A Single-Nucleus Transcriptome-Wide Association Study Implicates Novel Genes in Depression Pathogenesis

BACKGROUND

Depression, a common psychiatric illness and global public health problem, remains poorly understood across different life stages, which hampers the development of novel treatments.

METHODS

To identify new candidate genes for therapeutic development, we performed differential gene expression analysis of single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex of older adults (n = 424) in relation to antemortem depressive symptoms. Additionally, we integrated genome-wide association study results for depression (n = 500,199) along with genetic tools for inferring the expression of 14,048 unique genes in 7 cell types and 52 cell subtypes to perform a transcriptome-wide association study of depression followed by Mendelian randomization.

RESULTS

Our single-nucleus transcriptome-wide association study analysis identified 68 candidate genes for depression and showed the greatest number being in excitatory and inhibitory neurons. Of the 68 genes, 53 were novel compared to previous studies. Notably, gene expression in different neuronal subtypes had varying effects on depression risk. Traits with high genetic correlations with depression, such as neuroticism, shared more transcriptome-wide association study genes than traits that were not highly correlated with depression. Complementing these analyses, differential gene expression analysis across 52 neocortical cell subtypes showed that genes such as KCNN2, SCAI, WASF3, and SOCS6 were associated with late-life depressive symptoms in specific cell subtypes.

CONCLUSIONS

These 2 sets of analyses illustrate the utility of large single-nucleus RNA sequencing data both to uncover genes whose expression is altered in specific cell subtypes in the context of depressive symptoms and to enhance the interpretation of well-powered genome-wide association studies so that we can prioritize specific susceptibility genes for further analysis and therapeutic development.

Multicellular communities are perturbed in the aging human brain and Alzheimer's disease

The role of different cell types and their interactions in Alzheimer's disease (AD) is a complex and open question. Here, we pursued this question by assembling a high-resolution cellular map of the aging frontal cortex using single-nucleus RNA sequencing of 24 individuals with a range of clinicopathologic characteristics. We used this map to infer the neocortical cellular architecture of 638 individuals profiled by bulk RNA sequencing, providing the sample size necessary for identifying statistically robust associations. We uncovered diverse cell populations associated with AD, including a somatostatin inhibitory neuronal subtype and oligodendroglial states. We further identified a network of multicellular communities, each composed of coordinated subpopulations of neuronal, glial and endothelial cells, and we found that two of these communities are altered in AD. Finally, we used mediation analyses to prioritize cellular changes that might contribute to cognitive decline. Thus, our deconstruction of the aging neocortex provides a roadmap for evaluating the cellular microenvironments underlying AD and dementia.

A single-nucleus transcriptome-wide association study implicates novel genes in depression pathogenesis

Background

Depression is a common psychiatric illness and global public health problem. However, our limited understanding of the biological basis of depression has hindered the development of novel treatments and interventions.

Methods

To identify new candidate genes for therapeutic development, we examined single-nucleus RNA sequencing (snucRNAseq) data from the dorsolateral prefrontal cortex (N=424) in relation to ante-mortem depressive symptoms. To complement these direct analyses, we also used genome-wide association study (GWAS) results for depression (N=500,199) along with genetic tools for inferring the expression of 22,159 genes in 7 cell types and 55 cell subtypes to perform transcriptome-wide association studies (TWAS) of depression followed by Mendelian randomization (MR).

Results

Our single-nucleus TWAS analysis identified 71 causal genes in depression that have a role in specific neocortical cell subtypes; 59 of 71 genes were novel compared to previous studies. Depression TWAS genes showed a cell type specific pattern, with the greatest enrichment being in both excitatory and inhibitory neurons as well as astrocytes. Gene expression in different neuron subtypes have different directions of effect on depression risk. Compared to lower genetically correlated traits (e.g. body mass index) with depression, higher correlated traits (e.g., neuroticism) have more common TWAS genes with depression. In parallel, we performed differential gene expression analysis in relation to depression in 55 cortical cell subtypes, and we found that genes such as ANKRD36, MADD, TAOK3, SCAI and CHUK are associated with depression in specific cell subtypes.

Conclusions

These two sets of analyses illustrate the utility of large snucRNAseq data to uncover both genes whose expression is altered in specific cell subtypes in the context of depression and to enhance the interpretation of well-powered GWAS so that we can prioritize specific susceptibility genes for further analysis and therapeutic development.

A cellular and spatial map of the choroid plexus across brain ventricles and ages

The choroid plexus (ChP) in each brain ventricle produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier. Here, we construct a single-cell and spatial atlas of each ChP in the developing, adult, and aged mouse brain. We delineate diverse cell types, subtypes, cell states, and expression programs in epithelial and mesenchymal cells across ages and ventricles. In the developing ChP, we predict a common progenitor pool for epithelial and neuronal cells, validated by lineage tracing. Epithelial and fibroblast cells show regionalized expression by ventricle, starting at embryonic stages and persisting with age, with a dramatic transcriptional shift with maturation, and a smaller shift in each aged cell type. With aging, epithelial cells upregulate host-defense programs, and resident macrophages upregulate interleukin-1β (IL-1β) signaling genes. Our atlas reveals cellular diversity, architecture and signaling across ventricles during development, maturation, and aging of the ChP-brain barrier.

Percutaneous transluminal angioplasty versus endovascular stent placement in the treatment of venous stenoses in patients undergoing hemodialysis: intermediate results

PURPOSE

This report describes intermediate findings from an ongoing prospective randomized trial comparing the results of percutaneous transluminal angioplasty (PTA) with results of endovascular stent placement in patients undergoing hemodialysis.

PATIENTS AND METHODS

Among 87 consecutive patients with venous stenoses or occlusions, 47 (54%) were treated with PTA alone and 40 (46%) were treated with PTA and stent placement.

RESULTS

For peripheral sites, the primary patency rates for PTA at 60, 180, and 360 days were 55%, 31%, and 10%, respectively, and for stents were 36%, 27%, and 11%, respectively (P = .6528). The secondary patency rates for PTA at 60, 180, and 360 days were 94%, 80%, and 71%, respectively, and for stents were 73%, 64%, and 64%, respectively (P = .1677). For central sites, the primary patency rates for PTA at 60, 180, and 360 days were 81%, 23%, and 12%, respectively, and for stents were 67%, 11%, and 11%, respectively (P = .4595). The secondary patency rates for PTA were 100% at each interval, and for stents were 100%, 89%, and 78%, respectively (P = .5408).

CONCLUSION

Intermediate results suggest that, overall, there is no difference in the patency rates for peripheral venous stenoses in dialysis patients treated with PTA or PTA and endovascular stent placement. At this time, the numbers of patients are too small to conclude if certain sites such as larger central veins will respond better to one treatment or the other.

Myocardial hypertrophy and coronary artery disease in male cocaine users

We compared the heart weights and the incidence of atherosclerotic lesions in trauma fatalities testing positive for cocaine with the hearts of cocaine negative trauma fatalities, with the hearts of decedents dying from cocaine overdose, and with historic controls derived from the literature. There were 116 trauma victims, 83 men and 33 women, aged 20-50 years, and 26 men with cause of death listed as cocaine toxicity. The 32 cocaine (+) male trauma fatalities had a mean age 34 +/- 10 years and a mean heart weight of 375 +/- 82 grams. The 51 cocaine free males had a mean age 31 +/- 9 years, and mean heart weight 337 +/- 54 grams (P = .01). Heart weights in the cocaine using group were also significantly greater than historical controls from World War I, Korea, and Vietnam. The incidence of atherosclerotic changes was similar in both groups, but cocaine (+) men had more frequent coronary artery lesions involving multiple vessels (P = .01). Comparisons between 16 cocaine (+) females and 17 cocaine (-) female controls disclosed no significant differences in heart weight or the frequency of atherosclerotic lesions. The 26 men dying of cocaine overdose also had larger hearts than the controls (379 +/- 64 g, P = .004), and more severe CAD (30% had involvement of 2 or more vessels, P = .02). The degree of myocardial hypertrophy documented in this study was highly significant, but because the increase is modest (around 10%), it is likely to go unrecognized at autopsy.(ABSTRACT TRUNCATED AT 250 WORDS)

Transient reduction in renal function following arteriography: a radionuclide study

The effects of iodinated contrast agents upon renal function were determined in 11 patients undergoing arteriography. Serial radionuclide renograms were performed to calculate the glomerular filtration rate, effective renal plasma flow and filtration fraction before and after arteriography. The effective renal plasma flow was the parameter most adversely affected. The magnitude of renal dysfunction depended upon the amount of contrast medium administered, as well as probably pre-existing renal disease and site of injection.

Homicide by use of a pellet gun

This report relates the findings in a death by use of an air gun. It is believed to be the second reported homicidal air gun death in the United States. The fatal wound was unusual in that two pellets were loaded in "piggyback" fashion into the single shot .20 caliber Sheridan air gun. The lethal pellet penetrated the brain. Current literature on air gun deaths and injuries is reviewed.

Fluoroscopic placement of intestinal tubes

The authors have attempted to place fluoroscopically approximately 400 nasointestinal tubes in 7 years. The tube was guided into the jejunum in 39% of patients, into the third portion of the duodenum in 57%, and into the second portion in 76%.

Effects of coronary arteriography on myocardial blood flow

Myocardial blood flow responses to selective coronary arteriography were studied in 22 patients. Left coronary flow was estimated by the radioactive inert-gas ( 133 xenon) washout technic using precordial detection. Duplicate control studies were obtained before radiocontrast injection and test studies were performed at 1 min and 3, 5, or 7 min after angiography. Eleven patients received a single 7-ml injection of methylglucamine diatrizoate and 11 were given a series of injections (average total 40 ml), with the test blood flow studies after the final injection.

Myocardial flow increased in every patient 1 min after contrast injection (average control flow 66.3 ml/min/100 g; test flow 78.8, +18.9%, P < 0.001). Blood flow increased further in seven of 10 studied at 3 min (average 95.7 ml/min/100 g, +35.7%, P < 0.001) and remained elevated at 5 and 7 min. Systemic pressure was unchanged from the control level, so coronary vascular resistance decreased in proportion to the increase in flow. Blood flow responses in patients with coronary artery disease were no different from normal subjects. Sham injections of normal saline produced no increase in coronary flow.

Selective coronary arteriography results in a prompt increase in myocardial blood flow which persists for several minutes. The probable mechanism is coronary vasodilatation produced by the markedly hypertonic contrast material, an effect demonstrated previously in other vascular beds.

Complications of selective percutaneous transfemoral coronary arteriography and their prevention. A review of 445 consecutive examinations

Complications encountered during a typical 12-month period of routine work with the Judkins percutaneous transfemoral method of selective coronary arteriography are reviewed. In 445 examinations, 20 complications (16 local and four cardiac) occurred. Local complications included nine delayed hemorrhages, five thromboses of femoral arteries, and two peripheral emboli. Cardiac complications included one ventricular fibrillation, one significant bradyarrhythmia, and two myocardial infarctions. Causes of individual complications are analyzed and means for their prevention discussed. Guidelines of the procedure are proposed to minimize the complications of selective coronary arteriography. Emphasis is placed on patient evaluation, preparation for the procedure, and meticulous examination technique.