scholarly journals Decoding molecular and cellular heterogeneity of nucleus accumbens with high-throughput scRNA-seq and MERFISH

2021 ◽  
Author(s):  
Renchao Chen ◽  
Timothy R. Blosser ◽  
Mohamed N. Djekidel ◽  
Junjie Hao ◽  
Aritra Bhattacherjee ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
High Throughput ◽  
Spatial Information ◽  
Spatial Diversity ◽  
Cellular Heterogeneity ◽  
Spatially Resolved ◽  
A Cell ◽  
High Level ◽  
And Function ◽  
Neural Disorders

The nucleus accumbens (NAc) plays an important role in regulating multiple behaviors and its dysfunction has been linked to many neural disorders. However, the molecular, cellular and anatomic heterogeneity underlying its functional diversity remains incompletely understood. Here, we generate a cell census of the mouse NAc using high-throughput single cell RNA-sequencing and multiplexed error-robust FISH, revealing a high level of cell heterogeneity in this brain region. We show that the transcriptional and spatial diversity of neuron subtypes underlie NAc's anatomic and functional heterogeneity, and possibly contribute to the pathogenesis of different neurological disorders. These findings explain how the seemingly simple neuronal composition of the NAc achieves its highly heterogenous structure and diverse functions. Collectively, our study generates a spatially resolved cell taxonomy for understanding the NAc structure and function, which demonstrates the importance of combining molecular and spatial information in revealing the fundamental features of the nervous system.

scholarly journals Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord

2021 ◽  
Author(s):  
Felix Fiederling ◽  
Luke A. Hammond ◽  
David Ng ◽  
Carol Mason ◽  
Jane Dodd
Keyword(s):  
Spinal Cord ◽  
Sample Preparation ◽  
High Throughput ◽  
Adult Mouse ◽  
Spatial Information ◽  
Spinal Neurons ◽  
Mouse Spinal Cord ◽  
Single Block ◽  
And Function

Spinal neurons are highly heterogeneous in location, transcriptional identity and function. To understand their contributions to sensorimotor circuits, it is essential to map the positions of identified subsets of neurons in relation to others throughout the spinal cord (SC), but we lack tools for whole SC sample preparation, imaging and in toto analysis. To overcome this problem, we have (1) designed scaffolds (SpineRacks) that facilitate efficient and ordered cryo-sectioning of the entire SC in a single block, (2) constructed a 3D reference atlas of adult mouse SC and (3) developed software (SpinalJ) to register images of sections and for standardized analysis of cells and projections in atlas space. We have verified mapping accuracies for known neurons and demonstrated the usefulness of this platform to reveal unknown neuronal distributions. Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.

scholarly journals DSTG: Deconvoluting Spatial Transcriptomics Data through Graph-based Artificial Intelligence

2020 ◽  
Author(s):  
Jing Su ◽  
Qianqian Song
Keyword(s):  
Spatial Data ◽  
Spatial Information ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Superior Performance ◽  
Gene Expressions ◽  
Mouse Cortex ◽  
Hippocampus Slice ◽  
Transcriptomics Data ◽  
High Level

AbstractRecent development of spatial transcriptomics (ST) is capable of associating spatial information at different spots in the tissue section with RNA abundance of cells within each spot, which is particularly important to understand tissue cytoarchitectures and functions. However, for such ST data, since a spot is usually larger than an individual cell, gene expressions measured at each spot are from a mixture of cells with heterogenous cell types. Therefore, ST data at each spot needs to be disentangled so as to reveal the cell compositions at that spatial spot. In this study, we propose a novel method, named DSTG, to accurately deconvolute the observed gene expressions at each spot and recover its cell constitutions, thus achieve high-level segmentation and reveal spatial architecture of cellular heterogeneity within tissues. DSTG not only demonstrates superior performance on synthetic spatial data generated from different protocols, but also effectively identifies spatial compositions of cells in mouse cortex layer, hippocampus slice, and pancreatic tumor tissues. In conclusion, DSTG accurately uncovers the cell states and subpopulations based on spatial localization.

scholarly journals RefCell: Multi-dimensional analysis of image-based high-throughput screens based on ‘typical cells’

2018 ◽  
Author(s):  
Yang Shen ◽  
Nard Kubben ◽  
Julián Candia ◽  
Alexandre V. Morozov ◽  
Tom Misteli ◽  
...  
Keyword(s):  
Dimensional Analysis ◽  
High Throughput ◽  
High Throughput Screening ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Premature Aging ◽  
Cellular Heterogeneity ◽  
High Level ◽  
High Throughput Screens ◽  
High Throughput Imaging

AbstractBackgroundImage-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Cutting-edge high-dimensional analysis methods are successful in characterizing cellular heterogeneity, but they suffer from the “curse of dimensionality” and non-standardized outputs.ResultsHere we introduce RefCell, a multi-dimensional analysis pipeline for image-based HTS that reproducibly captures cells with typical combinations of features in reference states, and uses these “typical cells” as a reference for classification and weighting of metrics. RefCell quantitatively assesses the heterogeneous deviations from typical behavior for each analyzed perturbation or sample.ConclusionsWe apply RefCell to the analysis of data from a high-throughput imaging screen of a library of 320 ubiquitin protein targeted siRNAs selected to gain insights into the mechanisms of premature aging (progeria). RefCell yields results comparable to a more complex clustering based single cell analysis method, which both reveal more potential hits than conventional average based analysis.

scholarly journals Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Maeve O’Huallachain ◽  
Felice-Alessio Bava ◽  
Mary Shen ◽  
Carolina Dallett ◽  
Sri Paladugu ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Model Systems ◽  
Cellular Heterogeneity ◽  
Human Model ◽  
Targeted Analysis ◽  
Technological Advances ◽  
And Function

AbstractSingle-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers.

Materials Designed to Control and Examine The Function of Single Cells

1998 ◽  
Vol 530 ◽  
Author(s):  
C.H. Thomas ◽  
J.B. Lhoest ◽  
D.G. Castner ◽  
C.D. Mcfarland ◽  
K.E. Healy
Keyword(s):  
Mammalian Cells ◽  
Cell Function ◽  
Single Cells ◽  
Polymer Network ◽  
Interpenetrating Polymer Network ◽  
Cytoskeletal Organization ◽  
Spatially Resolved ◽  
Cell Organization ◽  
A Cell ◽  
And Function

AbstractStress levels imparted on a cell have been shown to alter cell organization and function, presumably as a result of morphological cues affecting cytoskeletal organization. Materials with spatially resolved surface chemistry were designed to isolate individual mammalian cells to determine the influence of projected area on cell proliferation and cytoskeletal organization. Surfaces were fabricated using a photolithographic process resulting in islands of cell binding N-(2-aminoethyl)-3-aminopropyl-trimethoxysilane (EDS) separated by a non-adhesive interpenetrating polymer network [poly acrylamide-co-ethylene glycol; P(AAm-co-EG)]. The surfaces contained over 3800 adhesive islands/cm2, allowing for isolation of single cells with projected areas ranging from 100µm2to 10,000µm2. These surfaces provide a useful tool for researching how cell morphology and mechanical forces affect cell function.

CD38 as an immunomodulator in cancer

2020 ◽  
Vol 16 (34) ◽  
pp. 2853-2861
Author(s):  
Yanli Li ◽  
Rui Yang ◽  
Limo Chen ◽  
Sufang Wu
Keyword(s):  
Multiple Myeloma ◽  
Cell Activation ◽  
Human Tissues ◽  
Transmembrane Glycoprotein ◽  
Cell Activation Marker ◽  
Research Findings ◽  
A Cell ◽  
And Function ◽  
Human Molecule

CD38 is a transmembrane glycoprotein that is widely expressed in a variety of human tissues and cells, especially those in the immune system. CD38 protein was previously considered as a cell activation marker, and today monoclonal antibodies targeting CD38 have witnessed great achievements in multiple myeloma and promoted researchers to conduct research on other tumors. In this review, we provide a wide-ranging review of the biology and function of the human molecule outside the field of myeloma. We focus mainly on current research findings to summarize and update the findings gathered from diverse areas of study. Based on these findings, we attempt to extend the role of CD38 in the context of therapy of solid tumors and expand the role of the molecule from a simple marker to an immunomodulator.

scholarly journals Maturation of the Na,K-ATPase in the Endoplasmic Reticulum in Health and Disease

2021 ◽  
Author(s):  
Vitalii Kryvenko ◽  
Olga Vagin ◽  
Laura A. Dada ◽  
Jacob I. Sznajder ◽  
István Vadász
Keyword(s):  
Endoplasmic Reticulum ◽  
Intracellular Signaling ◽  
Loss Of Function ◽  
Α Subunit ◽  
Rate Limiting Step ◽  
Atpase Subunits ◽  
A Cell ◽  
Health And Disease ◽  
And Function ◽  
Rate Limiting

Abstract The Na,K-ATPase establishes the electrochemical gradient of cells by driving an active exchange of Na+ and K+ ions while consuming ATP. The minimal functional transporter consists of a catalytic α-subunit and a β-subunit with chaperon activity. The Na,K-ATPase also functions as a cell adhesion molecule and participates in various intracellular signaling pathways. The maturation and trafficking of the Na,K-ATPase include co- and post-translational processing of the enzyme in the endoplasmic reticulum (ER) and the Golgi apparatus and subsequent delivery to the plasma membrane (PM). The ER folding of the enzyme is considered as the rate-limiting step in the membrane delivery of the protein. It has been demonstrated that only assembled Na,K-ATPase α:β-complexes may exit the organelle, whereas unassembled, misfolded or unfolded subunits are retained in the ER and are subsequently degraded. Loss of function of the Na,K-ATPase has been associated with lung, heart, kidney and neurological disorders. Recently, it has been shown that ER dysfunction, in particular, alterations in the homeostasis of the organelle, as well as impaired ER-resident chaperone activity may impede folding of Na,K-ATPase subunits, thus decreasing the abundance and function of the enzyme at the PM. Here, we summarize our current understanding on maturation and subsequent processing of the Na,K-ATPase in the ER under physiological and pathophysiological conditions. Graphic Abstract

scholarly journals Sialic Acid—Modified Nanoparticles—New Approaches in the Glioma Management—Perspective Review

2021 ◽  
Vol 22 (14) ◽  
pp. 7494
Author(s):  
Przemyslaw Wielgat ◽  
Katarzyna Niemirowicz-Laskowska ◽  
Agnieszka Z. Wilczewska ◽  
Halina Car
Keyword(s):  
Sialic Acid ◽  
Clinical Observation ◽  
Malignant Cell ◽  
Cellular Heterogeneity ◽  
Molecular Processes ◽  
Management Perspective ◽  
Therapeutic Tools ◽  
And Function ◽  
Worse Prognosis

The cell surface is covered by a dense and complex network of glycans attached to the membrane proteins and lipids. In gliomas, the aberrant sialylation, as the final stage of glycosylation, is an important regulatory mechanism of malignant cell behavior and correlates with worse prognosis. Better understanding of the role of sialylation in cellular and molecular processes opens a new way in the development of therapeutic tools for human brain tumors. According to the recent clinical observation, the cellular heterogeneity, activity of brain cancer stem cells (BCSCs), immune evasion, and function of the blood–brain barrier (BBB) are attractive targets for new therapeutic strategies. In this review, we summarize the importance of sialic acid-modified nanoparticles in brain tumor progression.

scholarly journals Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sunny Z. Wu ◽  
Daniel L. Roden ◽  
Ghamdan Al-Eryani ◽  
Nenad Bartonicek ◽  
Kate Harvey ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cells ◽  
Cellular Heterogeneity ◽  
Tumour Heterogeneity ◽  
Fresh Tissue ◽  
Human Cancers ◽  
Cryopreserved Cell ◽  
Single Cell Rna Sequencing

Abstract Background High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are logistically difficult, preclude histopathological triage of samples, and limit the ability to perform batch processing. This hindrance can often introduce technical biases when integrating patient datasets and increase experimental costs. Although tissue preservation methods have been previously explored to address such issues, it is yet to be examined on complex human tissues, such as solid cancers and on high throughput scRNA-Seq platforms. Methods Using the Chromium 10X platform, we sequenced a total of ~ 120,000 cells from fresh and cryopreserved replicates across three primary breast cancers, two primary prostate cancers and a cutaneous melanoma. We performed detailed analyses between cells from each condition to assess the effects of cryopreservation on cellular heterogeneity, cell quality, clustering and the identification of gene ontologies. In addition, we performed single-cell immunophenotyping using CITE-Seq on a single breast cancer sample cryopreserved as solid tissue fragments. Results Tumour heterogeneity identified from fresh tissues was largely conserved in cryopreserved replicates. We show that sequencing of single cells prepared from cryopreserved tissue fragments or from cryopreserved cell suspensions is comparable to sequenced cells prepared from fresh tissue, with cryopreserved cell suspensions displaying higher correlations with fresh tissue in gene expression. We showed that cryopreservation had minimal impacts on the results of downstream analyses such as biological pathway enrichment. For some tumours, cryopreservation modestly increased cell stress signatures compared to freshly analysed tissue. Further, we demonstrate the advantage of cryopreserving whole-cells for detecting cell-surface proteins using CITE-Seq, which is impossible using other preservation methods such as single nuclei-sequencing. Conclusions We show that the viable cryopreservation of human cancers provides high-quality single-cells for multi-omics analysis. Our study guides new experimental designs for tissue biobanking for future clinical single-cell RNA sequencing studies.

L2 acquisition of the bei passive in Mandarin Chinese: A constructionist approach

2020 ◽  
Vol 9 (2) ◽  
pp. 169-198
Author(s):  
Chen Chen ◽  
Feng-hsi Liu
Keyword(s):  
Mandarin Chinese ◽  
Choice Task ◽  
L2 Acquisition ◽  
Low Level ◽  
Passive Construction ◽  
Form And Function ◽  
L2 Learners ◽  
Constructionist Approach ◽  
High Level ◽  
And Function

Abstract A major claim in the constructionist approach to language acquisition is that grammar is learned by pairings of form and function. In this study we test this claim by examining how L2 learners of Mandarin Chinese acquire the bei passive construction, a construction that is associated with the meaning of adversity. Our goal is to find out whether L2 learners make the association between the passive and adversity. Participants performed a sentence choice task under four conditions: an adversative context with an adversative verb, an adversative context with a neutral verb, a neutral context with a neutral verb and a positive context with a neutral verb. In each context participants were asked to select either the bei passive construction or its active counterpart. We found that high-level learners consistently chose the bei passive significantly more in adversative contexts than in non-adversative contexts regardless of the connotations of the verbs, while low-level learners made the distinction half of the time. In addition, while low-level learners did not yet associate adversity with the form of the construction, high-level learners did. We conclude that L2 learners do learn the bei passive construction as a form-meaning pair. The constructionist approach is supported.

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