The human immune system displays substantial variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing (scRNA-seq) data from 1,267,758 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTLs, with most showing cell type–specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells that are transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to interindividual variation in immune function. Finally, using a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of interindividual variation in the immune system.

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNAo rigami nanostructures (DONs) presents an innovative pathwayf or the generation of stable,p olynucleotide brush-functionalized DNAn anostructures.W ed emonstrate that SI-TcEP can sitespecifically pattern DONs with brushes containing both natural and non-natural nucleotides.The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies.W ef ind that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly,and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes.The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to al arge range of functionalizedD ON architectures that would allowf or further supramolecular assembly,a nd for potential applications in smart nanoscale delivery systems.

CRISPR/Cas has opened the prospect of direct gene correction therapy for some inherited retinal diseases. Previous work has demonstrated the utility of adeno-associated virus (AAV) mediated delivery to retinal cells in vivo ; however, with the expanding repertoire of CRISPR/Cas endonucleases, it is not clear which of these are most efficacious for retinal editing in vivo . We sought to compare CRISPR/Cas endonuclease activity using both single and dual AAV delivery strategies for gene editing in retinal cells. Plasmids of a dual vector system with SpCas9, SaCas9, Cas12a, CjCas9 and a sgRNA targeting YFP , as well as a single vector system with SaCas9/YFP sgRNA were generated and validated in YFP-expressing HEK293A cell by flow cytometry and the T7E1 assay. Paired CRISPR/Cas endonuclease and its best performing sgRNA was then packaged into an AAV2 capsid derivative, AAV7m8, and injected intravitreally into CMV-Cre:Rosa26-YFP mice. SpCas9 and Cas12a achieved better knockout efficiency than SaCas9 and CjCas9. Moreover, no significant difference in YFP gene editing was found between single and dual CRISPR/SaCas9 vector systems. With a marked reduction of YFP-positive retinal cells, AAV7m8 delivered SpCas9 was found to have the highest knockout efficacy among all investigated endonucleases. We demonstrate that the AAV7m8-mediated delivery of CRISPR/SpCas9 construct achieves the most efficient gene modification in neurosensory retinal cells in vivo .

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si 3 N 4 ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si 3 N 4 substrates treated with a monolayer of hexamethyldisilazane (HMDS) (~1 0 13 ohms) than on native Si 3 N 4 substrates without HMDS (1 0 14 ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si 3 N 4 substrates reveal that DNA origami nanowires are ~1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.

CRISPR/Cas has opened the prospect of direct gene correction therapy for some inherited retinal diseases. Previous work has demonstrated the utility of adeno-associated virus (AAV) mediated delivery to retinal cells in vivo ; however, with the expanding repertoire of CRISPR/Cas endonucleases, it is not clear which of these are most efficacious for retinal editing in vivo . We sought to compare CRISPR/Cas endonuclease activity using both single and dual AAV delivery strategies for gene editing in retinal cells. Plasmids of a dual vector system with SpCas9, SaCas9, Cas12a, CjCas9 and sgRNA targeting YFP and a single vector system with SaCas9/YFP sgRNA were generated and validated in YFP-expressing HEK293A cell by flow cytometry and T7E1 assay.Paired CRISPR/Cas endonuclease and its best performing sgRNA was then packaged into an AAV2 capsid derivative, AAV7m8, and injected intravitreally into CMV-Cre::Rosa26-YFP mice. SpCas9and Cas12a achieved better knockout efficiency than SaCas9 and CjCas9. Moreover, no significant difference in YFP gene editing was found between single and dual CRISPR/SaCas9 vector systems.With a marked reduction of YFP-positive retinal cells, AAV7m8 delivered SpCas9 was found to have the highest knockout efficacy among all investigated endonucleases. We demonstrate that the AAV7m8-mediated delivery of CRISPR/SpCas9 construct achieves the most efficient gene modification in neurosensory retinal cells in vitro and in vivo .

ObjectiveTo investigate the differences in ocular surface characteristics, tear film quality, and the incidence of dry eye disease (DED) between Systemic Lupus Erythematosus (SLE) patients and healthy populations.MethodsThis age and gender-matched cross-sectional study included 96 SLE patients without secondary Sjögren's syndrome (SS) and 72 healthy subjects. The Ocular Surface Disease Index (OSDI), tear meniscus height (TMH), non-invasive tear film breakup time (NIKBUT), meibography, and tear film lipid layer grade were assessed. A receiver operative characteristic (ROC) curve was constructed to evaluate the predictive value of risk factors.ResultsCompared with the control subjects, a significantly greater proportion of SLE patients met the TFOS DEWS II DED diagnostic criteria (34.3 vs. 18.1%, P = 0.019). SLE patients without SS had higher OSDI scores [10.0 (4.5,18.0) vs. 5.0 (2.5,11.9), P < 0.001], and shorter NIKBUT [9.6 (6.6,15.0) vs. 12.3 (8.4, 15.8), P = 0.035]. Furthermore, TMH, Tear film lipid layer grade, and Meibomian gland (MG) dropout in SLE patients were worse than those in control subjects (all P < 0.05). For ROC analysis, the area under curve (AUC), sensitivity and specificity of prediction were 0.915, 75.8 and 92.1% for the combination of SLE disease activity index (SLEDAI), age and NIKBUT.ConclusionsSLE patients without SS exhibited a higher risk for DED than healthy subjects, and the poorer Meibomian gland function in SLE patients may potentially contribute to the development of DED. The combined parameters of SLEDAI, age and NIKBUT showed a high efficiency for the diagnosis of DED in SLE patients, with practical clinical applications.

PURPOSE: The exact pathogenesis of primary open-angle glaucoma (POAG) is poorly understood. Genome-wide association studies (GWAS) have recently uncovered many loci associated with variation in intraocular pressure (IOP); a crucial risk factor for POAG. Artificial intelligence (AI) can be used to interrogate the effect of specific genetic knockouts on the morphology of trabecular meshwork cells (TMCs), the regulatory cells of IOP. METHODS: Sixty-two genes at fifty-five loci associated with IOP variation were knocked out in primary TMC lines. All cells underwent high-throughput microscopy imaging after being stained with a five-channel fluorescent cell staining protocol. A convolutional neural network (CNN) was trained to distinguish between gene knockout and normal control cell images. The area under the receiver operator curve (AUC) metric was used to quantify morphological variation in gene knockouts to identify potential pathological perturbations. RESULTS: Cells where RALGPS1 had been perturbed demonstrated the greatest morphological variation from normal TMCs (AUC 0.851, SD 0.030), followed by LTBP2 (AUC 0.846, SD 0.029) and BCAS3 (AUC 0.845, SD 0.020). Of seven multi-gene loci, five had statistically significant differences in AUC (p<0.05) between genes, allowing for pathological gene prioritisation. The mitochondrial channel most frequently showed the greatest degree of morphological variation (33.9% of cell lines). CONCLUSIONS: We demonstrate a robust method for functionally interrogating genome-wide association signals using high-throughput microscopy and AI. Genetic variations inducing marked morphological variation can be readily identified, allowing for the gene-based dissection of loci associated with complex traits.

Combining surface‐initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI‐TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush‐functionalized DNA nanostructures. We demonstrate that SI‐TcEP can site‐specifically pattern DONs with brushes containing both natural and non‐natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse‐grained simulations predict the conformation of the brush‐functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush‐functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site‐specific growth of polynucleotide brushes. The ability to site‐specifically decorate DONs with brushes of natural and non‐natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.