Evaluating the Contribution of Cell Type-Specific Alternative Splicing to Variation in Lipid Levels.

BACKGROUND: Genome-wide association studies have identified hundreds of loci associated with lipid levels. However, the genetic mechanisms underlying most of these loci are not well-understood. Recent work indicates that changes in the abundance of alternatively spliced transcripts contribute to complex trait variation. Consequently, identifying genetic loci that associate with alternative splicing in disease-relevant cell types and determining the degree to which these loci are informative for lipid biology is of broad interest. METHODS: We analyze gene splicing in 83 sample-matched induced pluripotent stem cell (iPSC) and hepatocyte-like cell lines (n=166), as well as in an independent collection of primary liver tissues (n=96) to perform discovery of splicing quantitative trait loci (sQTLs). RESULTS: We observe that transcript splicing is highly cell type specific, and the genes that are differentially spliced between iPSCs and hepatocyte-like cells are enriched for metabolism pathway annotations. We identify 1384 hepatocyte-like cell sQTLs and 1455 iPSC sQTLs at a false discovery rate of <5% and find that sQTLs are often shared across cell types. To evaluate the contribution of sQTLs to variation in lipid levels, we conduct colocalization analysis using lipid genome-wide association data. We identify 19 lipid-associated loci that colocalize either with an hepatocyte-like cell expression quantitative trait locus or sQTL. Only 2 loci colocalize with both a sQTL and expression quantitative trait locus, indicating that sQTLs contribute information about genome-wide association studies loci that cannot be obtained by analysis of steady-state gene expression alone. CONCLUSIONS: These results provide an important foundation for future efforts that use iPSC and iPSC-derived cells to evaluate genetic mechanisms influencing both cardiovascular disease risk and complex traits in general.

Functional Characterization of Organoids Derived From Irreversibly Damaged Liver of Patients With NASH.

BACKGROUND AND AIMS: NASH will soon become the leading cause of liver transplantation in the United States and is also associated with increased COVID-19 mortality. Currently, there are no Food and Drug Administration-approved drugs available that slow NASH progression or address NASH liver involvement in COVID-19. Because animal models cannot fully recapitulate human NASH, we hypothesized that stem cells isolated directly from end-stage liver from patients with NASH may address current knowledge gaps in human NASH pathology. APPROACH AND RESULTS: We devised methods that allow the derivation, proliferation, hepatic differentiation, and extensive characterization of bipotent ductal organoids from irreversibly damaged liver from patients with NASH. The transcriptomes of organoids derived from NASH liver, but not healthy liver, show significant up-regulation of proinflammatory and cytochrome p450-related pathways, as well as of known liver fibrosis and tumor markers, with the degree of up-regulation being patient-specific. Functionally, NASH liver organoids exhibit reduced passaging/growth capacity and hallmarks of NASH liver, including decreased albumin production, increased free fatty acid-induced lipid accumulation, increased sensitivity to apoptotic stimuli, and increased cytochrome P450 metabolism. After hepatic differentiation, NASH liver organoids exhibit reduced ability to dedifferentiate back to the biliary state, consistent with the known reduced regenerative ability of NASH livers. Intriguingly, NASH liver organoids also show strongly increased permissiveness to severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) vesicular stomatitis pseudovirus as well as up-regulation of ubiquitin D, a known inhibitor of the antiviral interferon host response. CONCLUSION: Expansion of primary liver stem cells/organoids derived directly from irreversibly damaged liver from patients with NASH opens up experimental avenues for personalized disease modeling and drug development that has the potential to slow human NASH progression and to counteract NASH-related SARS-CoV-2 effects.

Multi-Trait Genome-Wide Association Study of Atherosclerosis Detects Novel Pleiotropic Loci.

Although affecting different arterial territories, the related atherosclerotic vascular diseases coronary artery disease (CAD) and peripheral artery disease (PAD) share similar risk factors and have shared pathobiology. To identify novel pleiotropic loci associated with atherosclerosis, we performed a joint analysis of their shared genetic architecture, along with that of common risk factors. Using summary statistics from genome-wide association studies of nine known atherosclerotic (CAD, PAD) and atherosclerosis risk factors (body mass index, smoking initiation, type 2 diabetes, low density lipoprotein, high density lipoprotein, total cholesterol, and triglycerides), we perform 15 separate multi-trait genetic association scans which resulted in 25 novel pleiotropic loci not yet reported as genome-wide significant for their respective traits. Colocalization with single-tissue eQTLs identified candidate causal genes at 14 of the detected signals. Notably, the signal between PAD and LDL-C at the PCSK6 locus affects PCSK6 splicing in human liver tissue and induced pluripotent derived hepatocyte-like cells. These results show that joint analysis of related atherosclerotic disease traits and their risk factors allowed identification of unified biology that may offer the opportunity for therapeutic manipulation. The signal at PCSK6 represent possible shared causal biology where existing inhibitors may be able to be leveraged for novel therapies.

Single cell transcriptomics of noncoding RNAs and their cell-specificity.

Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability. Technology for measuring ncRNA in single cell is still in development and most of the current single cell datasets have reliable measurements for only long noncoding RNA (lncRNA). Most works report that lncRNAs show lineage-specific restricted expression patterns, which suggest that they might determine, at least in part, lineage fates and cell subtypes. However, evidence is still inconclusive as to whether lncRNAs and other ncRNAs are more lineage-specific than protein-coding genes. Nevertheless, measurement of ncRNAs in single cells will be important for studies of cell types and single cell function. WIREs RNA 2017, 8:e1433. doi: 10.1002/wrna.1433 For further resources related to this article, please visit the WIREs website.

Dispositional Optimism and Incidence of Cognitive Impairment in Older Adults.

OBJECTIVE: Higher levels of optimism have been linked with positive health behaviors, biological processes, and health conditions that are potentially protective against cognitive impairment in older adults. However, the association between optimism and cognitive impairment has not been directly investigated. We examined whether optimism is associated with incident cognitive impairment in older adults. METHODS: Data are from the Health and Retirement Study. Optimism was measured by using the Life Orientation Test-R and cognitive impairment with a modified version of the Telephone Interview for Cognitive Status derived from the Mini-Mental State Examination. Using multiple logistic regression models, we prospectively assessed whether optimism was associated with incident cognitive impairment in 4624 adults 65 years and older during a 4-year period. RESULTS: Among participants, 312 women and 190 men developed cognitive impairment during the 4-year follow-up. Higher optimism was associated with decreased risk of incident cognitive impairment. When adjusted for sociodemographic factors, each standard deviation increase in optimism was associated with reduced odds (odds ratio [OR] = 0.70, 95% confidence interval [CI] = 0.61-0.81) of becoming cognitively impaired. A dose-response relationship was observed. Compared with those with the lowest levels of optimism, people with moderate levels had somewhat reduced odds of cognitive impairment (OR = 0.78, 95% CI = 0.59-1.03), whereas people with the highest levels had the lowest odds of cognitive impairment (OR = 0.52, 95% CI = 0.36-0.74). These associations remained after adjusting for health behaviors, biological factors, and psychological covariates that could either confound the association of interest or serve on the pathway. CONCLUSIONS: Optimism was prospectively associated with a reduced likelihood of becoming cognitively impaired. If these results are replicated, the data suggest that potentially modifiable aspects of positive psychological functioning such as optimism play an important role in maintaining cognitive functioning.

Potentially traumatic events and serious life stressors are prospectively associated with frequency of doctor visits and overnight hospital visits.

OBJECTIVE: Cumulative lifetime exposure to potentially traumatic events and serious life stressors has been linked with both mental and physical health problems; however, less is known about the association between exposure to potentially traumatic events and serious life stressors with health care use. We investigated whether a higher number of potentially traumatic events and serious life stressors were prospectively associated with an increased number of doctor visits and nights spent in the hospital. METHODS: Participants were drawn from the Health and Retirement Study, a prospective and nationally representative study of adults aged 50+ in the United States (n=7168). We analyzed the data using a generalized linear model with a gamma distribution and log link. RESULTS: A higher number of potentially traumatic events and serious life stressors were associated with an increased number of doctor visits and nights spent in the hospital. On a 10-point scale, each additional potentially traumatic event or serious life stressor was associated with an 8% increase in doctor visits after controlling for sociodemographic factors (RR=1.08, 95% CI=1.06-1.11; p<.001). Each additional potentially traumatic event or serious life stressor was also associated with an 18% increase in the number of nights spent in the hospital after controlling for sociodemographic factors (RR=1.18, 95% CI=1.10-1.27; p<.001). CONCLUSION: Exposure to potentially traumatic events and serious life stressors is associated with increased doctor visits and nights spent in the hospital, which may have important implications for the current standard of care.