Discovery of deaminase functions by structure-based protein clustering.

The elucidation of protein function and its exploitation in bioengineering have greatly advanced the life sciences. Protein mining efforts generally rely on amino acid sequences rather than protein structures. We describe here the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected deaminase proteins to analyze and identified many previously unknown properties. We were surprised to find that most proteins in the DddA-like clade were not double-stranded DNA deaminases. We engineered the smallest single-strand-specific cytidine deaminase, enabling efficient cytosine base editor (CBE) to be packaged into a single adeno-associated virus (AAV). Importantly, we profiled a deaminase from this clade that edits robustly in soybean plants, which previously was inaccessible to CBEs. These discovered deaminases, based on AI-assisted structural predictions, greatly expand the utility of base editors for therapeutic and agricultural applications.

Base editing of haematopoietic stem cells rescues sickle cell disease in mice.

Sickle cell disease (SCD) is caused by a mutation in the ß-globin gene HBB1. We used a custom adenine base editor (ABE8e-NRCH)2,3 to convert the SCD allele (HBBS) into Makassar ß-globin (HBBG), a non-pathogenic variant4,5. Ex vivo delivery of mRNA encoding the base editor with a targeting guide RNA into haematopoietic stem and progenitor cells (HSPCs) from patients with SCD resulted in 80% conversion of HBBS to HBBG. Sixteen weeks after transplantation of edited human HSPCs into immunodeficient mice, the frequency of HBBG was 68% and hypoxia-induced sickling of bone marrow reticulocytes had decreased fivefold, indicating durable gene editing. To assess the physiological effects of HBBS base editing, we delivered ABE8e-NRCH and guide RNA into HSPCs from a humanized SCD mouse6 and then transplanted these cells into irradiated mice. After sixteen weeks, Makassar ß-globin represented 79% of ß-globin protein in blood, and hypoxia-induced sickling was reduced threefold. Mice that received base-edited HSPCs showed near-normal haematological parameters and reduced splenic pathology compared to mice that received unedited cells. Secondary transplantation of edited bone marrow confirmed that the gene editing was durable in long-term haematopoietic stem cells and showed that HBBS-to-HBBG editing of 20% or more is sufficient for phenotypic rescue. Base editing of human HSPCs avoided the p53 activation and larger deletions that have been observed following Cas9 nuclease treatment. These findings point towards a one-time autologous treatment for SCD that eliminates pathogenic HBBS, generates benign HBBG, and minimizes the undesired consequences of double-strand DNA breaks.

Assigning functionality to cysteines by base editing of cancer dependency genes.

Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse human proteins. Determining which of these covalent binding events affect protein function, however, remains challenging. Here we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. The resulting atlas, which covers more than 13,800 cysteines on more than 1,750 cancer dependency proteins, confirms the essentiality of cysteines targeted by covalent drugs and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines in more than 160 cancer dependency proteins. We further show that a stereoselective and site-specific ligand targeting an essential cysteine in TOE1 inhibits the nuclease activity of this protein through an apparent allosteric mechanism. Our findings thus describe a versatile method and valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.

Sex differences in sleep architecture in a mouse model of Huntington's disease.

Sleep and circadian rhythm disturbances are common features of Huntington's disease (HD). HD is an autosomal dominant neurodegenerative disorder that affects men and women in equal numbers, but some epidemiological studies as well as preclinical work indicate there may be sex differences in disease presentation and progression. Since sex differences in HD could provide important insights to understand cellular and molecular mechanism(s), we used the bacterial artificial chromosome transgenic mouse model of HD (BACHD) to examine whether sex differences in sleep/wake cycles are detectable in an animal model of the disease. Electroencephalography/electromyography (EEG/EMG) was used to measure sleep/wake states and polysomnographic patterns in young adult (12-week-old) male and female wild-type and BACHD mice. Our findings show that male, but not female, BACHD mice exhibited increased variation in phases of the rhythms as compared to age- and sex-matched wild-types. For both rapid-eye movement (REM) and non-rapid eye movement (NREM) sleep, genotypic and sex differences were detected. In particular, the BACHD males spent less time in NREM sleep and exhibited a more fragmented sleep than the other groups. Finally, in response to 6 h of sleep deprivation, both genotypes and sexes displayed the predicted homeostatic responses to sleep loss. These findings suggest that females are relatively protected early in disease progression in this HD model.

Comparing the Drop Vertical Jump Tracking Performance of the Azure Kinect to the Kinect V2.

Traditional motion analysis systems are impractical for widespread screening of non-contact anterior cruciate ligament (ACL) injury risk. The Kinect V2 has been identified as a portable and reliable alternative but was replaced by the Azure Kinect. We hypothesize that the Azure Kinect will assess drop vertical jump (DVJ) parameters associated with ACL injury risk with similar accuracy to its predecessor, the Kinect V2. Sixty-nine participants performed DVJs while being recorded by both the Azure Kinect and the Kinect V2 simultaneously. Our software analyzed the data to identify initial coronal, peak coronal, and peak sagittal knee angles. Agreement between the two systems was evaluated using the intraclass correlation coefficient (ICC). There was poor agreement between the Azure Kinect and the Kinect V2 for initial and peak coronal angles (ICC values ranging from 0.135 to 0.446), and moderate agreement for peak sagittal angles (ICC = 0.608, 0.655 for left and right knees, respectively). At this point in time, the Azure Kinect system is not a reliable successor to the Kinect V2 system for assessment of initial coronal, peak coronal, and peak sagittal angles during a DVJ, despite demonstrating superior tracking of continuous knee angles. Alternative motion analysis systems should be explored.

Comparing a Portable Motion Analysis System against the Gold Standard for Potential Anterior Cruciate Ligament Injury Prevention and Screening.

Knee kinematics during a drop vertical jump, measured by the Kinect V2 (Microsoft, Redmond, WA, USA), have been shown to be associated with an increased risk of non-contact anterior cruciate ligament injury. The accuracy and reliability of the Microsoft Kinect V2 has yet to be assessed specifically for tracking the coronal and sagittal knee angles of the drop vertical jump. Eleven participants performed three drop vertical jumps that were recorded using both the Kinect V2 and a gold standard motion analysis system (Vicon, Los Angeles, CA, USA). The initial coronal, peak coronal, and peak sagittal angles of the left and right knees were measured by both systems simultaneously. Analysis of the data obtained by the Kinect V2 was performed by our software. The differences in the mean knee angles measured by the Kinect V2 and the Vicon system were non-significant for all parameters except for the peak sagittal angle of the right leg with a difference of 7.74 degrees and a p-value of 0.008. There was excellent agreement between the Kinect V2 and the Vicon system, with intraclass correlation coefficients consistently over 0.75 for all knee angles measured. Visual analysis revealed a moderate frame-to-frame variability for coronal angles measured by the Kinect V2. The Kinect V2 can be used to capture knee coronal and sagittal angles with sufficient accuracy during a drop vertical jump, suggesting that a Kinect-based portable motion analysis system is suitable to screen individuals for the risk of non-contact anterior cruciate ligament injury.

Reconstruction of evolving gene variants and fitness from short sequencing reads.

Directed evolution can generate proteins with tailor-made activities. However, full-length genotypes, their frequencies and fitnesses are difficult to measure for evolving gene-length biomolecules using most high-throughput DNA sequencing methods, as short read lengths can lose mutation linkages in haplotypes. Here we present Evoracle, a machine learning method that accurately reconstructs full-length genotypes (R2 = 0.94) and fitness using short-read data from directed evolution experiments, with substantial improvements over related methods. We validate Evoracle on phage-assisted continuous evolution (PACE) and phage-assisted non-continuous evolution (PANCE) of adenine base editors and OrthoRep evolution of drug-resistant enzymes. Evoracle retains strong performance (R2 = 0.86) on data with complete linkage loss between neighboring nucleotides and large measurement noise, such as pooled Sanger sequencing data (~US$10 per timepoint), and broadens the accessibility of training machine learning models on gene variant fitnesses. Evoracle can also identify high-fitness variants, including low-frequency 'rising stars', well before they are identifiable from consensus mutations.

Down Syndrome Candidate Region 1 Isoform 1L regulated tumor growth by targeting both angiogenesis and tumor cells.

Angiogenesis is critical for solid tumor growth beyond its minimal size. Previously, we reported that Down Syndrome Candidate Region 1 isoform 1L (DSCR1-1L) was one of the most up-regulated genes in endothelial cells induced by VEGF and histamine, and regulated endothelial cell proliferation, migration and angiogenesis. However, it was not known whether DSCR1-1L played a role in tumor growth. In this study, we found that DSCR1-1L shRNAs significantly inhibited the growth of transplanted melanoma in mice and its associated tumoral angiogenesis. In the gain of function assay, overexpression of DSCR1-1L cDNA in mouse endothelium is sufficient to significantly increase the tumor initiation induced by carcinogen, the growth of xenografted tumor, and the tumor metastasis in our endothelially-expressed DSCR1-1L transgenic mice, in which angiogenesis was induced. It was the first time to find that DSCR1-1L was also expressed in various tumor cells. DSCR1-1L shRNAs inhibited, but overexpression of DSCR1-1L cDNA increased, the tumor cell proliferation and migration. Most recently, we reported that DSCR1-1L modulated angiogenesis by down-regulation of VE-cadherin expression. Here, we found that DSCR1-1L down-regulated the expression of E-cadherin. Hence, DSCR1-1L is an excellent therapeutic target for cancers by regulation of both the endothelial and tumor cells through down-regulating (V)E-cadherin. DSCR1-1L shRNAs have the potential to be developed for clinical application.

Patient frailty association with cerebral arteriovenous malformation microsurgical outcomes and development of custom risk stratification score: an analysis of 16,721 nationwide admissions.

OBJECTIVE: Patient frailty is associated with poorer perioperative outcomes for several neurosurgical procedures. However, comparative accuracy between different frailty metrics for cerebral arteriovenous malformation (AVM) outcomes is poorly understood and existing frailty metrics studied in the literature are constrained by poor specificity to neurosurgery. This aim of this paper was to compare the predictive ability of 3 frailty scores for AVM microsurgical admissions and generate a custom risk stratification score. METHODS: All adult AVM microsurgical admissions in the National (Nationwide) Inpatient Sample (2002-2017) were identified. Three frailty measures were analyzed: 5-factor modified frailty index (mFI-5; range 0-5), 11-factor modified frailty index (mFI-11; range 0-11), and Charlson Comorbidity Index (CCI) (range 0-29). Receiver operating characteristic curves were used to compare accuracy between metrics. The analyzed endpoints included in-hospital mortality, routine discharge, complications, length of stay (LOS), and hospitalization costs. Survey-weighted multivariate regression assessed frailty-outcome associations, adjusting for 13 confounders, including patient demographics, hospital characteristics, rupture status, hydrocephalus, epilepsy, and treatment modality. Subsequently, k-fold cross-validation and Akaike information criterion-based model selection were used to generate a custom 5-variable risk stratification score called the AVM-5. This score was validated in the main study population and a pseudoprospective cohort (2018-2019). RESULTS: The authors analyzed 16,271 total AVM microsurgical admissions nationwide, with 21.0% being ruptured. The mFI-5, mFI-11, and CCI were all predictive of lower rates of routine discharge disposition, increased perioperative complications, and longer LOS (all p < 0.001). Their AVM-5 risk stratification score was calculated from 5 variables: age, hydrocephalus, paralysis, diabetes, and hypertension. The AVM-5 was predictive of decreased rates of routine hospital discharge (OR 0.26, p < 0.001) and increased perioperative complications (OR 2.42, p < 0.001), postoperative LOS (+49%, p < 0.001), total LOS (+47%, p < 0.001), and hospitalization costs (+22%, p < 0.001). This score outperformed age, mFI-5, mFI-11, and CCI for both ruptured and unruptured AVMs (area under the curve [AUC] 0.78, all p < 0.001). In a pseudoprospective cohort of 2005 admissions from 2018 to 2019, the AVM-5 remained significantly associated with all outcomes except for mortality and exhibited higher accuracy than all 3 earlier scores (AUC 0.79, all p < 0.001). CONCLUSIONS: Patient frailty is predictive of poorer disposition and elevated complications, LOS, and costs for AVM microsurgical admissions. The authors' custom AVM-5 risk score outperformed age, mFI-5, mFI-11, and CCI while using threefold less variables than the CCI. This score may complement existing AVM grading scales for optimization of surgical candidates and identification of patients at risk of postoperative medical and surgical morbidity.