scholarly journals Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming

2021 ◽  
Vol 7 (15) ◽  
pp. eabe8978
Author(s):  
Álvaro Herrero-Navarro ◽  
Lorenzo Puche-Aroca ◽  
Verónica Moreno-Juan ◽  
Alejandro Sempere-Ferràndez ◽  
Ana Espinosa ◽  
...  
Keyword(s):  
Molecular Diversity ◽  
Regional Identity ◽  
Brain Regions ◽  
Molecular Signature ◽  
Specific Gene ◽  
Thalamic Nuclei ◽  
Brain Repair ◽  
Cell Diversity ◽  
Regional Specificity ◽  
Epigenetic Signatures

Neural cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterized by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and astrocytes. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across these two brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis reveals the existence of common nucleus-specific progenitors for neurons and astrocytes. Consistent with their shared molecular signature, regional specificity is maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.

scholarly journals Astrocytes and neurons share brain region-specific transcriptional signatures

2020 ◽  
Author(s):  
Álvaro Herrero-Navarro ◽  
Lorenzo Puche-Aroca ◽  
Verónica Moreno-Juan ◽  
Alejandro Sempere-Ferràndez ◽  
Ana Espinosa ◽  
...  
Keyword(s):  
Molecular Diversity ◽  
Neuronal Cell ◽  
Brain Regions ◽  
Molecular Signature ◽  
Specific Gene ◽  
Thalamic Nuclei ◽  
Brain Repair ◽  
Cell Diversity ◽  
Regional Specificity ◽  
Epigenetic Signatures

SUMMARYNeuronal cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterised by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and glia. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis revealed the existence of common nucleus-specific progenitors for neurons and glia. Consistent with their shared molecular signature, regional specificity was maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.

scholarly journals Multiomics Identification of Potential Targets for Alzheimer Disease and Antrocin as a Therapeutic Candidate

Pharmaceutics ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1555
Author(s):  
Alexander T. H. Wu ◽  
Bashir Lawal ◽  
Li Wei ◽  
Ya-Ting Wen ◽  
David T. W. Tzeng ◽  
...  
Keyword(s):  
Early Stage ◽  
Brain Regions ◽  
Genetic Alterations ◽  
Molecular Signature ◽  
Support Vector ◽  
Specific Gene ◽  
Tor Signaling ◽  
Interacting Protein ◽  
Expression Levels ◽  
Neurodegenerative Dementia

Alzheimer’s disease (AD) is the most frequent cause of neurodegenerative dementia and affects nearly 50 million people worldwide. Early stage diagnosis of AD is challenging, and there is presently no effective treatment for AD. The specific genetic alterations and pathological mechanisms of the development and progression of dementia remain poorly understood. Therefore, identifying essential genes and molecular pathways that are associated with this disease’s pathogenesis will help uncover potential treatments. In an attempt to achieve a more comprehensive understanding of the molecular pathogenesis of AD, we integrated the differentially expressed genes (DEGs) from six microarray datasets of AD patients and controls. We identified ATPase H+ transporting V1 subunit A (ATP6V1A), BCL2 interacting protein 3 (BNIP3), calmodulin-dependent protein kinase IV (CAMK4), TOR signaling pathway regulator-like (TIPRL), and the translocase of outer mitochondrial membrane 70 (TOMM70) as upregulated DEGs common to the five datasets. Our analyses revealed that these genes exhibited brain-specific gene co-expression clustering with OPA1, ITFG1, OXCT1, ATP2A2, MAPK1, CDK14, MAP2K4, YWHAB, PARK2, CMAS, HSPA12A, and RGS17. Taking the mean relative expression levels of this geneset in different brain regions into account, we found that the frontal cortex (BA9) exhibited significantly (p < 0.05) higher expression levels of these DEGs, while the hippocampus exhibited the lowest levels. These DEGs are associated with mitochondrial dysfunction, inflammation processes, and various pathways involved in the pathogenesis of AD. Finally, our blood–brain barrier (BBB) predictions using the support vector machine (SVM) and LiCABEDS algorithm and molecular docking analysis suggested that antrocin is permeable to the BBB and exhibits robust ligand–receptor interactions with high binding affinities to CAMK4, TOMM70, and T1PRL. Our results also revealed good predictions for ADMET properties, drug-likeness, adherence to Lipinskís rules, and no alerts for pan-assay interference compounds (PAINS) Conclusions: These results suggest a new molecular signature for AD parthenogenesis and antrocin as a potential therapeutic agent. Further investigation is warranted.

scholarly journals Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Localization ◽  
Expression Profiles ◽  
Cell Types ◽  
Molecular Signature ◽  
Receptor Protein ◽  
Specific Gene ◽  
Specific Cell ◽  
Biological Processes ◽  
Endometrial Cells

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

scholarly journals To hum or not to hum: Neural transcriptome signature of courtship vocalization in a teleost fish

2020 ◽  
Author(s):  
Joel A. Tripp ◽  
Ni Y. Feng ◽  
Andrew H. Bass
Keyword(s):  
Gene Expression ◽  
Vocal Communication ◽  
Brain Regions ◽  
Vocal Behavior ◽  
Specific Gene ◽  
Motor Nucleus ◽  
Motor Behaviors ◽  
Behavioral States ◽  
Courtship Activity ◽  
Courtship Behaviors

AbstractFor many animal species, vocal communication is a critical social behavior, often a necessary component of reproductive success. In addition to the role of vocal behavior in social interactions, vocalizations are often demanding motor acts. Through understanding the genes involved in regulating and permitting vertebrate vocalization, we can better understand the mechanisms regulating vocal and, more broadly, motor behaviors. Here, we use RNA-sequencing to investigate neural gene expression underlying the performance of an extreme vocal behavior, the courtship hum of the plainfin midshipman fish (Porichthys notatus). Single hums can last up to two hours and may be repeated throughout an evening of courtship activity. We asked whether vocal behavioral states are associated with specific gene expression signatures in key brain regions that regulate vocalization by comparing transcript levels in humming versus non-humming males. We find that the circadian-related genes period3 and Clock are significantly upregulated in the vocal motor nucleus and preoptic area-anterior hypothalamus, respectively, in humming compared to non-humming males, indicating that internal circadian clocks may differ between these divergent behavioral states. In addition, we identify suites of differentially expressed genes related to synaptic transmission, ion channels and transport, hormone signaling, and metabolism and antioxidant activity that may permit or support humming behavior. These results underscore the importance of the known circadian control of midshipman humming and provide testable candidate genes for future studies of the neuroendocrine and motor control of energetically demanding courtship behaviors in midshipman fish and other vertebrate groups.

scholarly journals Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression

2019 ◽  
Vol 36 (3) ◽  
pp. 782-788 ◽  
Author(s):  
Jiebiao Wang ◽  
Bernie Devlin ◽  
Kathryn Roeder
Keyword(s):  
Gene Expression ◽  
Empirical Bayes ◽  
Brain Regions ◽  
Tissue Level ◽  
Supplementary Information ◽  
Specific Gene ◽  
Expression Data ◽  
Cell Type ◽  
Multiple Measurements ◽  
Cell Type Specific

Abstract Motivation Patterns of gene expression, quantified at the level of tissue or cells, can inform on etiology of disease. There are now rich resources for tissue-level (bulk) gene expression data, which have been collected from thousands of subjects, and resources involving single-cell RNA-sequencing (scRNA-seq) data are expanding rapidly. The latter yields cell type information, although the data can be noisy and typically are derived from a small number of subjects. Results Complementing these approaches, we develop a method to estimate subject- and cell-type-specific (CTS) gene expression from tissue using an empirical Bayes method that borrows information across multiple measurements of the same tissue per subject (e.g. multiple regions of the brain). Analyzing expression data from multiple brain regions from the Genotype-Tissue Expression project (GTEx) reveals CTS expression, which then permits downstream analyses, such as identification of CTS expression Quantitative Trait Loci (eQTL). Availability and implementation We implement this method as an R package MIND, hosted on https://github.com/randel/MIND. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Thalamic Functional Connectivity during Spatial Long-Term Memory and the Role of Sex

2020 ◽  
Vol 10 (12) ◽  
pp. 898
Author(s):  
Dylan S. Spets ◽  
Scott D. Slotnick
Keyword(s):  
Sex Differences ◽  
Functional Connectivity ◽  
Region Of Interest ◽  
Brain Regions ◽  
Long Term Memory ◽  
Thalamic Nuclei ◽  
Term Memory ◽  
Correlated Activity ◽  
Abstract Shapes

The thalamus has been implicated in many cognitive processes, including long-term memory. More specifically, the anterior (AT) and mediodorsal (MD) thalamic nuclei have been associated with long-term memory. Despite extensive mapping of the anatomical connections between these nuclei and other brain regions, little is known regarding their functional connectivity during long-term memory. The current study sought to determine which brain regions are functionally connected to AT and MD during spatial long-term memory and whether sex differences exist in the patterns of connectivity. During encoding, abstract shapes were presented to the left and right of fixation. During retrieval, shapes were presented at fixation, and participants made an “old-left” or “old-right” judgment. Activations functionally connected to AT and MD existed in regions with known anatomical connections to each nucleus as well as in a broader network of long-term memory regions. Sex differences were identified in a subset of these regions. A targeted region-of-interest analysis identified anti-correlated activity between MD and the hippocampus that was specific to females, which is consistent with findings in rodents. The current results suggest that AT and MD play key roles during spatial long-term memory and suggest that these functions may be sex specific.

scholarly journals Thiamine Deficiency Induced Neurochemical, Neuroanatomical, and Neuropsychological Alterations: A Reappraisal

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Raffaele Nardone ◽  
Yvonne Höller ◽  
Monica Storti ◽  
Monica Christova ◽  
Frediano Tezzon ◽  
...  
Keyword(s):  
Thiamine Deficiency ◽  
Cortical Cell ◽  
Cell Loss ◽  
Brain Regions ◽  
Experimental Models ◽  
Neurological Sequela ◽  
Thalamic Nuclei ◽  
Chronic Alcoholic ◽  
Ethanol Abuse ◽  
And Function

Nutritional deficiency can cause, mainly in chronic alcoholic subjects, the Wernicke encephalopathy and its chronic neurological sequela, the Wernicke-Korsakoff syndrome (WKS). Long-term chronic ethanol abuse results in hippocampal and cortical cell loss. Thiamine deficiency also alters principally hippocampal- and frontal cortical-dependent neurochemistry; moreover in WKS patients, important pathological damage to the diencephalon can occur. In fact, the amnesic syndrome typical for WKS is mainly due to the damage in the diencephalic-hippocampal circuitry, including thalamic nuclei and mammillary bodies. The loss of cholinergic cells in the basal forebrain region results in decreased cholinergic input to the hippocampus and the cortex and reduced choline acetyltransferase and acetylcholinesterase activities and function, as well as in acetylcholine receptor downregulation within these brain regions. In this narrative review, we will focus on the neurochemical, neuroanatomical, and neuropsychological studies shedding light on the effects of thiamine deficiency in experimental models and in humans.

scholarly journals Novel somatic mutations and distinct molecular signature in aldosterone-producing adenomas

2015 ◽  
Vol 22 (5) ◽  
pp. 735-744 ◽  
Author(s):  
Tobias Åkerström ◽  
Holger Sven Willenberg ◽  
Kenko Cupisti ◽  
Julian Ip ◽  
Samuel Backman ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Transcriptome Analysis ◽  
Somatic Mutations ◽  
Novel Mutation ◽  
Improve Patient Care ◽  
Molecular Signature ◽  
Specific Gene ◽  
Novel Mutations ◽  
Intracellular Ca ◽  
Improve Patient

Aldosterone-producing adenomas (APAs) are found in 1.5–3.0% of hypertensive patients in primary care and can be cured by surgery. Elucidation of genetic events may improve our understanding of these tumors and ultimately improve patient care. Approximately 40% of APAs harbor a missense mutation in the KCNJ5 gene. More recently, somatic mutations in CACNA1D, ATP1A1 and ATP2B3, also important for membrane potential/intracellular Ca2+ regulation, were observed in APAs. In this study, we analyzed 165 APAs for mutations in selected regions of these genes. We then correlated mutational findings with clinical and molecular phenotype using transcriptome analysis, immunohistochemistry and semiquantitative PCR. Somatic mutations in CACNA1D in 3.0% (one novel mutation), ATP1A1 in 6.1% (six novel mutations) and ATP2B3 in 3.0% (two novel mutations) were detected. All observed mutations were located in previously described hotspot regions. Patients with tumors harboring mutations in CACNA1D, ATP1A1 and ATP2B3 were operated at an older age, were more often male and had tumors that were smaller than those in patients with KCNJ5 mutated tumors. Microarray transcriptome analysis segregated KCNJ5 mutated tumors from ATP1A1/ATP2B3 mutated tumors and those without mutation. We observed significant transcription upregulation of CYP11B2, as well as the previously described glomerulosa-specific gene NPNT, in ATP1A1/ATP2B3 mutated tumors compared to KCNJ5 mutated tumors. In summary, we describe novel somatic mutations in proteins regulating the membrane potential/intracellular Ca2+ levels, and also a distinct mRNA and clinical signature, dependent on genetic alteration.

Music, Maestro, Please: Thalamic multisensory integration in music perception, processing and production

2019 ◽  
Vol 11 (2) ◽  
pp. 98
Author(s):  
Artur Jaschke
Keyword(s):  
Multisensory Integration ◽  
Music Perception ◽  
Initial Point ◽  
Initial Step ◽  
Brain Regions ◽  
Thalamic Nuclei ◽  
Brain Areas ◽  
Neural Connections ◽  
Parietal Lobes ◽  
The Brain

Music activates a wide array of brain areas involved in different functions such as   perception, processing and execution of music. Understanding musical processes in the brain has multiple implications in the neuro- and health sciences.  Challenging the brain with a multisensory stimulus such as music activates responses beyond the auditory cortex of the temporal lobe. Other areas that are involved include the frontal lobes, parietal lobes, areas of the limbic system such as the amygdala, hippocampus and thalamus, the cerebellum and the brainstem. Nonetheless, there has been no attempt to summarize all involved brain areas in music into one overall encompassing map. This may well be, as there has been no thorough theory introduced, which would allow an initial point of departure in creating such a mapTherefore, a thorough systematic review has been conducted to identify all mentioned neural connections involved in the perception, processing and execution of music.  Communication between the thalamic nuclei is the initial step in multisensory integration, which lies at the base of the neural networks as proposed in this paper. Against this background, this manuscript introduces the to our knowledge first map of all brain regions involved in the perception, processing and execution of music.Consequently, placing thalamic multisensory integration at the core of this atlas allowed us to create a preliminary theory to explain the complexity of music induced brain activation.

New docetaxel-peptide conjugate for the treatment of sortilin-positive triple-negative breast cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e12556-e12556
Author(s):  
Michel Demeule ◽  
Borhane Annabi ◽  
Jean-Christophe Currie ◽  
Alain Larocque ◽  
Cyndia Charfi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Tumor Regression ◽  
Cell Model ◽  
Molecular Signature ◽  
Specific Gene ◽  
Real Time System

e12556 Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease which still lacks defined molecular biomarkers. In the last decade, targeting of specific gene/protein molecular signature of tumors emerged among the best anticancer strategies. Recently, increased expression of the Sortilin (SORT1) receptor has been reported in TNBC patients. Given SORT1 functions in protein internalization, sorting and trafficking, we developed a new peptide-anticancer drug conjugation platform to target SORT1-positive breast cancer by linking Docetaxel to a peptide (KA-peptide) that specifically targets SORT1. Methods: MDA-MB-231 cells were used as a TNBC cell model for in vitro and in vivo xenograft (CD1 nude mice) assays. Cell migration was assessed using the xCELLigence real-time system, whereas MTT assay was used for cell proliferation analysis. Apoptosis biomarkers expression was assessed by immunoblotting. Results: In MDA-MB-231, the Docetaxel-KA-peptide conjugate (DoceKA) exerted potent anti-proliferative and anti-migratory activities in vitro. DoceKA triggered faster and higher cell death mechanisms than did free Docetaxel alone. The apoptotic and anti-migratory effects were reversed by the SORT1 ligands Neurotensin and Progranulin, and upon siRNA-mediated silencing of SORT1. DoceKA altered microtubules polymerization and triggered the down-regulation of IL-6, Survivin, Bcl-xL and mutant p53 pro-survival biomarkers. In vivo, DoceKA exhibited a greater tumor regression capacity with a prolonged survival in a murine MDA-MB-231 xenograft tumor model than did Docetaxel. Conclusions: Collectively, we demonstrate that DoceKA is specifically internalized through a receptor-mediated mechanism. Such property allows for targeting SORT1-positive breast cancers, and makes DoceKA a promising novel therapy for the treatment of TNBC.

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