The tumor associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA786940 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17160063_1.fastq.gz | Fastqsanger.gz | |||
| SRR17160063_2.fastq.gz | Fastqsanger.gz | |||
| SRR17160064_1.fastq.gz | Fastqsanger.gz | |||
| SRR17160064_2.fastq.gz | Fastqsanger.gz | |||
| SRR17160065_1.fastq.gz | Fastqsanger.gz |
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Project description:PRAME is a prominent member of the cancer germline antigen family of proteins, which triggers autologous T-cell mediated immune responses. Integrative genomic analysis in diffuse large B-cell lymphoma (DLBCL) uncovered recurrent, and highly focal deletions of 22q11.22 including the PRAME gene, which were associated with poor outcome. PRAME-deleted tumors showed cytotoxic T-cell immune escape and were associated with cold tumor microenvironments. In addition, PRAME down-modulation was strongly associated with somatic EZH2 Y641 mutations in DLBCL, and PRC2-regulated genes were repressed in isogenic PRAME KO vs. PRAME wt lymphoma cell lines, with PRAME directly interacting with EZH2 as a negative regulator. EZH2 inhibition with EPZ-6438 abrogated these extrinsic and intrinsic effects leading to PRAME and microenvironment restoration in vivo. Our data highlight multiple functions of PRAME during lymphomagenesis, and provide a preclinical rationale for synergistic therapies combining epigenetic re-programming with PRAME-targeted therapies.
2024-12-04 | GSE190403 | GEO
Project description:PRAME is a prominent member of the cancer testis antigen family of proteins, which triggers autologous T cell-mediated immune responses. Integrative genomic analysis in diffuse large B cell lymphoma (DLBCL) uncovered recurrent and highly focal deletions of 22q11.22, including the PRAME gene, which were associated with poor outcome. PRAME-deleted tumors showed cytotoxic T cell immune escape and were associated with cold tumor microenvironments. In addition, PRAME downmodulation was strongly associated with somatic EZH2 Y641 mutations in DLBCL. In turn, PRC2-regulated genes were repressed in isogenic PRAME-KO lymphoma cell lines, and PRAME was found to directly interact with EZH2 as a negative regulator. EZH2 inhibition with EPZ-6438 abrogated these extrinsic and intrinsic effects, leading to PRAME expression and microenvironment restoration in vivo. Our data highlight multiple functions of PRAME during lymphomagenesis and provide a preclinical rationale for synergistic therapies combining epigenetic reprogramming with PRAME-targeted therapies.
| S-EPMC9106353 | biostudies-literature
Project description:The human tumor antigen PRAME (Preferentially expressed antigen of melanoma) is frequently overexpressed in tumors. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in tumorigenesis remain largely elusive. We applied protein-complex purification strategies and identified PRAME as a substrate recognition subunit of a Cullin2-based E3 ubiquitin ligase. Genome-wide chromatin immunoprecipitation experiments revealed that PRAME is specifically enriched at NF-Y promoters that are transcriptionally active, suggesting a role in gene activation. Our results are consistent with the involvement of the PRAME ubiquitin ligase complex in NF-Y-mediated transcriptional regulation.
2011-07-29 | GSE26439 | GEO
Project description:The human tumor antigen PRAME (Preferentially expressed antigen of melanoma) is frequently overexpressed in tumors. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in tumorigenesis remain largely elusive. We applied protein-complex purification strategies and identified PRAME as a substrate recognition subunit of a Cullin2-based E3 ubiquitin ligase. Genome-wide chromatin immunoprecipitation experiments revealed that PRAME is specifically enriched at NF-Y promoters that are transcriptionally active, suggesting a role in gene activation. Our results are consistent with the involvement of the PRAME ubiquitin ligase complex in NF-Y-mediated transcriptional regulation. ChIP-seq binding profiles of PRAME (ChIP-seq using the preimmune serum was used as negative control), NFYA, and NFYB, and expression analysis by RNA-seq in K562 human leukemia cell line
2011-07-29 | E-GEOD-26439 | biostudies-arrayexpress
Project description:Preferentially Expressed Antigen in Melanoma (PRAME) is frequently overexpressed in a wide variety of cancers and it has been proposed as prognostic marker for clinical outcome. It belongs to a class of non-mutated genes whose expression seems to be mostly restricted to tumor cells. Osteosarcoma is the most common primary malignant bone tumor in children and young adults. Despite advances in the diagnosis and management of osteosarcoma, long-term survival has not envolved substantially in the past decades, justifying efforts in finding effective therapeutic targets. In order to assess transcriptome characteristics that could contribute to further comprehend PRAME association with cancer, the technique of gene expression profiling was used to compare PRAME-positive and PRAME-negative osteosarcoma samples. Keywords: disease state analysis Six tumor samples representing distinct histological classes of osteosarcoma (telangiectatic, giant cell, anaplastic, osteoblastic and chondroblastic) were included in this study. They were obtained from individual patients ranging from 5 to 29 years old. Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). This platform utilizes bioarrays consisting of 30-base, single pre-validated oligonucleotide probe per gene target. CodeLink UniSet Human I bioarrays, containing 10,000 human transcripts, were used for all experiments. Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A total of 12 arrays were hybridized, including 6 tumor samples (3 PRAME-positive and 3 PRAME-negative) and their respective technical replicates. Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).
2010-05-18 | E-GEOD-8079 | biostudies-arrayexpress
Project description:Preferentially Expressed Antigen of Melanoma (PRAME) is a cancer-testis antigen that is expressed in subsets of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), collectively termed keratinocyte carcinomas (KC). PRAME functions as a transcriptional co-repressor of retinoid signaling by guiding enhancer of zeste homologue 2 (EZH2), a repressive histone methyltransferase, to retinoic acid response elements (RARE) found in gene promoters. The functions and therapeutic relevance of PRAME expression in KC have not been investigated. In the present study, we evaluated the implications of PRAME expression upon KC development and response to retinoid-based therapeutics. High PRAME expression in tumors was negatively correlated with epidermal differentiation gene signatures. Similarly, PRAME overexpression (OE) downregulated epidermal differentiation gene signatures, and impaired epidermal differentiation. PRAME OE also attenuated retinoid-induced RARE activation, growth suppression and differentiation responses. Conversely, low-PRAME tumors and PRAME-depleted KC cells possessed enrichment of epidermal differentiation gene signatures. PRAME depletion also restored retinoid-induced RARE activation, suppression of KC growth, keratinization suppression in SCC cells and cell death signaling in BCC cells. Furthermore, EZH2 inhibitors potentiated the retinoid-induced RARE activation and suppress the growth of PRAME-expressing BCC and cSCC cells. We demonstrate that PRAME confers retinoid resistance in KC, and we contend that PRAME-mediated retinoid resistance in KC may be overcome by targeting EZH2.
2025-03-17 | GSE271108 | GEO
Project description:To investigate the transcriptomic changes associated with PRAME and BAP1 knockdown, RNA-seq was performed on A375SM melanoma cells stably expressing shRNA targeting PRAME (shPRAME), BAP1 (shBAP1), or a non-targeting control (shEmpty). This study aims to understand the role of PRAME and BAP1 in gene regulation and melanoma progression.
2025-09-02 | GSE306132 | GEO
Project description:To identify gene expression that distinguishes hematopoietic cells that express PRAME from those that do not, normal CD34+ cells with forced PRAME expression were compared to cells without PRAME expression in culture over time (days 4, 7, 14) using Affymetrix HU-133A microarrays
2009-11-01 | GSE17100 | GEO
Project description:Recurrent disease emerges in the majority of patients with ovarian cancer (OVCA). Adoptive T-cell therapies with T-cell receptors (TCRs) targeting tumor-associated antigens (TAAs) are considered promising solutions for less-immunogenic ‘cold’ ovarian tumors. In order to treat a broader patient population, more TCRs targeting peptides derived from different TAAs binding in various HLA class I molecules are essential. By performing a differential gene expression analysis using mRNA-seq datasets, PRAME, CTCFL and CLDN6 were selected as strictly tumor-specific TAAs, with high expression in ovarian cancer and at least 20-fold lower expression in all healthy tissues of risk. In primary OVCA patient samples and cell lines we confirmed expression and identified naturally expressed TAA-derived peptides in the HLA class I ligandome. Subsequently, high-avidity T-cell clones recognizing these peptides were isolated from the allo-HLA T-cell repertoire of healthy individuals. Three PRAME TCRs and one CTCFL TCR of the most promising T-cell clones were sequenced, and transferred to CD8+ T cells. The PRAME TCR-T cells demonstrated potent and specific antitumor reactivity in vitro and in vivo. The CTCFL TCR-T cells efficiently recognized primary patient-derived OVCA cells, and OVCA cell lines treated with demethylating agent 5-aza-2′-deoxycytidine (DAC). The identified PRAME and CTCFL TCRs are promising candidates for the treatment of patients with ovarian cancer, and are an essential addition to the currently used HLA-A*02:01 restricted PRAME TCRs. Our selection of differentially expressed genes, naturally expressed TAA peptides and potent TCRs can improve and broaden the use of T-cell therapies for patients with ovarian cancer or other PRAME or CTCFL expressing cancers.
2023-03-10 | PXD040651 | Pride
Project description:To identify gene expression that distinguishes hematopoietic cells that express PRAME from those that do not, normal CD34+ cells with forced PRAME expression were compared to cells without PRAME expression in culture over time (days 4, 7, 14) using Affymetrix HU-133A microarrays Normal CD34+ progenitor cells not expressing PRAME were transduced with either PRAME cDNA (no 3' utr) or a corresponding empty vector control by lentiviral vector infection. Two replicates were performed for each condition (PRAME and control) at three experimental time points (days 4, 7, and 14 in culture). A single-stranded linear amplification protocol was used to process total RNA (one microgram) for the microarrays. This protocols is described in detail in PMID 14706461.
2009-10-31 | E-GEOD-17100 | biostudies-arrayexpress