Although the prognosis for childhood Acute Lymphoblastic Leukemia (ALL) in general has improved tremendously over the last decades, the survival chances for infants (<1 year of age) with ALL remains poor.
Association of high-level MCL-1 expression with in vitro and in vivo prednisone resistance in MLL-rearranged infant acute lymphoblastic leukemia.
Sex, Specimen part, DiseaseView Samples
Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer
A stromal gene signature associated with inflammatory breast cancer.
Specimen part, Disease, Race, SubjectView Samples
To examine Ikaros tumor suppressor mechanisms, we have utilized inducible RNAi to dynamically restore endogenous Ikaros expression in BCR-ABL1+ B-ALL driven by its knockdown (Ikaros knockdown), and compared these tumors to tumors driven by BCR-ABL1 alone (control). Restoration of Ikaros causes rapid regression of tumor cells in vivo, significantly prolonging tumor transplant recipient survival. Using both transgenic and retroviral approaches, we conducted expression analysis of B-ALL by RNA-Seq and have identified a series of Ikaros-regulated genes within established tumor cell in vivo. Comparison of Ikaros-activated and Ikaros-repressed genes with human B-ALL expression data shows a set of conserved Ikaros target genes, some of which are associated with patient outcome (namely, CTNND1, IFITM3 and EMP1). Overall design: RNA-seq was performed on BCR-ABL1+ B-ALL with inducible Ikaros knockdown (Ikaros knockdown, n=8; transgenic n=5, retroviral n=3) or BCR-ABL1+ alone B-ALL (control, n=4; transgenic n=3, retroviral n=1) cells isolated from untreated and three 3-day Dox-treated mice. Samples were run on HiSeq or NextSeq platform. B-ALL B031 was run in technical duplicate. Extended Dox samples (B027: d7 and d10) and relapse samples for B027, B029 and B035 have also been analyzed in this dataset.
Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome.
Specimen part, Treatment, SubjectView Samples
Plants are known to be responsive to volatiles, but knowledge about the molecular players involved in transducing their perception remain scarce.
WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis.
Heterologous expression of the fungal pathogen Cladosporium fulvum Avr2 in Arabidopsis plants.
The Cladosporium fulvum virulence protein Avr2 inhibits host proteases required for basal defense.
No sample metadata fieldsView Samples
Title: Transcriptome analysis of human endometrial tissues from healthy post-menoupausal women reflecting the endometrial response to 3-weeks treatment with tibolone, E2 and E2+MPA.
Molecular analysis of human endometrium: short-term tibolone signaling differs significantly from estrogen and estrogen + progestagen signaling.
No sample metadata fieldsView Samples
Frozen tissue specimens from primary breast tumors were collected and profiled using Affymetrix U133 plus 2 expression microarrays.
Cyclin E2 overexpression is associated with endocrine resistance but not insensitivity to CDK2 inhibition in human breast cancer cells.
Specimen part, Disease, Disease stageView Samples
Mania is a serious neuropsychiatric condition associated with significant morbidity and mortality. Previous studies have suggested that environmental exposures can contribute to mania pathogenesis. We measured dietary exposures in a cohort of individuals with mania and other psychiatric disorders as well as in control individual without a psychiatric disorder. We found that a history of eating nitrated dry cured meat, but not other meat or fish products, was strongly and independently associated with current mania (adjusted odds ratio 3.49, 95% confidence interval (CI) 2.24-5.45, p<8.97x 10-8). Lower odds of association were found between eating nitrated dry cured meat and other psychiatric disorders. We further found that the feeding of meat preparations with added nitrate to rats resulted in alterations in behavior and changes in intestinal microbiota. Rats fed diets with added nitrate also showed alterations of brain pathways dysregulated in mania. These findings may lead to new methods for preventing mania and for developing novel therapeutic interventions
Nitrated meat products are associated with mania in humans and altered behavior and brain gene expression in rats.
Sex, Specimen partView Samples
Expression profiles of 917 pathway repoter genes were determined by AmpliSeq-RNA in primary human hepatocytes treated with Diclofenac and a test compound 3 hours after treatment. Overall design: Vehicle control, diclofenac, and three doses of the test compound (small-molecule neurotransmitter receptor antagonist) were applied to three primary cell lines, with three biological replicates in each group. In some treatment groups read-outs were only available for two samples. All together 41 samples were profiled.
Pathway reporter genes define molecular phenotypes of human cells.
No sample metadata fieldsView Samples
Breast cancer is a genetically and phenotypically complex disease. To understand the role of microRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer (BC) cell lines to discover miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.Using a microarray carrying LNA modified oligonucleotide capture probes (Exiqon), expression levels of 725 human miRNAs were measured in 51 BC cell lines. MiRNA expression was explored by unsupervised cluster analysis and then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer. Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 BC cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of BC cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters of which half were related to the ER-status of the cell lines. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group of cell lines, 39 miRNAs were associated with ERBB2 overexpression and 24 miRNAs with E-cadherin gene mutations, which are frequent in this subtype of BC cell lines. In contrast, 31 different miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in BC cell lines that are not of luminal origin. The differential expression of 30 miRNAs were associated with p16INK4 status while only a few differentially expressed miRNAs were associated with BRCA1, or PIK3CA/PTEN, TP53 mutation status of the cell lines (P-value < 0.05). Twelve miRNAs were associated with DNA copy number variation of the respective locus. Luminal-basal and epithelial-mesenchymal associated miRNAs determine the overall subdivision of miRNA transcriptome of BC cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4aor E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of the genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of BC cell lines, which can be exploited for functional studies of clinically important miRNAs.
miRNA expression profiling of 51 human breast cancer cell lines reveals subtype and driver mutation-specific miRNAs.
Cell lineView Samples