scholarly journals clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers

2018 ◽  
Author(s):  
Kieran R Campbell ◽  
Adi Steif ◽  
Emma Laks ◽  
Hans Zahn ◽  
Daniel Lai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cancer Cell ◽  
Cell Population ◽  
Rna Seq ◽  
Dna And Rna ◽  
Ovarian Cancer Cell Lines ◽  
Cell Population Growth ◽  
Cancer Cell Population ◽  
Scalable Methods

AbstractMeasuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we presentclonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We applyclonealignto triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.

scholarly journals Finsler-type estimators for the cancer cell population dynamics

2015 ◽  
Vol 98 (112) ◽  
pp. 53-69
Author(s):  
Vladimir Balan ◽  
Jelena Stojanov
Keyword(s):  
Dynamical System ◽  
Population Growth ◽  
Cancer Cell ◽  
Cell Population ◽  
Biological Models ◽  
Cell Population Dynamics ◽  
Finsler Structure ◽  
Cell Population Growth ◽  
Cancer Cell Population ◽  
The Difference

We introduce a Finslerian model related to the classical Garner dynamical system, which models the cancer cell population growth. The Finsler structure is determined by the energy of the deformation field-the difference of the fields, which describe the reduced and the proper biological models. It is shown that a certain locally-Minkowski anisotropic Randers structure, obtained by means of statistical fitting, is able to provide a Zermelo-type drift of the overall cancer cell population growth, which occurs due to significant changes within the cancerous process. The geometric background, the applicative advantages and perspective openings of the constructed geometric structure are discussed.

scholarly journals Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect

PLoS Biology ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. e3000399 ◽  
Author(s):  
Kaitlyn E. Johnson ◽  
Grant Howard ◽  
William Mo ◽  
Michael K. Strasser ◽  
Ernesto A. B. F. Lima ◽  
...  
Keyword(s):  
Population Growth ◽  
Cancer Cell ◽  
Cell Population ◽  
Growth Model ◽  
Growth Kinetics ◽  
Exponential Growth ◽  
Allee Effect ◽  
Cell Population Growth ◽  
Cancer Cell Population ◽  
Exponential Growth Model

Bulk and single-cell RNA-seq reveal dmrtb1 gene expression profiles during sex change in zig-zag eel (Mastacembelus armatus)

Aquaculture ◽  
2021 ◽  
pp. 737194
Author(s):  
Lingzhan Xue ◽  
Dan Jia ◽  
Luohao Xu ◽  
Zhen Huang ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Sex Change ◽  
Rna Seq ◽  
Mastacembelus Armatus

scholarly journals Simulation framework for generating intratumor heterogeneity patterns in a cancer cell population

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184229 ◽  
Author(s):  
Watal M. Iwasaki ◽  
Hideki Innan
Keyword(s):  
Cancer Cell ◽  
Cell Population ◽  
Intratumor Heterogeneity ◽  
Simulation Framework ◽  
Cancer Cell Population

scholarly journals Single cell RNA sequencing of calvarial and long bone endocortical cells

2019 ◽  
Author(s):  
Ugur M. Ayturk ◽  
Joseph P. Scollan ◽  
Alexander Vesprey ◽  
Christina M. Jacobsen ◽  
Paola Divieti Pajevic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cultured Cells ◽  
Neutralizing Antibody ◽  
Long Bone ◽  
Appendicular Skeleton ◽  
Rna Seq ◽  
Isolated Cells

ABSTRACTSingle cell RNA-seq (scRNA-seq) is emerging as a powerful technology to examine transcriptomes of individual cells. We determined whether scRNA-seq could be used to detect the effect of environmental and pharmacologic perturbations on osteoblasts. We began with a commonly used in vitro system in which freshly isolated neonatal mouse calvarial cells are expanded and induced to produce a mineralized matrix. We used scRNA-seq to compare the relative cell type abundances and the transcriptomes of freshly isolated cells to those that had been cultured for 12 days in vitro. We observed that the percentage of macrophage-like cells increased from 6% in freshly isolated calvarial cells to 34% in cultured cells. We also found that Bglap transcripts were abundant in freshly isolated osteoblasts but nearly undetectable in the cultured calvarial cells. Thus, scRNA-seq revealed significant differences between heterogeneity of cells in vivo and in vitro. We next performed scRNA-seq on freshly recovered long bone endocortical cells from mice that received either vehicle or Sclerostin-neutralizing antibody for 1 week. Bone anabolism-associated transcripts were also not significantly increased in immature and mature osteoblasts recovered from Sclerostin-neutralizing antibody treated mice; this is likely a consequence of being underpowered to detect modest changes in gene expression, since only 7% of the sequenced endocortical cells were osteoblasts, and a limited portion of their transcriptomes were sampled. We conclude that scRNA-seq can detect changes in cell abundance, identity, and gene expression in skeletally derived cells. In order to detect modest changes in osteoblast gene expression at the single cell level in the appendicular skeleton, larger numbers of osteoblasts from endocortical bone are required.

scholarly journals Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

2019 ◽  
Author(s):  
Marcus Alvarez ◽  
Elior Rahmani ◽  
Brandon Jew ◽  
Kristina M. Garske ◽  
Zong Miao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Types ◽  
Supervised Machine Learning ◽  
Data Sets ◽  
Rna Seq ◽  
Novel Approach ◽  
Single Nucleus ◽  
Downstream Analysis

AbstractSingle-nucleus RNA sequencing (snRNA-seq) measures gene expression in individual nuclei instead of cells, allowing for unbiased cell type characterization in solid tissues. Contrary to single-cell RNA seq (scRNA-seq), we observe that snRNA-seq is commonly subject to contamination by high amounts of extranuclear background RNA, which can lead to identification of spurious cell types in downstream clustering analyses if overlooked. We present a novel approach to remove debris-contaminated droplets in snRNA-seq experiments, called Debris Identification using Expectation Maximization (DIEM). Our likelihood-based approach models the gene expression distribution of debris and cell types, which are estimated using EM. We evaluated DIEM using three snRNA-seq data sets: 1) human differentiating preadipocytes in vitro, 2) fresh mouse brain tissue, and 3) human frozen adipose tissue (AT) from six individuals. All three data sets showed various degrees of extranuclear RNA contamination. We observed that existing methods fail to account for contaminated droplets and led to spurious cell types. When compared to filtering using these state of the art methods, DIEM better removed droplets containing high levels of extranuclear RNA and led to higher quality clusters. Although DIEM was designed for snRNA-seq data, we also successfully applied DIEM to single-cell data. To conclude, our novel method DIEM removes debris-contaminated droplets from single-cell-based data fast and effectively, leading to cleaner downstream analysis. Our code is freely available for use at https://github.com/marcalva/diem.

scholarly journals Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

2019 ◽  
Author(s):  
Wei Wang ◽  
Gang Ren ◽  
Ni Hong ◽  
Wenfei Jin
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Cell ◽  
Zinc Finger ◽  
Ctcf Binding ◽  
Rna Seq ◽  
Expression Noise ◽  
Genome Wide ◽  
Cell Variation ◽  
Variable Genes

Abstract Background: CCCTC-Binding Factor (CTCF), also known as 11-zinc finger protein, participates in many cellular processes, including insulator activity, transcriptional regulation and organization of chromatin architecture. Based on single cell flow cytometry and single cell RNA-FISH analyses, our previous study showed that deletion of CTCF binding site led to a significantly increase of cellular variation of its target gene. However, the effect of CTCF on genome-wide landscape of cell-to-cell variation is unclear. Results: We knocked down CTCF in EL4 cells using shRNA, and conducted single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells using Fluidigm C1 system. Principal component analysis of single cell RNA-seq data showed that WT and CTCF-KD cells concentrated in two different clusters on PC1, indicating gene expression profiles of WT and CTCF-KD cells were systematically different. Interestingly, GO terms including regulation of transcription, DNA binding, Zinc finger and transcription factor binding were significantly enriched in CTCF-KD-specific highly variable genes, indicating tissue-specific genes such as transcription factors were highly sensitive to CTCF level. The dysregulation of transcription factors potentially explain why knockdown of CTCF lead to systematic change of gene expression. In contrast, housekeeping genes such as rRNA processing, DNA repair and tRNA processing were significantly enriched in WT-specific highly variable genes, potentially due to a higher cellular variation of cell activity in WT cells compared to CTCF-KD cells. We further found cellular variation-increased genes were significantly enriched in down-regulated genes, indicating CTCF knockdown simultaneously reduced the expression levels and increased the expression noise of its regulated genes. Conclusions: To our knowledge, this is the first attempt to explore genome-wide landscape of cellular variation after CTCF knockdown. Our study not only advances our understanding of CTCF function in maintaining gene expression and reducing expression noise, but also provides a framework for examining gene function.

scholarly journals Comprehensive Quantification of Gene Expression Fluctuation by Single-cell RNA-seq

2016 ◽  
Vol 56 (6) ◽  
pp. 330-333
Author(s):  
Itoshi NIKAIDO
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Seq

scholarly journals Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

2018 ◽  
Vol 20 (4) ◽  
pp. 1583-1589 ◽  
Author(s):  
Shun H Yip ◽  
Pak Chung Sham ◽  
Junwen Wang
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Differentially Expressed Gene ◽  
Embryonic Stem ◽  
Rna Seq ◽  
Software Packages ◽  
Homogeneous Cell ◽  
Variable Gene ◽  
Cell Variation ◽  
Larger Sample

Abstract Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

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