Project description:The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison
Project description:To identify potential target genes of leukemia-related miRNAs such as miR-196b and miR-150 in human MLL-associated leukemia, we performed Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow (including 3 each of CD34+, CD33+, and MNC) cell samples.
Project description:Chronic lymphocytic leukemia shows a variable clinical course which is associated with distinct alterations such as chromosomal aberrations, gene mutations or IGHV mutation status. Refining biologic categories may help to improve clinical management with available and future treatment approaches. We used Affymetrix Exon 1.0 ST microarrays to investigate differences in CLL biology.
Project description:Chronic lymphocytic leukemia shows a variable clinical course which is associated with distinct alterations such as chromosomal aberrations, gene mutations or IGHV mutation status. Refining biologic categories may help to improve clinical management with available and future treatment, lymphoma/leukemia celllines and non-tumour cells of the microenvironment can be used for models to better categorize biologic CLL entities. We used Affymetrix Exon 1.0 ST microarrays to investigate differences in CLL biology.
Project description:To identify potential target genes of leukemia-related miRNAs such as miR-196b and miR-150 in human MLL-associated leukemia, we performed Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow (including 3 each of CD34+, CD33+, and MNC) cell samples. A total of 15 MLL-associated (9 primary untreated leukemia and 6 leukemia cell line) samples and 9 human normal bone marrow samples (including 3 each of CD34+ hematopoietic stem/progenitor, CD33+ myeloid, and mononuclear cell (MNC) samples) were analyzed by use of Affymetrix Human Exon 1.0 ST arrays (Affymetirx, Santa Clara, CA).
Project description:Failure to achieve complete elimination of triple negative breast cancer (TNBC) stem cells after adjuvant therapy is associated with poor outcomes. Aldehyde dehydrogenase 1 (ALDH1) is a marker of breast cancer stem cells (BCSCs), and its enzymatic activity regulates tumor stemness. Identifying upstream targets to control ALDH+ cells may facilitate TNBC tumor suppression. Here, we show that KK-LC-1 determines the stemness of TNBC ALDH+ cells via binding with FAT1 and subsequently promoting its ubiquitination and degradation. This compromised the Hippo pathway and led to nuclear translocation of YAP1 and ALDH1A1 transcription. These findings identified the KK-LC-1-FAT1-Hippo-ALDH1A1 pathway in TNBC ALDH+ cells as a therapeutic target. To reverse the malignancy due to KK-LC-1 expression, we employed a novel computational approach and discovered Z839878730 (Z8) as an small-molecule inhibitor which may disrupt KK-LC-1 and FAT1 binding. We demonstrate that Z8 suppressed TNBC tumor growth via a mechanism that reactivated the Hippo pathway and decreased TNBC ALDH+ cell stemness and viability.
Project description:Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC “stemness”. Using single cell RNAseq analysis, we identify a master regulator PU.1, whose LSC-specific expression determines the molecular signature and activity of LSC in the Pten-null T-ALL model. Although initiated by PTEN controlled β-catenin activation, PU.1 expression and LSC “stemness” are maintained by a β-catenin-PU.1-TIM-3 feedback loop, independent of the leukemogenic driver mutation. Perturbing any component of this loop, either genetically or pharmacologically, can prevent LSC formation or eradicate existing LSCs. LSCs lose their “stemness” when PU.1 expression is silenced by DNA methylation, which can be reactivated by 5-AZ. Importantly similar regulatory mechanisms are also present in human T-ALLs.
Project description:Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC “stemness”. Using single cell RNAseq analysis, we identify a master regulator PU.1, whose LSC-specific expression determines the molecular signature and activity of LSC in the Pten-null T-ALL model. Although initiated by PTEN controlled β-catenin activation, PU.1 expression and LSC “stemness” are maintained by a β-catenin-PU.1-TIM-3 feedback loop, independent of the leukemogenic driver mutation. Perturbing any component of this loop, either genetically or pharmacologically, can prevent LSC formation or eradicate existing LSCs. LSCs lose their “stemness” when PU.1 expression is silenced by DNA methylation, which can be reactivated by 5-AZ. Importantly similar regulatory mechanisms are also present in human T-ALLs.
