Project description:Despite ethical concerns and scientific drawbacks, fetal bovine serum (FBS) remains a common supplement of culture media for continuous cancer cell lines. FBS alternatives like human platelet lysate (hPL) as well as animal-component free, chemically defined media (CDM) are commercially available for many years. Nevertheless, the acceptance of such alternative media is limited because data verifying the stability of the phenotype and function of a cell line in the alternative media are often lacking. Here, we have adapted four widely used human cancer cell lines (HELA, HL-60, JIMT-1, K-562) to hPL supplemented media and different CDM. To evaluate the suitability of the FBS-free replacements in comparison to the FBS media, we systematically analyzed the different cultures in respect to recovery after cryopreservation, STR-profiles, proliferation, morphology and their transcriptomes. Neither alterations in STR-profiles nor difficulties after cryopreservation were detected. With the exception of K-562, FBS-free cultures showed a reduced proliferation rate and, in some conditions, slight morphological alterations in comparison to FBS cultures. Transcriptome-wide GSEA indicated that culture media affected expression of genes involved in cholesterol homeostasis in all cell lines, and genes involved in epithelial-mesenchymal transition in HELA and JIMT-1. However, their overall phenotypes remained stable. Hematopoietic differentiation markers were among the differentially expressed genes of HL-60 and K-562 cultures, but their main phenotypes remained very similar which was further confirmed by successful induction of differentiation of HL-60 in FBS-free media. In summary, our multiparametric approach delivers validated data supporting the transition to FBS-free media for the analyzed cancer models.
Project description:Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) which show deregulation of developmental transcription factors (TFs), representing major oncogenic drivers. Analysis of TF activities in these developmental entities helps understanding both their normal and aberrant expression and regulatory connections. Here, we focused on NKL-subclass homeodomain TF NKX6-3 which is active in normal B-cell progenitors and TCF3::PBX1-positive BCP-ALL cases. Performing siRNA-mediated knockdown and forced expression experiments in BCP-ALL model cell lines, we established a gene regulatory network for NKX6-3 together with NKL-TFs HLX, MSX1 and HHEX, TALE-class homeodomain TFs MEIS1 and IRX1, ETS-TFs ERG, ETS2 and SPIB, and additionally with PAX5, EBF1 and IRF4. NKX6-3 and TCF3::PBX1 were found to be mutual activators, underlying their co-expression. Furthermore, comparative expression profiling analysis of BCP-ALL patients revealed TGFb-pathway inhibitor CD109 as downregulated target gene of NKX6-3. TGFb in turn enhanced NKX6-3 expression, indicating mutual activation. Finally, RNA-seq analysis of BCP-ALL cell line RCH-ACV after NKX6-3 knockdown revealed MPP7 as upregulated target gene of both, NKX6-3 and TCF3::PBX1. Elevated MPP7 expression indicated an oncogenic role of the HIPPO-pathway in TCF3::PBX1 positive BCP-ALL. Collectively, our data add novel players and regulatory connections to normal and aberrant TF-networks in B-cell progenitors which may serve as diagnostic markers or therapeutic targets.
Project description:Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is an anaplastic lymphoma kinase-negative (ALKneg) T-cell lymphoma. Here, we provide RNA-seq data of four BIA-ALCL and four ALCL cell lines:TLBR-1, TLBR-2, TLBR-3, TLBR-4 and DEL (two replicates), KARPAS-299, KI-JK, SUP-M2 (two replicates), respectively.
Project description:Continuous cell lines are important and commonly used in vitro models in breast cancer (BC) research. Selection of the appropriate model cell line is crucial and requires consideration of their molecular characteristics. To characterize BC cell line models in depth, we profiled a panel of 29 authenticated and publicly available BC cell lines by mRNA-sequencing, mutation analysis, and immunoblotting. Gene expression profiles separated BC cell lines in two major clusters that represent basal-like (mainly triple-negative BC) and luminal BC subtypes, respectively. HER2-positive cell lines were located within the luminal cluster. Mutation calling highlighted the frequent aberration of TP53 and BRCA2 in BC cell lines, which, therefore, share relevant characteristics with primary BC. Furthermore, we showed that the data can be used to find novel, potential oncogenic fusion transcripts, e.g., FGFR2::CRYBG1 and RTN4IP1::CRYBG1 in cell line MFM-223, and to elucidate the regulatory circuit of IRX genes and KLF15 as novel candidate tumor suppressor genes in BC. Our data indicated that KLF15 was activated by IRX1 and inhibited by IRX3. Moreover, KLF15 inhibited IRX1 in cell line HCC-1599. Each BC cell line carries unique molecular features. Therefore, the molecular characteristics of BC cell lines described here might serve as a valuable resource to improve the selection of appropriate models for BC research. Raw fastq files are also published at BioStudies: S-BSST1200.
Project description:Retaining the mutational pattern of tumors, immortalized cell lines represent excellent tools for the molecular study of genetic aberrations. Tumors can consist of subclones which develop under selective forces driven by mutational alterations. This explains why after therapy, relapsed clones can be genetically distinct from clones at diagnosis. We analyzed the mutational patterns of pairs of cell lines raised at early and late phases of development from patients with a hematopoietic tumor named pre-B acute lymphoblastic leukemia (ALL). All cell lines tested showed mutations that typically occur in this tumor. We also observed clonal differences in sister cell lines, genetic aberrations developing during disease progression. Especially noteworthy was the presence of two mutations which are hitherto undescribed in cell lines.
Project description:For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and virus contamination. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) of the hundred authenticated leukemia-lymphoma cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. This part captures RNA-Seq. This data set will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
Project description:For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and virus contamination. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) of the hundred authenticated leukemia-lymphoma cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. This part captures WES. This data set will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
Project description:Retaining the mutational pattern of tumors, immortalized cell lines represent excellent tools for the molecular study of genetic aberrations. Tumors can consist of subclones which develop under selective forces driven by mutational alterations. This explains why after therapy, relapsed clones can be genetically distinct from clones at diagnosis. We analyzed the mutational patterns of pairs of cell lines raised at early and late phases of development from patients with a hematopoietic tumor named pre-B acute lymphoblastic leukemia (ALL). All cell lines tested showed mutations that typically occur in this tumor. We also observed clonal differences in sister cell lines, genetic aberrations developing during disease progression. Especially noteworthy was the presence of two mutations which are hitherto undescribed in cell lines.
Project description:Patients suffering from chronic lymphocytic leukemia (CLL) display highly diverse clinical courses ranging from indolent cases to aggressive disease with genetic and epigenetic features resembling this diversity. Here, we developed a comprehensive approach combining a variety of molecular and clinical data to identify translocation events disrupting long-range chromatin interactions and causing cancer-relevant transcriptional deregulation. Thereby, we identified a B cell specific cis-regulatory element restricting the expression of genes in the associated locus, including PRMT5 and DAD1, two factors with oncogenic potential. Examining the role of PRMT5 in CLL identified transcriptional programs associated with pathways of stress tolerance and growth support, maintaining MYC-driven gene expression in vivo and in vitro. Conversely, inhibition of PRMT5 impairs factors involved in DNA-repair and sensitizes cells for apoptosis. Finally, we show that artificial deletion of the regulatory element from its endogenous context resulted in upregulation of corresponding genes, including PRMT5. Furthermore, such disruption renders PRMT5 transcription vulnerable to additional stimuli and subsequently also alters the expression of downstream PRMT5 targets.