Delirium detection using wearable sensors and machine learning in patients with intracerebral hemorrhage.

Objective: Delirium is associated with worse outcomes in patients with stroke and neurocritical illness, but delirium detection in these patients can be challenging with existing screening tools. To address this gap, we aimed to develop and evaluate machine learning models that detect episodes of post-stroke delirium based on data from wearable activity monitors in conjunction with stroke-related clinical features. Design: Prospective observational cohort study. Setting: Neurocritical Care and Stroke Units at an academic medical center. Patients: We recruited 39 patients with moderate-to-severe acute intracerebral hemorrhage (ICH) and hemiparesis over a 1-year period [mean (SD) age 71.3 (12.20), 54% male, median (IQR) initial NIH Stroke Scale 14.5 (6), median (IQR) ICH score 2 (1)]. Measurements and main results: Each patient received daily assessments for delirium by an attending neurologist, while activity data were recorded throughout each patient's hospitalization using wrist-worn actigraph devices (on both paretic and non-paretic arms). We compared the predictive accuracy of Random Forest, SVM and XGBoost machine learning methods in classifying daily delirium status using clinical information alone and combined with actigraph data. Among our study cohort, 85% of patients (n = 33) had at least one delirium episode, while 71% of monitoring days (n = 209) were rated as days with delirium. Clinical information alone had a low accuracy in detecting delirium on a day-to-day basis [accuracy mean (SD) 62% (18%), F1 score mean (SD) 50% (17%)]. Prediction performance improved significantly (p < 0.001) with the addition of actigraph data [accuracy mean (SD) 74% (10%), F1 score 65% (10%)]. Among actigraphy features, night-time actigraph data were especially relevant for classification accuracy. Conclusions: We found that actigraphy in conjunction with machine learning models improves clinical detection of delirium in patients with stroke, thus paving the way to make actigraph-assisted predictions clinically actionable.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of the genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.

Estimating clinical risk in gene regions from population sequencing cohort data.

While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.

A molecular glue approach to control the half-life of CRISPR-based technologies.

Cas9 is a programmable nuclease that has furnished transformative technologies, including base editors and transcription modulators (e.g., CRISPRi/a), but several applications of these technologies, including therapeutics, mandatorily require precision control of their half-life. For example, such control can help avert any potential immunological and adverse events in clinical trials. Current genome editing technologies to control the half-life of Cas9 are slow, have lower activity, involve fusion of large response elements (> 230 amino acids), utilize expensive controllers with poor pharmacological attributes, and cannot be implemented in vivo on several CRISPR-based technologies. We report a general platform for half-life control using the molecular glue, pomalidomide, that binds to a ubiquitin ligase complex and a response-element bearing CRISPR-based technology, thereby causing the latter's rapid ubiquitination and degradation. Using pomalidomide, we were able to control the half-life of large CRISPR-based technologies (e.g., base editors, CRISPRi) and small anti-CRISPRs that inhibit such technologies, allowing us to build the first examples of on-switch for base editors. The ability to switch on, fine-tune and switch-off CRISPR-based technologies with pomalidomide allowed complete control over their activity, specificity, and genome editing outcome. Importantly, the miniature size of the response element and favorable pharmacological attributes of the drug pomalidomide allowed control of activity of base editor in vivo using AAV as the delivery vehicle. These studies provide methods and reagents to precisely control the dosage and half-life of CRISPR-based technologies, propelling their therapeutic development.

Estimating clinical risk in gene regions from population sequencing cohort data.

While pathogenic variants significantly increase disease risk in many genes, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2 , large cohort studies find no significant association between breast cancer and rare germline missense variants collectively. Here we introduce REGatta, a method to improve the estimation of clinical risk in gene segments. We define gene regions using the density of pathogenic diagnostic reports, and then calculate the relative risk in each of these regions using 109,581 exome sequences from women in the UK Biobank. We apply this method in seven established breast cancer genes, and identify regions in each gene with statistically significant differences in breast cancer incidence for rare missense carriers. Even in genes with no significant difference at the gene level, this approach significantly separates rare missense variant carriers at higher or lower risk ( BRCA2 regional model OR=1.46 [1.12, 1.79], p=0.0036 vs. BRCA2 gene model OR=0.96 [0.85,1.07] p=0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare with existing methods and the use of protein domains (Pfam) as regions, and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors which can potentially be used to improve risk assessment and clinical management.

Joint estimation and imputation of variant functional effects using high throughput assay data.

Deep mutational scanning assays enable the functional assessment of variants in high throughput. Phenotypic measurements from these assays are broadly concordant with clinical outcomes but are prone to noise at the individual variant level. We develop a framework to exploit related measurements within and across experimental assays to jointly estimate variant impact. Drawing from a large corpus of deep mutational scanning data, we collectively estimate the mean functional effect per AA residue position within each gene, normalize observed functional effects by substitution type, and make estimates for individual allelic variants with a pipeline called FUSE (Functional Substitution Estimation). FUSE improves the correlation of functional screening datasets covering the same variants, better separates estimated functional impacts for known pathogenic and benign variants (ClinVar BRCA1, p=2.24×10-51), and increases the number of variants for which predictions can be made (2,741 to 10,347) by inferring additional variant effects for substitutions not experimentally screened. For UK Biobank patients who carry a rare variant in TP53, FUSE significantly improves the separation of patients who develop cancer syndromes from those without cancer (p=1.77×10-6). These approaches promise to improve estimates of variant impact and broaden the utility of screening data generated from functional assays.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we have substantially improved the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.

Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria).

PURPOSE: This study aimed to explore whether evidence of pathogenicity from prior variant classifications in ClinVar could be used to inform variant interpretation using the American College of Medical Genetics and Genomics/Association for Molecular Pathology clinical guidelines. METHODS: We identified distinct single-nucleotide variants (SNVs) that are either similar in location or in functional consequence to pathogenic variants in ClinVar and analyzed evidence in support of pathogenicity using 3 interpretation criteria. RESULTS: Thousands of variants, including many in clinically actionable disease genes (American College of Medical Genetics and Genomics secondary findings v3.0), have evidence of pathogenicity from existing variant classifications, accounting for 2.5% of nonsynonymous SNVs within ClinVar. Notably, there are many variants with uncertain or conflicting classifications that cause the same amino acid substitution as other pathogenic variants (PS1, N = 323), variants that are predicted to cause different amino acid substitutions in the same codon as pathogenic variants (PM5, N = 7692), and loss-of-function variants that are present in genes in which many loss-of-function variants are classified as pathogenic (PVS1, N = 3635). Most of these variants have similar computational predictions of pathogenicity and splicing effect as their associated pathogenic variants. CONCLUSION: Broadly, for >1.4 million SNVs exome wide, information from previously classified variants could be used to provide evidence of pathogenicity. We have developed a pipeline to identify variants meeting these criteria that may inform interpretation efforts.

Peptide fusion improves prime editing efficiency.

Prime editing enables search-and-replace genome editing but is limited by low editing efficiency. We present a high-throughput approach, the Peptide Self-Editing sequencing assay (PepSEq), to measure how fusion of 12,000 85-amino acid peptides influences prime editing efficiency. We show that peptide fusion can enhance prime editing, prime-enhancing peptides combine productively, and a top dual peptide-prime editor increases prime editing significantly in multiple cell lines across dozens of target sites. Top prime-enhancing peptides function by increasing translation efficiency and serve as broadly useful tools to improve prime editing efficiency.

Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics.

The adenosine analogue remdesivir has emerged as a front-line antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness1.Prior clinical studies have identified adverse events1,2, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments7, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR-Cas9 screening and RNA sequencing, we show that remdesivir treatment leads to a repression of mitochondrial respiratory activity, and we identify five genes whose loss significantly reduces remdesivir cytotoxicity. In particular, we show that loss of the mitochondrial nucleoside transporter SLC29A3 mitigates remdesivir toxicity without a commensurate decrease in SARS-CoV-2 antiviral potency and that the mitochondrial adenylate kinase AK2 is a remdesivir kinase required for remdesivir efficacy and toxicity. This work elucidates the cellular mechanisms of remdesivir metabolism and provides a candidate gene target to reduce remdesivir cytotoxicity.

General fluid/inductive reasoning battery for a high-ability population.

The validity of studies investigating interventions to enhance fluid intelligence (Gf) depends on the adequacy of the Gf measures administered. Such studies have yielded mixed results, with a suggestion that Gf measurement issues may be partly responsible. The purpose of this study was to develop a Gf test battery comprising tests meeting the following criteria: (a) strong construct validity evidence, based on prior research; (b) reliable and sensitive to change; (c) varying in item types and content; (d) producing parallel tests, so that pretest-posttest comparisons could be made; (e) appropriate time limits; (f) unidimensional, to facilitate interpretation; and (g) appropriate in difficulty for a high-ability population, to detect change. A battery comprising letter, number, and figure series and figural matrix item types was developed and evaluated in three large-N studies (N = 3,067, 2,511, and 801, respectively). Items were generated algorithmically on the basis of proven item models from the literature, to achieve high reliability at the targeted difficulty levels. An item response theory approach was used to calibrate the items in the first two studies and to establish conditional reliability targets for the tests and the battery. On the basis of those calibrations, fixed parallel forms were assembled for the third study, using linear programming methods. Analyses showed that the tests and test battery achieved the proposed criteria. We suggest that the battery as constructed is a promising tool for measuring the effectiveness of cognitive enhancement interventions, and that its algorithmic item construction enables tailoring the battery to different difficulty targets, for even wider applications.