Single cell gene expression profiling of slow cycling and actively dividing mouse glioblastoma (GBM) cells isolated based on H2B-GFP label retention.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE228785 | GEO | 2023/04/03
REPOSITORIES: GEO
Similar Datasets
Project description:SUMMARY: Dormant or slow cycling tumour cells can form a residual chemoresistant reservoir responsible for relapse in patients, years after curative surgery and adjuvant therapy. Since their isolation from human tumors has been a long-stalled technical challenge preventing a direct study of their functional properties, we have adapted the pulse-chase expression and labeling approach using H2BeGFP (Tumbar et al., 2004, DOI:10.1126/science.1092436) to a doxycycline-inducible all-in-one lentiviral vector. In this manner we were able to label and isolate by FACS live slow cycling cancer cells (SCCC) from human colorectal, glioma and melanoma patient-derived tumors as well as from minitumors grown in matrigel (SW1222-cells) or in sphere culture (e225, e216 glioma models). We determined the differentially expressed transcriptional profiles in paired comparisons of slow-cycling cancer cell (SCCC) versus rapid cycling cancer cell (RCCC) sub-populations. H2BeGFP-retention revealed slow cycling as a transient cell state rather than a cellular entity. SCCC showed cancer-initiation potential and enhanced chemoresistance. Cells in this slow cycling status presented a distinctive non-genetic and cell-autonomous gene expression profile shared across different tumour types. We identified TET2 epigenetic enzyme as key factor controlling SCCC numbers and survival. 5-Hydroxymethylcytosine (5hmC), generated by TET2 enzymatic activity, labelled the SCCC genome in carcinomas and was a predictive biomarker of relapse and survival in cancer patients. We demonstrate the enhanced chemoresistance of SCCC, revealed 5hmC as a biomarker for their clinical identification, and identified TET2 as a potential drug-target for SCCC elimination that could extend patients' survival.Experimental Design: Cells from human patient-derived xenografts (PDX) and human cancer cell lines were infected with a doxycycline (DOX)-inducible all-in-one lentivirus coding for the histone2B-eGFP fusion protein. The models were as following: T70 (colorectal cancer); MMPG3 and MMLN9 (melanoma); e225 and e216 (glioma) and human SW1222 colorectal cancer cell line as an infected pool as well as a clone (Clone2) and the following SW1222 derivate cell lines: SW1222-shCTRL (stable expression of nonsilencing shRNA), SW1222-shTET2 (stable expression of TET2-specific shRNA).H2BeGFP-infected cells were isolated and grown/propagated and injected subcutaneously in the flanks of immunocompromised NOD-Scid mice as described (Puig et al., Clin. Cancer Res. 2013; doi: 10.1158/1078-0432.CCR-12-1740.). H2BeGFP-infected SW1222 cells and derivate cell lines were grown in matrigel drops as minitumors. H2BeGFP-infected patient-derived melanoma MMPG3 and MMLN9 minitumor and glioma models e216 and e225 were grown as sphere cultures in their respective conditions as indicated.H2BeGFP expression was induced by DOX treatment in all experimental systems in a pulse-chase fashion and H2BeGFP fusion protein integrated into the host genome labeling all cells. Consecutive cell divisions of proliferating cells diluted and finally eliminated the fluorescent mark in an exponential decay fashion (RCCC or sRCCC), whereas slow-cycling cells (SCCC) retained the fluorescent stain, allowing FACS separation and isolation. Total RNA was separately extracted from both sub-populations of cells of each system and submitted to microarray analyses for characterization.
2018-06-28 | E-MTAB-4004 | biostudies-arrayexpress
Project description:Slow-cycling subpopulations exist in bacteria, yeast, and mammalian systems. In the case of cancer, slow-cycling subpopulations have been proposed to give rise to drug resistance. However, the origin of slow-cycling human cells is poorly studied, in large part due to lack of markers to identify these rare cells. Slow-cycling cells pass through a non-cycling period marked by low CDK2 activity and high p21 levels. Here, we use this knowledge to isolate these naturally slow-cycling cells from a heterogeneous population and perform RNA-sequencing to delineate the transcriptome underlying the slow-cycling state. We show that cellular stress responses – the p53 transcriptional response and the integrated stress response – are the most salient causes of spontaneous entry into the slow-cycling state.
2019-02-28 | GSE122927 | GEO
Project description:We identified slow-cycling cells (SCCs) in Ewing sarcoma using a label retention assay with CFSE. We labeled cells of SK-ES-1, an Ewing sarcoma cell line, with CFSE. After 5 days culture, we isolated cells retaining strong fluorescence (upper, ~10%) as SCCs and other cells (lower, ~90%) as non-slow-cycling cells (non-SCCs) using FACS AriaTM Ⅲ cell sorter.
2022-10-17 | GSE204671 | GEO
Project description:Epimorphic regeneration commonly relies on the activation of quiescent stem cells to drive new cell production. The planarian Schmidtea mediterranea is among the best regenerators in nature, thanks to its large population of adult stem cells, called neoblasts. While neoblasts have long been known to drive regeneration, whether a subset of neoblasts is reserved for this purpose is unknown. Here, we revisited the idea of reserved neoblasts by approaching neoblast heterogeneity from a regulatory perspective. By implementing a new fluorescence-activated cell sorting strategy in planarians, we identified a population of neoblasts defined by low transcriptional activity. These RNAlow neoblasts are relatively slow-cycling at homeostasis and undergo a morphological regeneration response characterized by cell growth at 48 hours post-amputation. At this time, RNAlow neoblasts proliferated in a TOR-dependent manner. Additionally, knockdown of the tumour suppressor Lrig-1, which is enriched in RNAlow neoblasts, resulted in RNAlow neoblast growth and hyperproliferation at homeostasis, and ultimately delayed regeneration. We propose that slow-cycling RNAlow neoblasts represent a regeneration-reserved neoblast population.
2020-12-31 | GSE157860 | GEO
Project description:The dynamics of the hematopoietic flux responsible for blood cell production in native conditions remains a matter of debate. Using CITE-seq analyses, we uncovered a distinct progenitor population that displays a cell cycle gene signature similar to the one found in quiescent hematopoietic stem cells. We further determined that the CD62L marker can be used to phenotypically enrich this population in the Flt3+ multipotent progenitor (MPP4) compartment. Functional in vitro and in vivo analyses validated the heterogeneity of the MPP4 compartment and established the quiescent/slow-cycling properties of the CD62L– MPP4 cells. Furthermore, studies under native conditions revealed a novel hierarchical organization of the MPP compartments in which quiescent/slow-cycling MPP4 cells sustain a prolonged hematopoietic activity at steady state while giving rise to other lineage-biased MPP populations. Altogether, our data characterize a durable and productive quiescent/slow-cycling hematopoietic intermediary within the MPP4 compartment and highlight early paths of progenitor differentiation during unperturbed hematopoiesis.
2023-10-23 | GSE243197 | GEO
Project description:This study was performed to compare transcriptomic changes in the heterogeneous mouse skin epidermal stem cells and hair follicle stem cells (HFSC) populations during chronological aging. Slow-cycling stem cells (label retaining cells, LRCs), fast-cycling stem cells (non-label retaining cells, nLRCs) and hair follicle stem cells express unique gene signatures in young age (2 months old) and have independent stem cell identities. The changes in aging stem cells lineage identities have been a topic of discussion and here we examined if distinct stem cells cycling speed affects their aging process by comparing the transcriptomes of slow-and fast-cycling epidermal stem cells. Our data indicates the loss of unique stem cell identities in aging slow or fast-cycling epidermal stem cells or HFSC at 2 years of age with intermediary effects seen at 1.5 year old.
2022-10-01 | GSE185087 | GEO
Project description:A slow cycling Lgr5 tumour population mediates basal cell carcinoma relapse after therapy
| PRJNA482149 | ENA
Project description:Glioblastoma (GBM) is among the most aggressive cancers. Despite aggressive radiotherapy and treatment with the alkylating agent temozolomide (TMZ), patients ultimately succumb to the disease. Although much interest has focused on highly tumorigenic GBM stem cells (GSCs), adaption of a concept from microbial research proposes that a minor population of dormant âpersisterâ cells in cancer evade current therapies. To separate dormant and treatment-resistant tumor cells in human GBM tumorspheres, we have refined density gradient protocols previously used for separation of neurosphere-forming neural stem cells (NSCs). We find that a minor cell population in human GBM tumorsphere cultures and patient-derived tumor biopsies display increased cell density. These high-density GBM cells (HDGCs) display dormancy, variable expression of proposed GSC markers, and 10-100 fold higher levels of reprogramming gene expression compared to low-density GBM cells (LDGCs). Transcriptional profiling data confirmed the slow-cycling state of HDGCs. As a result, HDGCs show decreased tumorsphere formation capacity in vitro and reduced tumorigenicity in vivo. Using tumorspheres and xenografts, we demonstrated that HDGCs show increased treatment-resistance to ionizing radiation (IR) and temozolomide treatment compared to LDGCs. Similar to the NSC lineage, our data suggest that dormant HDGCs become increasingly sensitive to anti-proliferative therapies as they become activated and further differentiate. In conclusion, density gradients represents a marker-independent approach to separate dormant and treatment-resistant tumor cells in human GBMs and other solid cancers. 12 samples, no replicates, derived from 5 individual patients
2016-07-01 | E-GEOD-71116 | biostudies-arrayexpress
Project description:Identification of TOR-responsive slow-cycling neoblasts in planarians
| PRJNA662989 | ENA
Project description:Metabolic reprogramming has been described in rapidly growing tumors, which are thought to mostly contain fast-cycling cells (FCCs) that have impaired mitochondrial function and rely on aerobic glycolysis. Here, we characterize the metabolic landscape of glioblastoma (GBM) and explore metabolic specificities as targetable vulnerabilities. Our studies highlight the metabolic heterogeneity in GBM, in which FCCs harness aerobic glycolysis, and slow-cycling cells (SCCs) preferentially utilize mitochondrial oxidative phosphorylation for their functions. SCCs display enhanced invasion and chemoresistance, suggesting their important role in tumor recurrence. SCCs also demonstrate increased lipid contents that are specifically metabolized under glucose-deprived conditions. Increased fatty acid transport in SCCs is targetable by pharmacological inhibition or genomic deletion of FABP7, both of which sensitize SCCs to metabolic stress. Furthermore, FABP7 inhibition, whether alone or in combination with glycolysis inhibition, leads to overall increased survival. Our studies reveal the existence of GBM cell subpopulations with distinct metabolic requirements and suggest that FABP7 is central to lipid metabolism in SCCs and that targeting FABP7-related metabolic pathways is a viable therapeutic strategy.
| EGAS00001003251 | EGA