Functional characterization of Alzheimer's disease genetic variants in microglia.

Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens - assessing 18,905 protein-coding and 10,678 lncRNA loci - and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.

Graphical User Interface for Calculating Wave Intensity from Cardiac Catheterization Measurements.

Wave intensity analysis (WIA) as a framework to assess cardiovascular hemodynamics has been successfully used in many clinical applications. Typically, wave intensity calculations require the simultaneous acquisition of blood velocity and blood pressure at the same vascular site. Unfortunately, many hemodynamic parameters that are used to monitor pre-operative patient hemodynamic state use both invasively acquired blood pressure measurements in catheterization laboratory and non-invasively acquired blood velocity measurements. To utilize wave intensity analysis to assess patients undergoing cardiac interventional procedures, we have developed a graphical user interface (GUI) that uses standard clinical measurements which include invasive blood pressure waveforms and Doppler echocardiography images to calculate wave intensity parameters. The GUI consists of three main subroutines that allow clinicians to import raw data and extract and analyze the blood pressure and blood velocity signals separately. Using the electrocardiogram signals as an alignment marker, the re-formatted signals are aligned, and wave intensity is calculated. Wave intensity features such as forward compression wave (FCW), forward expansion wave (FEW) and wave speed are calculated and output in a table for statistical analysis. The GUI represents the first attempt to create a program that encourages clinicians to use WIA for hemodynamic assessment in patients undergoing cardiac catheterization procedures with the data they have already procured.

Assessing Single Ventricle Function in the Fontan Circulation using Wave Intensity Analysis.

Single ventricle hearts palliated with the Fontan operation present complications later in life as a result of increased venous pressures and abnormal ventricle function. Wave intensity analysis uses measurements of blood velocity and pressure to represent arterial hemodynamics as summations of energy waves. This methodology could potentially be a useful tool in assessment of Fontan patients. The clinical value of wave intensity parameters was utilized to evaluate the functional performance of the single ventricle in Fontan patients. A retrospective analysis of invasive hemodynamic data was retrospectively obtained from routine cardiac catheterization of patients with Fontan circulation (n = 20) and comparison to those with biventricular circulation (n = 10) who presented to the catheterization laboratory for closure of small patent ductus arteriosus (PDAs). Wave intensity analysis and wave energy flux was calculated using aortic pressure waveforms and echocardiography aortic Doppler measurements as previously described. Significant differences were seen in the peak forward compression wave (p = 0.013), early systolic energy flux (p = 0.005) and the systolic and diastolic ratio (p = 0.006) in Fontan patients versus controls. Within the Fontan group, there was a positive correlation (0.54, p = 0.02) between the wave speed and pulmonary vascular resistance. Early systolic energy flux was a potential individual indicator of a Fontan patients heart failure classification (AUC = 0.71). Wave intensity analysis could be a useful tool in screening Fontan patients and predicting clinical outcomes and Fontan failure. Future prospective analyses of Fontan hemodynamics and WIA are needed.