Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds.

SF3B is a multi-protein complex essential for branch site (BS) recognition and selection during pre-mRNA splicing. Several splicing modulators with antitumor activity bind SF3B and thereby modulate splicing. Here we report the crystal structure of a human SF3B core in complex with pladienolide B (PB), a macrocyclic splicing modulator and potent inhibitor of tumor cell proliferation. PB stalls SF3B in an open conformation by acting like a wedge within a hinge, modulating SF3B's transition to the closed conformation needed to form the BS adenosine-binding pocket and stably accommodate the BS/U2 duplex. This work explains the structural basis for the splicing modulation activity of PB and related compounds, and reveals key interactions between SF3B and a common pharmacophore, providing a framework for future structure-based drug design.

The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action.

Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1R1074H and PHF5AY36C The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure-activity relationship (SAR) on the PHF5AR38C mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.

Integrated management of HIV, diabetes, and hypertension in sub-Saharan Africa (INTE-AFRICA): a pragmatic cluster-randomised, controlled trial.

BACKGROUND: In sub-Saharan Africa, health-care provision for chronic conditions is fragmented. The aim of this study was to determine whether integrated management of HIV, diabetes, and hypertension led to improved rates of retention in care for people with diabetes or hypertension without adversely affecting rates of HIV viral suppression among people with HIV when compared to standard vertical care in medium and large health facilities in Uganda and Tanzania. METHODS: In INTE-AFRICA, a pragmatic cluster-randomised, controlled trial, we randomly allocated primary health-care facilities in Uganda and Tanzania to provide either integrated care or standard care for HIV, diabetes, and hypertension. Random allocation (1:1) was stratified by location, infrastructure level, and by country, with a permuted block randomisation method. In the integrated care group, participants with HIV, diabetes, or hypertension were managed by the same health-care workers, used the same pharmacy, had similarly designed medical records, shared the same registration and waiting areas, and had an integrated laboratory service. In the standard care group, these services were delivered vertically for each condition. Patients were eligible to join the trial if they were living with confirmed HIV, diabetes, or hypertension, were aged 18 years or older, were living within the catchment population area of the health facility, and were likely to remain in the catchment population for 6 months. The coprimary outcomes, retention in care (attending a clinic within the last 6 months of study follow-up) for participants with either diabetes or hypertension (tested for superiority) and plasma viral load suppression for those with HIV (>1000 copies per mL; tested for non-inferiority, 10% margin), were analysed using generalised estimating equations in the intention-to-treat population. This trial is registered with ISCRTN 43896688. FINDINGS: Between June 30, 2020, and April 1, 2021 we randomly allocated 32 health facilities (17 in Uganda and 15 in Tanzania) with 7028 eligible participants to the integrated care or the standard care groups. Among participants with diabetes, hypertension, or both, 2298 (75·8%) of 3032 were female and 734 (24·2%) of 3032 were male. Of participants with HIV alone, 2365 (70·3%) of 3365 were female and 1000 (29·7%) of 3365 were male. Follow-up lasted for 12 months. Among participants with diabetes, hypertension, or both, the proportion alive and retained in care at study end was 1254 (89·0%) of 1409 in integrated care and 1457 (89·8%) of 1623 in standard care. The risk differences were -0·65% (95% CI -5·76 to 4·46; p=0·80) unadjusted and -0·60% (-5·46 to 4·26; p=0·81) adjusted. Among participants with HIV, the proportion who had a plasma viral load of less than 1000 copies per mL was 1412 (97·0%) of 1456 in integrated care and 1451 (97·3%) of 1491 in standard care. The differences were -0·37% (one-sided 95% CI -1·99 to 1·26; pnon-inferiority<0·0001 unadjusted) and -0·36% (-1·99 to 1·28; pnon-inferiority<0·0001 adjusted). INTERPRETATION: In sub-Saharan Africa, integrated chronic care services could achieve a high standard of care for people with diabetes or hypertension without adversely affecting outcomes for people with HIV. FUNDING: European Union Horizon 2020 and Global Alliance for Chronic Diseases.

Duration of effectiveness of vaccines against SARS-CoV-2 infection and COVID-19 disease: results of a systematic review and meta-regression.

BACKGROUND: Knowing whether COVID-19 vaccine effectiveness wanes is crucial for informing vaccine policy, such as the need for and timing of booster doses. We aimed to systematically review the evidence for the duration of protection of COVID-19 vaccines against various clinical outcomes, and to assess changes in the rates of breakthrough infection caused by the delta variant with increasing time since vaccination. METHODS: This study was designed as a systematic review and meta-regression. We did a systematic review of preprint and peer-reviewed published article databases from June 17, 2021, to Dec 2, 2021. Randomised controlled trials of COVID-19 vaccine efficacy and observational studies of COVID-19 vaccine effectiveness were eligible. Studies with vaccine efficacy or effectiveness estimates at discrete time intervals of people who had received full vaccination and that met predefined screening criteria underwent full-text review. We used random-effects meta-regression to estimate the average change in vaccine efficacy or effectiveness 1-6 months after full vaccination. FINDINGS: Of 13 744 studies screened, 310 underwent full-text review, and 18 studies were included (all studies were carried out before the omicron variant began to circulate widely). Risk of bias, established using the risk of bias 2 tool for randomised controlled trials or the risk of bias in non-randomised studies of interventions tool was low for three studies, moderate for eight studies, and serious for seven studies. We included 78 vaccine-specific vaccine efficacy or effectiveness evaluations (Pfizer-BioNTech-Comirnaty, n=38; Moderna-mRNA-1273, n=23; Janssen-Ad26.COV2.S, n=9; and AstraZeneca-Vaxzevria, n=8). On average, vaccine efficacy or effectiveness against SARS-CoV-2 infection decreased from 1 month to 6 months after full vaccination by 21·0 percentage points (95% CI 13·9-29·8) among people of all ages and 20·7 percentage points (10·2-36·6) among older people (as defined by each study, who were at least 50 years old). For symptomatic COVID-19 disease, vaccine efficacy or effectiveness decreased by 24·9 percentage points (95% CI 13·4-41·6) in people of all ages and 32·0 percentage points (11·0-69·0) in older people. For severe COVID-19 disease, vaccine efficacy or effectiveness decreased by 10·0 percentage points (95% CI 6·1-15·4) in people of all ages and 9·5 percentage points (5·7-14·6) in older people. Most (81%) vaccine efficacy or effectiveness estimates against severe disease remained greater than 70% over time. INTERPRETATION: COVID-19 vaccine efficacy or effectiveness against severe disease remained high, although it did decrease somewhat by 6 months after full vaccination. By contrast, vaccine efficacy or effectiveness against infection and symptomatic disease decreased approximately 20-30 percentage points by 6 months. The decrease in vaccine efficacy or effectiveness is likely caused by, at least in part, waning immunity, although an effect of bias cannot be ruled out. Evaluating vaccine efficacy or effectiveness beyond 6 months will be crucial for updating COVID-19 vaccine policy. FUNDING: Coalition for Epidemic Preparedness Innovations.

Temperature-tunable UV generation using an Alexandrite laser and PPLN waveguides.

We present a simple and novel technique for achieving ultra-violet (UV) wavelength-tunable laser operation in the continuous-wave regime. Wavelength tunable operation in the near infrared is obtained from a compact two-mirror Alexandrite laser cavity by temperature tuning of the laser crystal. Second-harmonic-generation to the UV is then achieved at 376-379 nm and 384-386 nm by temperature tuning of a periodically-poled lithium-niobate (PPLN) waveguide. A maximum UV power of 1.3 mW from 185 mW infra-red pump throughput is obtained from a third-order PPLN Λ=6.1µm grating. These results show promising potential for simple and wavelength tunable access to wavelengths at 360-400 nm.

Short single-frequency self-pulsing Brillouin-Raman distributed feedback fiber laser.

We demonstrate that the stimulated Brillouin scattering of a 250 mm long distributed feedback Raman fiber laser can self-pulse with repetition rates up to 7 MHz, pulse widths of 25 ns, and peak powers of 1.2 W. While both CW and pulsed lasing are produced from a bespoke grating at 1119 nm this laser design could be constructed at almost any wavelength, as the Raman and Brillouin gain regions are relative to the pump wavelength. The laser has a low lasing threshold for a Raman laser of 0.55 W, a peak slope efficiency of 14 %, and a maximum average output of 0.25 W. An investigation of beating between pure Raman and Raman-pumped Brillouin lasing shows that the outputs of the two processes are highly correlated and thus the Brillouin lasing is essentially single-frequency when CW and near transform limited for pulsed operation. A phenomenological model of the Raman-Brillouin interaction shows that the pulsing behaviour of such a cavity is expected and produces very similar pulsing to that the seen in experimental results.

Human Challenge Studies to Accelerate Coronavirus Vaccine Licensure.

Controlled human challenge trials of SARS-CoV-2 vaccine candidates could accelerate the testing and potential rollout of efficacious vaccines. By replacing conventional phase 3 testing of vaccine candidates, such trials may subtract many months from the licensure process, making efficacious vaccines available more quickly. Obviously, challenging volunteers with this live virus risks inducing severe disease and possibly even death. However, we argue that such studies, by accelerating vaccine evaluation, could reduce the global burden of coronavirus-related mortality and morbidity. Volunteers in such studies could autonomously authorize the risks to themselves, and their net risk could be acceptable if participants comprise healthy young adults, who are at relatively low risk of serious disease following natural infection, if they have a high baseline risk of natural infection, and if during the trial they receive frequent monitoring and, following any infection, the best available care.

The R882H DNMT3A hot spot mutation stabilizes the formation of large DNMT3A oligomers with low DNA methyltransferase activity.

DNMT3A (DNA methyltransferase 3A) is a de novo DNA methyltransferase responsible for establishing CpG methylation patterns within the genome. DNMT3A activity is essential for normal development, and its dysfunction has been linked to developmental disorders and cancer. DNMT3A is frequently mutated in myeloid malignancies with the majority of mutations occurring at Arg-882, where R882H mutations are most frequent. The R882H mutation causes a reduction in DNA methyltransferase activity and hypomethylation at differentially-methylated regions within the genome, ultimately preventing hematopoietic stem cell differentiation and leading to leukemogenesis. Although the means by which the R882H DNMT3A mutation reduces enzymatic activity has been the subject of several studies, the precise mechanism by which this occurs has been elusive. Herein, we demonstrate that in the context of the full-length DNMT3A protein, the R882H mutation stabilizes the formation of large oligomeric DNMT3A species to reduce the overall DNA methyltransferase activity of the mutant protein as well as the WT-R882H complex in a dominant-negative manner. This shift in the DNMT3A oligomeric equilibrium and the resulting reduced enzymatic activity can be partially rescued in the presence of oligomer-disrupting DNMT3L, as well as DNMT3A point mutations along the oligomer-forming interface of the catalytic domain. In addition to modulating the oligomeric state of DNMT3A, the R882H mutation also leads to a DNA-binding defect, which may further reduce enzymatic activity. These findings provide a mechanistic explanation for the observed loss of DNMT3A activity associated with the R882H hot spot mutation in cancer.

CW demonstration of SHG spectral narrowing in a PPLN waveguide generating 2.5 W at 780†nm.

Periodically poled lithium niobate (PPLN) waveguides are a proven and popular means for efficient wavelength conversion. However, conventional PPLN waveguides typically have small mode field diameters (MFD) (≲6 µm) or significant insertion and/or propagation losses, limiting their ability to operate at multi-watt power levels. In this work we utilise zinc indiffused PPLN ridge waveguides that have a larger MFD, favourable pump/SHG modal overlap, and low insertion losses. Here for the first time, we have demonstrated continuous wave (CW) spectral narrowing from a PPLN waveguide, both with high efficiency and multi-watt second harmonic generation (SHG). 2.5 W of 780 nm has been produced by SHG of an amplified 1560 nm telecom laser with a device efficiency of 58% in a 4.0-cm long ridge waveguide. We have modelled conversion efficiency and applied experimentally measured waveguide parameters to show excellent agreement to the SHG spectra. Spectral narrowing of the full width half maximum (FWHM) of 35.7% has been measured as the nonlinear drive is increased. This work demonstrates that single-pass, multi-watt, CW SHG at 780 nm is feasible from our PPLN waveguide in the large conversion regime.

Upconversion detection of 1.25 Gb/s mid-infrared telecommunications using a silicon avalanche photodiode.

With an ever-increasing interest in secure and reliable free-space optical communication, upconversion detectors enabled through nonlinear optical processes are an attractive route to transmitting data as a mid-infrared signal. This spectral region is known to have a higher transmissivity through the atmosphere. In this work, we present an upconversion scheme for detection in the silicon absorption band using magnesium-oxide doped periodically poled lithium niobate to generate 21 mW of a 3.4 µm signal from commercial laser sources using a difference frequency generation process. Following a further nonlinear frequency conversion, via sum-frequency generation, the resulting signal at 809 nm is detected. We achieve >50 µW of signal and bit error rates of 10-7 from a single-pass nonlinear conversion for both the transmitter and receiver systems without the need for additional optical amplifiers at the receiving end. The error rates due to potentially reduced laser powers at the receiver end are investigated and laser noise transfer through our system is discussed.

Highly-chirped Bragg gratings for integrated silica spectrometers.

A blazed chirped Bragg grating in a planar silica waveguide device was used to create an integrated diffractive element for a spectrometer. The grating diffracts light from a waveguide and creates a wavelength dependent focus in a manner similar to a bulk diffraction grating spectrometer. An external imaging system is used to analyse the light, later device iterations plan to integrate detectors to make a fully integrated spectrometer. Devices were fabricated with grating period chirp rates in excess of 100 nm mm-1, achieving a focal length of 5.5 mm. Correction of coma aberrations resulted in a device with a footprint of 20 mm×10 mm, a peak FWHM resolution of 1.8 nm, a typical FWHM resolution of 2.6 nm and operating with a 160 nm bandwidth centered at 1550 nm.

Individual inscription of spectrally multiplexed Bragg gratings in optical multicore fibers using small spot direct UV writing.

We have demonstrated the inscription of Bragg gratings into five individual cores of a seven core fiber using small spot direct UV writing. With this technique, we defined spectrally multiplexed Bragg gratings consecutively in separate cores as well as spectrally multiplexed gratings at the same longitudinal location in different cores. The effect of bending on the optical spectrum was evaluated to allow the differentiation between cross-exposure and cross-talk, and an alignment process to reduce cross-exposure by 13 dB was found.

213 nm laser written waveguides in Ge-doped planar silica without hydrogen loading.

In this paper we present the first example of waveguides fabricated by UV writing in non-hydrogen loaded Ge-doped planar silica with 213 nm light. Single mode waveguides were fabricated and the numerical apertures and mode field diameters were measured for a range of writing fluences. A peak index change of 5.3 x 10-3 was inferred for the waveguide written with 70 kJ cm-2. The refractive index change is sufficient to match the index structure of standard optical fiber. Uniformity of the written structures was measured and a propagation loss of 0.39 ± 0.03 dB cm-1 was determined through cutback measurements.

Metabolic disposition of H3B-8800, an orally available small-molecule splicing modulator, in rats, monkeys, and humans.

H3B-8800, a novel orally available modulator of the SF3b complex, which potently and preferentially kills spliceosome-mutant tumor cells, is in clinical development for the treatment of advanced myeloid malignancies. We characterized the pharmacokinetics, metabolism and disposition of H3B-8800 in rats, monkeys and humans.In vitro, H3B-8800 is a substrate of CYP3A4/5, flavin-containing monooxygenases (FMOs) and P-glycoprotein (P-gp), and showed a favorable drug-drug interaction profile as a perpetrator.Following oral dosing of 14C-H3B-8800 in bile-duct cannulated SD rats, 54.7% of the dosed radioactivity was excreted in the bile, with less found in feces (36.8%). The low amount in urine (3.7%), suggests that renal elimination is a minor pathway of clearance for H3B-8800.In Long-Evans rats, radioactivity derived from 14C-H3B-8800 was rapidly absorbed, with the highest distribution in the ocular, metabolic/excretory, and gastrointestinal tract tissues. No radioactivity was detected in the central nervous system.Seven metabolites were observed in human plasma following 4 daily doses of 40 mg H3B-8800. H3B-68736 (N-desmethyl), H3B-77176 (N-oxide), and unchanged H3B-8800 were the prominent components in human plasma, at 27.3%, 18.1%, and 33.2%, respectively, of the total drug-related material in a pooled AUC0-24h sample. The same 7 metabolites were observed in monkey plasma.

Zinc-indiffused MgO:PPLN waveguides for blue/UV generation via VECSEL pumping.

We present the design and characterization of a zinc-indiffused periodically poled lithium-niobate ridge waveguide for second-harmonic generation of ∼390nm light from 780 nm. We use a newly developed, broadband near-infrared vertical external-cavity surface-emitting laser (VECSEL) to investigate the potential for lower-footprint nonlinear optical pump sources as an alternative to larger commercial laser systems. We demonstrate a VECSEL with an output power of 500 mW, containing an intracavity birefringent filter for spectral narrowing and wavelength selection. In this first demonstration of using a VECSEL to pump a nonlinear waveguide, we present the ability to generate 1 mW of ∼390nm light with further potential for increased efficiency and size reduction.

Neuronal cytoskeletal gene dysregulation and mechanical hypersensitivity in a rat model of Rett syndrome.

Children with Rett syndrome show abnormal cutaneous sensitivity. The precise nature of sensory abnormalities and underlying molecular mechanisms remain largely unknown. Rats with methyl-CpG binding protein 2 (MeCP2) mutation, characteristic of Rett syndrome, show hypersensitivity to pressure and cold, but hyposensitivity to heat. They also show cutaneous hyperinnervation by nonpeptidergic sensory axons, which include subpopulations encoding noxious mechanical and cold stimuli, whereas peptidergic thermosensory innervation is reduced. MeCP2 knockdown confined to dorsal root ganglion sensory neurons replicated this phenotype in vivo, and cultured MeCP2-deficient ganglion neurons showed augmented axonogenesis. Transcriptome analysis revealed dysregulation of genes associated with cytoskeletal dynamics, particularly those controlling actin polymerization and focal-adhesion formation necessary for axon growth and mechanosensory transduction. Down-regulation of these genes by topoisomerase inhibition prevented abnormal axon sprouting. We identified eight key affected genes controlling actin signaling and adhesion formation, including members of the Arhgap, Tiam, and cadherin families. Simultaneous virally mediated knockdown of these genes in Rett rats prevented sensory hyperinnervation and reversed mechanical hypersensitivity, indicating a causal role in abnormal outgrowth and sensitivity. Thus, MeCP2 regulates ganglion neuronal genes controlling cytoskeletal dynamics, which in turn determines axon outgrowth and mechanosensory function and may contribute to altered pain sensitivity in Rett syndrome.

Evaluation of Convalescent Plasma for Ebola Virus Disease in Guinea.

BACKGROUND: In the wake of the recent outbreak of Ebola virus disease (EVD) in several African countries, the World Health Organization prioritized the evaluation of treatment with convalescent plasma derived from patients who have recovered from the disease. We evaluated the safety and efficacy of convalescent plasma for the treatment of EVD in Guinea. METHODS: In this nonrandomized, comparative study, 99 patients of various ages (including pregnant women) with confirmed EVD received two consecutive transfusions of 200 to 250 ml of ABO-compatible convalescent plasma, with each unit of plasma obtained from a separate convalescent donor. The transfusions were initiated on the day of diagnosis or up to 2 days later. The level of neutralizing antibodies against Ebola virus in the plasma was unknown at the time of administration. The control group was 418 patients who had been treated at the same center during the previous 5 months. The primary outcome was the risk of death during the period from 3 to 16 days after diagnosis with adjustments for age and the baseline cycle-threshold value on polymerase-chain-reaction assay; patients who had died before day 3 were excluded. The clinically important difference was defined as an absolute reduction in mortality of 20 percentage points in the convalescent-plasma group as compared with the control group. RESULTS: A total of 84 patients who were treated with plasma were included in the primary analysis. At baseline, the convalescent-plasma group had slightly higher cycle-threshold values and a shorter duration of symptoms than did the control group, along with a higher frequency of eye redness and difficulty in swallowing. From day 3 to day 16 after diagnosis, the risk of death was 31% in the convalescent-plasma group and 38% in the control group (risk difference, -7 percentage points; 95% confidence interval [CI], -18 to 4). The difference was reduced after adjustment for age and cycle-threshold value (adjusted risk difference, -3 percentage points; 95% CI, -13 to 8). No serious adverse reactions associated with the use of convalescent plasma were observed. CONCLUSIONS: The transfusion of up to 500 ml of convalescent plasma with unknown levels of neutralizing antibodies in 84 patients with confirmed EVD was not associated with a significant improvement in survival. (Funded by the European Union's Horizon 2020 Research and Innovation Program and others; ClinicalTrials.gov number, NCT02342171.).

Direct UV written integrated planar waveguides using a 213 nm laser.

We present the first demonstration of integrated waveguides in planar silica devices fabricated using direct UV writing with 213 nm laser light. Waveguides were produced with different writing fluences and the NA and MFD of each were measured. Single mode waveguides were achieved at fluence values one-tenth that typically required when operating with a 244 nm laser, allowing for more rapid fabrication. A maximum in-plane index change of 2.4 ×10-3 for a writing fluence of 5 kJ cm-2 was estimated from NA measurements. Finally cutback measurements were performed and a propagation loss of 0.42 ± 0.07 dB cm-1 was directly measured, though losses as low as 0.2 ± 0.03 dB/cm are indicated through calculations.

Integrated polarizer based on 45° tilted gratings.

We report the first integrated implementation of a polarizer based on the use of 45° tilted gratings in planar waveguides. The waveguides and gratings are fabricated by direct UV writing in a hydrogenated germanium-doped silica-on-silicon chip. We experimentally demonstrate a polarization extinction ratio per unit length of 0.25 dB mm -1 with a modelled wavelength dependence smaller than 0.3 dB for a 20 mm device over the C band from 1530-1570 nm. We also present a novel numerical study and analytical description of the architecture that are in good agreement with each other and the experimental data.