scholarly journals Single Cell Clones Derived from a Patient's AML Xenograft Display Genetic and Functional Heterogeneity

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1450-1450
Author(s):  
Christina Maria Zeller ◽  
Daniel Richter ◽  
Binje Vick ◽  
Tobias Herold ◽  
Johannes Bagnoli ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Multiple Hypothesis Testing ◽  
Targeted Sequencing ◽  
Functional Heterogeneity ◽  
Nras Mutation ◽  
In Vivo Experiments ◽  
Cell Clones

Introduction: Acute myeloid leukemia (AML) shows substantial genetic and epigenetic heterogeneity, even within an individual patient. Due to treatment resistance and ability to induce relapse, adverse subclones present a major clinical challenge in determining the patient's prognosis. Here, we aimed at characterizing the genetic and functional heterogeneity within a single AML patient, and at identifying adverse subclones that result in therapy failure or give rise to relapse. Methods: Leukemic cells from an AML patient at first and second relapse were transplanted into immuno-compromised mice to generate patient-derived xenografts (PDX). PDX AML cells allowed serial transplantation and genetic engineering by lentiviruses. To distinguish single cells and generate PDX AML clones derived from a single cell (single cell clones, SCC), cells were transduced with a genetic barcode and transplanted into recipient mice near leukemia initiating cell frequency. Resulting SCC were genetically marked to express recombinant fluorochromes to enable flow cytometry analysis. All SCC were characterized for known subclonal mutations of the AML patient by targeted sequencing. Additionally, transcriptome and methylome analysis were performed by SCRB-seq and methylation array, respectively. Results: We successfully generated thirteen serially transplantable PDX SCC from a single AML patient, expressing combinations of up to four fluorochromes to enable competitive in vitro and in vivo experiments. In targeted sequencing, we found that SCC originated from at least four genetically distinct AML subclones and were distinguished by mutations in KRAS (4/13), NRAS (5/13), EZH2 (2/13) or EZH2 and NRAS (2/13). While the NRAS mutation was detected in a minority of bulk cells over serial passages (<10%) from both the first and second relapse, 50% of SCC carried the NRAS mutation. This indicates that NRAS mutated AML cells have an increased stem cell capacity upon transplantation of low cell numbers. Transcriptome analysis revealed 442 genes as differentially expressed between SCC and up to four biological replicates after adjustment for multiple hypothesis testing. Unsupervised clustering demonstrated a strong correlation of gene expression profiles with the respective genotype. In competitive in vivo experiments, homing capability was comparable between the four genetically distinct subclones. However, 2/2 EZH2-mutated SCC overgrew all other clones showing a clear growth advantage within two weeks of in vivo growth. The EZH2-mutated SCC (2/2) were resistant towards in vivo treatment with Cytarabine, whereas the KRAS (4/4), NRAS (5/5) mutated as well as the EZH2 and NRAS double-mutated SCC (2/2) responded to treatment. Conclusion: Taken together, we experimentally prove the existence of genetically and functionally diverse subclones within an individual AML sample. Our approach allows not only genetic, but also functional in vitro and in vivo characterization of adverse subclones. Our approach can be used to identify novel therapeutic approaches in order to specifically target the most adverse cells within patients' AML sample. Disclosures Metzeler: Celgene: Honoraria, Research Funding; Daiichi Sankyo: Honoraria; Otsuka: Honoraria.

scholarly journals A qPCR method for genome editing efficiency determination and single-cell clone screening in human cells

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo Li ◽  
Naixia Ren ◽  
Lele Yang ◽  
Junhao Liu ◽  
Qilai Huang
Keyword(s):  
Single Cell ◽  
Genome Editing ◽  
Cell Clone ◽  
Editing Efficiency ◽  
Base Editing ◽  
Single Cell Clone ◽  
Cell Clones ◽  
Nucleotide Mismatch

AbstractCRISPR/Cas9 technology has been widely used for targeted genome modification both in vivo and in vitro. However, an effective method for evaluating genome editing efficiency and screening single-cell clones for desired modification is still lacking. Here, we developed this real time PCR method based on the sensitivity of Taq DNA polymerase to nucleotide mismatch at primer 3′ end during initiating DNA replication. Applications to CRISPR gRNAs targeting EMX1, DYRK1A and HOXB13 genes in Lenti-X 293 T cells exhibited comprehensive advantages. Just in one-round qPCR analysis using genomic DNA from cells underwent CRISPR/Cas9 or BE4 treatments, the genome editing efficiency could be determined accurately and quickly, for indel, HDR as well as base editing. When applied to single-cell clone screening, the genotype of each cell colony could also be determined accurately. This method defined a rigorous and practical way in quantify genome editing events.

scholarly journals Single Cell RNA-Seq Characterises Pre-Leukemic Transformation Driven By CEBPA N321D in the Hoxb8-FL Cell Line

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3887-3887
Author(s):  
Moosa Qureshi ◽  
Fernando Calero-Nieto ◽  
Iwo Kucinski ◽  
Sarah Kinston ◽  
George Giotopoulos ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Single Cell ◽  
Cell Line ◽  
Single Cells ◽  
Mutant Form ◽  
Rna Seq ◽  
Wild Type ◽  
Leukemic Transformation

Abstract The C/EBPα transcription factor plays a pivotal role in myeloid differentiation and E2F-mediated cell cycle regulation. Although CEBPA mutations are common in acute myeloid leukaemia (AML), little is known regarding pre-leukemic alterations caused by mutated CEBPA. Here, we investigated early events involved in pre-leukemic transformation driven by CEBPA N321D in the LMPP-like cell line Hoxb8-FL (Redecke et al., Nat Methods 2013), which can be maintained in vitro as a self-renewing LMPP population using Flt3L and estradiol, as well as differentiated both in vitro and in vivo into myeloid and lymphoid cell types. Hoxb8-FL cells were retrovirally transduced with Empty Vector (EV), wild-type CEBPA (CEBPA WT) or its N321D mutant form (CEBPA N321D). CEBPA WT-transduced cells showed increased expression of cd11b and SIRPα and downregulation of c-kit, suggesting that wild-type CEBPA was sufficient to promote differentiation even under LMPP growth conditions. Interestingly, we did not observe the same phenotype in CEBPA N321D-transduced cells. Upon withdrawal of estradiol, both EV and CEBPA WT-transduced cells differentiated rapidly into a conventional dendritic cell (cDC) phenotype by day 7 and died within 12 days. By contrast, CEBPA N321D-transduced cells continued to grow for in excess of 56 days, with an initial cDC phenotype but by day 30 demonstrating a plasmacytoid dendritic cell precursor phenotype. CEBPA N321D-transduced cells were morphologically distinct from EV-transduced cells. To test leukemogenic potential in vivo, we performed transplantation experiments in lethally irradiated mice. Serial monitoring of peripheral blood demonstrated that Hoxb8-FL derived cells had disappeared by 4 weeks, and did not reappear. However, at 6 months CEBPA N321D-transduced cells could still be detected in bone marrow in contrast to EV-transduced cells but without any leukemic phenotype. To identify early events involved in pre-leukemic transformation, the differentiation profiles of EV, CEBPA WT and CEBPA N321D-transduced cells were examined with single cell RNA-seq (scRNA-seq). 576 single cells were taken from 3 biological replicates at days 0 and 5 post-differentiation, and analysed using the Automated Single-Cell Analysis Pipeline (Gardeux et al., Bioinformatics 2017). Visualisation by t-SNE (Fig 1) demonstrated: (i) CEBPA WT-transduced cells formed a distinct cluster at day 0 before withdrawal of estradiol; (ii) CEBPA N321D-transduced cells separated from EV and CEBPA WT-transduced cells after 5 days of differentiation, (iii) two subpopulations could be identified within the CEBPA N321D-transduced cells at day 5, with a cluster of five CEBPA N321D-transduced single cells distributed amongst or very close to the day 0 non-differentiated cells. Differential expression analysis identified 224 genes upregulated and 633 genes downregulated specifically in the CEBPA N321D-transduced cells when compared to EV cells after 5 days of differentiation. This gene expression signature revealed that CEBPA N321D-transduced cells switched on a HSC/MEP/CMP transcriptional program and switched off a myeloid dendritic cell program. Finally, in order to further dissect the effect of the N321D mutation, the binding profile of endogenous and CEBPA N321D was compared by ChIP-seq before and after 5 days of differentiation. Integration with scRNA-seq data identified 160 genes specifically downregulated in CEBPA N321D-transduced cells which were associated with the binding of the mutant protein. This list of genes included genes previously implicated in dendritic cell differentiation (such as NOTCH2, JAK2), as well as a number of genes not previously implicated in the evolution of AML, representing potentially novel therapeutic targets. Disclosures No relevant conflicts of interest to declare.

scholarly journals Single-cell RNA-seq revealed the role of Alkbh5 in reproduction

2021 ◽  
Author(s):  
Xiaozhong Shen ◽  
Gangcai Xie
Keyword(s):  
Single Cell ◽  
Messenger Rna ◽  
Single Cells ◽  
Rna Seq ◽  
Single Cell Sequencing ◽  
Differential Gene ◽  
Higher Eukaryotes

AbstractN(6)-methyladenosine (m(6)a) is the most common internal modification of messenger RNA (mRNA) in higher eukaryotes. According to previous literature reports, alkbh5, as another demethylase in mammals, can reverse the expression of m(6)a gene in vivo and in vitro. In order to reveal the effect of Alkbh5 deletion on the level of single cells in the testis during spermatogenesis in mice, the data were compared using single-cell sequencing. In this article, we discussed the transcription profile and cell type identification of mouse testis, the expression of mitochondrial and ribosomal genes in mice, the analysis of differential gene expression, and the effects of Alkbh5 deletion, and try to explain the role and influence of Alkbh5 on reproduction at the level of single-cell sequencing.

scholarly journals Injury-Free In Vivo Delivery and Engraftment into the Cornea Endothelium Using Extracellular Matrix Shrink-Wrapped Cells

2021 ◽  
Author(s):  
Rachelle N. Palchesko ◽  
Yiqin Du ◽  
Moira L. Geary ◽  
Santiago Carrasquilla ◽  
Daniel J. Shiwarski ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Single Cells ◽  
Tissue Level ◽  
Cell Junctions ◽  
Small Island ◽  
Corneal Endothelial Cells ◽  
Corneal Blindness

AbstractCell injection has emerged as a widespread approach for therapeutic delivery of healthy cells into diseased and damaged tissues to achieve regeneration. However, cell retention, viability and integration at the injection site has generally been poor, driving the need for improved approaches. Additionally, it is unknown how efficiently single cells can integrate and repair tissue level function. Here we have developed a technique to address these issues by engineering islands of interconnected cells on ECM nanoscaffolds that can be non-destructively released from the surface via thermal dissolution of the underlying thermo-responsive polymer. Upon dissolution of the polymer, the ECM nanoscaffold shrink-wraps around the small island of cells, creating a small patch of cells that maintain their cell-cell junctions and cytoskeletal structure throughout collection, centrifugation and injection that we have termed μMonolayers. These μMonolayers were made with corneal endothelial cells, as a model system, as single cell injections of corneal endothelial cells have been used with some success clinically to treat corneal blindness. In vitro our μMonolayers exhibited increased integration compared to single cells into low density corneal endothelial monolayers and in vivo into the high-density healthy rabbit corneal endothelium. These results indicate that this technique could be used to increase the integration of healthy cells into existing tissues to treat not only corneal blindness, but also other conditions such as cystic fibrosis, myocardial infarction, diabetes, etc.One Sentence SummarySmall monolayers of interconnected endothelial cells are shrinkwrapped in a thin layer of ECM and exhibit enhanced adhesion and integration in vivo compared to single cell suspensions.

scholarly journals Puromycin reactivity does not accurately localize translation at the subcellular level

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Syed Usman Enam ◽  
Boris Zinshteyn ◽  
Daniel H Goldman ◽  
Madeline Cassani ◽  
Nathan M Livingston ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Single Cell ◽  
In Vivo Experiments ◽  
Cell Assays ◽  
Translation Inhibitor ◽  
Polypeptide Chains ◽  
Subcellular Level ◽  
Biology Research

Puromycin is a tyrosyl-tRNA mimic that blocks translation by labeling and releasing elongating polypeptide chains from translating ribosomes. Puromycin has been used in molecular biology research for decades as a translation inhibitor. The development of puromycin antibodies and derivatized puromycin analogs has enabled the quantification of active translation in bulk and single-cell assays. More recently, in vivo puromycylation assays have become popular tools for localizing translating ribosomes in cells. These assays often use elongation inhibitors to purportedly inhibit the release of puromycin-labeled nascent peptides from ribosomes. Using in vitro and in vivo experiments in various eukaryotic systems, we demonstrate that, even in the presence of elongation inhibitors, puromycylated peptides are released and diffuse away from ribosomes. Puromycylation assays reveal subcellular sites, such as nuclei, where puromycylated peptides accumulate post-release and which do not necessarily coincide with sites of active translation. Our findings urge caution when interpreting puromycylation assays in vivo.

scholarly journals Vimentin fibers orient traction stress

2017 ◽  
Vol 114 (20) ◽  
pp. 5195-5200 ◽  
Author(s):  
Nancy Costigliola ◽  
Liya Ding ◽  
Christoph J. Burckhardt ◽  
Sangyoon J. Han ◽  
Edgar Gutierrez ◽  
...  
Keyword(s):  
Cell Migration ◽  
Single Cell ◽  
Graph Matching ◽  
Single Cells ◽  
Mechanical Strain ◽  
Migration Direction ◽  
Human Foreskin Fibroblasts ◽  
And Migration

The intermediate filament vimentin is required for cells to transition from the epithelial state to the mesenchymal state and migrate as single cells; however, little is known about the specific role of vimentin in the regulation of mesenchymal migration. Vimentin is known to have a significantly greater ability to resist stress without breaking in vitro compared with actin or microtubules, and also to increase cell elasticity in vivo. Therefore, we hypothesized that the presence of vimentin could support the anisotropic mechanical strain of single-cell migration. To study this, we fluorescently labeled vimentin with an mEmerald tag using TALEN genome editing. We observed vimentin architecture in migrating human foreskin fibroblasts and found that network organization varied from long, linear bundles, or “fibers,” to shorter fragments with a mesh-like organization. We developed image analysis tools employing steerable filtering and iterative graph matching to characterize the fibers embedded in the surrounding mesh. Vimentin fibers were aligned with fibroblast branching and migration direction. The presence of the vimentin network was correlated with 10-fold slower local actin retrograde flow rates, as well as spatial homogenization of actin-based forces transmitted to the substrate. Vimentin fibers coaligned with and were required for the anisotropic orientation of traction stresses. These results indicate that the vimentin network acts as a load-bearing superstructure capable of integrating and reorienting actin-based forces. We propose that vimentin's role in cell motility is to govern the alignment of traction stresses that permit single-cell migration.

Single-Cell Analysis of Lymphoid-Primed Multipotent Progenitors (LMPPs) Reveal Alterations in Lineage Commitment during Aging

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 244-244
Author(s):  
Sneha Borikar ◽  
Vivek Philip ◽  
Jennifer J. Trowbridge
Keyword(s):  
Single Cell ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Progenitor Cell ◽  
Conflicts Of Interest ◽  
Single Cells ◽  
Differentiation Potential ◽  
Increased Risk

Abstract During aging, the hematopoietic compartment undergoes lineage skewing, biased toward myeloid differentiation at the expense of lymphoid differentiation. This skewing clinically presents as impaired adaptive immunity and an increased risk of myeloproliferative disorders. However, little is known of the regulatory mechanisms underlying these changes in differentiation potential due in part to the inadequacy of current analytic techniques to evaluate lineage potency of individual progenitor cells. Recent demonstration that long-lived hematopoietic progenitor cells drive steady-state hematopoiesis has shifted focus onto the progenitor cell compartment to understand clonal dynamics of native hematopoiesis. Here, we critically assess the functional and molecular alterations in the multipotent progenitor cell pool with aging at the single-cell level. We developed novel in vitro and in vivo assays to define the heterogeneity of the LMPP population and test cell-fate potential from single cells. Our results demonstrate, for the first time, distinct, intrinsic lineage potential of single in vitro LMPPs at the cellular and molecular level. We find that clonal alterations in the lymphoid-primed multipotent progenitor (LMPP) compartment contributes to the functional alterations in hematopoiesis observed during aging. Unbiased single-cell transcriptome analysis reveals that true multipotential clones and lymphoid-restricted clones are reduced with aging, while bipotential and myeloid-restricted clones are modestly expanded. Furthermore, myeloid-restricted clones gain myc driver signatures, molecularly identifying clones emerging during aging that are susceptible to transformation. Our study reveals that aging alters the clonal composition of multipotential progenitor cells, directly contributing to the global loss of the lymphoid compartment and increased susceptibility to myeloid transformation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Oscillation between B-lymphoid and myeloid lineages in Myc-induced hematopoietic tumors following spontaneous silencing/reactivation of the EBF/Pax5 pathway

Blood ◽  
2003 ◽  
Vol 101 (5) ◽  
pp. 1950-1955 ◽  
Author(s):  
Duonan Yu ◽  
David Allman ◽  
Michael H. Goldschmidt ◽  
Michael L. Atchison ◽  
John G. Monroe ◽  
...  
Keyword(s):  
B Cell ◽  
Single Cell ◽  
Target Genes ◽  
Myeloid Differentiation ◽  
Target Cells ◽  
Cell Clones ◽  
B Lymphoid ◽  
Secondary Lymphoma

B lymphomagenesis is an uncontrolled expansion of immature precursors that fail to complete their differentiation program. This failure could be at least partly explained by inappropriate expression of several oncogenic transcription factors, such as Pax5 and Myc. Both Pax5 and c-Myc are implicated in the pathogenesis of non-Hodgkin lymphomas. To address their role in lymphomagenesis, we analyzed B-cell lymphomas derived from p53-null bone marrow progenitors infected in vivo by a Myc-encoding retrovirus. All Myc-induced lymphomas invariably maintained expression of Pax5, which is thought to be incompatible with terminal differentiation. However, upon culturing in vitro, several cell lines spontaneously down-regulated Pax5 and its target genes CD19, N-Myc, and MB1. Unexpectedly, other B-cell markers (eg, CD45R) were also down-regulated, and markers of myeloid lineage (CD11b and F4/80 antigen) were acquired instead. Moreover, cells assumed the morphology reminiscent of myeloid cells. A pool of F4/80-positive cells as well as several single-cell clones were obtained and reinjected into syngeneic mice. Remarkably, pooled cells rapidly re-expressed Pax5 and formed tumors of relatively mature lymphoid phenotype, with surface immunoglobulins being abundantly expressed. Approximately half of tumorigenic single-cell clones also abandoned myeloid differentiation and gave rise to B lymphomas. However, when secondary lymphoma cells were returned to in vitro conditions, they once again switched to myeloid differentiation. This process could be curbed via enforced expression of retrovirally encoded Pax5. Our data demonstrate that some Myc target cells are bipotent B-lymphoid/myeloid progenitors with the astonishing capacity to undergo successive rounds of lineage switching.

scholarly journals Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

2017 ◽  
Author(s):  
Yohei Sasagawa ◽  
Hiroki Danno ◽  
Hitomi Takada ◽  
Masashi Ebisawa ◽  
Kaori Tanaka ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Single Cells ◽  
Embryonic Stem ◽  
Stromal Vascular Fraction ◽  
Rna Seq ◽  
Sequencing Method ◽  
Unique Molecular Identifier

AbstractHigh-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts (at a rate of 30%–50%) and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes in total from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

scholarly journals CSIG-17. SIGNALING PATHWAY-BASED CLUSTERING OF MASS CYTOMETRY DATA UNCOVERS CELLS ASSOCIATED WITH CLINICAL PROGRESSION IN GLIOBLASTOMA

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi47-vi47
Author(s):  
Alvaro Alvarado ◽  
Tyler Alban ◽  
Ichiro Nakano ◽  
Justin Lathia ◽  
Steven Goldman ◽  
...  
Keyword(s):  
Single Cell ◽  
Stem Cell Markers ◽  
Mass Cytometry ◽  
Cancer Stem Cell Markers ◽  
In Vivo Experiments ◽  
Lineage Markers ◽  
Cell Expression ◽  
Machine Readable

Abstract Recent advances in single cell expression technology have allowed us to appreciate the complexity in tumoral heterogeneity of solid tumors such as glioblastoma (GBM), which remains uniformly fatal despite aggressive therapies. Currently, there is no knowledge about cell identities and functional characteristics of the different tumoral populations. To this end, we created a 28-marker mass cytometry panel composed of signaling markers, including phospho-proteins, and lineage markers that have been associated with GBM or are considered putative cancer stem cell markers. We evaluated lines established from core and edge (periphery) areas from the same patient and validated to be functionally different with RNA expression and in vivo experiments. We first clustered the cells from all samples using the signaling markers in order to establish differences based on pathway utilization, and then we evaluated the expression of all markers. We found clusters shared by cells from both regions as well as region-specific ones. In order to better characterize these, we used marker enrichment modeling (MEM) and generated machine-readable labels. These were compared to MEM labels generated after using the same signaling markers to cluster primary samples from newly diagnosed or recurrent patients. Similarly, MEM labels were obtained from patients in a clinical trial treated with capecitabine that had positive or negative responses. Clusters from edge cells were found in higher proportion in recurrent tumors and were correlated with negative responses to the chemotherapeutic agent. Initial analyses have also been done correlating immune clusters with tumor clusters in the same samples. We are currently conducting in vitro studies and analyzing additional lines from other patients in order to validate these findings. Our studies exploit single cell cytometry to underscore pathways that are preferentially use by different cell populations with the ultimate goal of establishing therapeutic efforts to extend patient survival.

Sign in / Sign up

Export Citation Format

Share Document