Distinct properties in ventral pallidum projection neuron subtypes

The ventral pallidum (VP), a major component of the basal ganglia, plays a critical role in motivational disorders. It sends projections to many different brain regions but it is not yet known whether and how these projections differ in their cellular properties, gene expression patterns, connectivity and role in reward seeking. In this study, we focus on four major outputs of the VP - to the lateral hypothalamus (LH), ventral tegmental area (VTA), mediodorsal thalamus (MDT), and lateral habenula (LHb) - and examine the differences between them in 1) baseline gene expression profiles using projection-specific RNA-sequencing; 2) physiological parameters using whole-cell patch clamp; and 3) their influence on cocaine reward using chemogenetic tools. We show that these four VP efferents differ in all three aspects and highlight specifically differences between the projections to the LH and the VTA. These two projections originate largely from separate populations of neurons, express distinct sets of genes related to neurobiological functions, and show opposite physiological and behavioral properties. Collectively, our data demonstrates for the first time that VP neurons exhibit distinct molecular and cellular profiles in a projection-specific manner, suggesting that they represent different cell types.

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Scopolamine-induced Delirium Promotes Neuroinflammation and Neuropsychiatric Disorder in Mice

10.21203/rs.3.rs-126768/v1 ◽

2020 ◽

Author(s):

So Yeong Cheon ◽

Bon-Nyeo Koo ◽

So Yeon Kim ◽

Eun Hee Kam ◽

Junhyun Nam ◽

...

Keyword(s):

Gene Expression ◽

Inflammatory Cytokines ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Brain Regions ◽

Mice Model ◽

Tnf Α ◽

Compare Gene Expression ◽

Pro Inflammatory Cytokines

Abstract BackgroundPostoperative delirium is a common neuropsychiatric syndrome resulting in a high postsurgical mortality rate and decline in postdischarge function. Extensive research has been performed on both human and animal delirium models due to their clinical significance, focusing on systemic inflammation and consequent neuroinflammation playing a key in the pathogenesis of postoperative cognitive dysfunctions. Since animal models are widely utilized for pathophysiological study of neuropsychiatric disorders, this study aimed at examining the validity of the scopolamine-induced delirium mice model with respect to the neuroinflammatory hypothesis of delirium. MethodsMale C57BL/6 mice were treated with intraperitoneal scopolamine (2 mg/kg). Neurobehavioural tests were performed to evaluate the changes in cognitive functions, including learning and memory, and the level of anxiety after surgery or scopolamine treatment. The levels of pro-inflammatory cytokines (IL-1ꞵ, IL-18, and TNF-α) and inflammasome components (NLRP3, ASC, and caspase-1) in different brain regions were measured. Gene expression profiles were also examined using whole-genome RNA sequencing analyses to compare gene expression patterns of different mice models.Results Scopolamine treatment showed significant increase in the level of anxiety and impairments in memory and cognitive function associated with increased level of pro-inflammatory cytokines and NLRP3 inflammasome components. Genetic analysis confirmed the different expression patterns of the genes involved in immune response and inflammation and those related with the development of the nervous system in both surgery and scopolamine-induced mice models. Conclusions The scopolamine-induced delirium mice model successfully showed that analogous neuropsychiatric changes coincide with the neuroinflammatory hypothesis for pathogenesis of delirium.

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Feasibility assessment of GI tumor stroma gene expression profiles with microarray technology in formalin-fixed, paraffin-embedded (FFPE) specimens.

Journal of Clinical Oncology ◽

10.1200/jco.2011.29.4_suppl.232 ◽

2011 ◽

Vol 29 (4_suppl) ◽

pp. 232-232

Author(s):

S. X. Wang ◽

J. Wang ◽

M. S. Beg ◽

E. Ozhegov ◽

A. X. Qu ◽

...

Keyword(s):

Gene Expression ◽

Gene Annotation ◽

Expression Profiles ◽

Expression Patterns ◽

Critical Role ◽

Gene Expression Profiles ◽

Tumor Stroma ◽

Pancreatic Tissue ◽

Feasibility Assessment ◽

Study Gene Expression

232 Background: Cancer stroma plays a critical role in tumorigenesis. Microarrays are widely used to study gene expression patterns in tumor frozen tissue to explore tumorigenesis and predict recurrence. Here we explored the feasibility of applying microarrays to tumor stroma using FFPE specimens. Methods: Ten samples were obtained from one colon and one pancreatic cancer specimen. Tumor stroma and normal stroma were microdissected. RNA was extracted, amplified, and labeled using Nugene FFPE kit, with array analysis using Affymetrix Human Gene 1.0. To assess reproducibility, each stroma sample was run twice in parallel. To test the reproducibility of sampling, the specimen was microdissected twice at a different stroma location. GenePattern software was used; correlation between parallel samples and the repeat dissection samples was calculated and ComparativeMarkerSelection program with two-sided T test was used to study gene profiles in pancreatic and colon stroma. To validate the array results, the profile differences were analyzed against public databases. Results: The correlation between the duplicate samples was in the range of 0.978-0.988. The correlation between the original versus the repeat dissection at a different stroma site was 0.953-0.967. 19,319 probes with gene annotation were examined, and pancreatic stroma was compared to colon stroma. We found that 90% of these genes were expressed at similar levels. Using a cutoff of 1.3, we identified 50 genes that were expressed greater than 30% in pancreatic stroma compared to colon stroma. We researched these 50 genes against GeneNote, GNF, Unigene and SAGE databases. Upregulation of 95% of these genes in pancreatic stroma is consistent with the public databases. Moreover, among these genes we identified PNLIP, CPB1 CPA2, PRSS1/PRSS2, AMY1A, AMY1B, AMY1C, and AMY2A, known to be highly expressed in pancreatic tissue. Conclusions: Gene expression microarray is a tool that can be effectively used to analyze normal and tumor stroma in GI cancer. FFPE tissue is suitable for such an analysis, as evidenced by high reproducibility and biologic consistency of the obtained data. No significant financial relationships to disclose.

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Scopolamine promotes neuroinflammation and delirium-like neuropsychiatric disorder in mice

Scientific Reports ◽

10.1038/s41598-021-87790-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

So Yeong Cheon ◽

Bon-Nyeo Koo ◽

So Yeon Kim ◽

Eun Hee Kam ◽

Junhyun Nam ◽

...

Keyword(s):

Gene Expression ◽

Inflammatory Cytokines ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Brain Regions ◽

Mice Model ◽

Tnf Α ◽

Compare Gene Expression ◽

Pro Inflammatory Cytokines

AbstractPostoperative delirium is a common neuropsychiatric syndrome resulting a high postsurgical mortality rate and decline in postdischarge function. Extensive research has been performed on both human and animal delirium-like models due to their clinical significance, focusing on systematic inflammation and consequent neuroinflammation playing a key role in the pathogenesis of postoperative cognitive dysfunctions. Since animal models are widely utilized for pathophysiological study of neuropsychiatric disorders, this study aimed at examining the validity of the scopolamine-induced delirium-like mice model with respect to the neuroinflammatory hypothesis of delirium. Male C57BL/6 mice were treated with intraperitoneal scopolamine (2 mg/kg). Neurobehavioral tests were performed to evaluate the changes in cognitive functions, including learning and memory, and the level of anxiety after surgery or scopolamine treatment. The levels of pro-inflammatory cytokines (IL-1β, IL-18, and TNF-α) and inflammasome components (NLRP3, ASC, and caspase-1) in different brain regions were measured. Gene expression profiles were also examined using whole-genome RNA sequencing analyses to compare gene expression patterns of different mice models. Scopolamine treatment showed significant increase in the level of anxiety and impairments in memory and cognitive function associated with increased level of pro-inflammatory cytokines and NLRP3 inflammasome components. Genetic analysis confirmed the different expression patterns of genes involved in immune response and inflammation and those related with the development of the nervous system in both surgery and scopolamine-induced mice models. The scopolamine-induced delirium-like mice model successfully showed that analogous neuropsychiatric changes coincides with the neuroinflammatory hypothesis for pathogenesis of delirium.

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Scopolamine-Induced Delirium Promotes Neuroinflammation and Neuropsychiatric Disorder in Mice

10.21203/rs.3.rs-132211/v1 ◽

2020 ◽

Author(s):

So Yeong Cheon ◽

Bon-Nyeo Koo ◽

So Yeon Kim ◽

Eun Hee Kam ◽

Junhyun Nam ◽

...

Keyword(s):

Gene Expression ◽

Inflammatory Cytokines ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Brain Regions ◽

Mice Model ◽

Tnf Α ◽

Compare Gene Expression ◽

Pro Inflammatory Cytokines

Abstract Postoperative delirium is a common neuropsychiatric syndrome resulting a high postsurgical mortality rate and decline in postdischarge function. Extensive research has been performed on both human and animal delirium models due to their clinical significance, focusing on systematic inflammation and consequent neuroinflammation playing a key role in the pathogenesis of postoperative cognitive dysfunctions. Since animal models are widely utilized for pathophysiological study of neuropsychiatric disorders, this study aimed at examining the validity of the scopolamine-induced delirium mice model with respect to the neuroinflammatory hypothesis of delirium. Male C57BL/6 mice were treated with intraperitoneal scopolamine (2 mg/kg). Neurobehavioral tests were performed to evaluate the changes in cognitive functions, including learning and memory, and the level of anxiety after surgery or scopolamine treatment. The levels of pro-inflammatory cytokines (IL-1ꞵ, IL-18, and TNF-α) and inflammasome components (NLRP3, ASC, and caspase-1) in different brain regions were measured. Gene expression profiles were also examined using whole-genome RNA sequencing analyses to compare gene expression patterns of different mice models.Scopolamine treatment showed significant increase in the level of anxiety and impairments in memory and cognitive function associated with increased level of pro-inflammatory cytokines and NLRP3 inflammasome components. Genetic analysis confirmed the different expression patterns of genes involved in immune response and inflammation and those related with the development of the nervous system in both surgery and scopolamine-induced mice models. The scopolamine-induced delirium mice model successfully showed that analogous neuropsychiatric changes coincides with the neuroinflammatory hypothesis for pathogenesis of delirium.

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Automated Sorting of Monocytes from Whole Blood for Reproducible Gene Expression Profiling.

Blood ◽

10.1182/blood.v110.11.3840.3840 ◽

2007 ◽

Vol 110 (11) ◽

pp. 3840-3840

Author(s):

Carsten Poggel ◽

Timo Adams ◽

Sabine Martin ◽

Carola Pickel ◽

Nicole Prahl ◽

...

Keyword(s):

Gene Expression ◽

Blood Cell ◽

Gene Expression Profiling ◽

Whole Blood ◽

Expression Profiling ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Cell Types ◽

Specific Gene

Abstract Microarray-based gene expression profiling has been used to develop clinically relevant molecular classifiers for many different diseases. Furthermore, it has been shown for various chronic diseases that specific gene expression patterns are reflected at the level of blood cells. However, blood is a complex tissue comprising numerous cell types. Therefore, the contribution of rare cell types to a whole blood expression profile might not be detected and a substantial proportion of what is usually reported as “up-regulation” or “down-regulation” might actually be the result of a shift in cell populations and not of a true regulatory process. In order to circumvent these problems, several techniques have been established to analyze purified subpopulations rather than whole blood samples. Previously, it has been shown, for example, that reproducible gene expression profiles can be generated by positive selection of blood cell subsets from PBMCs1. As the preparation of PBMCs by, for example, Ficoll is time-consuming, inconvenient, and not amenable to automation, we have set up a combined direct whole blood cell separation and gene expression profiling protocol. By using Whole Blood CD14 MicroBeads in combination with the autoMACS Pro™ Separator, the separation protocol generally allowed enrichment of monocytes from whole blood within 30 min with purities higher than 90%. In combination with the depletion of neutrophils, the major source of contaminating RNA, purities increased to over 95% for all tested blood donors. Monocytes included the CD14bright/CD16− as well as the CD14dim/CD16+ populations. To assess the reproducibility of gene expression profiles and the influence of several experimental parameters, monocytes were sorted from 5 ml whole blood. RNA was extracted and hybridized to microarrays and the Pearson correlation coefficients of pairwise comparisons were calculated. Technical repeats of monocyte analysis from blood donated at different days showed a higher correlation coefficient than whole blood RNA. Blood storage at room temperature resulted in a strong deregulation of many genes, whereas blood stored at 4°C showed minimal changes, which is in agreement with previous studies. Skipping the centrifugation step, which is used to remove unbound MicroBeads did not alter the gene expression profiles. Incubation of sorted cells in PrepProtect™ Stabilization Buffer showed no alteration of gene expression thus enabling the shipping of cells without liquid nitrogen. Monocytes play a crucial role in diseases like atherosclerosis. Our rapid and simple protocol for combined direct cell sorting from whole blood and gene expression profiling of monocytes might help to ease the discovery of new biomarkers and to screen and monitor patients. 1 Lyons et al., BMC Genomics (2007), 8:64.

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Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

Nature Communications ◽

10.1038/s41467-021-22331-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Bing He ◽

Ping Chen ◽

Sonia Zambrano ◽

Dina Dabaghie ◽

Yizhou Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Kidney ◽

Cell Types ◽

Model Organisms ◽

Mural Cell ◽

Glomerular Cell ◽

Individual Gene ◽

The Individual

AbstractMolecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

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Discovering Distinct Patterns in Gene Expression Profiles

Journal of Integrative Bioinformatics ◽

10.1515/jib-2008-105 ◽

2008 ◽

Vol 5 (2) ◽

Cited By ~ 1

Author(s):

Li Teng ◽

Laiwan Chan

Keyword(s):

Gene Expression ◽

Large Scale ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Clustering Methods ◽

Gene Expressions ◽

Real Gene ◽

Large Scale Dataset ◽

Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

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CFTR ΔF508 mutation has minimal effect on the gene expression profile of differentiated human airway epithelia

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00065.2005 ◽

2005 ◽

Vol 289 (4) ◽

pp. L545-L553 ◽

Cited By ~ 29

Author(s):

Joseph Zabner ◽

Todd E. Scheetz ◽

Hakeem G. Almabrazi ◽

Thomas L. Casavant ◽

Jian Huang ◽

...

Keyword(s):

Gene Expression ◽

Cystic Fibrosis ◽

Large Scale ◽

Expression Profiles ◽

Expression Patterns ◽

Primary Cultures ◽

Gene Expression Profiles ◽

Filter Method ◽

Tissue Destruction ◽

Airway Epithelia

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial chloride channel regulated by phosphorylation. Most of the disease-associated morbidity is the consequence of chronic lung infection with progressive tissue destruction. As an approach to investigate the cellular effects of CFTR mutations, we used large-scale microarray hybridization to contrast the gene expression profiles of well-differentiated primary cultures of human CF and non-CF airway epithelia grown under resting culture conditions. We surveyed the expression profiles for 10 non-CF and 10 ΔF508 homozygote samples. Of the 22,283 genes represented on the Affymetrix U133A GeneChip, we found evidence of significant changes in expression in 24 genes by two-sample t-test ( P < 0.00001). A second, three-filter method of comparative analysis found no significant differences between the groups. The levels of CFTR mRNA were comparable in both groups. There were no significant differences in the gene expression patterns between male and female CF specimens. There were 18 genes with significant increases and 6 genes with decreases in CF relative to non-CF samples. Although the function of many of the differentially expressed genes is unknown, one transcript that was elevated in CF, the KCl cotransporter (KCC4), is a candidate for further study. Overall, the results indicate that CFTR dysfunction has little direct impact on airway epithelial gene expression in samples grown under these conditions.

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Dynamical consequences of regional heterogeneity in the brain’s transcriptional landscape

10.1101/2020.10.28.359943 ◽

2020 ◽

Cited By ~ 1

Author(s):

Gustavo Deco ◽

Kevin Aquino ◽

Aurina Arnatkevičiūtė ◽

Stuart Oldham ◽

Kristina Sabaroedin ◽

...

Keyword(s):

Gene Expression ◽

Large Scale ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Brain Regions ◽

Biophysical Model ◽

Neuronal Dynamics ◽

Regional Heterogeneity ◽

Magnetic Resonance Imaging Mri

AbstractBrain regions vary in their molecular and cellular composition, but how this heterogeneity shapes neuronal dynamics is unclear. Here, we investigate the dynamical consequences of regional heterogeneity using a biophysical model of whole-brain functional magnetic resonance imaging (MRI) dynamics in humans. We show that models in which transcriptional variations in excitatory and inhibitory receptor (E:I) gene expression constrain regional heterogeneity more accurately reproduce the spatiotemporal structure of empirical functional connectivity estimates than do models constrained by global gene expression profiles and MRI-derived estimates of myeloarchitecture. We further show that regional heterogeneity is essential for yielding both ignition-like dynamics, which are thought to support conscious processing, and a wide variance of regional activity timescales, which supports a broad dynamical range. We thus identify a key role for E:I heterogeneity in generating complex neuronal dynamics and demonstrate the viability of using transcriptional data to constrain models of large-scale brain function.

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Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

10.1101/2020.08.26.266494 ◽

2020 ◽

Author(s):

Alexander Calderwood ◽

Jo Hepworth ◽

Shannon Woodhouse ◽

Lorelei Bilham ◽

D. Marc Jones ◽

...

Keyword(s):

Gene Expression ◽

Brassica Rapa ◽

Regulatory Networks ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Detailed Comparison ◽

Developmental Time ◽

Floral Transition ◽

Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

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