scholarly journals Expression of genes in the16p11.2locus during human fetal cortical neurogenesis

2019 ◽  
Author(s):  
Sarah Morson ◽  
Yifei Yang ◽  
David J. Price ◽  
Thomas Pratt
Keyword(s):  
Cell Cycle ◽  
Cerebral Cortex ◽  
Gene Dosage ◽  
Cell Types ◽  
Autism Spectrum ◽  
Cycle Phase ◽  
Human Cerebral Cortex ◽  
Proliferating Cells ◽  
Protein Coding ◽  
Expression Of Genes

AbstractThe 593 kbp16p11.2copy number variation (CNV) affects the gene dosage of 29 protein coding genes, with heterozygous16p11.2microduplication or microdeletion implicated in about 1% of autism spectrum disorder (ASD) cases. The16p11.2CNV is frequently associated with macrocephaly or microcephaly indicating early defects of neurogenesis may contribute to subsequent ASD symptoms, but it is unknown which16p11.2transcripts are expressed in progenitors and whose levels are likely, therefore, to influence neurogenesis. Analysis of human fetal gene expression data revealed that of all the16p11.2transcripts only two,ALDOAandKIF22, are significantly enriched in progenitors. To investigate the role ofALDOAandKIF22in human cerebral cortex development we used immunohistochemical staining to describe their expression in late first and early second trimester human cerebral cortex. KIF22 protein is restricted to proliferating cells with its levels increasing during the cell cycle and peaking at mitosis. ALDOA protein is expressed in all cell types and does not vary with cell-cycle phase. Our expression analysis suggests the hypothesis that the simultaneous changes in KIF22 and ALDOA dosage in cortical progenitors causes defects in neurogenesis that may contribute to ASD in16p11.2CNV patients.

PCNA and total nuclear protein content as markers of cell proliferation in pea tissue

1992 ◽  
Vol 102 (1) ◽  
pp. 71-78 ◽  
Author(s):  
SANDRA CITTERIO ◽  
SERGIO SGORBATI ◽  
MARISA LEVI ◽  
BRUNO MARIA COLOMBO ◽  
ELIO SPARVOLI
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Protein Content ◽  
Time Course ◽  
Nuclear Protein ◽  
Flow Cytometric Analysis ◽  
Nuclear Antigen ◽  
Cycle Phase ◽  
Proliferating Cells ◽  
Embryo Cells

The identification of cell proliferation markers has been shown to be a useful tool with which to study basic mechanisms of cell cycle progression. The use of immunofluorescence techniques revealed the presence of the proliferating cell nuclear antigen (PCNA) in pea tissue, where we observed a high PCNA expression in proliferating cells of the root meristem compared to noncycling cells of the differentiated leaf. The presence of PCNA was monitored also during the time-course of seed germination, before, during and after the cell cycle resumption of the embryo cells. PCNA is present in embryo cells not only during and after resumption of the cell cycle but also before, when cells have not yet begun replicating their genome. A bivariate flow cytometric analysis of DNA and nuclear protein content was used to localize precisely the cells of the examined pea tissues in different cell cycle phase subcompartments. A high correlation was found between the degree of cell proliferation and the protein content of G1 nuclei, on the one hand, and the percentage of PCNA positive cells on the other.

scholarly journals The effects of proliferation status and cell cycle phase on the responses of single cells to chemotherapy

2020 ◽  
Vol 31 (8) ◽  
pp. 845-857 ◽  
Author(s):  
Adrián E. Granada ◽  
Alba Jiménez ◽  
Jacob Stewart-Ornstein ◽  
Nils Blüthgen ◽  
Simone Reber ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Information Theory ◽  
Tumor Cells ◽  
Single Cells ◽  
Residual Tumor ◽  
Cell Cycle Phase ◽  
Cycle Phase ◽  
Proliferating Cells ◽  
Probability Of Death

DNA-damaging chemotherapy often leaves residual tumor cells. Combining single-cell long-term live imaging with information theory, we found an unexpected effect: highly proliferative cells were more likely to arrest than to die, whereas more slowly proliferating cells showed a higher probability of death.

scholarly journals Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

2019 ◽  
Author(s):  
Chiaowen Joyce Hsiao ◽  
PoYuan Tung ◽  
John D. Blischak ◽  
Jonathan E. Burnett ◽  
Kenneth A. Barr ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Single Cell ◽  
Cell Cycle Progression ◽  
Cell Types ◽  
Cell Cycle Phase ◽  
Cellular Heterogeneity ◽  
Cycle Phase ◽  
Cycle Progression ◽  
Cellular Environment

AbstractCellular heterogeneity in gene expression is driven by cellular processes such as cell cycle and cell-type identity, and cellular environment such as spatial location. The cell cycle, in particular, is thought to be a key driver of cell-to-cell heterogeneity in gene expression, even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity, and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs). Using these data, we developed a novel approach to characterize cell cycle progression. While standard methods assign cells to discrete cell cycle stages, our method goes beyond this, and quantifies cell cycle progression on a continuum. We found that, on average, scRNA-seq data from only five genes predicted a cell’s position on the cell cycle continuum to within 14% of the entire cycle, and that using more genes did not improve this accuracy. Our data and predictor of cell cycle phase can directly help future studies to account for cell-cycle-related heterogeneity in iPSCs. Our results and methods also provide a foundation for future work to characterize the effects of the cell cycle on expression heterogeneity in other cell types.

scholarly journals The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

2021 ◽  
Author(s):  
Helle Samdal ◽  
Siv Anita Hegre ◽  
Konika Chawla ◽  
Nina-Beate Liabakk ◽  
Per Arne Aas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Phase Distribution ◽  
Cell Types ◽  
Metabolic Reprogramming ◽  
Cycle Phase ◽  
Cell Type ◽  
Chip Sequencing ◽  
Cell Cycle Phase Distribution

AbstractThe long non-coding RNA (lncRNA) EPB41L4A-AS1 is aberrantly expressed in various cancers and has been reported to be involved in metabolic reprogramming and as a repressor of the Warburg effect. Although the biological relevance of EPB41L4A-AS1 is evident, its functional role seems to vary depending on cell type and state of disease. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we previously identified EPB41L4A-AS1 to be one of 59 lncRNAs with potential cell cycle functions. Here, we demonstrate that EPB41L4A-AS1 exists as bright foci and regulates gene expression in the nucleus in both cis and trans. Specifically, we find that EPB41L4A-AS1 positively regulates its sense overlapping gene EPB41L4A and influences expression of hundreds of other genes, including genes involved in cell proliferation. Finally, we show that EPB41L4A-AS1 affects cell cycle phase distribution, though these effects vary between cell types.

scholarly journals Plk4 triggers autonomous de novo centriole biogenesis and maturation

2021 ◽  
Vol 220 (5) ◽  
Author(s):  
Catarina Nabais ◽  
Delphine Pessoa ◽  
Jorge de-Carvalho ◽  
Thomas van Zanten ◽  
Paulo Duarte ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
De Novo ◽  
Cell Types ◽  
Proliferating Cells ◽  
Cycle Progression ◽  
Controlled System ◽  
Pericentriolar Material ◽  
Centriole Assembly ◽  
Critical Components

Centrioles form centrosomes and cilia. In most proliferating cells, centrioles assemble through canonical duplication, which is spatially, temporally, and numerically regulated by the cell cycle and the presence of mature centrioles. However, in certain cell types, centrioles assemble de novo, yet by poorly understood mechanisms. Herein, we established a controlled system to investigate de novo centriole biogenesis, using Drosophila melanogaster egg explants overexpressing Polo-like kinase 4 (Plk4), a trigger for centriole biogenesis. We show that at a high Plk4 concentration, centrioles form de novo, mature, and duplicate, independently of cell cycle progression and of the presence of other centrioles. Plk4 concentration determines the temporal onset of centriole assembly. Moreover, our results suggest that distinct biochemical kinetics regulate de novo and canonical biogenesis. Finally, we investigated which other factors modulate de novo centriole assembly and found that proteins of the pericentriolar material (PCM), and in particular γ-tubulin, promote biogenesis, likely by locally concentrating critical components.

Effect of salmonella typhimurium A1-R on quiescent cancer cells that do not respond to standard chemotherapy.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e13576-e13576
Author(s):  
Shuya Yano ◽  
Yong Zhang ◽  
Fuminari Uehara ◽  
Yukihiko Hiroshima ◽  
Shinji Miwa ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Salmonella Typhimurium ◽  
Cancer Cells ◽  
Nude Mice ◽  
Fluorescent Protein ◽  
Confocal Imaging ◽  
Cytotoxic Agents ◽  
Cycle Phase ◽  
Solid Cancer ◽  
Proliferating Cells

e13576 Background: Quiescent cancer cells are a major impediment to treating solid cancer with chemotherapy, since in most tumors the majority of the cells are quiescent. Methods: The cell-cycle phase of each human MKN45 gastric cancer cell was imaged using a fluorescence ubiquitination cell cycle indicator (FUCCI). With FUCCI, quiescent cancer cells express mKusabira-Orange fluorescent protein (red) and proliferating cells express mAzami-Green fluorescent protein (green). FUCCI-labeled cancer cells in tumor spheres and subcutaneous tumor in nude mice were treated with Salmonella typhimurium A1-R. Results: Time-lapse confocal imaging showed that cancer cells in tumor spheres in serum-free culture become and remained quiescent. S. typhimurium A1-R infected and killed quiescent cancer cells in tumor spheres. In contrast, cytotoxic agents did not kill the quiescent cancer cells in the tumor spheres. S. typhimurium A1-R targeting of FUCCI-expressing subcutaneous tumors growing in nude mice resulted in the killing of quiescent cancer cells resistant to cytotoxic agents. Conclusions: S. typhimurium A1-R can kill quiescent cancer cells which suggests a new therapeutic paradigm potentially more effective than current therapeutics which are ineffective against quiescent cancer cells.

scholarly journals Droplet sample preparation for single-cell proteomics applied to the cell cycle

2021 ◽  
Author(s):  
Andrew Leduc ◽  
R. Gray Huffman ◽  
Nikolai Slavov
Keyword(s):  
Cell Cycle ◽  
Sample Preparation ◽  
Single Cell ◽  
Cell Mass ◽  
Cell Types ◽  
Single Cell Protein ◽  
Cell Protein ◽  
Cycle Phase ◽  
Protein Markers ◽  
Cell Cycle Protein

Many biological functions, such as the cell division cycle, are intrinsically single-cell processes regulated in part by protein synthesis and degradation. Investigating such processes has motivated the development of single-cell mass spectrometry (MS) proteomics. To further advance single-cell MS proteomics, we developed a method for automated nano-ProteOmic sample Preparation (nPOP). nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and performs all subsequent preparation steps in small droplets on a hydrophobic slide. This allows massively parallel sample preparation, including lysing, digesting, and labeling individual cells in volumes below 20 nl. Single-cell protein analysis using nPOP classified cells by cell type and by cell cycle phase. Furthermore, the data allowed us to quantify the covariation between cell cycle protein markers and thousands of proteins. Based on this covariation, we identify cell cycle associated proteins and functions that are shared across cell types and those that differ between cell types.

scholarly journals The Number of Chandelier and Basket Cells Are Differentially Decreased in Prefrontal Cortex in Autism

2016 ◽  
Vol 28 (2) ◽  
pp. 411-420 ◽  
Author(s):  
Jeanelle Ariza ◽  
Haille Rogers ◽  
Ezzat Hashemi ◽  
Stephen C Noctor ◽  
Verónica Martínez-Cerdeño
Keyword(s):  
Cerebral Cortex ◽  
Prefrontal Cortex ◽  
Translational Research ◽  
Intercellular Communication ◽  
Cell Types ◽  
Human Cerebral Cortex ◽  
Perineuronal Net ◽  
Vicia Villosa ◽  
Vicia Villosa Lectin ◽  
System Functioning

Abstract An interneuron alteration has been proposed as a source for the modified balance of excitation / inhibition in the cerebral cortex in autism. We previously demonstrated a decreased number of parvalbumin (PV)-expressing interneurons in prefrontal cortex in autism. PV-expressing interneurons include chandelier (Ch) and basket (Bsk) cells. We asked whether the decreased PV+ interneurons affected both Ch cells and Bsk cells in autism. The lack of single markers to specifically label Ch cells or Bsk cells presented an obstacle for addressing this question. We devised a method to discern between PV-Ch and PV-Bsk cells based on the differential expression of Vicia villosa lectin (VVA). VVA binds to N-acetylgalactosamine, that is present in the perineuronal net surrounding some cell types where it plays a role in intercellular communication. N-acetylgalactosamine is present in the perineuronal net surrounding Bsk but not Ch cells. We found that the number of Ch cells is consistently decreased in the prefrontal cortex of autistic (n = 10) when compared with control (n = 10) cases, while the number of Bsk cells is not as severely affected. This finding expand our understanding of GABAergic system functioning in the human cerebral cortex in autism, which will impact translational research directed towards providing better treatment paradigms for individuals with autism.

scholarly journals Highly reproducible human brain organoids recapitulate cerebral cortex cellular diversity.

2019 ◽  
Author(s):  
Silvia Velasco ◽  
Bruna Paulsen ◽  
Paola Arlotta
Keyword(s):  
Cerebral Cortex ◽  
Human Brain ◽  
Single Cells ◽  
Cell Types ◽  
Previous Method ◽  
Human Cerebral Cortex ◽  
Rich Diversity ◽  
Single Cell Rna Sequencing ◽  
The Rich ◽  
Detailed Protocol

Abstract Human brain organoids hold an unprecedented opportunity to observe, perturb, and study the early stages of human cortical development. Several protocols to generate brain organoids have been described in recent years[1, 2]. However, incomplete characterization and lack of organoid-to-organoid reproducibility has limited their application as an experimental model[3]. Here we describe a detailed protocol for the generation of human dorsal forebrain organoids that show highly reproducible generation of the rich diversity of cell types present in the developing human cerebral cortex. This protocol is a modification of a previous method described by Kadoshima et al.[4]. We also include a detailed description of the protocol used to dissociate organoids into single cells for single-cell RNA-sequencing.

scholarly journals Plk4 triggers autonomous de novo centriole biogenesis and maturation

2020 ◽  
Author(s):  
Catarina Nabais ◽  
Delphine Pessoa ◽  
Jorge de-Carvalho ◽  
Thomas van Zanten ◽  
Paulo Duarte ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
De Novo ◽  
Cell Types ◽  
Proliferating Cells ◽  
Cycle Progression ◽  
Controlled System ◽  
Centriole Assembly ◽  
Critical Components ◽  
Kinetics Of

AbstractCentrioles form centrosomes and cilia. In most proliferating cells, centrioles assemble through canonical duplication, which is spatially, temporally and numerically regulated by the cell cycle and the presence of mature centrioles. However, in certain cell-types, centrioles assemble de novo, yet by poorly understood mechanisms. Here, we established a controlled system to investigate de novo centriole biogenesis, using Drosophila melanogaster egg explants overexpressing Polo-like kinase 4 (Plk4), a trigger for centriole biogenesis. We show that at high Plk4 concentration, centrioles form de novo, mature and duplicate, independently of cell cycle progression and of the presence of other centrioles. Plk4 concentration determines the kinetics of centriole assembly. Moreover, our results suggest Plk4 operates in a switch-like manner to control the onset of de novo centriole formation, and that distinct biochemical kinetics regulate de novo and canonical biogenesis. Finally, we investigated which other factors modulate de novo centriole assembly and reveal that proteins of the pericentriolar matrix (PCM) promote biogenesis, likely by locally concentrating critical components.

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