Recent advances in large-scale gene expression profiling necessitate concurrent development of biostatistical approaches to reveal meaningful biological relationships. Most analyses rely on ...significance thresholds for identifying differentially expressed genes. We use an approach to compare gene expression datasets using 'threshold-free' comparisons. Significance cut-offs to identify genes shared between datasets may be too stringent and may miss concordant patterns of gene expression with potential biological relevance. A threshold-free approach gaining popularity in several research areas, including neuroscience, is Rank-Rank Hypergeometric Overlap (RRHO). Genes are ranked by their p-value and effect size direction, and ranked lists are compared to identify significantly overlapping genes across a continuous significance gradient rather than at a single arbitrary cut-off. We have updated the previous RRHO analysis by accurately detecting overlap of genes changed in the same and opposite directions between two datasets. Here, we use simulated and real data to show the drawbacks of the previous algorithm as well as the utility of our new algorithm. For example, we show the power of detecting discordant transcriptional patterns in the postmortem brain of subjects with psychiatric disorders. The new R package, RRHO2, offers a new, more intuitive visualization of concordant and discordant gene overlap.
Global changes in gene expression underlying circuit and behavioral dysregulation associated with cocaine addiction remain incompletely understood. Here, we show how a history of cocaine ...self-administration (SA) reprograms transcriptome-wide responses throughout the brain’s reward circuitry at baseline and in response to context and/or cocaine re-exposure after prolonged withdrawal (WD).
We assigned male mice to one of six groups: saline/cocaine SA + 24-hour WD or saline/cocaine SA + 30-day WD + an acute saline/cocaine challenge within the previous drug-paired context. RNA sequencing was conducted on six interconnected brain reward regions. Using pattern analysis of gene expression and factor analysis of behavior, we identified genes that are strongly associated with addiction-related behaviors and uniquely altered by a history of cocaine SA. We then identified potential upstream regulators of these genes.
We focused on three patterns of gene expression that reflect responses to 1) acute cocaine, 2) context re-exposure, and 3) drug + context re-exposure. These patterns revealed region-specific regulation of gene expression. Further analysis revealed that each of these gene expression patterns correlated with an addiction index—a composite score of several addiction-like behaviors during cocaine SA—in a region-specific manner. Cyclic adenosine monophosphate response element binding protein and nuclear receptor families were identified as key upstream regulators of genes associated with such behaviors.
This comprehensive picture of transcriptome-wide regulation in the brain’s reward circuitry by cocaine SA and prolonged WD provides new insight into the molecular basis of cocaine addiction, which will guide future studies of the key molecular pathways involved.
The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some distinct functions related to motor control, ...cognitive processing, motivation, and reward. Previously, we used a "time-of-death" approach to identify diurnal rhythms in RNA transcripts in human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. Core circadian clock genes are rhythmic across all three regions and show strong phase concordance across regions. However, the putamen contains a much larger number of significantly rhythmic transcripts than the other two regions. Moreover, there are many differences in pathways that are rhythmic across regions. Strikingly, the top rhythmic transcripts in NAc (but not the other regions) are predominantly small nucleolar RNAs and long noncoding RNAs, suggesting that a completely different mechanism might be used for the regulation of diurnal rhythms in translation and/or RNA processing in the NAc versus the other regions. Further, although the NAc and putamen are generally in phase with regard to timing of expression rhythms, the NAc and caudate, and caudate and putamen, have several clusters of discordant rhythmic transcripts, suggesting a temporal wave of specific cellular processes across the striatum. Taken together, these studies reveal distinct transcriptome rhythms across the human striatum and are an important step in helping to understand the normal function of diurnal rhythms in these regions and how disruption could lead to pathology.
Right heart failure (RHF) is a common, yet difficult to manage, complication of severe acute respiratory distress syndrome requiring extracorporeal membrane oxygenation (ECMO) that is associated with ...increased mortality. Reports of the use of percutaneous mechanical circulatory support devices for concurrent right heart and respiratory failure are limited. This series describes the percutaneous cannulation of the pulmonary artery for conversion from veno-venous to veno-pulmonary artery return ECMO in 21 patients who developed secondary RHF. All patients cannulated between May 2019 and September 2021 were included. Either a 19 or 21 French venous cannula was placed percutaneously into the pulmonary artery via the internal jugular or subclavian vein, providing a total of 821 days of support (median 23 4-71 days per patient) with flows up to 6 L/min. Five patients underwent cannulation at the bedside, with the remainder performed in the cardiac catheterization laboratory. Pulmonary artery cannulation occurred after 12 8.5-23.5 days of ECMO support. Vasoactive infusion requirements decreased significantly within 24 hours of pulmonary artery cannula placement (p = 0.0004). Nonetheless, 75% of these patients expired after a median of 12 4-63 days of support, with three patients found to have had significant pericardial effusions peri-arrest. This cannulation technique may be an effective alternative to veno-arterial ECMO cannulation or the placement of a dual-lumen cannula for the treatment of RHF.
Psychosis is a defining feature of schizophrenia and highly prevalent in bipolar disorder. Notably, individuals with these illnesses also have major disruptions in sleep and circadian rhythms, and ...disturbances of sleep and circadian rhythms can precipitate or exacerbate psychotic symptoms. Psychosis is associated with the striatum, though to our knowledge, no study to date has directly measured molecular rhythms and determined how they are altered in the striatum of subjects with psychosis.
We performed RNA sequencing and both differential expression and rhythmicity analyses to investigate diurnal alterations in gene expression in human postmortem striatal subregions (nucleus accumbens, caudate, and putamen) in subjects with psychosis (n = 36) relative to unaffected comparison subjects (n = 36).
Across regions, we found differential expression of immune-related transcripts and a substantial loss of rhythmicity in core circadian clock genes in subjects with psychosis. In the nucleus accumbens, mitochondrial-related transcripts had decreased expression in subjects with psychosis, but only in those who died at night. Additionally, we found a loss of rhythmicity in small nucleolar RNAs and a gain of rhythmicity in glutamatergic signaling in the nucleus accumbens of subjects with psychosis. Between-region comparisons indicated that rhythmicity in the caudate and putamen was far more similar in subjects with psychosis than in matched comparison subjects.
Together, these findings reveal differential and rhythmic gene expression differences across the striatum that may contribute to striatal dysfunction and psychosis in psychotic disorders.
Women are approximately two times as likely to be diagnosed with major depressive disorder (MDD) compared to men. While sex differences in MDD might be driven by circulating gonadal hormones, we ...hypothesized that developmental hormone exposure and/or genetic sex might play a role. Mice were gonadectomized in adulthood to isolate the role of developmental hormones. We examined the effects of developmental gonadal and genetic sex on anhedonia-/depressive-like behaviors under non-stress and chronic stress conditions and performed RNA-sequencing in three mood-relevant brain regions. We used an integrative network approach to identify transcriptional modules and stress-specific hub genes regulating stress susceptibility, with a focus on whether these differed by sex. After identifying sex differences in anhedonia-/depressive-like behaviors (female > male), we show that both developmental hormone exposure (gonadal female > gonadal male) and genetic sex (XX > XY) contribute to the sex difference. The top biological pathways represented by differentially expressed genes were related to immune function; we identify which differentially expressed genes are driven by developmental gonadal or genetic sex. There was very little overlap in genes affected by chronic stress in males and females. We also identified highly co-expressed gene modules affected by stress, some of which were affected in opposite directions in males and females. Since all mice had equivalent hormone exposure in adulthood, these results suggest that sex differences in gonadal hormone exposure during sensitive developmental periods program adult sex differences in mood, and that these sex differences are independent of adult circulating gonadal hormones.
Women are twice as likely as men to be diagnosed with major depressive disorder (MDD). Recent studies report distinct molecular changes in depressed men and women across mesocorticolimbic brain ...regions. However, it is unclear which sex-related factors drive distinct MDD-associated pathology. The goal of this study was to use mouse experimental systems to investigate sex-specific mechanisms underlying the distinct molecular profiles of MDD in men and women. We used unpredictable chronic mild stress to induce an elevated anxiety-/depressive-like state and “four core genotypes” (FCG) mice to probe for sex-specific mechanisms. As predicted, based on previous implications in mood, stress impacted the expression of several dopamine-, GABA-, and glutamate-related genes. Some of these effects, specifically in the prefrontal cortex, were genetic sex-specific, with effects in XX mice but not in XY mice. Stress also impacted gene expression differently across the mesocorticolimbic circuit, with increased expression of mood-related genes in the prefrontal cortex and nucleus accumbens, but decreased expression in basolateral amygdala. Our results suggest that females are sensitive to the effects of chronic stress, partly due to their genetic sex, independent of gonadal hormones. Furthermore, these results point to the prefrontal cortex as the node in the mesocorticolimbic circuitry with the strongest female-specific effects.
To assess depression, anxiety, and burnout among health care workers using well-established validated scales and to examine associations of these mental health outcomes with personal protective ...equipment (PPE) and high-risk patient contact.
This prospective survey was conducted between August and October 2020 among 970 essential health care workers from 2 health systems in central Texas. The survey captured basic demographic, occupational, and baseline health information including history of mental health disorders. Depression, anxiety, and burnout were assessed with the 8-item Patient Health Questionnaire, 7-item Generalized Anxiety Disorder Scale, and 23-item Burnout Assessment Tool. Questions about clinical contact with patients with suspected or known COVID-19 were also incorporated.
Approximately 24% of respondents had moderate or severe anxiety, 14% had moderate or severe depression, and 7% were at high risk for burnout. Statistically significant associations were found between perceived PPE adequacy and the 3 mental health outcomes, while accounting for age, gender, and education. Hours of contact with COVID-19 patients during aerosolizing procedures was positively correlated with measures of anxiety, burnout, and depression after adjustment for age, gender, and occupational role. Perception of PPE adequacy was inversely correlated with measures of depression, anxiety, and burnout among essential members of 2 health care systems, whose roles precluded working remotely during the pandemic.
This study highlights the correlations of perceptions of PPE adequacy and contact hours with COVID-19 patients undergoing aerosolizing procedures and employee mental well-being. Future work confirming the findings can help identify ways that systems can support their employees through similarly stressful and demanding events.
Abstract Several forms of hippocampal-dependent learning rely upon activation of the N -methyl- d -aspartate (NMDA) subtype of glutamate receptor. Here we have investigated the effects of ...administration of the NMDA receptor antagonist (±)-3-(2-carboxypiperazin-4-yl)propyl-1-phosphonic acid (CPP) on the performance of rats in an object displacement task and the possible role of extracellular signal-regulated kinase (ERK) in this form of learning. The data show that rats injected intraperitoneally with CPP (10 mg/kg) before, but not after, training in the object displacement task displayed impairments in spatial learning when compared with saline-injected controls. The NMDAR may thus be involved in the acquisition, but not the consolidation, of this type of memory. In addition, a significant positive correlation was observed between learning and the expression of activated ERK in the dentate gyrus. No such correlation was apparent in the rest of the hippocampal formation. This study implicates the NMDARs in the acquisition phase of spatial learning and provides evidence for a role for ERK in spatial learning in the dentate gyrus of the rat.
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