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Genome-wide maps of Ets21C and Pointed isoforms PntP1 and PntP2 binding sites in intestinal stem cells (ISCs) and transcriptome profiling of ISCs over-expressing Spitz, Ets21C, PntP1, or PntP2

ABSTRACT: Genome-wide maps of Ets21C and Pointed isoforms PntP1 and PntP2 binding sites in intestinal stem cells (ISCs) and transcriptome profiling of ISCs over-expressing Spitz, Ets21C, PntP1, or PntP2

PROVIDER: PRJNA752599 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15359700.fastq.gz	Fastqsanger.gz
	SRR15359701.fastq.gz	Fastqsanger.gz
	SRR15359702.fastq.gz	Fastqsanger.gz
	SRR15359703.fastq.gz	Fastqsanger.gz
	SRR15359704.fastq.gz	Fastqsanger.gz

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Genome-wide maps of Ets21C and Pointed isoforms PntP1 and PntP2 binding sites in intestinal stem cells (ISCs) and transcriptome profiling of ISCs over-expressing Spitz, Ets21C, PntP1, or PntP2

Project description:Purpose: The ETS transcription factors Ets21C and Pnt are downstream effectors of EGFR signaling pathway regulating intestinal stem cell (ISC) proliferation. ISC-specific DNA binding mapping using DamID and mRNA expression profiling were performed to identify the role of Ets21C and Pnt downstream of EGFR signaling. Methods: For DamID, ISC were FACS sorted and their genomic DNA extracted, amplified, and sequenced. For RNA-Seq, ISC were FACS sorted and their total RNA extracted, amplified (only for Pnt samples), and sequenced. Conclusions: We found that Ets21C and Pnt have a role in driving both ISC proliferation and metabolic changes.

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Array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas

Project description:Distinguishing between Spitz nevus and melanoma presents a challenging task for clinicians and pathologists. Most of these lesions are submitted entirely in formalin for histologic analysis by conventional hematoxylin and eosin-stained sections, and fresh-frozen material for ancillary studies is rarely collected. Molecular techniques, such as comparative genomic hybridization (CGH), can detect chromosomal alterations in tumor DNA that differ between these 2 lesions. This study investigated the ability of high-resolution array-based CGH to serve as a diagnostic test in distinguishing Spitz nevus and melanoma using DNA isolated from formalin-fixed and paraffin-embedded samples. Two of 3 Spitz nevi exhibited no significant chromosomal alterations, while the third showed gain of the short arm of chromosome 11p. The latter finding has previously been described as characteristic of a subset of Spitz nevi. The 2 melanomas showed multiple copy number alterations characteristic of melanoma such as 1q amplification and chromosome 9 deletion. This study has shown the utility of array-based CGH as a potential molecular test in distinguishing Spitz nevus from melanoma. The assay is capable of using archival paraffin-embedded, formalin-fixed material; is technically easier to perform as compared with conventional CGH; is more sensitive than conventional CGH in being able to detect focal alterations; and can detect copy number alterations even with relatively small amounts of lesional tissue as is typical of many skin tumors. Series_type = clinical_history_design A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Keywords: other

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Determination of Shavenbaby target genes in Intestinal Stem Cells (ISCs) [RNAseq_ISC]

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Transcription profiling of Drosophila eye antennal imaginal disc expressing either activated Ras or secreted Spitz

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Project description:The newest WHO classification suggests eliminating cases with BRAF and NRAS mutations from the categories of Spitz tumors (ST) and Spitz melanoma (SM). We aimed to better characterize the genomics of Spitz neoplasms and assess whether integrating genomic data with morphologic diagnosis improves classification and prognostication. We performed DNA and RNA sequencing on 80 STs, 26 SMs, and 22 melanomas with Spitzoid features (MSF). NGS data was used to reclassify tumors by moving BRAF/NRAS-mutated cases to MSF. Eighty-one percent of STs harbored kinase fusions/truncations. Of SMs, 77% had fusions/truncations, 8 involving MAP3K8. Novel fusions identified were MYO5A-FGFR1, MYO5A-ERBB4, and PRKDC-CTNNB1. The majority of MSFs (84%) had BRAF, NRAS, or NF1 mutations, and 62% had TERT promoter mutations. Only after reclassification, the following was observed: 1) mRNA expression showed distinct clustering of MSF; 2) 6/7 cases with recurrence and all distant metastases were MSFs; 3) RFS was worse in MSF than ST and SM groups (p=0.0073); 4) classification incorporating genomic data was highly predictive of recurrence (OR 13.20, p=0.0197). The majority of STs and SMs have kinase fusions as primary initiating genomic events. Eliminating BRAF/NRAS-mutated neoplasms from these categories results in improved classification and prognostication of melanocytic neoplasms with Spitzoid cytomorphology.

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