Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex

Background

Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Computational methods for deconvolution have been developed and benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or immunohistochemistry reference data. A major limitation in developing improved deconvolution algorithms has been the lack of integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue sample. Deconvolution algorithm performance has not yet been evaluated across different RNA extraction methods (cytosolic, nuclear, or whole cell RNA), different library preparation types (mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets.

Results

A rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq (across six library/extraction RNA-seq combinations), and RNAScope/Immunofluorescence (RNAScope/IF) for six broad cell types. The Mean Ratio method, implemented in the DeconvoBuddies R package, was developed for selecting cell type marker genes. Six computational deconvolution algorithms were evaluated in DLPFC and predicted cell type proportions were compared to orthogonal RNAScope/IF measurements.

Conclusions

Bisque and hspe were the most accurate methods, were robust to differences in RNA library types and extractions. This multi-assay dataset showed that cell size differences, marker genes differentially quantified across RNA libraries, and cell composition variability in reference snRNA-seq impact the accuracy of current deconvolution methods.

[The effects of enalapril on basal arterial pressure at rest and during exercise and on cardiac performance in hypertensive athletes]

A dose of 10 mg of enalapril was administered once a day to regularly trained hypertensive athletes (mean age 39 +/- 8.9 range 29-51) in order to evaluate the effect of the drug on ambulatory blood pressure and on blood pressure and physical performance during stress testing. STUDY DESIGN. This investigation was a randomized, double blind, cross-over versus placebo trial. At first, subjects whose blood pressure met the entry criteria (casual diastolic blood pressure greater than or equal to 95 mmHg), were subjected to 24-hour ambulatory blood pressure monitoring and maximal upright bicycle stress testing including measurement of O2 uptake. Then they were randomly assigned to treatment with placebo or enalapril. After one month they repeated stress testing and then they were crossed over. Stress testing was repeated in all subjects after two months. The 24-hour ambulatory blood pressure monitoring was repeated in all subjects during enalapril treatment only, by a non-blind investigator. RESULTS. Ambulatory blood pressure decreased significantly during enalapril and no changes in heart rate were observed during the monitoring. The results of bicycle stress testing, both in basal and during the placebo test were comparable as regards blood pressure response, maximal workload, effort duration, maximal heart rate and VO2 max. With enalapril systolic and diastolic blood pressure decreased significantly during stress testing both versus basal test and placebo test at each workload considered including maximal workload. No changes were observed during enalapril as regards maximal workload, effort duration, maximal heart rate and VO2 max. CONCLUSION. Our results suggest that enalapril could be effective in treating hypertensive athletes because it reduces blood pressure during physical effort without affecting physical performance. We conclude that enalapril could be considered a first-choice drug in hypertensive athletes doing aerobic sports.