous characterization of circRNA-specific exon-intron structures by long-read sequencing (LRS). Two different sequencing approaches are provided: (1) Global circRNA sequencing (the circNick-LRS strategy) relying on circRNA enrichment from total RNA followed by total circRNA long-read sequencing, and (2) targeted circRNA sequencing (the circPanel-LRS strategy) where a preselected panel of circRNA are sequenced without prior circRNA enrichment. Both methods were originally described in Karim et al. (Rahimi et al., Nat Commun 12: 4825, 2021) where they were applied to characterize the exon-intron structure of >10.000 circRNAs in mouse and human brains.

Transfer RNA-derived small RNAs (tsRNAs) - categorized as tRNA-derived fragments (tRFs), tRNA-derived stress-induced RNAs (tiRNAs) and internal tRF (itRF) - are small non-coding RNAs that participate in various cellular processes such as translation inhibition and responses to cellular stress. We here identified tsRNA profiles within susceptible tissues in animal models of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD) to pinpoint disease-specific tsRNAs and those shared across neurodegenerative diseases. We performed small RNA sequencing in the SOD1(G93A) and TDP43(A315T) mouse models of ALS (spinal cord), the Tau(P301S) model of FTD (hippocampus), and the parkin/POLG model of PD (substantia nigra). Bioinformatic analysis showed higher expression of 5 ' tiRNAs selectively in the two ALS models, lower expression of 3 ' tRFs in both the ALS and FTD mouse models, and lower expression of itRF Arg in the PD model. Experimental validation confirmed the expression of tsRNAs. Gene Ontology analysis of targets associated with validated 3 ' tRFs indicated functions in the regulation of synaptic and neuronal pathways. Our profiling of tsRNAs indicates disease-specific fingerprints in animal models of neurodegeneration, which require validation in human disease.

Brain functionality relies on finely tuned regulation of gene expression by networks of non -coding RNAs (ncRNAs) such as the one composed by the circular RNA ciRS-7 (also known as CDR1as), the microRNA miR-7, and the long ncRNA Cyrano. We describe ischemia-induced alterations in the ncRNA network both in vitro and in vivo and in transgenic mice lacking ciRS-7 or miR-7. Our data show that cortical neurons downregulate ciRS-7 and Cyrano and upregulate miR-7 expression during ischemia. Mice lacking ciRS-7 exhibit reduced lesion size and motor impairment, while the absence of miR-7 alone results in increased ischemia-induced neuronal death. Moreover, miR-7 levels in pyramidal excitatory neurons regulate neurite morphology and glutamatergic signaling, suggesting a potential molecular link to the in vivo phenotype. Our data reveal the role of ciRS-7 and miR-7 in modulating ischemic stroke outcome, shedding light on the pathophysiological function of intracellular ncRNA networks in the brain.

In cancer molecular imaging, selecting binders with high specificity and affinity for biomarkers is paramount for achieving high-contrast imaging within clinical time frames. Nanobodies have emerged as potent candidates, surpassing antibodies in pre-clinical imaging due to their convenient production, rapid renal clearance, and deeper tissue penetration. Multimerization of nanobodies is a popular strategy to enhance their affinity and pharmacokinetics; however, traditional methods are laborious and may yield heterogeneous products. In this study, we employ a Holliday junction (HJ)-like nucleic acid-based scaffold to create homogeneous nanostructures with precise multivalent and multiparatopic nanobody displays. The plugand-play assembly allowed the screening of several nanobody multimer configurations for the detection of the breast cancer In vitro studies demonstrated significant improvements in binding avidity, particularly with the biparatopic construct exhibiting high sensitivity, surpassing that of traditional antibody-based cell binding. Furthermore, our HJ platform allowed for adaptation from fluorescence-based to nuclear imaging, as demonstrated in xenografted mice, thereby allowing for future in vivo applications. This work highlights the potential of nucleic acid-mediated multimerization to markedly enhance nanobody binding, by exploring synergistic combinations and offering versatility for both in vitro diagnostics and cancer molecular imaging with prospects for future theranostic applications.

Remote ischemic conditioning (RIC) by brief periods of limb ischemia and reperfusion protects against ischemia-reperfusion injury. However, the mechanism is unknown. We studied the role of exosomes for mediating the cardioprotective signal and whether they accumulate in injured myocardium. Blood samples from 12 healthy male volunteers were obtained prior to and one hour after RIC. Plasma obtained before and after RIC (n=4) (P-Pre and P-Post) was used to evaluate the transferability of RIC. Pre- and Post-RIC plasma (n=8) was separated into an exosome rich fraction (Exo-Pre and Exo-Post) and an exosome depleted fraction (Prot-Pre and Prot-Post) by size exclusion chromatography. All studies were carried out in duplicate samples from each volunteer. Infarct size was compared in Sprague-Dawley rat hearts perfused with plasma, exosomes and exosome depleted fractions in a Langendorff model. We investigated changes in the miRNA content of the exosomes after RIC by a human miRNA panel. Additionally, fluorescently labeled exosomes isolated from C2C12 cells were used to assess accumulation in injured myocardium in an in vivo rat model. Rats were divided into an infarct group (n=6) (left anterior descending artery ligation) and a sham group (n=6) (without ligation). Labelled exosomes were injected in the femoral vein prior to reperfusion. Exosome-accumulation in infarcted or sham myocardium was evaluated. P-Post reduced infarct size by 15% points compared with P-Pre (55±4% vs 70±6%, p=0.03) (Fig. 1a). Exo-Post reduced infarct size by 16% points compared with Exo-Pre (53±15% vs 68±12%, p=0.03) (Fig. 1b). Prot-Post did not affect infarct size compared to Prot-Pre (64±3% and 68±10%, p>0.99). We found miRNA-16, miRNA-144 and miRNA-451 to be upregulated in exosomes after RIC and the mTOR-pathway as a potential target for these miRNAs. In the in vivo model, labelled exosomes accumulated more intensively in the infarct area than in remote areas and sham hearts (Fig. 1c). Cardioprotection by RIC is mediated by exosomes with a changed miRNA profile and exosomes accumulate in injured myocardium. Figure 1 Type of funding source: Private company. Main funding source(s): Novo synergy

Remote ischemic conditioning (RIC) is a procedure that can attenuate ischemic-reperfusion injury by conducting brief cycles of ischemia and reperfusion in the arm or leg. Extracellular vesicles (EVs) circulating in the bloodstream can release their content into recipient cells to confer protective function on ischemia-reperfusion injured (IRI) organs. Skeletal muscle cells are potential candidates to release EVs as a protective signal during RIC. In this study, we used C2C12 cells as a model system and performed cyclic hypoxia-reoxygenation (HR) to mimic RIC. EVs were collected and subjected to small RNA profiling and proteomics. HR induced a distinct shift in the miRNA profile and protein content in EVs. HR EV treatment restored cell viability, dampened inflammation, and enhanced tube formation in in vitro assays. In vivo, HR EVs showed increased accumulation in the ischemic brain compared to EVs secreted from normoxic culture (N EVs) in a mouse undergoing transient middle cerebral artery occlusion (tMCAO). We conclude that HR conditioning changes the miRNA and protein profile in EVs released by C2C12 cells and enhances the protective signal in the EVs to recipient cells in vitro.

Significance Temporal lobe epilepsy is commonly drug resistant and is associated with dysregulated hippocampal gene expression. MicroRNAs are short noncoding RNAs which control protein levels by binding target mRNAs via Argonaute proteins. We sequenced Argonaute-bound microRNAs from the hippocampus of three rodent epilepsy models, identifying common and unique functioning microRNAs at each stage of epileptogenesis. We designed oligonucleotide inhibitors against six microRNAs shared among models in chronic epilepsy and show three of these protected against acute and spontaneous seizures in a mouse model. We demonstrate that normal brain physiology is not obviously disrupted by these treatments and used a multiomics approach to identify a common mechanistic pathway for the therapeutic protective effects. Overall, these studies reveal potential treatments for drug-resistant epilepsy. Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by microRNAs. To systematically assess their significance, we sequenced Argonaute-loaded microRNAs to define functionally engaged microRNAs in the hippocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated microRNAs for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 unique microRNAs detected per model. Approximately half of the detected microRNAs were dysregulated in each epilepsy model. We prioritized commonly up-regulated microRNAs that were fully conserved in humans and designed custom antisense oligonucleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three microRNAs reduced spontaneous seizures in epileptic mice. Proteomic data, RNA sequencing, and pathway analysis on predicted and validated targets of these microRNAs implicated derepressed TGF-β signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-β signaling occluded the antiseizure effects of the antagomirs. Together, these results identify shared, dysregulated, and functionally active microRNAs during the pathogenesis of epilepsy which represent therapeutic antiseizure targets.

Multipotent stem cells (MSCs) are used in various therapeutic applications based on their paracrine secretion activity. Here, we set out to identify and characterize the paracrine factors released during osteoblastogenesis, with a special focus on small non-coding RNAs released in extracellular vesicles (EVs). Bone marrow stem cells (BMSCs) and adipose stem cells (ASCs) from healthy human donors were used as representatives of MSCs. We isolated EVs secreted before and after induction of osteoblastic differentiation and found that the EVs contained a specific subset of microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNA) compared to their parental cells. Osteoblastic differentiation had a larger effect on the small RNA profile of BMSC-EVs relative to ASC-EVs. Our data showed that EVs from different MSC origin exhibited distinct expression profiles of small RNA profiles when undergoing osteoblastogenesis, a factor that should be taken into consideration for stem cell therapy.

Extracellular and circulating RNAs (exRNA) are produced by many cell types of the body and exist in numerous bodily fluids such as saliva, plasma, serum, milk and urine. One subset of these RNAs are the posttranscriptional regulators - microRNAs (miRNAs). To delineate the miRNAs produced by specific cell types, in vitro culture systems can be used to harvest and profile exRNAs derived from one subset of cells. The secreted factors of mesenchymal stem cells are implicated in alleviating numerous diseases and is used as the in vitro model system here. This paper describes the process of collection, purification of small RNA and library generation to sequence extracellular miRNAs. ExRNAs from culture media differ from cellular RNA by being low RNA input samples, which calls for optimized procedures. This protocol provides a comprehensive guide to small exRNA sequencing from culture media, showing quality control checkpoints at each step during exRNA purification and sequencing.

MicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in the hippocampus of three different animal models at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures. The commonly upregulated miRNAs were selected for a functional in vivo screen using oligonucleotide inhibitors. This revealed anti-seizure phenotypes upon inhibition of miR-10a-5p, miR-21a-5p and miR-142a-5p as well as neuroprotection-only effects for inhibition of miR-27a-3p and miR-431-5p. Proteomic data and pathway analysis on predicted and validated targets of these miRNAs indicated a role for TGFβ signaling in a shared seizure-modifying mechanism. Together, these results identify functional miRNAs in the hippocampus and a pipeline of new targets for seizure control in epilepsy.

Background: Up to 80% of mesial temporal lobe epilepsy patients with hippocampal sclerosis (mTLE-HS) are resistant to pharmacological treatment, often necessitating surgical resection. Deep brain stimulation (DBS) has emerged as an alternative treatment for patients who do not qualify for resective brain surgery. Brain stimulation may also exert disease-modifying effects, and noncoding microRNAs have recently been proposed to shape the gene expression landscape in epilepsy. Objective: We compared the effect of DBS of 4 different hippocampal target regions on epileptogenesis and manifest epilepsy in a rat model of mTLE-HS. To explore mechanisms, we profiled the effect of the most effective DBS paradigm on hippocampal microRNA levels. Methods: MTLE-HS was induced by electrical stimulation of the perforant pathway (PP) in rats. This paradigm leads to spontaneous seizures within 4 weeks. We investigated DBS of 4 targets: PP, fimbria fornix (FF) formation, dentate gyrus (DG) and ventral hippocampal commissure (VHC). We applied both high- (130 Hz) and low-frequency (5 Hz or 1 Hz) stimulation. Functional microRNAs were identified in the hippocampus immediately after VHC-DBS and after a 97-day recording period by sequencing small RNAs bound to Argonaute-2, a component of the miRNA silencing complex. Results: Low frequency DBS of the VHC significantly delayed the occurrence of the first spontaneous recurrent seizure in the PPS model by ∼300%, from 19 to 56 days. No other stimulation regime altered the latency phase. Upregulation of 5 microRNAs during epileptogenesis was suppressed by VHC-stimulation. Conclusion: We conclude that DBS of the VHC delays epilepsy in the PPS model in rats and is associated with differential regulation of several miRNAs. Additional studies are required to determine whether VHC-regulated miRNAs serve causal roles in the anti-epileptogenic effects of this DBS model.

Plants contain various factors that transiently interact with subunits or intermediates of the thylakoid multiprotein complexes, promoting their stable association and integration. Hence, assembly factors are essential for chloroplast development and the transition from heterotrophic to phototrophic growth. Snowy cotyledon 2 (SCO2) is a DNAJ-like protein involved in thylakoid membrane biogenesis and interacts with the light-harvesting chlorophyll-binding protein LHCB1. In Arabidopsis thaliana, SCO2 function was previously reported to be restricted to cotyledons. Here we show that disruption of SCO2 in Lotus japonicus results not only in paler cotyledons but also in variegated true leaves. Furthermore, smaller and palegreen true leaves can also be observed in A. thaliana sco2 (atsco2) mutants under short-day conditions. In both species, SCO2 is required for proper accumulation of PSII-LHCII complexes. In contrast to other variegated mutants, inhibition of chloroplastic translation strongly affects L. japonicus sco2 mutant development and fails to suppress their variegated phenotype. Moreover, inactivation of the suppressor of variegation AtClpR1 in the atsco2 background results in an additive double-mutant phenotype with variegated true leaves. Taken together, our results indicate that SCO2 plays a distinct role in PSII assembly or repair and constitutes a novel factor involved in leaf variegation.

Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.