scholarly journals Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis

2021 ◽  
Vol 22 (16) ◽  
pp. 8802
Author(s):  
Anastasia N. Vaganova ◽  
Ramilya Z. Murtazina ◽  
Taisiia S. Shemyakova ◽  
Andrey D. Prjibelski ◽  
Nataliia V. Katolikova ◽  
...  
Keyword(s):  
Brain Structures ◽  
Gene Expression Omnibus ◽  
Brain Atlas ◽  
Potential Contribution ◽  
Brain Functions ◽  
Neuropsychiatric Diseases ◽  
Human Protein Atlas ◽  
Olfactory Input ◽  
Socially Relevant ◽  
Novel Target

Trace amine-associated receptors (TAAR) recognize organic compounds, including primary, secondary, and tertiary amines. The TAAR5 receptor is known to be involved in the olfactory sensing of innate socially relevant odors encoded by volatile amines. However, emerging data point to the involvement of TAAR5 in brain functions, particularly in the emotional behaviors mediated by the limbic system which suggests its potential contribution to the pathogenesis of neuropsychiatric diseases. TAAR5 expression was explored in datasets available in the Gene Expression Omnibus, Allen Brain Atlas, and Human Protein Atlas databases. Transcriptomic data demonstrate ubiquitous low TAAR5 expression in the cortical and limbic brain areas, the amygdala and the hippocampus, the nucleus accumbens, the thalamus, the hypothalamus, the basal ganglia, the cerebellum, the substantia nigra, and the white matter. Altered TAAR5 expression is identified in Down syndrome, major depressive disorder, or HIV-associated encephalitis. Taken together, these data indicate that TAAR5 in humans is expressed not only in the olfactory system but also in certain brain structures, including the limbic regions receiving olfactory input and involved in critical brain functions. Thus, TAAR5 can potentially be involved in the pathogenesis of brain disorders and represents a valuable novel target for neuropsychopharmacology.

scholarly journals A robust image registration interface for large volume brain atlas

2018 ◽  
Author(s):  
Hong Ni ◽  
Chaozhen Tan ◽  
Zhao Feng ◽  
Shangbin Chen ◽  
Zoutao Zhang ◽  
...  
Keyword(s):  
Large Volume ◽  
Three Dimensional ◽  
Brain Structures ◽  
Cellular Level ◽  
Brain Atlas ◽  
Biological Images ◽  
Brain Functions ◽  
Streak Image ◽  
Dataset Size ◽  
The Brain

AbstractMapping the brain structures in three-dimensional accurately is critical for an in-depth understanding of the brain functions. By using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficiently use of various datasets. However, because of the heterogeneous and non-uniform characteristics of the brain structures at cellular level brought with the recently developed high-resolution whole-brain microscopes, traditional registration methods are difficult to apply to the robust mapping of various large volume datasets. Here, we proposed a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large volume datasets at cellular level by introducing the extract regional features of the anatomically invariant method and a strategy of parameter acquisition and large volume transformation. By performing validation on model data and biological images, BrainsMapi can not only achieve robust registration on sample tearing and streak image datasets, different individual and modality datasets accurately, but also are able to complete the registration of large volume dataset at cellular level which dataset size reaches 20 TB. Besides, it can also complete the registration of historical vectorized dataset. BrainsMapi would facilitate the comparison, reuse and integration of a variety of brain datasets.

scholarly journals CircFAM13B promotes the proliferation of hepatocellular carcinoma by sponging miR-212, upregulating E2F5 expression and activating the P53 pathway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Xie ◽  
Xiaofeng Hang ◽  
Wensheng Xu ◽  
Jing Gu ◽  
Yuanjing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
In Vivo Studies ◽  
Circular Rnas ◽  
Novel Target ◽  
Underlying Mechanisms

Abstract Background Most of the biological functions of circular RNAs (circRNAs) and the potential underlying mechanisms in hepatocellular carcinoma (HCC) have not yet been discovered. Methods In this study, using circRNA expression data from HCC tumor tissues and adjacent tissues from the Gene Expression Omnibus database, we identified out differentially expressed circRNAs and verified them by qRT-PCT. Functional experiments were performed to evaluate the effects of circFAM13B in HCC in vitro and in vivo. Results We found that circFAM13B was the most significantly differentially expressed circRNA in HCC tissue. Subsequently, in vitro and in vivo studies also demonstrated that circFAM13B promoted the proliferation of HCC. Further studies revealed that circFAM13B, a sponge of miR-212, is involved in the regulation of E2F5 gene expression by competitively binding to miR-212, inhibits the activation of the P53 signalling pathway, and promotes the proliferation of HCC cells. Conclusions Our findings revealed the mechanism underlying the regulatory role played by circFAM13B, miR-212 and E2F5 in HCC. This study provides a new theoretical basis and novel target for the clinical prevention and treatment of HCC.

scholarly journals Homologous laminar organization of the mouse and human subiculum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael S. Bienkowski ◽  
Farshid Sepehrband ◽  
Nyoman D. Kurniawan ◽  
Jim Stanis ◽  
Laura Korobkova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hippocampal Formation ◽  
Expression Patterns ◽  
Pyramidal Cells ◽  
Brain Structures ◽  
Longitudinal Axis ◽  
Brain Atlas ◽  
Fiber Density ◽  
Laminar Organization ◽  
Hybridization Data

AbstractThe subiculum is the major output component of the hippocampal formation and one of the major brain structures most affected by Alzheimer’s disease. Our previous work revealed a hidden laminar architecture within the mouse subiculum. However, the rotation of the hippocampal longitudinal axis across species makes it unclear how the laminar organization is represented in human subiculum. Using in situ hybridization data from the Allen Human Brain Atlas, we demonstrate that the human subiculum also contains complementary laminar gene expression patterns similar to the mouse. In addition, we provide evidence that the molecular domain boundaries in human subiculum correspond to microstructural differences observed in high resolution MRI and fiber density imaging. Finally, we show both similarities and differences in the gene expression profile of subiculum pyramidal cells within homologous lamina. Overall, we present a new 3D model of the anatomical organization of human subiculum and its evolution from the mouse.

scholarly journals Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Norio Takata ◽  
Nobuhiko Sato ◽  
Yuji Komaki ◽  
Hideyuki Okano ◽  
Kenji F. Tanaka
Keyword(s):  
Mouse Brain ◽  
Brain Structures ◽  
Brain Atlas ◽  
Resting State Functional Connectivity ◽  
Brain Science ◽  
Step Procedure ◽  
Public Resources ◽  
Large Brain ◽  
Magnetic Resonance Imaging Mri ◽  
And Function

AbstractA brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher’s necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.

scholarly journals Transcriptional Profiling and Functional Analysis of N1/N2 Neutrophils Reveal an Immunomodulatory Effect of S100A9-Blockade on the Pro-Inflammatory N1 Subpopulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Andreea C. Mihaila ◽  
Letitia Ciortan ◽  
Razvan D. Macarie ◽  
Mihaela Vadana ◽  
Sergiu Cecoltan ◽  
...  
Keyword(s):  
Inflammatory Diseases ◽  
Transcriptional Profiling ◽  
Innate Immune ◽  
Potential Contribution ◽  
Functional Differences ◽  
Elevated Expression ◽  
Pharmacological Blockade ◽  
Novel Target ◽  
Increased Activity ◽  
Homogenous Population

Neutrophils have been classically viewed as a homogenous population. Recently, neutrophils were phenotypically classified into pro-inflammatory N1 and anti-inflammatory N2 sub-populations, but the functional differences between the two subtypes are not completely understood. We aimed to investigate the phenotypic and functional differences between N1 and N2 neutrophils, and to identify the potential contribution of the S100A9 alarmin in neutrophil polarization. We describe distinct transcriptomic profiles and functional differences between N1 and N2 neutrophils. Compared to N2, the N1 neutrophils exhibited: i) higher levels of ROS and oxidative burst, ii) increased activity of MPO and MMP-9, and iii) enhanced chemotactic response. N1 neutrophils were also characterized by elevated expression of NADPH oxidase subunits, as well as activation of the signaling molecules ERK and the p65 subunit of NF-kB. Moreover, we found that the S100A9 alarmin promotes the chemotactic and enzymatic activity of N1 neutrophils. S100A9 inhibition with a specific small-molecule blocker, reduced CCL2, CCL3 and CCL5 chemokine expression and decreased MPO and MMP-9 activity, by interfering with the NF-kB signaling pathway. Together, these findings reveal that N1 neutrophils are pro-inflammatory effectors of the innate immune response. Pharmacological blockade of S100A9 dampens the function of the pro-inflammatory N1 phenotype, promoting the alarmin as a novel target for therapeutic intervention in inflammatory diseases.

scholarly journals Targeting brain functions from the scalp: Transcranial brain atlas based on large-scale fMRI data synthesis

NeuroImage ◽  
2020 ◽  
Vol 210 ◽  
pp. 116550 ◽  
Author(s):  
Yihan Jiang ◽  
Zheng Li ◽  
Yang Zhao ◽  
Xiang Xiao ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Brain Atlas ◽  
Fmri Data ◽  
Data Synthesis ◽  
Brain Functions

Identification of the PCA29 gene signature as a predictor in prostate cancer

2019 ◽  
Vol 17 (03) ◽  
pp. 1940006 ◽  
Author(s):  
Jung-Yu Lee ◽  
Si-Yu Lin ◽  
Chun-Yu Lin ◽  
Yi-Huan Chuang ◽  
Sing-Han Huang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Signature ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Gene Expressions ◽  
Scoring Method ◽  
Clinical Issue ◽  
Targeting Therapy ◽  
Human Protein Atlas

Prostate cancer (PCa) is the second leading cause of cancer death among men worldwide. About 70% of PCa patients were diagnosed at later stage, and metastasis has been observed. Additionally, the cure rate of PCa closely relies on the early diagnosis with biomarkers. The identification of biomarkers for diagnosis and prognosis is an urgent clinical issue for PCa. Here, we developed a novel scoring strategy, including cluster score (CS) and predicting score (PS), to identify 29 PCa genes (called PCa29) for early diagnostic biomarkers from two datasets in Gene Expression Omnibus. The result indicates that PCa29 can discriminate between normal and tumor tissues and are specific for prostate cancer. To validate PCa29, we found that 97% of PCa29 were consistently significant with these gene expressions in The Cancer Genome Atlas; furthermore, [Formula: see text]70% of PCa29 are consensus to the protein expression in The Human Protein Atlas. Finally, we examined 10 genes in PCa29 on three PCa cell lines by real-time quantitative polymerase chain reaction. The experimental results show that the trend of the differential PCa29 expression is consistent with the analyzed results from our novel scoring method. We believe that our method is useful and PCa29 are potential biomarkers that provide the clues to develop targeting therapy for PCa.

scholarly journals Downregulated SPINK4 is associated with poor survival in colorectal cancer

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiaojie Wang ◽  
Qian Yu ◽  
Waleed M. Ghareeb ◽  
Yiyi Zhang ◽  
Xingrong Lu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Expression Data ◽  
Poor Survival ◽  
Protein Levels ◽  
Normal Tissues ◽  
Human Protein Atlas ◽  
Cancer Genome Atlas ◽  
Independent Indicator

Abstract Background SPINK4 is known as a gastrointestinal peptide in the gastrointestinal tract and is abundantly expressed in human goblet cells. The clinical significance of SPINK4 in colorectal cancer (CRC) is largely unknown. Methods We retrieved the expression data of 1168 CRC patients from 3 Gene Expression Omnibus (GEO) datasets (GSE24551, GSE39582, GSE32323) and The Cancer Genome Atlas (TCGA) to compare the expression level of SPINK4 between CRC tissues and normal colorectal tissues and to evaluate its value in predicting the survival of CRC patients. At the protein level, these results were further confirmed by data mining in the Human Protein Atlas and by immunohistochemical staining of samples from 81 CRC cases in our own center. Results SPINK4 expression was downregulated in CRC compared with that in normal tissues, and decreased SPINK4 expression at both the mRNA and protein levels was associated with poor prognosis in CRC patients from all 3 GEO datasets, the TCGA database and our cohort. Additionally, lower SPINK4 expression was significantly related to higher TNM stage. Moreover, in multivariate regression, SPINK4 was confirmed as an independent indicator of poor survival in CRC patients in all databases and in our own cohort. Conclusions We concluded that reduced expression of SPINK4 relates to poor survival in CRC, functioning as a novel indicator.

Visual and sensorimotor cortices mapping during awake resection of lesion on the right periatrium: a case report on brainwaves and their peculiar patterns

2014 ◽  
Vol 2 (1-4) ◽  
Author(s):  
Zamzuri Idris ◽  
Ch’ng Chee How ◽  
Jafri Malin Abdullah
Keyword(s):  
Visual Field ◽  
Brain Mapping ◽  
New Technologies ◽  
Visual Stimulation ◽  
Brain Atlas ◽  
Brain Functions ◽  
Eloquent Areas ◽  
Neurosurgical Planning ◽  
Visual Field Deficits ◽  
Visual Evoked

AbstractAdvances in neurosurgery have allowed for more sophisticated mapping of various eloquent neural structures including the visual cortex. Applications of various modalities of new technologies allow accurate brain mapping for neurosurgical planning and preservation of functions in patients with lesions involving the eloquent cortex. The authors demonstrate the use of various new technologies for accurate presurgical planning, preservation of brain functions, and depiction of patterns of cortical brainwaves, which relate to motor networks and continuous visual stimuli.A patient with a right periatrial lesion involving the optic radiation with no visual field deficits was operated under an awake state and under continuous contralateral electrocorticography and visual monitoring. Presurgically, extra-operative brain mapping for visual-, sensory-, and motor-evoked magnetic fields were completed using magnetoencephalography (MEG). The dipole areas were identified, and the images were fused with a 116-region cortical brain atlas. The ideal trajectory was planned based on these images and diffusion tensor imaging (tractography). The trans-sulcal approachA good agreement for eloquent areas was identified based on extra-operative MEG and intra-operative neurostimulation mappings. The patient had no new neurological or visual-field deficits after the surgery. Certain patterns of brainwaves for motor cortex and visual stimulation were obtained: (a) spikes at the contralateral sensorimotor area when the motor strip was stimulated and (b) up-down and dense-loose continuous visual-evoked brainwaves at the occipital pole toward flashing checkerboard visual stimulation.A combination of extra- and intra-operative brain mappings should ideally be done in patients harboring lesions near eloquent areas. The continuous visual-evoked potential monitoring, using a grid electrode and flashing checkerboard and contralateral sensorimotor responses, observed in our case is interesting and needs further studies.

scholarly journals Fractalkine Attenuates Microglial Cell Activation Induced by Prenatal Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Joanna Ślusarczyk ◽  
Ewa Trojan ◽  
Katarzyna Głombik ◽  
Katarzyna Chamera ◽  
Adam Roman ◽  
...  
Keyword(s):  
Prenatal Stress ◽  
Cell Activation ◽  
Inflammatory Factors ◽  
Potential Contribution ◽  
Fractalkine Receptor ◽  
Neuropsychiatric Diseases ◽  
Prenatally Stressed ◽  
The Brain ◽  
Receptor Cx3cr1

The potential contribution of inflammation to the development of neuropsychiatric diseases has recently received substantial attention. In the brain, the main immune cells are the microglia. As they are the main source of inflammatory factors, it is plausible that the regulation of their activation may be a potential therapeutic target. Fractalkine (CX3CL1) and its receptor CX3CR1 play a crucial role in the control of the biological activity of the microglia. In the present study, using microglial cultures we investigated whether fractalkine is able to reverse changes in microglia caused by a prenatal stress procedure. Our study found that the microglia do not express fractalkine. Prenatal stress decreases the expression of the fractalkine receptor, which in turn is enhanced by the administration of exogenous fractalkine. Moreover, treatment with fractalkine diminishes the prenatal stress-induced overproduction of proinflammatory factors such as IL-1β, IL-18, IL-6, TNF-α, CCL2, or NO in the microglial cells derived from prenatally stressed newborns. In conclusion, the present results revealed that the pathological activation of microglia in prenatally stressed newborns may be attenuated by fractalkine administration. Therefore, understanding of the role of the CX3CL1-CX3CR1 system may help to elucidate the mechanisms underlying the neuron-microglia interaction and its role in pathological conditions in the brain.

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