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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse.

ABSTRACT: Retrospective investigation of genetic background of rapid progression of multiple myeloma into extramedullary relapse. Array-CGH showed chromothripsis in chromosome 18, hyperdiploidy, structural copy-number alterations. Utilization of novel NGS leukemia-related gene custom panel revealed patholological mutation in NRAS (c.181C>A; p.Gln61Lys) or variants of unknown significance in TP53, CUX1 and POU4F1.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Jan Smetana

PROVIDER: E-MTAB-6036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse.

Project description:Retrospective investigation of genetic background of rapid progression of multiple myeloma into extramedullary relapse. Array-CGH showed chromothripsis in chromosome 18, hyperdiploidy, structural copy-number alterations. Utilization of novel NGS leukemia-related gene custom panel revealed patholological mutation in NRAS (c.181C>A; p.Gln61Lys) or variants of unknown significance in TP53, CUX1 and POU4F1.

2017-10-31 | E-MTAB-6033 | biostudies-arrayexpress

Clonal cytogenetics changes in progression of multiple myeloma to extramedullary relapse and plasmocellular leukemia – case report

Project description:Extramedullary relapse (EM) of multiple myeloma (MM) is defined as infiltration of plasma cells (PC) outside of the bone marrow. EM is an aggressive form of the disease with a dismal outcome. We present cytogenetic findings of a 52-year-old female patient who was diagnosed with MM in 2008 and progression of MM to EM and plasmocellular leukemia retrospective analysis of TP53 mutation status showed presence of 2 known missense mutations in exon 6 (c.632C>T) and exon 7 (c.700T>C). EM relapse of this patient was connected to a change of the entire genome profile. We suppose that the extramedullary lesion originated by an expansion of one clone of tumor plasma cells from the bone marrow, which was confirmed by identical genomic profile of both tested samples. Thus, change of ploidy status should be considered as potential hallmark of adverse course of the disease.

2015-10-06 | E-MTAB-3600 | biostudies-arrayexpress

Clonal cytogenetics changes in progression of multiple myeloma to extramedullary relapse and plasmocellular leukemia – case report

2015-10-10 | E-MTAB-3577 | biostudies-arrayexpress

Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.

2015-11-27 | E-MTAB-3961 | biostudies-arrayexpress

Genomic studies controvert the existence of the CUX1 p75 isoform

Project description:CUX1, a homeodomain-containing transcription factor, is recurrently deleted or mutated in multiple tumor types. In myeloid neoplasms, CUX1 deletion or mutation carries a poor prognosis. We have previously established that CUX1 functions as a tumor suppressor in hematopoietic cells across multiple organisms. Others, however, have described oncogenic functions of CUX1 in solid tumors, often attributed to truncated CUX1 isoforms, p75 and p110. Given the clinical relevance, it is imperative to clarify these discrepant activities. Herein, we sought to determine the CUX1 isoforms expressed in hematopoietic cells, and find that they express the full-length p200 isoform. Through the course of this analysis, we found no evidence of the p75 alternative transcript in any cell type examined. Using an array of orthogonal approaches, including biochemistry, proteomics, CRISPR/Cas9 genomic editing, and analysis of functional genomics datasets across a spectrum of normal and malignant tissue types, we found no data to support the existence of the CUX1 p75 isoform generated by an alternative transcriptional start site. Based on these results, prior studies of p75 require reevaluation, including the interpretation of oncogenic roles attributed to CUX1.

2022-02-17 | PXD027527 | Pride

Genes regulated by miR-181c

Project description:We found frequently down-regulation of microRNA-181c in human gastric cancer cases. To identify the potential target of miR-181c, we introduced miR-181c into a gastric cancer cell line KATO-III　and analyzed significant changes of gene expression which was induced after introducing miR-181c. Keywords: dose response

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CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [CUT&RUN]

Project description:CUX1 is a HOX-family transcription factor that is essential for development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor suppressive functions of CUX1. Herein, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 functions as a pioneer factor to epigenetically regulate hematopoietic lineage commitment and homeostasis, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.

2023-10-01 | GSE235303 | GEO

CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ChIP-seq]

2023-10-01 | GSE235301 | GEO

CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ATAC-seq]

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Functional genomic analysis of the haploinsufficient tumor suppressor, CUX1

Project description:CUX1 is a homeodomain-containing transcription factor that is conserved, ubiquitous, and essential in vertebrates and invertebrates. CUX1 is mutated or deleted in high-risk myeloid neoplasms and solid tumors, resulting in haploinsufficiency and tumor growth. Here we provide the first analysis of endogenous, whole genome, CUX1 DNA binding. We demonstrate that CUX1 binds with transcriptional activators and cohesin at distal enhancers across three different human cell types. Haploinsufficiency of CUX1 altered the expression of a large number of genes, including cell cycle regulators, with concomitant increased cellular proliferation. Surprisingly, CUX1 occupancy decreased genome-wide in the haploinsufficient state, and binding site affinity did not correlate with differential gene expression. Instead, differentially expressed genes had multiple, low-affinity CUX1 binding sites, consistent with an analog model for CUX1 gene regulation. A machine-learning algorithm determined that chromatin accessibility, enhancer activity, and distance to the transcription start site are features of functional CUX1 DNA binding. Moreover, CUX1 is enriched at sites of DNA looping, and these loops connect CUX1 to the promoters of target genes. We propose that CUX1 is an analog transcription factor that regulates target genes through higher order genome architecture.

2017-03-29 | GSE92882 | GEO

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