Epigenetic Based Enrichment of Cancer Stem Cells: Mechanistic and Clinical Implications for Liver Cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE24520 | GEO | 2011/10/04
SECONDARY ACCESSION(S): PRJNA132603
REPOSITORIES: GEO
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Project description:Global transcriptiome changes between SP and NSP cells of liver cancer cell lines w and w/o Zebularine treatment Huh7,WRL68, KMCH FACS sorted in SP and NSP w and w/o Zebularine and subjected to illumina microarray analysis.
2011-10-03 | E-GEOD-24520 | biostudies-arrayexpress
Project description:Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescencent dye H33342 and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays this study investigated differential gene expression between SP and non-SP (NSP) cells isolated from the CAL-51 human mammary carcinoma cell line. Keywords: cell type comparison To characterize differential gene expression between CAL-51 breast cancer SP and NSP cells, three consecutive cell culture passages of CAL-51 were independently subjected to H33342 labeling and dual wavelength fluorescence analysis and were then flow cytometrically sorted into SP and NSP cell fractions. Subsequently, each of the six cell preparations was subjected to global transcriptional profiling using Affymetrix HG U133 Plus 2.0 expression microarrays.
2009-12-31 | E-GEOD-18773 | biostudies-arrayexpress
Project description:Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescencent dye H33342 and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays this study investigated differential gene expression between SP and non-SP (NSP) cells isolated from the CAL-51 human mammary carcinoma cell line. Keywords: cell type comparison
2009-12-31 | GSE18773 | GEO
Project description:Difference of DNA methylation and Chromatin accessibility of T24 SP cell and T24 NSP cell
2020-01-30 | GSE130641 | GEO
Project description:We report the application of single-cell RNA sequencing data on Side Population (SP) cells and their Non-Side Population (NSP) counterparts in a mouse model of undifferentiated pleomorphic sarcoma (UPS). SP cells exhibit tumor propagting cell properties characterized by enhanced tumorigenicity and self-renewal potential. The purpose of this experiment is to investigate cellular heterogeneity at the gene expression level in UPS tumors and lineage relationships between different subpopulation of tumor cells. We generated the gene expression profiles of individual cells in the SP and NSP compartments of mouse UPS.
2022-01-07 | GSE162847 | GEO
Project description:Immature cell populations, including stem cells and progenitor cells, can be found in M-bM-^@M-^\side-population (SP)M-bM-^@M-^] cells. Although SP cells isolated from some adult tissues have been reported elsewhere, isolation and characterization of human trophoblast SP cells remained to be reported. We used microarrays to detail the global program of gene expression underlying cell differentiation and identified up-regulated genes of SP HTR-8/SVneo SP cells or NSP cells were isolated using a FACS Vantage fluorescence-activated cell sorter (BD Bioscience, San Jose, California) using dual wavelength analysis (blue, 424 - 444nm; red 675 nm) after excitation with 350 nm UV light. PI-positive dead cells were excluded from the analysis. Sorted SP and NSP cells' RNA had been analyzed by microarray analysis.
2014-09-18 | E-GEOD-61547 | biostudies-arrayexpress
Project description:Transcriptomic changes in human liver cancer cell lines caused by the demethylating drug zebularine. Epigenomic changes such as aberrant hypermethylation and subsequent atypical gene silencing are characteristic features of human cancer. Here, we report a comprehensive characterization of epigenomic modulation caused by zebularine, an effective DNA methylation inhibitor, in human liver cancer. Using transcriptomic and epigenomic profiling, we identified a zebularine signature that classified liver cancer cell lines into two major subtypes with different drug-responses. In drug-sensitive cell lines, zebularine caused inhibition of proliferation coupled with increased apoptosis, whereas drug-resistant cell lines were associated with upregulation of oncogenic networks (e.g. E2F1, MYC, and TNF) driving liver cancer growth in vitro and in mice. Assessment of zebularine-based therapy in xenograft mouse models demonstrated potent therapeutic effects against tumors established from zebularine-sensitive but not zebularine-resistant liver cancer cells leading to increased survival and decreased pulmonary metastasis. Integration of zebularine gene expression and demethylation response signatures differentiated patients with HCC according to their survival and disease recurrence and identified a subclass of patients within the poor survivors likely to benefit from therapeutic agents that target the cancer epigenome.
2011-07-31 | GSE23991 | GEO
Project description:The discovery of the benefits of castration for prostate cancer treatment in 1941 led to androgen deprivation therapy, which remains a mainstay of the treatment of men with advanced prostate cancer. However, as early as this original publication, the inevitable development of castration-resistant prostate cancer was recognized. Resistance first manifests as a sustained rise in the androgen-responsive gene, PSA, consistent with reactivation of the androgen receptor axis. Evaluation of clinical specimens demonstrates that castration-resistant prostate cancer cells remain addicted to androgen signalling and adapt to chronic low-testosterone states. Paradoxically, results of several studies have suggested that treatment with supraphysiological levels of testosterone can retard prostate cancer growth. Insights from these studies have been used to investigate administration of supraphysiological testosterone to patients with prostate cancer for clinical benefits, a strategy that is termed bipolar androgen therapy (BAT). BAT involves rapid cycling from supraphysiological back to near-castration testosterone levels over a 4-week cycle. Understanding how BAT works at the molecular and cellular levels might help to rationalize combining BAT with other agents to achieve increased efficacy and tumour responses.
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Project description:Background: Possible outcomes of acne lesions are atrophic scars which may cause serious physical and psychological distress. Current treatments of post-acne scarring remain difficult and often require invasive procedures. Pathophysiological studies on acne scaring investigated only the first week of papule life. Objectives: Study the pathophysiology of atrophic acne scar formation to identify molecular and cellular pathways that can lead to new therapies for the prevention of acne scarring. Methods: Large-scale gene expression profiling of uninvolved acne skin and acne papules of 48 hours and 3 weeks of age, respectively, of both, scar-prone (SP) and non-scar-prone (NSP) patients was performed. Immunohistochemistry techniques were applied to confirm transcriptomics results on the protein and cellular level. Results: Gene expression and immunohistochemistry analyses showed a very similar immune response in 48 hours-old papules in SP and NSP populations characterized by elevated numbers of T cells, neutrophils and macrophages. However, only in SP patients the immune response persisted in 3 week-old papules, and was characterized by an important infiltrate of B cells. Transient down-modulation of genes related to lipid metabolism was observed in 48 hours-old papules in NSP patients, followed by normalization of gene expression levels after 3 weeks. In contrast, in SP patients a drastic reduction of lipid metabolizing enzymes was observed in 3 week-old papules, suggesting irreversible modifications. The affected lipid metabolism genes were found preferentially expressed in human sebaceous glands, pointing to a destruction of sebaceous gland structures after 3 weeks of inflammatory remodelling in SP acne patients.
2018-04-30 | GSE108110 | GEO
Project description:Transcriptomic changes in human liver cancer cell lines caused by the demethylating drug zebularine. Epigenomic changes such as aberrant hypermethylation and subsequent atypical gene silencing are characteristic features of human cancer. Here, we report a comprehensive characterization of epigenomic modulation caused by zebularine, an effective DNA methylation inhibitor, in human liver cancer. Using transcriptomic and epigenomic profiling, we identified a zebularine signature that classified liver cancer cell lines into two major subtypes with different drug-responses. In drug-sensitive cell lines, zebularine caused inhibition of proliferation coupled with increased apoptosis, whereas drug-resistant cell lines were associated with upregulation of oncogenic networks (e.g. E2F1, MYC, and TNF) driving liver cancer growth in vitro and in mice. Assessment of zebularine-based therapy in xenograft mouse models demonstrated potent therapeutic effects against tumors established from zebularine-sensitive but not zebularine-resistant liver cancer cells leading to increased survival and decreased pulmonary metastasis. Integration of zebularine gene expression and demethylation response signatures differentiated patients with HCC according to their survival and disease recurrence and identified a subclass of patients within the poor survivors likely to benefit from therapeutic agents that target the cancer epigenome. Each cell line was mock treated or treated with 100uM and 200uM zebularine for 7 days, respectively *** This Series represents the gene expression component of the study.
2011-07-30 | E-GEOD-23991 | biostudies-arrayexpress