Future directions for medicinal chemistry in the field of oligonucleotide therapeutics.

In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.

Effects of a comprehensive brain computed tomography deep learning model on radiologist detection accuracy.

OBJECTIVES: Non-contrast computed tomography of the brain (NCCTB) is commonly used to detect intracranial pathology but is subject to interpretation errors. Machine learning can augment clinical decision-making and improve NCCTB scan interpretation. This retrospective detection accuracy study assessed the performance of radiologists assisted by a deep learning model and compared the standalone performance of the model with that of unassisted radiologists. METHODS: A deep learning model was trained on 212,484 NCCTB scans drawn from a private radiology group in Australia. Scans from inpatient, outpatient, and emergency settings were included. Scan inclusion criteria were age ≥ 18 years and series slice thickness ≤ 1.5 mm. Thirty-two radiologists reviewed 2848 scans with and without the assistance of the deep learning system and rated their confidence in the presence of each finding using a 7-point scale. Differences in AUC and Matthews correlation coefficient (MCC) were calculated using a ground-truth gold standard. RESULTS: The model demonstrated an average area under the receiver operating characteristic curve (AUC) of 0.93 across 144 NCCTB findings and significantly improved radiologist interpretation performance. Assisted and unassisted radiologists demonstrated an average AUC of 0.79 and 0.73 across 22 grouped parent findings and 0.72 and 0.68 across 189 child findings, respectively. When assisted by the model, radiologist AUC was significantly improved for 91 findings (158 findings were non-inferior), and reading time was significantly reduced. CONCLUSIONS: The assistance of a comprehensive deep learning model significantly improved radiologist detection accuracy across a wide range of clinical findings and demonstrated the potential to improve NCCTB interpretation. CLINICAL RELEVANCE STATEMENT: This study evaluated a comprehensive CT brain deep learning model, which performed strongly, improved the performance of radiologists, and reduced interpretation time. The model may reduce errors, improve efficiency, facilitate triage, and better enable the delivery of timely patient care. KEY POINTS: • This study demonstrated that the use of a comprehensive deep learning system assisted radiologists in the detection of a wide range of abnormalities on non-contrast brain computed tomography scans. • The deep learning model demonstrated an average area under the receiver operating characteristic curve of 0.93 across 144 findings and significantly improved radiologist interpretation performance. • The assistance of the comprehensive deep learning model significantly reduced the time required for radiologists to interpret computed tomography scans of the brain.

An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.

Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.

Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers.

In many prokaryotes, type III clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) systems detect and degrade invasive genetic elements by an RNA-guided, RNA-targeting multisubunit interference complex. The CRISPR-associated protein Csm6 additionally contributes to interference by functioning as a standalone RNase that degrades invader RNA transcripts, but the mechanism linking invader sensing to Csm6 activity is not understood. Here we show that Csm6 proteins are activated through a second messenger generated by the type III interference complex. Upon target RNA binding by the interference complex, its Cas10 subunit converts ATP into a cyclic oligoadenylate product, which allosterically activates Csm6 by binding to its CRISPR-associated Rossmann fold (CARF) domain. CARF domain mutations that abolish allosteric activation inhibit Csm6 activity in vivo, and mutations in the Cas10 Palm domain phenocopy loss of Csm6. Together, these results point to an unprecedented mechanism for regulation of CRISPR interference that bears striking conceptual similarity to oligoadenylate signalling in mammalian innate immunity.

Corneal cross-linking in patients with keratoconus: up to 13 years of follow-up.

INTRODUCTION: To evaluate long-term safety and efficacy of corneal collagen cross-linking (CXL) in patients with keratoconus up to 13 years. MATERIALS AND METHODS: In this mono-centre exploratory study, we included all consecutive patients who underwent CXL in our cornea centre from 01/01/2007 to 12/30/2011 and met the inclusion criteria. CXL was performed in all patients according to the Dresden protocol. Evaluation included best-corrected visual acuity (BCVA), topographic keratometry by Scheimpflug corneal tomography and endothelial cell count (ECC). Follow-up measurements were taken up to 13 years after treatment were compared with baseline values. RESULTS: The study enrolled 168 eyes. The mean age of our patients was 26.3 years ± 7.8 years. A complete topographic dataset was available 1 year postoperatively for 142 eyes, 5 years postoperatively for 105 eyes, 10 years postoperatively for 61 eyes and 13 years postoperatively for 9 eyes. BCVA increased statistically significant after 1 year, 5 years and 10 years and non-significantly after 13 years. All keratometric parameters with exception of posterior astigmatism showed a statistically significant decrease after 1 year, 5 years and 10 years. After 13 years, the decrease was statistically significant only in Kmax, K2 and thinnest cornea. No significant changes in ECC were detected. Three eyes received Re-CXL, none of the eyes received penetrating keratoplasty and no infections occurred in this cohort. CONCLUSIONS: CXL can slow down or even stop the progression of keratoconus in the majority of cases. The effect is long-lasting with excellent safety.

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome.

Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5'-extended isoform, iso-miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso-miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA.

TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA.

The telomere specific shelterin complex, which includes TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, prevents spurious recognition of telomeres as double-strand DNA breaks and regulates telomerase and DNA repair activities at telomeres. TIN2 is a key component of the shelterin complex that directly interacts with TRF1, TRF2 and TPP1. In vivo, the large majority of TRF1 and TRF2 are in complex with TIN2 but without TPP1 and POT1. Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, previous cell-based assays only provide information on downstream effects after the loss of TRF1/TRF2 and TIN2. Here, we investigated DNA structures promoted by TRF2-TIN2 using single-molecule imaging platforms, including tracking of compaction of long mouse telomeric DNA using fluorescence imaging, atomic force microscopy (AFM) imaging of protein-DNA structures, and monitoring of DNA-DNA and DNA-RNA bridging using the DNA tightrope assay. These techniques enabled us to uncover previously unknown unique activities of TIN2. TIN2S and TIN2L isoforms facilitate TRF2-mediated telomeric DNA compaction (cis-interactions), dsDNA-dsDNA, dsDNA-ssDNA and dsDNA-ssRNA bridging (trans-interactions). Furthermore, TIN2 facilitates TRF2-mediated T-loop formation. We propose a molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres.

The role of maternal trauma and discipline types in emotional processing among Syrian refugee children.

Stressful experiences in armed conflict incur intergenerational effects through parental behaviors with their children. A recent study reported that among Syrian refugee families, mothers' (but not fathers') post-traumatic stress (PTS) impacted children's emotional processing. In this study, we aim to shed further light on this phenomenon by analyzing how the parenting practices in the context of post-traumatic stress confers protection or risk for children's emotional processing. Participants were 6-18-year-old children (n = 212) and their mothers (n = 94), who fled from Syria and were residing in Turkish communities. We used the computer-based emotional processing task including photos of facial movements typically associated with different emotions to measure children's capacity for emotional processing. Mothers reported their PTS and the discipline types they use, as well as the contextual factors related to their refugee background. Linear mixed effect models were constructed first, to find out the discipline types that are most strongly associated with emotional processing of the child, and second, to examine whether these discipline types moderate the effect of maternal PTS on children's emotional processing. Finally, generalized linear models were constructed to examine which contextual factors are associated with the use of these discipline types by mothers. We found that spanking as a discipline type was associated with poorer child emotional processing, whereas withholding of media access was associated with better emotional processing. Younger and less religious mothers were more prone to use spanking. The study underlines the need for parenting programs alongside with efforts to address mental health issues among mothers living under armed conflict.

Tranexamic acid as a novel adjunct in the management of vessel perforation complicating Endovascular Clot Retrieval.

AIM: To assess the safety and utility of tranexamic acid (TXA) as an adjunct salvage therapy in iatrogenic vessel perforation complicating endovascular clot retrieval. Iatrogenic vessel perforation and extravasation are known and potentially fatal complications of endovascular clot retrieval (ECR). Various methods of establishing haemostasis post perforation have been reported. TXA is widely utilised intraoperatively to reduce bleeding in various surgical specialities. The use of TXA in endovascular procedures has not been previously described in the literature. METHODS: Retrospective case control study of all cases that underwent ECR. Cases where arterial rupture occurred were identified. Details of management and functional status at 3 months were recorded. Modified Rankin score (mRS) 0-2 was considered a good functional outcome. Comparison of proportions analysis was performed. RESULTS: Of 1378 cases of ECR, rupture complicated 36 (2.6%). TXA was administered in addition to standard care in 11 cases (31%). At 3 months, 4 of 11 cases (36%) where TXA was administered had a good functional outcome compared to 3 of 22 (12%) in the standard care group (P=0.09). Mortality at 3 months occurred in 4 of 11 cases (41.7%) where TXA was administered compared to 16 of 25 (64%) where it was not (P=0.13). CONCLUSION: Tranexamic acid administration in iatrogenic vessel rupture was associated with a lower mortality rate and a larger proportion of patients achieving a good functional outcome at 3 months. This effect trended towards but was not statistically significant. TXA administration was not associated with adverse effects.

Chemically Synthesized, Self-Assembling Small Interfering RNA-Prohead RNA Molecules Trigger Dicer-Independent Gene Silencing.

RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three-way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA-3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA-3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA-3WJs transfected into Dicer-deficient cell lines trigger potent gene silencing. Interestingly, siRNA-3WJs transfected into an Argonaute 2-deficient cell line also retain some gene silencing activity. siRNA-3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5' of the 3WJ (5'-siRNA-3WJ) relative to 3' of the 3WJ (3'-siRNA-3WJ). This work sheds light on the functional properties of siRNA-3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.

An artificial intelligence model correlated with morphological and genetic features of blastocyst quality improves ranking of viable embryos.

RESEARCH QUESTION: Can better methods be developed to evaluate the performance and characteristics of an artificial intelligence model for evaluating the likelihood of clinical pregnancy based on analysis of day-5 blastocyst-stage embryos, such that performance evaluation more closely reflects clinical use in IVF procedures, and correlations with known features of embryo quality are identified? DESIGN: De-identified images were provided retrospectively or collected prospectively by IVF clinics using the artificial intelligence model in clinical practice. A total of 9359 images were provided by 18 IVF clinics across six countries, from 4709 women who underwent IVF between 2011 and 2021. Main outcome measures included clinical pregnancy outcome (fetal heartbeat at first ultrasound scan), embryo morphology score, and/or pre-implantation genetic testing for aneuploidy (PGT-A) results. RESULTS: A positive linear correlation of artificial intelligence scores with pregnancy outcomes was found, and up to a 12.2% reduction in time to pregnancy (TTP) was observed when comparing the artificial intelligence model with standard morphological grading methods using a novel simulated cohort ranking method. Artificial intelligence scores were significantly correlated with known morphological features of embryo quality based on the Gardner score, and with previously unknown morphological features associated with embryo ploidy status, including chromosomal abnormalities indicative of severity when considering embryos for transfer during IVF. CONCLUSION: Improved methods for evaluating artificial intelligence for embryo selection were developed, and advantages of the artificial intelligence model over current grading approaches were highlighted, strongly supporting the use of the artificial intelligence model in a clinical setting.

Delivery of oligonucleotides to bone marrow to modulate ferrochelatase splicing in a mouse model of erythropoietic protoporphyria.

Erythropoietic protoporphyria (EPP) is a rare genetic disease in which patients experience acute phototoxic reactions after sunlight exposure. It is caused by a deficiency in ferrochelatase (FECH) in the heme biosynthesis pathway. Most patients exhibit a loss-of-function mutation in trans to an allele bearing a SNP that favors aberrant splicing of transcripts. One viable strategy for EPP is to deploy splice-switching oligonucleotides (SSOs) to increase FECH synthesis, whereby an increase of a few percent would provide therapeutic benefit. However, successful application of SSOs in bone marrow cells is not described. Here, we show that SSOs comprising methoxyethyl-chemistry increase FECH levels in cells. We conjugated one SSO to three prototypical targeting groups and administered them to a mouse model of EPP in order to study their biodistribution, their metabolic stability and their FECH splice-switching ability. The SSOs exhibited distinct distribution profiles, with increased accumulation in liver, kidney, bone marrow and lung. However, they also underwent substantial metabolism, mainly at their linker groups. An SSO bearing a cholesteryl group increased levels of correctly spliced FECH transcript by 80% in the bone marrow. The results provide a promising approach to treat EPP and other disorders originating from splicing dysregulation in the bone marrow.

Medicinal Chemistry of Oligonucleotide Drugs - Milestones of the Past and Visions for the Future.

The oligonucleotide therapeutics field has blossomed in recent years, with thirteen approved drugs today and the promise of accelerated growth in coming years. Much of the progress in this field is due to advances in the medicinal chemistry of oligonucleotides,combined with a judicious choice of molecular targets and disease areas. In this perspective, we describe the growth of this new class of drugs highlighting selected milestones in oligonucleotide medicinal chemistry.

Inosine Substitutions in RNA Activate Latent G-Quadruplexes.

It is well-accepted that gene expression is heavily influenced by RNA structure. For instance, stem-loops and G-quadruplexes (rG4s) are dynamic motifs in mRNAs that influence gene expression. Adenosine-to-inosine (A-to-I) editing is a common chemical modification of RNA which introduces a nucleobase that is iso-structural with guanine, thereby changing RNA base-pairing properties. Here, we provide biophysical, chemical, and biological evidence that A-to-I exchange can activate latent rG4s by filling incomplete G-quartets with inosine. We demonstrate the formation of inosine-containing rG4s (GI-quadruplexes) in vitro and verify their activity in cells. GI-quadruplexes adopt parallel topologies, stabilized by potassium ions. They exhibit moderately reduced thermal stability compared to conventional G-quadruplexes. To study inosine-induced structural changes in a naturally occurring RNA, we use a synthetic approach that enables site-specific inosine incorporation in long RNAs. In summary, RNA GI-quadruplexes are a previously unrecognized structural motif that may contribute to the regulation of gene expression in vivo.

Single Nucleotide Resolution RNA-Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow.

RNA-protein interactions mediate many intracellular processes. CLIR-MS (cross-linking of isotope-labeled RNA and tandem mass spectrometry) allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a single experiment. Using isotopically labeled RNA segments for UV-light-induced cross-linking generates characteristic isotope patterns that constrain the sequence database searches, increasing spatial resolution. Whereas the use of segmentally isotopically labeled RNA is effective, it is technically involved and not applicable in some settings, e.g., in cell or tissue samples. Here we introduce an extension of the CLIR-MS workflow that uses unlabeled RNA during cross-linking and subsequently adds an isotopic label during sample preparation for MS analysis. After RNase and protease digests of a cross-linked complex, the nucleic acid part of a peptide-RNA conjugate is labeled using the enzyme T4 polynucleotide kinase and a 1:1 mixture of heavy 18O4-γ-ATP and light ATP. In this simple, one-step reaction, three heavy oxygen atoms are transferred from the γ-phosphate to the 5'-end of the RNA, introducing an isotopic shift of 6.01 Da that is detectable by mass spectrometry. We applied this approach to the RNA recognition motif (RRM) of the protein FOX1 in complex with its cognate binding substrate, FOX-binding element (FBE) RNA. We also labeled a single phosphate within an RNA and unambiguously determined the cross-linking site of the FOX1-RRM binding to FBE at single residue resolution on the RNA and protein level and used differential ATP labeling for relative quantification based on isotope dilution. Data are available via ProteomeXchange with the identifier PXD024010.

Chimeric Flaviviral RNA-siRNA Molecules Resist Degradation by The Exoribonuclease Xrn1 and Trigger Gene Silencing in Mammalian Cells.

RNA is an emerging platform for drug delivery, but the susceptibility of RNA to nuclease degradation remains a major barrier to its implementation in vivo. Here, we engineered flaviviral Xrn1-resistant RNA (xrRNA) motifs to host small interfering RNA (siRNA) duplexes. The xrRNA-siRNA molecules self-assemble in vitro, resist degradation by the conserved eukaryotic 5' to 3' exoribonuclease Xrn1, and trigger gene silencing in 293T cells. The resistance of the molecules to Xrn1 does not translate to stability in blood serum. Nevertheless, our results demonstrate that flavivirus-derived xrRNA motifs can confer Xrn1 resistance on a model therapeutic payload and set the stage for further investigations into using the motifs as building blocks in RNA nanotechnology.

Design and Application of Mini-libraries of miRNA Probes for an Efficient and Versatile miRNA-mRNA Cross-linking.

MicroRNAs constitute a class of endogenous, non-coding RNAs that influence various processes within the cell. By base-pairing to partially-complementary sites located in the 3' untranslated region of target messenger RNAs, microRNAs participate in post-transcriptional regulation of the majority of human protein-coding genes. Their dysregulation has been related to many pathological processes and diseases. Thus, an in-depth understanding of the microRNA mechanisms of action is crucial. Here, we present a new concept of probe design to achieve an efficient and sequence-independent miRNA-mRNA cross-linking. The new strategy is based on the utilization of a controlled mixture of probes for a chosen miRNA, in which a trioxsalen moiety is introduced at the N4 -position of a selected cytidine through short oligoethylene glycol-based linkers. In vitro photo-cross-linking experiments with mini-libraries of probes for microRNAs of interest showed variable cross-linking efficiencies, demonstrating a general applicability of the presented approach.

Structural basis of a small molecule targeting RNA for a specific splicing correction.

Splicing modifiers promoting SMN2 exon 7 inclusion have the potential to treat spinal muscular atrophy, the leading genetic cause of infantile death. These small molecules are SMN2 exon 7 selective and act during the early stages of spliceosome assembly. Here, we show at atomic resolution how the drug selectively promotes the recognition of the weak 5' splice site of SMN2 exon 7 by U1 snRNP. The solution structure of the RNA duplex formed following 5' splice site recognition in the presence of the splicing modifier revealed that the drug specifically stabilizes a bulged adenine at this exon-intron junction and converts the weak 5' splice site of SMN2 exon 7 into a stronger one. The small molecule acts as a specific splicing enhancer cooperatively with the splicing regulatory network. Our investigations uncovered a novel concept for gene-specific alternative splicing correction that we coined 5' splice site bulge repair.

Contemporary Treatment of Intracranial Blood Blister Aneurysms - A Systematic Review.

INTRODUCTION: Blood blister aneurysms (BBAs) are rare aneurysms affecting non-branched points of intracerebral arteries. Due to their small size and fragility, BBAs are prone to rupture, and can be challenging to diagnose and treat. Several treatment options have been suggested yet there is no consensus regarding the best modality to reduce morbidity and mortality. MATERIALS AND METHODS: A systematic review of the literature was conducted searching for articles discussing the treatment of BBAs. Inclusion criteria included: articles published between January 2010 and August 2020, English language, with each paper including at least 15 patients. Studies included required detailed reporting of patient demographics, treatment, and patient outcomes (including complications, recurrence, neurologic functional status, and mortality). RESULTS AND DISCUSSION: A total of 25 studies with 883 patients were included. Most were female (n = 594, 67.3%) and aneurysms were overwhelmingly located in the supraclinoid internal carotid artery (99%). Aneurysms were variable in size and mostly presented with subarachnoid haemorrhage. Endovascular treatment (n = 518, 58.7%) was more common than microsurgery (n = 365, 41.1%) while only 2 patients were managed conservatively. Complications were more common in patients treated microsurgically. Microsurgical procedures had an unfavorable outcome (mRS 4-6, GOS 1-3) rate of 27.8% (n = 100/360) while that of endovascular procedures was 14.7% (n = 70/477). Endovascular procedures had a lower mortality rate than microsurgical interventions (8.4% vs 11%). CONCLUSION: This review demonstrates that endovascular treatment of blood blister aneurysm has reduced morbidity and mortality when compared with microsurgical treatment. Small sample sizes and substantial study heterogeneity makes strong conclusions difficult.

Rapid Versus Laboratory-Based Testing for HIV and Hepatitis C at a Drug Detoxification Treatment Center: A Randomized Trial.

BACKGROUND: A health department survey revealed nearly half employ laboratory-based HIV and HCV testing (LBT) over rapid testing (RT) in nonhospital settings such as drug detoxification centers. LBT has higher sensitivity for acute HIV infection compared to RT but LBT is not point of care and may result in fewer diagnoses due to loss to follow-up before result delivery. METHODS: We conducted a randomized trial comparing real-world case notification of RT (Orasure) vs LBT (HIV Combo Ag/Ab EIA, HCV EIA) for HIV and HCV at a drug detoxification center. Primary outcome was receipt of test results within 2 weeks. RESULTS: Among 341 individuals screened (11/2016-7/2017), 200 met inclusion criteria; 58% injected drugs and 31% shared needles in the previous 6 months. Of the 200 randomized, 98 received RT and 102 LBT. Among all participants, 0.5% were positive for HIV and 48% for HCV; 96% received test results in the RT arm and 42% in the LBT arm (odds ratio, 28.72; 95% confidence interval, 10.27-80.31). Real-world case notification was 95% and 93% for HIV and HCV RT, respectively, compared to 42% for HIV and HCV LBT. CONCLUSIONS: RT has higher real-world case notification than LBT at drug detoxification centers.Clinical trials registration: NCT02869776.