Creation of a human T-ALL cell line online database.
Ontology highlight
ABSTRACT:
SUBMITTER: Squiban B
PROVIDER: S-EPMC5526728 | biostudies-literature | 2017 Nov
REPOSITORIES: biostudies-literature
Publications
Creation of a human T-ALL cell line online database.
Squiban Barbara B Ahmed Syed Talha ST Frazer J Kimble JK
Leukemia & lymphoma 20170613 11
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Project description:BackgroundCell-based and chimerism-based therapies represent a promising approach for tolerance induction in transplantation. We propose a new cell therapy of the ex vivo created human hematopoietic chimeric cells (HHCC) as an alternative approach to bone marrow (BM)-based therapies in support of solid organ and vascularized composite allotransplantation (VCA). This study aimed to characterize in vitro the phenotype, genotype, clonogenic, and tolerogenic properties of HHCC.MethodsThirty ex vivo fusions of CD34+ cells from two unrelated human BM donors were performed. CD34+ cells were stained separately with PKH26 and PKH67 membrane dyes and fused using polyethylene glycol (PEG). Creation of human HHCC and chimeric state was confirmed by flow cytometry (FC), confocal microscopy (CM) and electron microscopy (EM). HHCC's phenotype (CD34, CD133, CD117, CD4, CD19, CD4/CD25) was assessed by FC, viability by Trypan Blue, LIVE/DEAD and apoptosis by AnnexinV/Sytox Blue and TUNEL assay, while mixed lymphocyte reaction (MLR) assay assessed HHCC's immunogenicity and tolerogenic properties. HHCC differentiation, proliferation and clonogenic potential were assessed by the colony forming unit (CFU). Polyploidy was evaluated by fluorescence in situ hybridization (FISH), whereas polymerase chain reaction-reverse sequence-specific oligonucleotide probe (PCR-rSSOP) and short tandem repeats-polymerase chain reaction (STR-PCR) assessed HHCC's genotype, and chimerism. Reverse transcription polymerase chain reaction (RT-PCR) analyzed cytokines secretion [interleukin (IL)-10, transforming growth factor-β (TGF-β) and tumor necrosis factor-α (TNF-α)] up to 14 days post-fusion.ResultsFC and CM confirmed creation of HHCC by fusion of CD34+ cells from two unrelated human donors. After fusion, maintenance of hematopoietic markers and increased expression of Treg-cells (CD4/CD25) was confirmed. Moreover, high HHCC viability (99%) and a low apoptosis rate (1.2%) were revealed HHCC presented decreased immunogenicity by MLR, and significant, 40-fold increase of IL-10 the pro-tolerogenic cytokine at 21 days after fusion (RT-PCR) P<0.0001. The number of polyploid cells was negligible (0.48%). PCR-rSSOP of HHCC after fusion confirmed presence of human leukocyte antigen (HLA) class I and class II-alleles and presence of the loci specific for both CD34+ cells BM donors by STR-PCR.ConclusionsWe have created a new hematopoietic cell line of HHCC from two unrelated human donors, and have successfully characterized in vitro, viability, phenotype, genotype, clonogenic, and tolerogenic properties of HHCC. These unique immunomodulatory and tolerogenic properties introduce HHCC as a novel therapeutic approach for tolerance induction in VCA and solid organ transplantation.
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Project description:OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.
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Project description:BackgroundPolypharmacology plays an important part in drug discovery, and remains a major challenge in drug development. Identification of the underlying polypharmacology of a drug, as well as development of polypharmacological drugs, have become important issues in the pharmaceutical industry and academia.DescriptionHerein, through data mining of the Protein Data Bank (PDB), a free, Internet-accessible database called the Multiple Target Ligand Database (MTLD; www.mtdcadd.com) was constructed. The MTLD contains 1,732 multiple-target ligands (MTLs) which bind to 14,996 binding sites extracted from 12,759 PDB structures. Among MTLs, 222 entries are approved drugs and 1,334 entries are drug-like compounds. The MTLD could be an extremely useful tool in the development of polypharmacological drugs. It also sheds light on the side effects of drugs through anticipation of their multiple functions and similarities in the binding sites of multiple targets. The entire database is free for online searching, browsing, and downloading.ConclusionAs a crucial expansion of the PDB, increasing numbers of MTLs will be included in the MTLD. Eventually, it will become an efficient platform to obtain useful information on MTLs and their underlying polypharmacology.
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Project description:Flexible, rapid, and predictive approaches that do not require the use of large numbers of vertebrate test animals are needed because the chemical universe remains largely untested for potential hazards. Development of robust new approach methodologies and nontesting approaches requires the use of existing information via curated, integrated data sets. The ecological threshold of toxicological concern (ecoTTC) represents one such new approach methodology that can predict a conservative de minimis toxicity value for chemicals with little or no information available. For the creation of an ecoTTC tool, a large, diverse environmental data set was developed from multiple sources, with harmonization, characterization, and information quality assessment steps to ensure that the information could be effectively organized and mined. The resulting EnviroTox database contains 91 217 aquatic toxicity records representing 1563 species and 4016 unique Chemical Abstracts Service numbers and is a robust, curated database containing high-quality aquatic toxicity studies that are traceable to the original information source. Chemical-specific information is also linked to each record and includes physico-chemical information, chemical descriptors, and mode of action classifications. Toxicity data are associated with the physico-chemical data, mode of action classifications, and curated taxonomic information for the organisms tested. The EnviroTox platform also includes 3 analysis tools: a predicted-no-effect concentration calculator, an ecoTTC distribution tool, and a chemical toxicity distribution tool. Although the EnviroTox database and tools were originally developed to support ecoTTC analysis and development, they have broader applicability to the field of ecological risk assessment. Environ Toxicol Chem 2019;9999:1-12. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
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Project description:BackgroundPathway-oriented experimental and computational studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gene regulation events, and metabolic reaction events. A pathway consists of a series of molecular pathway events that link molecular entities such as proteins, genes, and metabolites. There are approximately 300 biological pathway resources as of April 2009 according to the Pathguide database; however, these pathway databases generally have poor coverage or poor quality, and are difficult to integrate, due to syntactic-level and semantic-level data incompatibilities.ResultsWe developed the Human Pathway Database (HPD) by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web sites. Integration of pathway data at syntactic, semantic, and schematic levels was based on a unified pathway data model and data warehousing-based integration techniques. HPD provides a comprehensive online view that connects human proteins, genes, RNA transcripts, enzymes, signaling events, metabolic reaction events, and gene regulatory events. At the time of this writing HPD includes 999 human pathways and more than 59,341 human molecular entities. The HPD software provides both a user-friendly Web interface for online use and a robust relational database backend for advanced pathway querying. This pathway tool enables users to 1) search for human pathways from different resources by simply entering genes/proteins involved in pathways or words appearing in pathway names, 2) analyze pathway-protein association, 3) study pathway-pathway similarity, and 4) build integrated pathway networks. We demonstrated the usage and characteristics of the new HPD through three breast cancer case studies.ConclusionHPD http://bio.informatics.iupui.edu/HPD is a new resource for searching, managing, and studying human biological pathways. Users of HPD can search against large collections of human biological pathways, compare related pathways and their molecular entity compositions, and build high-quality, expanded-scope disease pathway models. The current HPD software can help users address a wide range of pathway-related questions in human disease biology studies.
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Project description:We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de .
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Project description:Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG) was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry.BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure.By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.
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Project description:BackgroundAnalysis of the functional consequences and treatment response of rare CFTR variants is challenging due to the limited availability of primary airways cells.MethodsA Flp recombination target (FRT) site for stable expression of CFTR was incorporated into an immortalized CF bronchial epithelial cell line (CFBE41o-). CFTR cDNA was integrated into the FRT site. Expression was evaluated by western blotting and confocal microscopy and function measured by short circuit current. RNA sequencing was used to compare the transcriptional profile of the resulting CF8Flp cell line to primary cells and tissues.ResultsFunctional CFTR was expressed from integrated cDNA at the FRT site of the CF8Flp cell line at levels comparable to that seen in native airway cells. CF8Flp cells expressing WT-CFTR have a stable transcriptome comparable to that of primary cultured airway epithelial cells, including genes that play key roles in CFTR pathways.ConclusionCF8Flp cells provide a viable substitute for primary CF airway cells for the analysis of CFTR variants in a native context.
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Project description:Circular RNA (circRNA) is a highly stable, single-stranded, closed-loop RNA that works as RNA or as a protein decoy to regulate gene expression. In humans, thousands of circRNA transcriptional products precisely express in specific developmental stages, tissues and cell types. Due to their stability and specificity, circRNAs are ideal biomarkers for cancer diagnosis and prognosis. To provide an integrated and standardized circRNA expression profile for human cancers, we performed extensive data curation across 11 technical platforms, collecting 48 expression profile data sets for 18 cancer types and amassing 860 751 expression records. We also identified 189 193 differential expression signatures that are significantly different between normal and cancer samples. All the pre-calculated expression analysis results are organized into 132 plain text files for bulk download. Our online interface, circExp, provides data browsing and search functions. For each data set, a dynamic expression heatmap provides a profile overview. Based on the processed data, we found that 52 circRNAs were consistently and differentially expressed in 20 or more processed analyses. By mapping those circRNAs to their parent protein-coding genes, we found that they may have profoundly affected the survival of 10 797 patients in the The Cancer Genome Atlas pan-cancer data set. In sum, we developed circExp and demonstrated that it is useful to identify circRNAs that have potential diagnostic and prognostic significance for a variety of cancer types. In this online and reusable database, found at http://soft.bioinfo-minzhao.org/circexp, we have provided pre-calculated expression data about circRNAs and their parental genes, as well as data browsing and searching functions. Database URL: http://soft.bioinfominzhao.org/circexp/.
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