Decoding schizophrenia through postmortem human brain transcriptomics.

Author response: Tau polarizes an aging transcriptional signature to excitatory neurons and glia

Zebrafish model of human Zellweger syndrome reveals organ-specific accumulation of distinct fatty acid species and widespread gene expression changes

STUDY QUESTIONIs labour, both at term and preterm, associated with alterations in decidual lymphocyte densities and widespread changes to the decidual transcriptome?SUMMARY ANSWERThe onset of parturition, both at term and preterm, is associated with widespread gene expression changes in the decidua, many of which are related to inflammatory signalling, but is not associated with changes in the number of any of the decidual lymphocyte populations examined.WHAT IS KNOWN ALREADYGiven its location, directly at the maternal–foetal interface, the decidua is likely to play a pivotal role in the onset of parturition, however, the molecular events occurring in the decidua in association with the onset of labour, both at term and preterm, remain relatively poorly defined. Using flow cytometry and microarray analysis, the present study aimed to investigate changes to the immune cell milieu of the decidua in association with the onset of parturition and define the decidual gene signature associated with term and preterm labour (PTL).STUDY DESIGN, SIZE, DURATIONThis study used decidual samples collected from 36 women across four clinical groups: term (38–42 weeks of gestation) not in labour, TNL; term in labour, TL; preterm (<35 weeks of gestation)not in labour, PTNL; and preterm in labour, PTL.PARTICIPANTS/MATERIALS, SETTING, METHODSDecidual lymphocytes were isolated from fresh decidual tissue collected from women in each of our four patient groups and stained with a panel of antibodies (CD45, CD3, CD19, CD56, CD4, CD8 and TCRVα24-Jα18) to investigate lymphocyte populations present in the decidua (TNL, n = 8; TL, n = 7; PTNL, n = 5; PTL, n = 5). RNA was extracted from decidual tissue and subjected to Illumina HT-12v4.0 BeadChip expression microarrays (TNL, n = 11; TL, n = 8; PTNL, n = 7; PTL, n = 10). Quantitative real-time PCR (qRT-PCR) was used to validate the microarray results.MAIN RESULTS AND THE ROLE OF CHANCEThe relative proportions of decidual lymphocytes (T cells, NK cells, B cells and invariant natural killer (iNKT) cells) were unaffected by either gestation or labour status. However, we found elevated expression of the non-classical MHC-protein, CD1D, in PTL decidua samples (P < 0.05), suggesting the potential for increased activation of decidual invariant NKT (iNKT) cells in PTL. Both term and PTL were associated with widespread gene expression changes, particularly related to inflammatory signalling. Up-regulation of candidate genes in TL (IL-6, PTGS2, ATF3, IER3 and TNFAIP3) and PTL (CXCL8, MARCO, LILRA3 and PLAU) were confirmed by qRT-PCR analysis.LARGE SCALE DATAMicroarray data are available at www.ebi.ac.uk/arrayexpress under accession number E-MTAB-5353.LIMITATIONS REASONS FOR CAUTIONWhilst no changes in lymphocyte number were observed across our patient samples, we did not investigate the activation state of any of the immune cell sub-populations examined, therefore, it is possible that the function of these cells may be altered in association with labour onset. Additionally, the results of our transcriptomic analyses are descriptive and at this stage, we cannot prove direct causal link with the up-regulation of any of the genes examined and the onset of either term or PTL.WIDER IMPLICATIONS OF THE FINDINGSOur findings demonstrate that the onset of parturition is associated with widespread changes to the decidual transcriptome, and there are distinct gene expression changes associated with term and PTL. We confirmed that an inflammatory signature is present within the decidua, and we also report the up-regulation of several genes involved in regulating the inflammatory response. The identification of genes involved in regulating the inflammatory response may provide novel molecular targets for the development of new, more effective therapies for the prevention of preterm birth (PTB). Such targets are urgently required.STUDY FUNDING AND COMPETING INTEREST(S)This work was supported by Medical Research Council (grant number MR/L002657/1) and Tommy's, the baby charity. Jane Norman has had research grants from the charity Tommy's and from the National Institute for Health Research on PTB during the lifetime of this project. Jane Norman also sits on a data monitoring committee for GSK for a study on PTB prevention and her institution receives financial recompense for this. The other authors do not have any conflicts of interest to declare.

BackgroundThe cellular mechanism(s) underlying autism spectrum disorders (ASDs) are not completely understood, but ASDs are thought to ultimately result from disrupted synaptogenesis. However, studies have also shown that glial cell numbers and function are abnormal in post-mortem brain tissue from autistic patients. Direct assessment of glial cells in post-mortem human brain tissue is technically challenging, limiting glial research in human ASD studies. Therefore, we attempted to determine if glial cell-type specific markers may be altered in autistic brain tissue in a manner that is consistent with known cellular findings, such that they could serve as a proxy for glial cell numbers and/or activation patterns.MethodsWe assessed the relative expression of five glial-specific markers and two neuron-specific markers via qRT-PCR. We studied tissue samples from the prefrontal cortex (PFC) and cerebellum of nine post-mortem autistic brain samples and nine neurologically-normal controls. Relative fold-change in gene expression was determined using the ΔΔCt method normalized to housekeeping gene β-actin, with a two-tailed Student’s t-test P <0.05 between groups considered as significant.ResultsBoth astrocyte- and microglial-specific markers were significantly more highly expressed in autistic PFC as compared to matched controls, while in the cerebellum only astrocyte markers were elevated in autistic samples. In contrast, neuron-specific markers showed significantly lower expression in both the PFC and cerebellum of autistic patients as compared to controls.ConclusionsThese results are in line with previous findings showing increased glial cell numbers and up-regulation of glial cell gene expression in autistic post-mortem brain tissue, particularly in the PFC, as well as decreased number of neurons in both the PFC and cerebellum of autistic patients. The concordance of these results with cell-level studies in post-mortem autistic brain tissue suggests that expression of glial cell-type specific markers may serve as a useful alternative to traditional cellular characterization methods, especially when appropriately-preserved post-mortem tissue is lacking. Additionally, these results demonstrate abnormal glial-specific gene expression in autistic brains, supporting previous studies that have observed altered glial cell numbers or activation patterns in ASDs. Future work should directly assess the correlation between cell-type specific marker levels and cell number and activation patterns.

Phenotypic plasticity, the ability of an organism to alter its phenotype in response to an environmental cue, facilitates rapid adaptation to changing environments. Plastic changes in morphology and behavior are underpinned by widespread gene expression changes. However, it is unknown if, or how, genomes are structured to ensure these robust responses. Here, we use repression of honeybee worker ovaries as a model of plasticity. We show that the honeybee genome is structured with respect to plasticity; genes that respond to an environmental trigger are colocated in the honeybee genome in a series of gene clusters, many of which have been assembled in the last 80 My during the evolution of the Apidae. These clusters are marked by histone modifications that prefigure the gene expression changes that occur as the ovary activates, suggesting that these genomic regions are poised to respond plastically. That the linear sequence of the honeybee genome is organized to coordinate widespread gene expression changes in response to environmental influences and that the chromatin organization in these regions is prefigured to respond to these influences is perhaps unexpected and has implications for other examples of plasticity in physiology, evolution, and human disease.

Back to table of contents Previous article Next article Clinical & Research NewsFull AccessEvidence Builds For Glutamate Link to SchizophreniaJoan Arehart-TreichelJoan Arehart-TreichelPublished Online:21 Sep 2001https://doi.org/10.1176/pn.36.18.0017bDuring the last decade of the 20th century, it became increasingly apparent that glutamate, not dopamine, is probably the major nerve-transmitter culprit in schizophrenia—and this in spite of the fact that the level of dopamine activity is known to be markedly higher in the brains of schizophrenia patients than in the brains of healthy persons and to be strongly linked with the positive symptoms of schizophrenia.In other words, it started to look increasingly as if glutamate might do the initial dirty work in the brain as schizophrenia develops, then bring dopamine in on the act. Or as Jack Gorman, M.D., a professor of psychiatry at Columbia University, put it at APA's 2000 annual meeting, an underdevelopment of glutamate-using neurons might cause an overabundance of dopamine-containing neurons, which then would unleash schizophrenia symptoms (Psychiatric News, July 7, 2000).Now that the 21st century has arrived, the case continues to build that glutamate and company are heavily involved in schizophrenia. Take, for instance, three new studies reported in the September American Journal of Psychiatry.David Lewis, M.D., a professor of psychiatry and neuroscience at the University of Pittsburgh, and coworkers measured, in postmortem brain tissue taken from 20 persons with schizophrenia, the amount of a putative marker for glutamate. The team used neurons that originate in the thalamus area of the brain and terminate in the prefrontal cortex.They also measured the amount of the marker in postmortem brain tissue taken from 20 healthy controls and compared that amount with the amount in the tissue from the schizophrenia subjects. They found less of the marker in tissue from individuals with schizophrenia than in tissue from controls, implying that a paucity of glutamate-using neurons, at least in the thalamus and prefrontal cortex regions, might be implicated in schizophrenia.Robert E. Smith, M.D., Ph.D., a resident at the University of Michigan's Psychiatry Residency Research Branch, and his colleagues focused on three proteins that are used for reuptake of glutamate by brain neurons. They compared the genetic expression of these proteins in postmortem brain tissue taken from 12 persons with schizophrenia with that in postmortem brain tissue from eight healthy controls. The tissue came from the thalamus region.The investigators found greater genetic expression for two out of three of the proteins in tissue taken from the individuals with schizophrenia than in tissue taken from the healthy controls, implying that excessive genetic expression of the proteins, at least in the thalamus, might underlie schizophrenia.In addition, Stella Dracheva, Ph.D., a professor of psychiatry at Mount Sinai School of Medicine, and her colleagues compared the genetic expression of three different subunits of NMDA receptors in postmortem brain tissue taken from 26 persons with schizophrenia with the expression of the subunits in postmortem brain tissue taken from 13 healthy controls and with the expression of the subunits in postmortem brain tissue taken from 10 people with Alzheimer's disease. The NMDA receptor is one of the neuron receptors for glutamate; NMDA stands for N-methyl-D-aspartate.The tissue samples came from the prefrontal cortex and occipital cortex regions of the brain.Expression for two of the three subunits, the investigators reported, was higher in tissue from people with schizophrenia than in tissue from both healthy controls and Alzheimer's subjects, suggesting that excessive genetic expression of these two subunits, at least in the prefrontal cortex and occipital cortex regions, might be involved in schizophrenia.How all these findings fit together and how they might mesh with previous discoveries on the subject is far from clear at this point. For instance, how might the finding from Dracheva and her team that there is excessive NMDA receptor gene expression in schizophrenia be reconciled with a report in the June 1, 2000, Journal of Neuroscience that antipsychotic drugs enhance the function and consequent gene expression of NMDA receptors?Nonetheless, schizophrenia investigators remain optimistic that all the pieces will ultimately fit together and give a coherent picture of the origins of schizophrenia. For instance, Carol Tamminga, M.D., a professor of psychiatry at the University of Maryland, wrote in an editorial accompanying the study reports that emerging results "will be the basis not only for understanding the pathophysiology of schizophrenia, but also for postulating novel drug targets." And in a review of the subject that accompanies the study reports, Donald Goff, M.D., and Joseph Coyle, M.D., professors of psychiatry and neuroscience at Harvard University, concluded: "Dysfunction of glutamatergic neurotransmission may play an important role in the pathophysiology of schizophrenia, especially of the negative symptoms and cognitive impairments associated with the disorder, and is a promising target for drug development."The study reports, editorial, and review mentioned in this article can be read online at www.ajp.psychiatryonline by searching under the September issue. ▪ ISSUES NewArchived

Postmortem brain tissue has been reported to be suitable to delineate regional pattern of possible disturbances underlying epigenetic functionality. However, from many parameters that have been detected in postmortem brain regions it is noteworthy that an effect of postmortem interval (PMI), storage time and premortem parameters should not be underestimated. Our previous investigation revealed that tryptophan (TRP) levels in postmortem brain tissue is affected by PMI and storage time. Since, alteration in TRP levels are assumed to be due to protein degradation, we further investigated whether TRP correlates to variables such as RNA, proteins and DNA modulators. In addition, we aimed to elucidate whether established postmortem variables may influence epigenetic parameters. These were investigated in well characterized postmortem human brain tissue originating from the European Brain Bank consortium II (BNEII). We could confirm previous findings, in which some protein levels alter because of prolonged PMI. Similarly, we demonstrated an influence of increased storage period on TRP levels, which might indicate degradation of proteins. Still not all proteins degrade in a similar manner, therefore a specific analysis for the protein of interest would be recommended. We found that methyltransferase- and acetyltransferase-activities were relatively preserved with PMI and storage duration. In conclusion, preservation of acetyltransferase- and methyltransferase-activities provides possible evidence of stability for epigenetic studies using postmortem tissue.

Postmortem studies of schizophrenia have yielded definitive evidence for abnormalities of cortical GABAergic neurons. However, few studies have delineated how the GABA neurons are functionally impaired and how their abnormalities cause symptoms of the illness. Thelin et al. (in this issue) recorded in vivo task-related spike firings of individual neurons in the primary auditory cortex in a mouse model of the 15q13.3 microdeletion syndrome, which is associated with an approximately 10-fold increased risk for developing schizophrenia. This article is protected by copyright. All rights reserved.

Parkinson's disease (PD) is a prevalent neurodegenerative disorder, and recent evidence suggests that pathogenesis may be in part mediated by inflammatory processes, the molecular and cellular architectures of which are largely unknown. To identify and characterize selectively vulnerable brain cell populations in PD, we performed single-nucleus transcriptomics and unbiased proteomics to profile the prefrontal cortex from postmortem human brains of six individuals with late-stage PD and six age-matched controls. Analysis of nearly 80,000 nuclei led to the identification of eight major brain cell types, including elevated brain-resident T cells in PD, each with distinct transcriptional changes in agreement with the known genetics of PD. By analyzing Lewy body pathology in the same postmortem brain tissues, we found that α-synuclein pathology was inversely correlated with chaperone expression in excitatory neurons. Examining cell-cell interactions, we found a selective abatement of neuron-astrocyte interactions and enhanced neuroinflammation. Proteomic analyses of the same brains identified synaptic proteins in the prefrontal cortex that were preferentially down-regulated in PD. By comparing this single-cell PD dataset with a published analysis of similar brain regions in Alzheimer's disease (AD), we found no common differentially expressed genes in neurons but identified many shared differentially expressed genes in glial cells, suggesting that the disease etiologies, especially in the context of neuronal vulnerability, in PD and AD are likely distinct.

Alzheimer’s disease (AD) is a neurodegenerative disease with no effective cure that attacks the brain’s cells resulting in memory loss and changes in behavior and language skills. Alternative splicing is a highly regulated process influenced by specific cell types and has been implicated in age-related disorders such as neurodegenerative diseases. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem brain tissue can provide valuable insights into AD pathology. Here, we provided cell-level ASEs in postmortem brain tissue by employing bioinformatics pipelines on a bulk RNA sequencing study sorted by cell types and two single-cell RNA sequencing studies from the prefrontal cortex. This comprehensive analysis revealed previously overlooked splicing and expression changes in AD patient brains. Among the observed alterations were changed in the splicing and expression of transcripts associated with chaperones, including CLU in astrocytes and excitatory neurons, PTGDS in astrocytes and endothelial cells, and HSP90AA1 in microglia and tauopathy-afflicted neurons, which were associated with differential expression of the splicing factor DDX5. In addition, novel, unknown transcripts were altered, and structural changes were observed in lncRNAs such as MEG3 in neurons. This work provides a novel strategy to identify the notable ASEs at the cell level in neurodegeneration, which revealed cell type-specific splicing changes in AD. This finding may contribute to interpreting associations between splicing and neurodegenerative disease outcomes.

Estrogen regulation of spine density and excitatory synapses in rat prefrontal and somatosensory cerebral cortex

BackgroundAlzheimer’s disease is defined by deposition of pathological proteins in spatially reproducible patterns within the tissue of affected individuals. Prominent pathological protein species found in Alzheimer’s disease are amyloid beta plaques and phospho‐tau tangles, which spread through a succession of brain areas. As this pathology spreads and worsens, it is accompanied by glial reactivity and activation and neuronal loss. Characterization of cell types changing or lost during disease progression and where those changes occur will be important for finding mechanisms of disease onset and progression.MethodsnRNAseq analysis from Alzheimer’s donors was used to determine which cell types are present and what changes in gene expression, if any, can be observed at the highest resolution of cell type identity: the supertype. We mapped these supertypes using highly multiplexed spatial transcriptomics on the same donor set to determine where these supertypes are in the tissue, where vulnerable types are lost at which stages, and whether gene expression changes can be observed in specific types near pathology.ResultWe have found that certain vulnerable cellular supertypes are more likely to be affected early, and a reproducible sequence of neuronal loss follows with increasing pathology. Surprisingly, one of the first neuronal subtypes to be affected are somatostatin inhibitory neurons, followed by L2/3IT excitatory neurons and parvalbumin inhibitory neurons. We have corroborated these results in human donor tissue using spatial transcriptomics to map and characterize loss of abundance of vulnerable cell types. We find that vulnerable neuronal types are predominately localized in supragranular layers.ConclusionSpatial methods are key to relating these neuronal vulnerabilities with pathological protein locations and specific locations within affected tissue. We have adapted spatial profiling and analysis methods to characterize the spatial relationships between specific neuronal types, amyloid plaques, tau tangles, and observed changes in gene expression. These data will offer novel insight into cell and molecular changes occurring at each phase of the disease and may inform the development of promising therapeutic interventions.

Women are at elevated risk for certain cardiovascular diseases, including pulmonary arterial hypertension, Alzheimer's disease, and vascular complications of diabetes. Angiotensin II (AngII), a circulating stress hormone, is elevated in cardiovascular disease; however, our knowledge of sex differences in the vascular effects of AngII are limited. We therefore analyzed sex differences in human endothelial cell response to AngII treatment. Male and female endothelial cells were treated with AngII for 24h and analyzed by RNA sequencing. We then used endothelial and mesenchymal markers, inflammation assays, and oxidative stress indicators to measure female and male endothelial cell functional changes in response to AngII. Our data show that female and male endothelial cells are transcriptomically distinct. Female endothelial cells treated with AngII had widespread gene expression changes related to inflammatory and oxidative stress pathways, while male endothelial cells had few gene expression changes. While both female and male endothelial cells maintained their endothelial phenotype with AngII treatment, female endothelial cells showed increased release of the inflammatory cytokine interleukin-6 and increased white blood cell adhesion following AngII treatment concurrent with a second inflammatory cytokine. Additionally, female endothelial cells had elevated reactive oxygen species production compared to male endothelial cells after AngII treatment, which may be partially due to nicotinamide adenine dinucleotide phosphate oxidase-2 (NOX2) escape from X-chromosome inactivation. These data suggest that endothelial cells have sexually dimorphic responses to AngII, which could contribute to increased prevalence of some cardiovascular diseases in women. The online version contains supplementary material available at 10.1007/s12195-023-00762-2.

OP0063 Impact of baseline interferon pathway activation on widespread gene expression changes with disease flare in lupus patients: Interim report from the bold (biomarkers of lupus disease) study

The retrosplenial cortex (RSC) is a critical brain region that is activated during spatial memory tasks and plays a crucial role in the consolidation of long-term memory. Various classes of RSC excitatory neurons across different laminar layers serve as the central hub for neuronal connections between the RSC and other brain regions, such as the hippocampus. Despite the established role of the RSC in spatial memory, the transcriptomic signature of the neuronal subtypes in the RSC during spatial memory consolidation remained elusive. Here, we used unbiased and targeted spatial transcriptomics to identify the RSC transcriptional signature after a spatial memory task. Genes related to transcription regulation, protein folding, and mitogen-activated protein kinase pathways were upregulated in the RSC during an early time window of memory consolidation. Furthermore, cell-type and excitatory neuronal layer-specific changes in gene expression were resolved using Xenium spatial transcriptomics. A deep learning computational tool uncovered cell-type-specific molecular activation patterns within the RSC after learning. Conversely, in a mouse model of Alzheimer's disease and related dementia (ADRD) exhibiting tau hyperphosphorylation in the RSC, there was a reduction in predicted neuronal activation following learning. Notably, learning-induced Fos expression was decreased in excitatory neurons of the RSC in the ADRD mice. Finally, we observed that blocking RSC excitatory neurons during the early temporal window after learning using a chemogenetic approach impaired long-term spatial memory in adult mice. Our results reveal a molecular signature of the RSC after learning and emphasize the role of RSC excitatory neurons during spatial memory consolidation.