RNAseq analysis of MM13 and MM2 metastatic melanoma PDX cells overexpressing TINCR
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517676 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8502852_1.fastq.gz | Fastqsanger.gz | |||
| SRR8502852_2.fastq.gz | Fastqsanger.gz | |||
| SRR8502853_1.fastq.gz | Fastqsanger.gz | |||
| SRR8502853_2.fastq.gz | Fastqsanger.gz | |||
| SRR8502854_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Purpose: Study the changes in cell transcriptome upon overexpression of lncRNA TINCR Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins Results: we found that TINCR overexpression induces partial reversion of invasive phenotype
2020-11-25 | GSE125834 | GEO
Project description:Differential gene expression analysis of FaDu cells overexpressing TINCR-HA-FLAG or an empty vector.
2024-07-16 | GSE180301 | GEO
Project description:Gene expression profiling of FaDu cells overexpressing TINCR-HA-FLAG
| PRJNA747713 | ENA
Project description:Purpose: Study the changes in mRNA translation upon silencing of lncRNA TINCR Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins Results: we found that TINCR silencing induces activation of ATF4 translation
2020-11-25 | GSE125832 | GEO
Project description:Purpose: Study the changes in the transcriptome of metastatic melanoma PDX cells upon combination treatment with AURKA and MEK inhibitors Methods: RNAseq analysis of melanoma PDX cells treated with AURKA inhibitor Alisertib (500nM) and MEK inhibitor trametinib (100nM) for 72 h
2023-07-07 | GSE207645 | GEO
Project description:Long non-coding RNA TINCR suppresses metastatic melanoma dissemination by preventing ATF4 translation
| PRJNA517668 | ENA
Project description:Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high mRNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a suite of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25 nucleotide M-bM-^@M-^\TINCR boxM-bM-^@M-^] motif which is strongly enriched in interacting mRNAs and required for TINCR binding. A high-throughput screen to analyze TINCR binding capacity to ~9,400 human recombinant proteins revealed direct binding of TINCR RNA to the Staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay (SMD), however, lacked differentiation impacts. Instead, the TINCR/STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through inducible lncRNA binding to differentiation mRNAs to ensure their expression. Examination of TINCR-binding RNAs using two independent pools of TINCR-targeting oligos
2012-10-10 | E-GEOD-40121 | biostudies-arrayexpress
Project description:Although high clinical response rates are seen for immune checkpoint blockade (ICB) of metastatic melanoma, both intrinsic and acquired ICB resistance remain formidable challenges. Combination ICB shows improved clinical benefit, but is associated with severe adverse events and exceedingly high cost. Therefore, there is a dire need to stratify individual patients for their likelihood of responding to either anti-PD-1 or anti-CTLA-4 monotherapy, or the combination. Since it is conceivable that ICB responses are influenced by both tumor cell-intrinsic and stromal factors, we hypothesized that a predictive classifier ought to mirror both of these distinct features. We used a panel of melanoma patient-derived xenografts (PDX), in which human stromal cells upon transplantation are naturally replaced by their murine counterparts, to computationally subtract PDX RNA expression signals from those in patients’ melanomas. We thus derived both “Stromal immune” (SIM) and tumor cell-specific “Tumor-autonomous inflammation” (TAF) signatures. Here we report that the SIM signature predicts response to anti-CTLA-4 but not anti-PD-1 treatment, whereas the tumor TAF signature predicts response to anti-PD-1 but not anti-CTLA-4. Moreover, when used in conjunction, the signatures accurately predict response in two independent patient cohorts treated with the anti-CTLA-4 + anti-PD-1 combination. These signatures may be clinically exploited for personalized treatment advice based on the predicted benefit from either anti-CTLA-4 or anti-PD-1 monotherapy or their combination.
2020-04-27 | GSE129127 | GEO
Project description:Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high mRNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a suite of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25 nucleotide “TINCR box” motif which is strongly enriched in interacting mRNAs \and required for TINCR binding. A high-throughput screen to analyze TINCR binding capacity to ~9,400 human recombinant proteins revealed direct binding of TINCR RNA to the Staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay (SMD), however, lacked differentiation impacts. Instead, the TINCR/STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through inducible lncRNA binding to differentiation mRNAs to ensure their expression. Gene expression analysis: To establish a gene expression signature for regenerated human epidermis depleted of TINCR, as well as STAU1, total RNA was isolated in biologic duplicate from organotypic cultures of cells with a non-targeting siRNA, or an siRNA to the gene of interest. This RNA was processed and then hybridized to Affymetrix HG-U133 2.0 Plus arrays.
2012-10-10 | E-GEOD-40122 | biostudies-arrayexpress
Project description:The therapeutic landscape of melanoma is rapidly changing. While targeted inhibitors yield significant responses, their clinical benefit is often limited by the early onset of drug resistance. This motivates the pursuit to establish more durable clinical responses, by developing combinatorial therapies. But while potential new combinatorial targets steadily increase in numbers, they cannot possibly all be tested in patients. Similarly, while genetically engineered mouse melanoma models have great merit, they do not capture the enormous genetic diversity and heterogeneity typical in human melanoma. Furthermore, whereas in vitro studies have many advantages, they lack the presence of micro-environmental factors, which can have a profound impact on tumor progression and therapy response. This prompted us to develop an in vivo model for human melanoma that allows for studying the dynamics of tumor progression and drug response, with concurrent evaluation and optimization of new treatment regimens. Here, we present a collection of patient-derived xenografts (PDX), derived from BRAFV600E, NRASQ61 or BRAFWT/NRASWT melanoma metastases. The BRAFV600E PDX melanomas were acquired both prior to treatment with the BRAF inhibitor vemurafenib and after resistance had occurred, including six matched pairs. We find that PDX resemble their human donors’ melanomas regarding biomarkers, chromosomal aberrations, RNA expression profiles, mutational spectrum and targeted drug resistance patterns. Mutations, previously identified to cause resistance to BRAF inhibitors, are captured in PDX derived from resistant melanomThis melanoma PDX platform represents a comprehensive public resource to study both fundamental and translational aspects of melanoma progression and treatment in a physiologically relevant setting.
2016-05-27 | GSE73737 | GEO