Splicing quality control mediated by DHX15 and its G-patch activator SUGP1.

Pre-mRNA splicing is surveilled at different stages by quality control (QC) mechanisms. The leukemia-associated DExH-box family helicase hDHX15/scPrp43 is known to disassemble spliceosomes after splicing. Here, using rapid protein depletion and analysis of nascent and mature RNA to enrich for direct effects, we identify a widespread splicing QC function for DHX15 in human cells, consistent with recent in vitro studies. We find that suboptimal introns with weak splice sites, multiple branch points, and cryptic introns are repressed by DHX15, suggesting a general role in promoting splicing fidelity. We identify SUGP1 as a G-patch factor that activates DHX15's splicing QC function. This interaction is dependent on both DHX15's ATPase activity and on SUGP1's U2AF ligand motif (ULM) domain. Together, our results support a model in which DHX15 plays a major role in splicing QC when recruited and activated by SUGP1.

Design of a chimeric ACE-2/Fc-silent fusion protein with ultrahigh affinity and neutralizing capacity for SARS-CoV-2 variants.

Background: As SARS-CoV-2 continues to mutate into Variants of Concern (VOC), there is growing and urgent need to develop effective antivirals to combat COVID-19. Monoclonal antibodies developed earlier are no longer capable of effectively neutralizing currently active VOCs. This report describes the design of variant-agnostic chimeric molecules consisting of an Angiotensin-Converting Enzyme 2 (ACE-2) domain mutated to retain ultrahigh affinity binding to a wide variety of SARS-CoV-2 variants, coupled to an Fc-silent immunoglobulin domain that eliminates antibody-dependent enhancement and extends biological half-life. Methods: Molecular modeling, Surrogate Viral Neutralization tests (sVNTs) and infection studies of human airway organoid cultures were performed with synthetic chimeras, SARS-CoV-2 spike protein mimics and SARS-CoV-2 Omicron variants B.1.1.214, BA.1, BA.2 and BA.5. Results: ACE-2 mutations L27, V34 and E90 resulted in ultrahigh affinity binding of the LVE-ACE-2 domain to the widest variety of VOCs, with KDs of 93 pM and 73 pM for binding to the Alpha B1.1.7 and Omicron B.1.1.529 variants, and notably, 78fM, 133fM and 1.81pM affinities to the Omicron BA.2, BA2.75 and BQ.1.1 subvariants, respectively. sVNT assays revealed titers of ≥4.9 ng/ml, for neutralization of recombinant viral proteins corresponding to the Alpha, Delta and Omicron variants. The values above were obtained with LVE-ACE-2/mAB chimeras containing the FcRn-binding Y-T-E sequence which extends biological half-life 3-4-fold. Conclusions: The ACE-2-mutant/Fc silent fusion proteins described have ultrahigh affinity to a wide variety of SARS-CoV-2 variants including Omicron. It is proposed that these chimeric ACE-2/mABs will constitute variant-agnostic and cost-effective prophylactics against SARS-CoV-2, particularly when administered nasally.

The DNA binding domain and the C-terminal region of DNA Ligase IV specify its role in V(D)J recombination.

DNA Ligase IV is responsible for the repair of DNA double-strand breaks (DSB), including DSBs that are generated during V(D)J recombination. Like other DNA ligases, Ligase IV contains a catalytic core with three subdomains-the DNA binding (DBD), the nucleotidyltransferase (NTD), and the oligonucleotide/oligosaccharide-fold subdomain (OBD). Ligase IV also has a unique C-terminal region that includes two BRCT domains, a nuclear localization signal sequence and a stretch of amino acid that participate in its interaction with XRCC4. Out of the three mammalian ligases, Ligase IV is the only ligase that participates in and is required for V(D)J recombination. Identification of the minimal domains within DNA Ligase IV that contribute to V(D)J recombination has remained unresolved. The interaction of the Ligase IV DNA binding domain with Artemis, and the interaction of its C-terminal region with XRCC4, suggest that both of these regions that also interact with the Ku70/80 heterodimer are important and might be sufficient for mediating participation of DNA Ligase IV in V(D)J recombination. This hypothesis was investigated by generating chimeric ligase proteins by swapping domains, and testing their ability to rescue V(D)J recombination in Ligase IV-deficient cells. We demonstrate that a fusion protein containing Ligase I NTD and OBDs flanked by DNA Ligase IV DBD and C-terminal region is sufficient to support V(D)J recombination. This chimeric protein, which we named Ligase 37, complemented formation of coding and signal joints. Coding joints generated with Ligase 37 were shorter than those observed with wild type DNA Ligase IV. The shorter length was due to increased nucleotide deletions and decreased nucleotide insertions. Additionally, overexpression of Ligase 37 in a mouse pro-B cell line supported a shift towards shorter coding joints. Our findings demonstrate that the ability of DNA Ligase IV to participate in V(D)J recombination is in large part mediated by its DBD and C-terminal region.

Digital Papillary Adenocarcinoma in the Dorsal Proximal Ring Finger.

Digital papillary adenocarcinoma (DPA) is a rare and aggressive tumor arising from the eccrine sweat glands. It is found on the hands and feet and most commonly occurs on the volar and distal finger tips. In this report, we describe a DPA in a 45-year-old woman who presented with a slowly enlarging mass on the dorsal aspect of her proximal ring finger. This report shows that DPA may clinically present as a relatively benign-appearing mass and in an atypical location. Surgical excision, followed by histologic and immunohistochemical evaluations of even benign-appearing digital masses, is important because this is the only way a DPA can be diagnosed.

Assessing eukaryotic initiation factor 4F subunit essentiality by CRISPR-induced gene ablation in the mouse.

Eukaryotic initiation factor (eIF) 4F plays a central role in the ribosome recruitment phase of cap-dependent translation. This heterotrimeric complex consists of a cap binding subunit (eIF4E), a DEAD-box RNA helicase (eIF4A), and a large bridging protein (eIF4G). In mammalian cells, there are two genes encoding eIF4A (eIF4A1 and eIF4A2) and eIF4G (eIF4G1 and eIF4G3) paralogs that can assemble into eIF4F complexes. To query the essential nature of the eIF4F subunits in normal development, we used CRISPR/Cas9 to generate mouse strains with targeted ablation of each gene encoding the different eIF4F subunits. We find that Eif4e, Eif4g1, and Eif4a1 are essential for viability in the mouse, whereas Eif4g3 and Eif4a2 are not. However, Eif4g3 and Eif4a2 do play essential roles in spermatogenesis. Crossing of these strains to the lymphoma-prone Eµ-Myc mouse model revealed that heterozygosity at the Eif4e or Eif4a1 loci significantly delayed tumor onset. Lastly, tumors derived from Eif4e∆38 fs/+/Eµ-Myc or Eif4a1∆5 fs/+/Eµ-Myc mice show increased sensitivity to the chemotherapeutic agent doxorubicin, in vivo. Our study reveals that eIF4A2 and eIF4G3 play non-essential roles in gene expression regulation during embryogenesis; whereas reductions in eIF4E or eIF4A1 levels are protective against tumor development in a murine Myc-driven lymphoma setting.

Trans-spliced mRNA products produced from circRNA expression vectors.

Circular (circ) RNA expression vectors are used as a method of identifying and characterizing RNA sequences that harbor internal ribosome entry site (IRES) activity. During the course of developing a vector series tailored for IRES discovery, we found evidence for the occurrence of trans-spliced mRNAs arising when sequences with promoter activity were embedded between the upstream CTD and downstream NTD exons of the pre-mRNA. These trans-spliced products regenerate the same open reading frame expected from a circRNA and can lead to false-positive signals in screens relying on circRNA expression vectors for IRES discovery. Our results caution against interpretations of IRES activity solely based on results obtained from circRNA expression vectors.

A Community Orthopaedic Residency Approach to Education and Training During the COVID-19 Pandemic.

BACKGROUND: The COVID-19 pandemic has rapidly affected all facets of everyday life including the practice of medicine. Hospital systems and medical practices have evolved to protect patients, physicians, and staff and conserve personal protective equipment and resources. Orthopaedic practices have been specifically affected by social distancing and stay at home guidelines, limiting in-office practice and elective surgery restrictions. This, in turn, has had an effect on resident education. Previous literature has been published regarding how academic programs have adjusted to these changes. However, the effects on smaller orthopaedic residencies with nonacademic faculty has not been discussed. The orthopaedic residency at Baylor University Medical Center of Dallas is a fifteen-resident program with a combination of hospital employed and private practice faculty. We adjusted our resident education in mid-March 2020 to keep residents safe while trying to maximize surgical and clinical education and outside research. GOALS: Our goals were to come up with a plan allowed for continuing high-level patient care and resident education while protecting residents and limiting burnout. MODEL: We devised a four-team system with five-day call periods. Interactions between teams were strictly minimized. We also moved to a web-based academic curriculum and devised a system for safe resident participation in surgical cases. The model has been adjusted based on attending and resident feedback. CONCLUSION: Until we develop effective treatments or vaccination for COVID-19, there is a possibility that it will be an ongoing threat. Resident education must also adapt to the changing environment while continuing to provide residents safe opportunities for patient care, didactic education, and research. We believe we have come up with a sustainable, adaptable model for resident education during this challenging time.

iRHOM2: A Regulator of Palmoplantar Biology, Inflammation, and Viral Susceptibility.

The palmoplantar epidermis is a specialized area of the skin that undergoes high levels of mechanical stress. The palmoplantar keratinization and esophageal cancer syndrome, tylosis with esophageal cancer, is linked to mutations in RHBDF2 encoding the proteolytically inactive rhomboid protein, iRhom2. Subsequently, iRhom2 was found to affect palmoplantar thickening to modulate the stress keratin response and to mediate context-dependent stress pathways by p63. iRhom2 is also a direct regulator of the sheddase, ADAM17, and the antiviral adaptor protein, stimulator of IFN genes. In this perspective, the pleiotropic functions of iRhom2 are discussed with respect to the skin, inflammation, and the antiviral response.

Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5' leader regions.

Hippuristanol (Hipp) is a natural product that selectively inhibits protein synthesis by targeting eukaryotic initiation factor (eIF) 4A, a DEAD-box RNA helicase required for ribosome recruitment to mRNA templates. Hipp binds to the carboxyl-terminal domain of eIF4A, locks it in a closed conformation, and inhibits its RNA binding. The dependencies of mRNAs for eIF4A during initiation is contingent on the degree of secondary structure within their 5' leader region. Interest in targeting eIF4A therapeutically in cancer and viral-infected settings stems from the dependencies that certain cellular (e.g. pro-oncogenic, pro-survival) and viral mRNAs show towards eIF4A. Using a CRISPR/Cas9-based variomics screen, we identify functional EIF4A1 Hipp-resistant alleles, which in turn allowed us to link the translation-inhibitory and cytotoxic properties of Hipp to eIF4A1 target engagement. Genome-wide translational profiling in the absence or presence of Hipp were undertaken and our validation studies provided insight into the structure-activity relationships of eIF4A-dependent mRNAs. We find that mRNA 5' leader length, overall secondary structure and cytosine content are defining features of Hipp-dependent mRNAs.

Structure-Guided Design of Substituted Biphenyl Butanoic Acid Derivatives as Neprilysin Inhibitors.

Inhibition of neprilysin (NEP) is widely studied as a therapeutic target for the treatment of hypertension, heart failure, and kidney disease. Sacubitril/valsartan (LCZ696) is a drug approved to reduce the risk of cardiovascular death in heart failure patients with reduced ejection fraction. LBQ657 is the active metabolite of sacubitril and an inhibitor of NEP. Previously, we have reported the crystal structure of NEP bound with LBQ657, whereby we noted the presence of a subsite in S1' that has not been explored before. We were also intrigued by the zinc coordination made by one of the carboxylic acids of LBQ657, leading us to explore alternative linkers to efficiently engage zinc for NEP inhibition. Structure-guided design culminated in the synthesis of selective, orally bioavailable, and subnanomolar inhibitors of NEP. A 17-fold boost in biochemical potency was observed upon addition of a chlorine atom that occupied the newly found subsite in S1'. We report herein the discovery and preclinical profiling of compound 13, which paved the path to our clinical candidate.

Rocaglates Induce Gain-of-Function Alterations to eIF4A and eIF4F.

Rocaglates are a diverse family of biologically active molecules that have gained tremendous interest in recent years due to their promising activities in pre-clinical cancer studies. As a result, this family of compounds has been significantly expanded through the development of efficient synthetic schemes. However, it is unknown whether all of the members of the rocaglate family act through similar mechanisms of action. Here, we present a comprehensive study comparing the biological activities of >200 rocaglates to better understand how the presence of different chemical entities influences their biological activities. Through this, we find that most rocaglates preferentially repress the translation of mRNAs containing purine-rich 5' leaders, but certain rocaglates lack this bias in translation repression. We also uncover an aspect of rocaglate mechanism of action in which the pool of translationally active eIF4F is diminished due to the sequestration of the complex onto RNA.

Accuracy and Workflow Improvements for Responsive Neurostimulation Hippocampal Depth Electrode Placement Using Robotic Stereotaxy.

Background: Robotic stereotaxy is increasingly common in epilepsy surgery for the implantation of stereo-electroencephalography (sEEG) electrodes for intracranial seizure monitoring. The use of robots is also gaining popularity for permanent stereotactic lead implantation applications such as in deep brain stimulation and responsive neurostimulation (RNS) procedures. Objective: We describe the evolution of our robotic stereotactic implantation technique for placement of occipital-approach hippocampal RNS depth leads. Methods: We performed a retrospective review of 10 consecutive patients who underwent robotic RNS hippocampal depth electrode implantation. Accuracy of depth lead implantation was measured by registering intraoperative post-implantation fluoroscopic CT images and post-operative CT scans with the stereotactic plan to measure implantation accuracy. Seizure data were also collected from the RNS devices and analyzed to obtain initial seizure control outcome estimates. Results: Ten patients underwent occipital-approach hippocampal RNS depth electrode placement for medically refractory epilepsy. A total of 18 depth electrodes were included in the analysis. Six patients (10 electrodes) were implanted in the supine position, with mean target radial error of 1.9 ± 0.9 mm (mean ± SD). Four patients (8 electrodes) were implanted in the prone position, with mean radial error of 0.8 ± 0.3 mm. The radial error was significantly smaller when electrodes were implanted in the prone position compared to the supine position (p = 0.002). Early results (median follow-up time 7.4 months) demonstrate mean seizure frequency reduction of 26% (n = 8), with 37.5% achieving ≥50% reduction in seizure frequency as measured by RNS long episode counts. Conclusion: Prone positioning for robotic implantation of occipital-approach hippocampal RNS depth electrodes led to lower radial target error compared to supine positioning. The robotic platform offers a number of workflow advantages over traditional frame-based approaches, including parallel rather than serial operation in a bilateral case, decreased concern regarding human error in setting frame coordinates, and surgeon comfort.

EEG education in neurology residency: background knowledge and focal challenges.

To assess the baseline EEG knowledge among adult neurology residents at our institution and their perspectives on EEG learning experience during residency. We evaluated baseline EEG knowledge and resident perception of EEG education utilizing an EEG quiz and an online EEG survey, respectively. The EEG quiz was divided in two parts, composed of normal (n=27) and abnormal (n=10) EEG examples. The EEG survey focused on the importance of EEG, EEG milestones and EEG education. Twenty-one residents completed the EEG quiz; all 21 completed the normal EEG part whereas 19 of these 21 completed the abnormal EEG part. The overall score (mean±SEM) was 42±4.5% for the normal EEG part and 44±5.5% for the abnormal EEG part. The EEG survey was completed by 28 residents. Forty-three percent of the respondents reported not being able to read EEGs even with supervision. The most commonly reported education barriers were insufficient exposure, insufficient responsibility to read EEGs, and inability to link EEG learning to direct patient care. On average, adult neurology residents were able to correctly identify less than half of normal and abnormal EEG findings. Almost half of residents reported not being able to read EEGs even with supervision.

Impact of prior hysterectomy on surgical outcomes for laparoscopic adnexal surgery.

BACKGROUND: Adnexal surgery is believed to be more complex in patients with prior hysterectomy; however, there is little data regarding surgical outcomes. Understanding of individualized risks improves counseling, informed consent, and preoperative planning. METHODS: We performed a retrospective cohort study with a control group; we evaluated 744 patients undergoing laparoscopic adnexal surgery at an academic tertiary care center from 2011 to 2015. Comparisons were made using Chi square, Fisher's exact, or Wilcoxon-rank sum tests. We used log-binomial regression to calculate risk ratio and 95% confidence interval. RESULTS: Patients with prior hysterectomy were more likely to have intraoperative or postoperative complications at the time of laparoscopic adnexal surgery when compared to patients without prior hysterectomy [17.7% vs. 10.2%, p = 0.02, risk ratio (RR) 1.7, 95% confidence interval (CI) 1.1-2.7]. Patients with prior hysterectomy were four times more likely to have intraoperative complications (3.2% vs. 0.8%, p = 0.047, RR 4.0, 95% CI 1.1-14.7), and five times more likely to have conversion to laparotomy (5.6% vs. 1.1%, p = 0.004, RR 5.0, 95% CI 1.8-14.0). Patients with prior hysterectomy were more likely to need additional procedures, including lysis of adhesions (69.4% vs. 26.0%, p < 0.001), ureterolysis (15.3% vs. 4.8%, p < 0.001), and cystoscopy (28.2% vs. 8.1%, p < 0.001). They had longer operative time [101.5 min (IQR 59.5-135.0) vs. 78.0 min (IQR 53.0-109.0, p < 0.001)], and were less likely to have outpatient surgery (56.5% vs. 84.8%, p < 0.01). Postoperative complications were also more common (15.3% vs. 9.4%, p = 0.046). CONCLUSIONS: Patients with prior hysterectomy were 70% more likely to have a complication at the time of laparoscopic adnexal surgery than patients without hysterectomy. Increased risk of complications in subsequent adnexal surgery may influence the informed consent process or decisions regarding ovarian conservation. Awareness of potential need for additional surgical procedures may guide availability of equipment, choice of operating site, or referral to an advanced pelvic surgeon.

Amidino-Rocaglates: A Potent Class of eIF4A Inhibitors.

Rocaglates share a common cyclopenta[b]benzofuran core that inhibits eukaryotic translation initiation by modifying the behavior of the RNA helicase, eIF4A. Working as interfacial inhibitors, rocaglates stabilize the association between eIF4A and RNA, which can lead to the formation of steric barriers that block initiating ribosomes. There is significant interest in the development and expansion of rocaglate derivatives, as several members of this family have been shown to possess potent anti-neoplastic activity in vitro and in vivo. To further our understanding of rocaglate diversity and drug design, herein we explore the RNA clamping activity of >200 unique rocaglate derivatives. Through this, we report on the identification and characterization of a potent class of synthetic rocaglates called amidino-rocaglates. These compounds are among the most potent rocaglates documented to date and, taken together, this work offers important information that will guide the future design of rocaglates with improved biological properties.

Intercepted Retro-Nazarov Reaction: Syntheses of Amidino-Rocaglate Derivatives and Their Biological Evaluation as eIF4A Inhibitors.

Rocaglates are a family of natural products isolated from the genus Aglaia which possess a highly substituted cyclopenta[b]benzofuran skeleton and inhibit cap-dependent protein synthesis. Rocaglates are attractive compounds due to their potential for inhibiting tumor cell maintenance in vivo by specifically targeting eukaryotic initiation factor 4A (eIF4A) and interfering with recruitment of ribosomes to mRNA. In this paper, we describe an intercepted retro-Nazarov reaction utilizing intramolecular tosyl migration to generate a reactive oxyallyl cation on the rocaglate skeleton. Trapping of the oxyallyl cation with a diverse range of nucleophiles has been used to generate over 50 novel amidino-rocaglate (ADR) and amino-rocaglate derivatives. Subsequently, these derivatives were evaluated for their ability to inhibit cap-dependent protein synthesis where they were found to outperform previous lead compounds including the rocaglate hydroxamate CR-1-31-B.

Do GLP-1RAs and SGLT-2is reduce cardiovascular events in black patients with type 2 diabetes? A systematic review and meta-analysis.

AIMS: While recent cardiovascular safety trials (CVST) concerning newer diabetes medications included mostly white participants, results are being generalized to all races in recent guidelines. This raises a controversial question regarding the appropriateness of applying CVST data to black patients with type 2 diabetes. MATERIALS AND METHODS: We searched for randomized trials comparing diabetes medications to placebo in type 2 diabetes and investigated three- or four-point major adverse cardiovascular events (MACE). Data concerning black patients were then extracted. As the American Diabetes Association (ADA) and the European Association for the Study of Diabetes (EASD) updated their recommendations for patients with established cardiovascular risk based on the CVST showing cardiovascular benefit, we performed a sensitivity analysis by including those trials only. RESULTS: A total of 11 trials were included, investigating a glucagon-like peptide-1 receptor agonist (GLP-1RA) in five, a sodium-glucose co-transporter-2 inhibitor (SGLT-2i) in two and dipeptidyl peptidase-4 inhibitors (DPP-4i) in four. Of the 102 416 participants enrolled in the included trials, only 4601 were black (4.5%). Pooled results showed no significant difference in the incidence of MACE among diabetes medications (GLP-1RA, SGLT-2i or DPP-4i) and placebo in black patients with type 2 diabetes (relative risk [RR] [95% CI], 0.94 [0.77,1.16]). Restricting the analysis to different classes of diabetes medication, the results remained non-significant. Restricting the analysis to CVST with significant outcomes, the results remained non-significant (RR [95% CI], 0.97 [0.68,1.39]). CONCLUSIONS: Given that black patients with type 2 diabetes were not well represented in CVSTs and such trials were underpowered to evaluate racial differences, it remains unclear whether GLP-1RAs or SGLT-2is would reduce cardiovascular risk in such patients, and additional studies targeting black patients are urgently needed.