scholarly journals Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karsten Bach ◽  
Sara Pensa ◽  
Marija Zarocsinceva ◽  
Katarzyna Kania ◽  
Julie Stockis ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Genetically Engineered ◽  
Cell Of Origin ◽  
Loss Of Function ◽  
Time Resolved ◽  
Genetically Engineered Mouse Models ◽  
Tumour Formation ◽  
Luminal Progenitor Cell ◽  
Single Cell Profiling

AbstractIt is unclear how genetic aberrations impact the state of nascent tumour cells and their microenvironment. BRCA1 driven triple negative breast cancer (TNBC) has been shown to arise from luminal progenitors yet little is known about how BRCA1 loss-of-function (LOF) and concomitant mutations affect the luminal progenitor cell state. Here we demonstrate how time-resolved single-cell profiling of genetically engineered mouse models before tumour formation can address this challenge. We found that perturbing Brca1/p53 in luminal progenitors induces aberrant alveolar differentiation pre-malignancy accompanied by pro-tumourigenic changes in the immune compartment. Unlike alveolar differentiation during gestation, this process is cell autonomous and characterised by the dysregulation of transcription factors driving alveologenesis. Based on our data we propose a model where Brca1/p53 LOF inadvertently promotes a differentiation program hardwired in luminal progenitors, highlighting the deterministic role of the cell-of-origin and offering a potential explanation for the tissue specificity of BRCA1 tumours.

Digitonin-facilitated delivery of imaging probes enables single-cell analysis of AKT signalling activities in suspension cells

The Analyst ◽  
2021 ◽  
Author(s):  
Siwen Wang ◽  
Nicole G. Perkins ◽  
Fei Ji ◽  
Rohit Chaudhuri ◽  
Zhili Guo ◽  
...  
Keyword(s):  
Single Cell ◽  
Cyclic Peptide ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Suspension Cells ◽  
Time Resolved ◽  
Imaging Probes ◽  
Single Cell Profiling

Digitonin allows the delivery of cyclic peptide-based imaging probes into suspension cells. This method enables time-resolved single-cell profiling of AKT signalling activities.

scholarly journals ATRT-13. DIFFERENT CELLS OF ORIGIN PAVE THE WAY FOR MOLECULAR HETEROGENEITY IN RHABDOID TUMORS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii278-iii278
Author(s):  
Monika Graf ◽  
Marta Interlandi ◽  
Natalia Moreno ◽  
Dörthe Holdhof ◽  
Viktoria Melcher ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
Time Frame ◽  
Precursor Cells ◽  
Genetically Engineered ◽  
Molecular Heterogeneity ◽  
Loss Of Function ◽  
Cellular Origin ◽  
Cells Of Origin ◽  
Rhabdoid Tumors

Abstract Rhabdoid tumors (RT) are rare but highly aggressive pediatric neoplasms. These tumors carry homozygous loss-of-function alterations of SMARCB1 in almost all cases with an otherwise low mutational load. RT arise at different intracranial (ATRT) as well as extracranial (MRT) anatomical sites. Three main molecular subgroups (ATRT-SHH, ATRT-TYR, ATRT-MYC) have been characterized for ATRT which are epigenetically and clinically diverse, while MRT show remarkable similarities with ATRT-MYC distinct from ATRT-SHH and ATRT-TYR. Even though there are hypotheses about various cells of origin among RT subgroups, precursor cells of RT have not yet been identified. Previous studies on the temporal control of SMARCB1 knockout in genetically engineered mouse models have unveiled a tight vulnerable time frame during embryogenesis with regard to the susceptibility of precursor cells to result in RT. In this study, we employed single-cell RNA sequencing to describe the intra- and intertumoral heterogeneity of murine ATRT-SHH and -MYC as well as extracranial MYC tumor cells. We defined subgroup-specific tumor markers for all RT classes but also observed a notable overlap of gene expression patterns in all MYC subgroups. By comparing these single-cell transcriptomes with available single-cell maps of early embryogenesis, we gained first insights into the cellular origin of RT. Finally, unsupervised clustering of published human RT methylation data and healthy control tissues confirmed the existence of different cells of origin for intracranial SHH tumors and MYC tumors independent of their anatomical localizations.

scholarly journals ETMR-06. DISSECTING THE MOLECULAR AND DEVELOPMENTAL BASIS OF PINEOBLASTOMA THROUGH GENOMICS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii323-iii324
Author(s):  
Brian Gudenas ◽  
Bernhard Englinger ◽  
Anthony P Y Liu ◽  
Yiai Tong ◽  
David Meredith ◽  
...  
Keyword(s):  
Pineal Gland ◽  
Single Cell ◽  
Outcome Data ◽  
Genetically Engineered ◽  
Developmental Trajectory ◽  
Transcriptional Analysis ◽  
Molecular Heterogeneity ◽  
Developmental Origins ◽  
Cell Of Origin ◽  
Molecular Features

Abstract Pineoblastoma (PB) is an aggressive embryonal brain tumor comprising 1% of pediatric CNS tumors. The clinico-molecular heterogeneity and developmental origins underlying PB are poorly understood; therefore, we have assembled a molecular cohort of histologically defined PBs (n=43) with corresponding outcome data. Methylation profiling revealed four molecularly and clinically distinct PB subgroups, including two novel entities. Mutational and transcriptional analysis identified characteristic molecular features of each subgroup, such as mutations in the miRNA processing pathway or FOXR2 proto-oncogene overexpression. Furthermore, subgroups exhibited differences in propensity for metastasis, cytogenetics, and clinical outcomes. To dissect PB developmental origins and resolve PB subgroup biology, we have employed a combination of single-cell genomics and genetically engineered mouse modeling. We created a single-cell transcriptional atlas of the developing murine pineal gland across 11 timepoints and are currently integrating these data with single nuclei RNA-seq data of human PB (n=25). Single-cell analysis of the developing pineal gland revealed three distinct populations of pinealocytes, referred to as early, mid and late pinealocytes, which segregate by developmental stage yet lie along a single developmental trajectory. Preliminary results implicate significant associations between PBs and the early pinealocyte population as well as subgroup-specific differences in intratumoral heterogeneity. Furthermore, this knowledge has informed the downstream generation of biologically faithful disease models, including a transgenic mouse model of the PB-RB subgroup. Remarkably, this model shows up-regulation of key markers of PB such as Crx, Asmt and Otx2 and substantiates early pinealocytes as the probable cell-of-origin for this PB subgroup.

Highly efficient single-cell analysis of microbial cells by time-resolved inductively coupled plasma mass spectrometry

2014 ◽  
Vol 29 (9) ◽  
pp. 1598-1606 ◽  
Author(s):  
Shin-ichi Miyashita ◽  
Alexander S. Groombridge ◽  
Shin-ichiro Fujii ◽  
Ayumi Minoda ◽  
Akiko Takatsu ◽  
...  
Keyword(s):  
Single Cell ◽  
Inductively Coupled Plasma ◽  
Single Cell Analysis ◽  
High Time Resolution ◽  
Time Resolved ◽  
Microbial Cells ◽  
Inductively Coupled ◽  
Highly Efficient ◽  
Icp Ms ◽  
Plasma Mass Spectrometry

Highly efficient single-cell elemental analysis of microbial cells was achieved using a developed ICP-MS system with approximately 100% cell introduction efficiency and high time resolution.

scholarly journals Modular transcriptional programs separately define axon and dendrite connectivity

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yerbol Z Kurmangaliyev ◽  
Juyoun Yoo ◽  
Samuel A LoCascio ◽  
S Lawrence Zipursky
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Transcriptional Control ◽  
Surface Proteins ◽  
Synaptic Connectivity ◽  
Loss Of Function ◽  
Neuronal Connectivity ◽  
Cell Surface Proteins ◽  
Single Cell Rna Sequencing ◽  
Single Cell Profiling

Patterns of synaptic connectivity are remarkably precise and complex. Single-cell RNA sequencing has revealed a vast transcriptional diversity of neurons. Nevertheless, a clear logic underlying the transcriptional control of neuronal connectivity has yet to emerge. Here, we focused on Drosophila T4/T5 neurons, a class of closely related neuronal subtypes with different wiring patterns. Eight subtypes of T4/T5 neurons are defined by combinations of two patterns of dendritic inputs and four patterns of axonal outputs. Single-cell profiling during development revealed distinct transcriptional programs defining each dendrite and axon wiring pattern. These programs were defined by the expression of a few transcription factors and different combinations of cell surface proteins. Gain and loss of function studies provide evidence for independent control of different wiring features. We propose that modular transcriptional programs for distinct wiring features are assembled in different combinations to generate diverse patterns of neuronal connectivity.

scholarly journals Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Chee Wai Chua ◽  
Nusrat J Epsi ◽  
Eva Y Leung ◽  
Shouhong Xuan ◽  
Ming Lei ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Progenitor Cells ◽  
Neuroendocrine Differentiation ◽  
Tumor Formation ◽  
Genetically Engineered ◽  
Cell Of Origin ◽  
Genetically Engineered Mouse Models ◽  
Pten Deletion ◽  
A Cell

Master regulatory genes of tissue specification play key roles in stem/progenitor cells and are often important in cancer. In the prostate, androgen receptor (AR) is a master regulator essential for development and tumorigenesis, but its specific functions in prostate stem/progenitor cells have not been elucidated. We have investigated AR function in CARNs (CAstration-Resistant Nkx3.1-expressing cells), a luminal stem/progenitor cell that functions in prostate regeneration. Using genetically--engineered mouse models and novel prostate epithelial cell lines, we find that progenitor properties of CARNs are largely unaffected by AR deletion, apart from decreased proliferation in vivo. Furthermore, AR loss suppresses tumor formation after deletion of the Pten tumor suppressor in CARNs; however, combined Pten deletion and activation of oncogenic Kras in AR-deleted CARNs result in tumors with focal neuroendocrine differentiation. Our findings show that AR modulates specific progenitor properties of CARNs, including their ability to serve as a cell of origin for prostate cancer.

scholarly journals Sandwich cortical lamination and single-cell analysis decodes the developing spatial processing system

2019 ◽  
Author(s):  
Yong Liu ◽  
Tobias Bergmann ◽  
Julie Lee ◽  
Ulrich Pfisterer ◽  
Louis-Francois Handfield ◽  
...  
Keyword(s):  
Single Cell ◽  
Entorhinal Cortex ◽  
Pyramidal Neurons ◽  
Single Cell Analysis ◽  
Processing System ◽  
Cell Types ◽  
Inhibitory Neurons ◽  
Spatial Processing ◽  
Single Cell Profiling ◽  
Perception Of Time

SummaryThe entorhinal cortex consists of several important cell types including, the grid cells, speed cells, border cells and head-direction cells and is important for memory, spatial navigation and perception of time. Here, we trace in detail the development of the entorhinal cortex. Using single-cell profiling we provide unique transcriptional signatures for glia, excitatory and inhibitory neurons existing in the region, including RELN+ cells in layer (L) II and superficial pyramidal neurons. We identified a sandwich layered cortex, where LII emerges prior to LIII and superficial cells maintain a deep layer molecular identity after birth. Our findings contribute to the understanding of the formation of the brain’s cognitive memory and spatial processing system and provides insight into the transcriptional identity and spatial position of the entorhinal cells.

scholarly journals SAVER: Gene expression recovery for UMI-based single cell RNA sequencing

2017 ◽  
Author(s):  
Mo Huang ◽  
Jingshu Wang ◽  
Eduardo Torre ◽  
Hannah Dueck ◽  
Sydney Shaffer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cell Analysis ◽  
Specific Gene ◽  
Recovery Method ◽  
Single Cell Rna Sequencing ◽  
Cell Gene Expression ◽  
Single Cell Profiling ◽  
Downstream Analysis

AbstractRapid advances in massively parallel single cell RNA sequencing (scRNA-seq) is paving the way for high-resolution single cell profiling of biological samples. In most scRNA-seq studies, only a small fraction of the transcripts present in each cell are sequenced. The efficiency, that is, the proportion of transcripts in the cell that are sequenced, can be especially low in highly parallelized experiments where the number of reads allocated for each cell is small. This leads to unreliable quantification of lowly and moderately expressed genes, resulting in extremely sparse data and hindering downstream analysis. To address this challenge, we introduce SAVER (Single-cell Analysis Via Expression Recovery), an expression recovery method for scRNA-seq that borrows information across genes and cells to impute the zeros as well as to improve the expression estimates for all genes. We show, by comparison to RNA fluorescence in situ hybridization (FISH) and by data down-sampling experiments, that SAVER reliably recovers cell-specific gene expression concentrations, cross-cell gene expression distributions, and gene-to-gene and cell-to-cell correlations. This improves the power and accuracy of any downstream analysis involving genes with low to moderate expression.

scholarly journals UHRF1 drives the poor prognosis associated with RB loss in osteosarcoma

2020 ◽  
Author(s):  
Stephanie C. Wu ◽  
Jocelyne Lopez ◽  
Kelsey Salcido ◽  
Loredana Zocchi ◽  
Jie Wu ◽  
...  
Keyword(s):  
Poor Prognosis ◽  
Ring Finger ◽  
Current Treatment ◽  
Genetically Engineered ◽  
Loss Of Function ◽  
Genetically Engineered Mouse Models ◽  
Downstream Effector ◽  
Downstream Effectors ◽  
Type Plasminogen Activator ◽  
Poor Therapeutic Outcome

ABSTRACTLoss of function mutations at the retinoblastoma (RB1) gene are associated with increased mortality, metastasis and poor therapeutic outcome in several cancers, including osteosarcoma. However, the mechanism(s) through which RB1 loss worsens clinical outcome remain to be elucidated. Ubiquitin-like with PHD and Ring Finger domains 1 (UHRF1) has been identified as a critical downstream effector of the RB/E2F signaling pathway that is overexpressed in various cancers. Here, we show that UHRF1 upregulation is critical in rendering osteosarcoma cells more aggressive. We confirmed that UHRF1 is transcriptionally regulated by the RB/E2F pathway and overexpressed in osteosarcoma. Using novel genetically engineered mouse models, we determined that Uhrf1 loss dramatically reverses the effects of Rb1 loss. Based on gain- and loss-of-function assays, we report that UHRF1 promotes cell proliferation, migration, invasion, and metastasis. Furthermore, transcriptome analyses revealed the involvement of urokinase-type plasminogen activator (uPA) in UHRF1-mediated cell mobility. Our work presents a new mechanistic insight into RB1 loss-associated poor prognosis, revealing UHRF1 as a critical driver of tumor promotion, progression, and metastasis in osteosarcoma. This study provides substantial support for targeting UHRF1 or its downstream effectors as novel therapeutic options to improve current treatment for osteosarcoma and other cancers with RB/E2F pathway inactivation.

scholarly journals EPCO-12. SINGLE CELL PROFILING OF LONG NON-CODING RNAS IN GLIOMA

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii71-ii71
Author(s):  
Bharati Mehani ◽  
Hye-Jung Chung ◽  
Russell Bandle ◽  
Sarah Young ◽  
Michael Kelly ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Glioma Cells ◽  
Specific Expression ◽  
Lncrna Expression ◽  
Tumor Tissues ◽  
Single Cell Profiling ◽  
Non Coding Rnas ◽  
And Migration ◽  
Cell Data

Abstract Non-coding RNAs have critical functions across biological processes that regulate glioma initiation and progression, and deregulated expression of long non-coding RNAs (lncRNAs) have been implicated in the onset and progression of malignancies. The majority of these transcripts exhibit tissue- and cancer-specific expression but little has been investigated at the single-cell level. We performed single cell RNA Sequencing (10x Genomics) for 9 IDH-wild-type glioblastomas from 7 patients. In total 66,825 cells dissociated from tumor tissues and not sorted were included in this analysis which encompassed 41,989 mean sequencing reads and 2,619 median coding genes per cell. Single cell analysis of lncRNAs in captured 190 median lncRNAs per cell and demonstrated a distinct lncRNA expression profile for glioma cells compared to the non-tumor cells with SOX2-OT significantly upregulated (2X) in glioma cells. Consistent with this finding, SOX2-OT is known to be overexpressed in a variety of cancers and has been previously implicated in glioma proliferation and migration. We then examined patterns of lncRNA expression in GBM expression subtypes. Subtype correlation indicated overexpression of RMST (classical subtype), PCED1B-AS1 (mesenchymal) and LINC00689 (proneural) lncRNAs in these expression subtypes. Consistent with these findings, upregulation of each of these 3 lncRNAs have previously been implicated on pro-tumorigenic effects, including in glioma. Examination of an independent published single cell GBM dataset also validated PCED1B-AS1 in the mesenchymal subtype. Comparison with bulk tumor GBM profiles (IDHwt TCGA GBM dataset) also showed correlations with the expression of RMST, PCED1B-AS1 and LINC00689 lncRNAs in the classical, mesenchymal and proneural subtypes respectively. Overall, these results indicate lncRNA expression can be determined in 10x-generated glioma single cell data and may reveal additional insights about cellular state and glioma biology.

Sign in / Sign up

Export Citation Format

Share Document