Refining the impact of genetic evidence on clinical success.

The cost of drug discovery and development is driven primarily by failure1, with only about 10% of clinical programmes eventually receiving approval2-4. We previously estimated that human genetic evidence doubles the success rate from clinical development to approval5. In this study we leverage the growth in genetic evidence over the past decade to better understand the characteristics that distinguish clinical success and failure. We estimate the probability of success for drug mechanisms with genetic support is 2.6 times greater than those without. This relative success varies among therapy areas and development phases, and improves with increasing confidence in the causal gene, but is largely unaffected by genetic effect size, minor allele frequency or year of discovery. These results indicate we are far from reaching peak genetic insights to aid the discovery of targets for more effective drugs.

Differential Cognitive Effects of Unilateral Subthalamic Nucleus Deep Brain Stimulation for Parkinson's Disease.

OBJECTIVE: The aim of this study was to investigate the cognitive effects of unilateral directional versus ring subthalamic nucleus deep brain stimulation (STN DBS) in patients with advanced Parkinson's disease. METHODS: We examined 31 participants who underwent unilateral STN DBS (left n = 17; right n = 14) as part of an National Institutes of Health (NIH)-sponsored randomized, double-blind, crossover study contrasting directional versus ring stimulation. All participants received unilateral DBS implants in the hemisphere more severely affected by motor parkinsonism. Measures of cognition included verbal fluency, auditory-verbal memory, and response inhibition. We used mixed linear models to contrast the effects of directional versus ring stimulation and implant hemisphere on longitudinal cognitive function. RESULTS: Crossover analyses showed no evidence for group-level changes in cognitive performance related to directional versus ring stimulation. Implant hemisphere, however, impacted cognition in several ways. Left STN participants had lower baseline verbal fluency than patients with right implants (t [20.66 = -2.50, p = 0.02]). Verbal fluency declined after left (p = 0.013) but increased after right STN DBS (p < 0.001), and response inhibition was faster following right STN DBS (p = 0.031). Regardless of hemisphere, delayed recall declined modestly over time versus baseline (p = 0.001), and immediate recall was unchanged. INTERPRETATION: Directional versus ring STN DBS did not differentially affect cognition. Similar to prior bilateral DBS studies, unilateral left stimulation worsened verbal fluency performance. In contrast, unilateral right STN surgery increased performance on verbal fluency and response inhibition tasks. Our findings raise the hypothesis that unilateral right STN DBS in selected patients with predominant right brain motor parkinsonism could mitigate declines in verbal fluency associated with the bilateral intervention. ANN NEUROL 2024.

New alleles of nlp-2 , nlp-22 , and nlp-23 demonstrate that they are dispensable for stress-induced sleep in C. elegans.

Sleep is ancient and genetically conserved across phylogeny. Neuropeptide signaling plays a fundamental role in the regulation of sleep for mammals, fish, and invertebrates like Caenorhabditis elegans . Developmentally timed-sleep and stress-induced sleep of C. elegans are controlled by distinct and overlapping neuropeptide pathways. The RPamide neuropeptides nlp-2 , nlp-22 , and nlp-23 , play antagonistic roles during the regulation of developmentally-timed sleep, however, their role in stress-induced sleep has not been explored. These genes are linked on the X chromosome, which has made genetic analyses challenging. Here we used CRISPR to generate new alleles of nlp-22 and nlp-23 , nlp-22 ; nlp-23 double mutants, and nlp-2 ; nlp-22 ; nlp-23 triple mutants. Confirming previous studies, we find that nlp-22 is required for developmentally-timed sleep, and show that nlp-23 is also required. However, all three genes are dispensable for stress-induced sleep.

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.

Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.

Resveratrol differentially affects MMP-9 release from neurons and glia; implications for therapeutic efficacy.

Resveratrol, a naturally occurring polyphenol that activates sirtuin 1 (SIRT1), has been shown to reduce overall levels of matrix metalloprotease-9 (MMP-9) in cerebrospinal fluid (CSF) samples from patients with Alzheimer's dementia (AD). Depending on the site of release, however, MMP-9 has the potential to improve or impair cognition. In particular, its release from microglia or pericytes proximal to the blood brain barrier can damage the basement membrane, while neuronal activity-dependent release of this protease from glutamatergic neurons can instead promote dendritic spine expansion and long-term potentiation of synaptic plasticity. In the present study, we test the hypothesis that resveratrol reduces overall MMP-9 levels in CSF samples from patients with APOE4, an allele associated with increased glial inflammation. We also examine the possibility that resveratrol reduces inflammation-associated MMP release from cultured glia but spares neuronal activity-dependent release from cultured cortical neurons. We observe that resveratrol decreases overall levels of MMP-2 and MMP-9 in CSF samples from AD patients. Resveratrol also reduces CSF levels of tissue inhibitor of metalloproteinases-1 (TIMP-1), glial-derived protein that restricts long-term potentiation of synaptic transmission, in individuals homozygous for APOE4. Consistent with these results, we observe that resveratrol reduces basal and lipopolysaccharide (LPS)-stimulated MMP and TIMP-1 release from cultured microglia and astrocytes. In contrast, however, resveratrol does not inhibit release of MMP-9 from cortical neurons. Overall, these results are consistent with the possibility that while resveratrol reduces potentially maladaptive MMP and TIMP-1 release from activated glia, neuroplasticity-promoting MMP release from neurons is spared. In contrast, resveratrol reduces release of neurocan and brevican, extracellular matrix components that restrict neuroplasticity, from both neurons and glia. These data underscore the diversity of resveratrol's actions with respect to affected cell types and molecular targets and also suggest that further studies may be warranted to determine if its effects on glial MMP release could make it a useful adjunct for AD- and/or anti-amyloid therapy-related damage to the blood brain barrier.

Introducing DEPDOSE, a Tool to Calculate Dose Coefficients to Members of the Public for Radioactive Aerosols.

ABSTRACT: This paper presents DEPDOSE, an open-source computer application that combines the KDEP respiratory tract deposition fractions for inhaled aerosols with DC_PAK committed equivalent dose coefficients for a unit deposition in each region of the respiratory tract. DEPDOSE allows the user to rapidly produce tables of dose coefficients for workers and members of the public inhaling precisely defined, user-specified aerosols using the ICRP Publication 60 methodology. Combined with a plume dispersion modeling system, such as the Quick Urban & Industrial Complex (QUIC) Dispersion Modeling System, this makes it possible to predict radiation doses downstream from an accidental or intentional release of radioactive materials. For this work, a radioactive plume was calculated to members of the public downstream from a dirty bomb in Chicago. DEPDOSE is published under an open source license, and can be downloaded at https://github.com/lanl/DEPDOSE .

An easy and inexpensive method for determining the rate of individual phoretic events of nematodes.

Considering their limited locomotory capabilities, the cosmopolitan distribution of free-living nematodes may rely on phoretic dispersal. We describe a new, inexpensive device to investigate individual phoretic events of the nematode Caenorhabditis elegans using the pomace flies Drosophila melanogaster and Drosophila hydei over short time periods. Using our device, we replicated previous findings demonstrating that phoresis requires C. elegans to be in the dauer stage and capable of nictation. Additionally, we find that phoresis can happen on the order of seconds, and does not increase linearly with time of interaction. Using this approach can facilitate the investigation of nematode biogeography, which could provide useful insight into their, and their vector's, control.

Review of particle deposition to and removal from clothing, skin, and hair after a radioactive airborne dispersal event.

Explosive Radiological Dispersal Devices (RDD) - aka dirty bombs - are seen as a credible method to carry out a radiological terror attack. After exploding a radioactive source, the radionuclide-laden plume will be blown downwind of ground zero, with particles falling out and potentially depositing on people caught in and under the cloud. Some of these people may not show any sign of radiation sickness and therefore not realize they have been contaminated and may take the radioactive particulate with them on their daily activities, thus spreading the radioactive particulate outside the initially contaminated area. This paper reviews the scientific literature to better understand the rate at which particulate deposits on and is removed from the different "surfaces" of a person, i.e., hair, skin, and clothing. Prior research indicates that: 1) particle deposition is usually higher on skin than on hair and clothing; 2) particle deposition is greater for a person with higher skin moisture, 3) stronger wind increases the deposition flux onto a person, and 4) the fraction of particulate deposited on the hair, skin, and clothing respectively depends on the length of the hair, assuming all the hair surface is available for deposition. The studies taken into consideration show that the largest uncertainty in particulate deposition onto a person is due to clothing type because of the different possible weave arrangements and tightness which translate into differences in actual surface area and surface roughness. A factor of 2-to-20 variation in deposition rate was found. Removal of the particulate from the contaminated person may be due to wind, a person's movement, and/or contact transfer, i.e., by touching a different clean surface. Experiments show that the majority of the particulate is resuspended within 2-6 h mostly depending on the intensity of physical activity. The largest uncertainty in particulate removal from skin depends on the skin moisture, transfer rate of single-contact, and how many objects/people a person touches per hour. No data for hair were found for particle removal and resuspension. The studies considered did not utilize radionuclides directly; however, data on adhesion of radioactive vs. their non-radioactive counterpart have shown that the uncertainty due to the radioactivity of the particles is lower than that due to other factors. An idealized scenario involving a single building in the path of the cloud showed the impact of building-influenced flow on the cloud transport path and mixing, which affects the radiological dose the downwind population is exposed to and consequently the health effects.

The causal mutation leading to sweetness in modern white lupin cultivars.

Lupins are high-protein crops that are rapidly gaining interest as hardy alternatives to soybean; however, they accumulate antinutritional alkaloids of the quinolizidine type (QAs). Lupin domestication was enabled by the discovery of genetic loci conferring low QA levels (sweetness), but the precise identity of the underlying genes remains uncertain. We show that pauper, the most common sweet locus in white lupin, encodes an acetyltransferase (AT) unexpectedly involved in the early QA pathway. In pauper plants, a single-nucleotide polymorphism (SNP) strongly impairs AT activity, causing pathway blockage. We corroborate our hypothesis by replicating the pauper chemotype in narrow-leafed lupin via mutagenesis. Our work adds a new dimension to QA biosynthesis and establishes the identity of a lupin sweet gene for the first time, thus facilitating lupin breeding and enabling domestication of other QA-containing legumes.

The neuropeptide receptor npr-38 regulates avoidance and stress-induced sleep in Caenorhabditis elegans.

Although essential and conserved, sleep is not without its challenges that must be overcome; most notably, it renders animals vulnerable to threats in the environment. Infection and injury increase sleep demand, which dampens sensory responsiveness to stimuli, including those responsible for the initial insult. Stress-induced sleep in Caenorhabditis elegans occurs in response to cellular damage following noxious exposures the animals attempted to avoid. Here, we describe a G-protein-coupled receptor (GPCR) encoded by npr-38, which is required for stress-related responses including avoidance, sleep, and arousal. Overexpression of npr-38 shortens the avoidance phase and causes animals to initiate movement quiescence and arouse early. npr-38 functions in the ADL sensory neurons, which express neuropeptides encoded by nlp-50, also required for movement quiescence. npr-38 regulates arousal by acting on the DVA and RIS interneurons. Our work demonstrates that this single GPCR regulates multiple aspects of the stress response by functioning in sensory and sleep interneurons.

Virtual family-centered rounds: a quality improvement initiative to adapt inpatient care during COVID-19 using a human-centred participatory design approach.

BACKGROUND: Family-centered rounds (FCR) are fundamental to pediatric inpatient care. During the COVID-19 pandemic, we aimed to design and implement a virtual family-centered rounds (vFCR) process that allowed continuation of inpatient rounds while following physical distancing guidelines and preserving personal protective equipment (PPE). METHODS: A multidisciplinary team developed the vFCR process using a participatory design approach. From April through July 2020, quality improvement methods were used to iteratively evaluate and improve the process. Outcome measures included satisfaction, perceived effectiveness, and perceived usefulness of vFCR. Data were collected via questionnaire distributed to patients, families, staff and medical staff, and analyzed using descriptive statistics and content analysis. Virtual auditors monitored time per patient round and transition time between patients as balancing measures. RESULTS: Seventy-four percent (51/69) of health care providers surveyed and 79% (26/33) of patients and families were satisfied or very satisfied with vFCR. Eighty eight percent (61/69) of health care providers and 88% (29/33) of patients and families felt vFCR were useful. Audits revealed an average vFCR duration of 8.4 min (SD = 3.9) for a single patient round and transition time between patients averaged 2.9 min (SD = 2.6). CONCLUSION: Virtual family-centered rounds are an acceptable alternative to in-person FCR in a pandemic scenario, yielding high levels of stakeholder satisfaction and support. We believe vFCR are a useful method to support inpatient rounds, physical distancing, and preservation of PPE that may also be valuable beyond the pandemic. A rigorous process evaluation of vFCR is underway.

The search for commercial sweet white lupin (Lupinus albus L.) adaptive to Ethiopian growing condition seems not successful: what should be done?

The study was conducted to find new adaptive commercial sweet white lupin (Lupinus albus L.) varieties and evaluate the effect of inoculum on herbage and seed yields of white and blue lupin varieties in Ethiopia for two growing seasons in two locations. For the experiment a factorial arrangement (seven variety * two inoculation) in a randomized complete block design with three replication was used. Three sweet blue (Bora, Sanabor and Vitabor), three sweet white (Dieta, Energy and Feodora) and one bitter white local landrace lupin varieties were tested in the experiment. Analysis of variance was done using the general linear model procedure in SAS. The effects of location and inoculum were insignificant (P ≥ 0.0761) on yield and yield parameters. The effect of variety was observed (P ≤ 0.035) only on plant height, fresh biomass yield and thousand seed weight in both seasons except for fresh biomass yield in season two. However, its effect on other parameters was not shown (P ≥ 0.134) in both growing seasons or only shown in either season. The mean dry matter yield of all varieties was 2.45 ton per ha. However, sweet blue entries performed better than white entries. The mean seed yield of blue sweet lupin entries and white local check was 2.6 ton per ha. Sweet blue and white local landrace varieties were found tolerant while, commercial sweet white lupin varieties were susceptible for anthracnose and fusarium diseases that occurred immediately after flowering. As a result imported commercial sweet white varieties failed to give seed yield. Developing adaptive, disease resistant and high yielding sweet white lupin through crossing the local and commercial varieties and looking for species specific inoculum should be the future research agendas.

Dirty bomb source term characterization and downwind dispersion: Review of experimental evidence.

Dirty bombs are considered one of the easiest forms of radiological terrorism, a form of terrorism based on the deliberate use of radiological material to cause adverse effects in a target population. One U.S. Government official has even described a dirty bomb attack as "all but inevitable". While people in the vicinity of the blast may experience acute radiation effects, people downwind may unknowingly be contaminated by the radioactive airborne particulate and face increased long-term cancer risk. The likelihood of increased cancer risk depends on the radionuclide used and its specific activity, its aerosolization potential, the particle sizes generated in the blast, and where a person is with respect to the detonation. Different studies have reported that plausible radionuclides for dirty bomb include 60Co, 90Sr, 137Cs, 192Ir, 241Am based on their availability in commercial sources as well as safeguards, the amount needed for adverse health effects, previous mishandling of radionuclides and malicious uses. In order to have increased long-term cancer risk, the radionuclide would have to deposit inside the body by entering the respiratory tract and then possibly migrate to other organs or bones (ground shine is not considered in this paper because areas affected by the event will likely become inaccessible). This implies that the particles will have to be smaller than 10 µm to be inhaled. Experiments involving the detonation of dirty bombs have shown that particles or droplets smaller than 10 µm are generated, independently from the initial radionuclide or its state (e.g., powder, solution). Atmospheric tests have shown that in unobstructed terrain, the radionuclide laden cloud can travel kilometers downwind even for relatively small amounts of explosives. Buildings in the path of the cloud can change the dose rate. For instance, in one experiment with a single building, the dose rate was 1-2 orders of magnitude lower behind the obstacle compared to its front face. For people walking around, the amount of particulate deposited on them and inhaled will depend on their path relative to the cloud, resulting in the counterintuitive result that the closer people may actually not be the ones more at risk because they could simply miss the bulk of the cloud in their wandering. In summary, the long-term cancer risk for people caught in a dirty bomb cloud away from the detonation requires considering where and when the people are, which radionuclide was used, and the layout of the obstacles (e.g., buildings, vegetation) in the path of the cloud.

Differential cognitive effects of unilateral left and right subthalamic nucleus deep brain stimulation for Parkinson disease.

Objective: To investigate hemispheric effects of directional versus ring subthalamic nucleus (STN) deep brain stimulation (DBS) surgery on cognitive function in patients with advanced Parkinson's disease (PD). Methods: We examined 31 PD patients (Left STN n = 17; Right STN n = 14) who underwent unilateral subthalamic nucleus (STN) DBS as part of a NIH-sponsored randomized, cross-over, double-blind (ring vs directional) clinical trial. Outcome measures were tests of verbal fluency, auditory-verbal memory, and response inhibition. First, all participants were pooled together to study the effects of directional versus ring stimulation. Then, we stratified the groups by surgery hemisphere and studied the longitudinal changes in cognition post-unilateral STN DBS. Results: Relative to pre-DBS cognitive baseline performances, there were no group changes in cognition following unilateral DBS for either directional or ring stimulation. However, assessment of unilateral DBS by hemisphere revealed a different pattern. The left STN DBS group had lower verbal fluency than the right STN group (t(20.66 = -2.50, p = 0.02). Over a period of eight months post-DBS, verbal fluency declined in the left STN DBS group (p = 0.013) and improved in the right STN DBS group over time (p < .001). Similarly, response inhibition improved following right STN DBS (p = 0.031). Immediate recall did not significantly differ over time, nor was it affected by implant hemisphere, but delayed recall equivalently declined over time for both left and right STN DBS groups (left STN DBS p = 0.001, right STN DBS differ from left STN DBS p = 0.794). Conclusions: Directional and ring DBS did not differentially or adversely affect cognition over time. Regarding hemisphere effects, verbal fluency decline was observed in those who received left STN DBS, along with the left and right STN DBS declines in delayed memory. The left STN DBS verbal fluency decrement is consistent with prior bilateral DBS research, likely reflecting disruption of the basal-ganglia-thalamocortical network connecting STN and inferior frontal gyrus. Interestingly, we found an improvement in verbal fluency and response inhibition following right STN DBS. It is possible that unilateral STN DBS, particularly in the right hemisphere, may mitigate cognitive decline.

Future prospects for human genetics and genomics in drug discovery.

Evidence from human genetics supporting the therapeutic hypothesis increases the likelihood that a drug will succeed in clinical trials. Rare and common disease genetics yield a wide array of alleles with a range of effect sizes that can proxy for the effect of a drug in disease. Recent advances in large scale population collections and whole genome sequencing approaches have provided a rich resource of human genetic evidence to support drug target selection. As the range of phenotypes profiled increases and ever more alleles are discovered across world-wide populations, these approaches will increasingly influence multiple stages across the lifespan of a drug discovery programme.

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.

Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development.

Using human genetics to improve safety assessment of therapeutics.

Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.

Corrigendum: How could the use of crop wild relatives in breeding increase the adaptation of crops to marginal environments?

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A reference human induced pluripotent stem cell line for large-scale collaborative studies.

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.

A Psychological Resilience Briefing Intervention for Helicopter Emergency Medical Service Observers.

OBJECTIVE: Helicopter emergency medical services (HEMS) observers may be at risk of negative psychological effects associated with exposure to traumatic events during shifts. This article describes a quality improvement project for HEMS observers at Essex & Herts Air Ambulance. METHODS: A psychological resilience briefing intervention (PRBi) was developed and delivered during induction training with 60 HEMS observers. The PRBi aimed to raise awareness of traumatic events that observers may experience and provided basic education on 5 domains, including likely forms of trauma exposure, possible psychological reactions, advice on coping strategies and supporting colleagues, and resources that they could use if required. The intervention was intended to bolster resilience and reduce posttraumatic stress disorder symptoms, and to encourage adaptive coping styles in observers. RESULTS: Observers learned from and valued the PRBi; statistically significant increases were observed in awareness of the 5 domains from pre- to post-delivery, and free-text responses cited a variety of benefits to the observers. There was no indication that the PRBi caused harm. CONCLUSION: The PRBi has now been included in the routine induction of observers at Essex & Herts Air Ambulance and has the potential to be repurposed for use in other settings, including medical schools.