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Intra-tumor heterogeneity caused by clonal evolution is a major problem in cancer treatment. To address this problem, we performed label-free quantitative proteomics on primary acute myeloid leukemia (AML) samples. We identified 50 leukemia-enriched plasma membrane proteins enabling the prospective isolation of genetically distinct subclones from individual AML patients. Subclones differed in their regulatory phenotype, drug sensitivity, growth, and engraftment behavior, as determined by RNA sequencing, DNase I hypersensitive site mapping, transcription factor occupancy analysis, in vitro culture, and xenograft transplantation. Finally, we show that these markers can be used to identify and longitudinally track distinct leukemic clones in patients in routine diagnostics. Our study describes a strategy for a major improvement in stratifying cancer diagnosis and treatment.
Pubmed ID: 30245083 RIS Download
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Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsSoftware application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
View all literature mentionsThis unknown targets Rabbit IgG Control
View all literature mentionsThis monoclonal targets Prokaryotic recombninant protein corresponding to external domain
View all literature mentionsThis monoclonal targets Human CD117 (CD117 (C-kit); c-kit; SCF receptor)
View all literature mentionsThis monoclonal targets CD34
View all literature mentionsThis monoclonal targets CD7
View all literature mentionsThis monoclonal targets CD49e
View all literature mentionsThis monoclonal targets CD135
View all literature mentionsThis monoclonal targets CD47
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets CD34
View all literature mentionsThis monoclonal targets CD22
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets CD366
View all literature mentionsThis monoclonal targets CD103
View all literature mentionsThis monoclonal targets CD49f
View all literature mentionsThis monoclonal targets CD123
View all literature mentionsThis monoclonal targets CD45RA
View all literature mentionsThis monoclonal targets CD99
View all literature mentionsThis monoclonal targets CD97
View all literature mentionsThis monoclonal targets CD82
View all literature mentionsThis monoclonal targets CD25
View all literature mentionsThis polyclonal targets Human GATA-2
View all literature mentionsThis monoclonal targets SEMA4D
View all literature mentionsThis monoclonal targets Human CD155 / PVR
View all literature mentionsThis monoclonal targets Human JAM-C Phycoerythrin MAb (Clone 208212)
View all literature mentionsThis unknown targets Human Integrin beta 7
View all literature mentionsThis monoclonal targets Human IL-6 R
View all literature mentionsThis monoclonal targets Human IL-1 RAcP/IL-1 R3 Phycoerythrin MAb (Cl 89412)
View all literature mentionsThis monoclonal targets Human IFN-gamma R1
View all literature mentionsThis monoclonal targets Human ESAM
View all literature mentionsThis monoclonal targets Human MICL Phycoerythrin MAb (Cl 687317)
View all literature mentionsThis monoclonal targets Human MMR/CD206 Phycoerythrin MAb (Clone 685641)
View all literature mentionsThis monoclonal targets Human CD200 Phycoerythrin MAb (Clone 325516)
View all literature mentionsThis monoclonal targets Human CD151
View all literature mentionsGraphic design software which can be used for vector illustration and page layout, web design, and photo editing. Features include: search, preview, application and transformation capabilities for both vector pattern and bitmap pattern fills; a fill engine with complete control over fountain, bitmap pattern and vector pattern fills; templates for website design; and vector shaping and page layout tools.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsSoftware package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
View all literature mentionsBioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsUltrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
View all literature mentionsSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
View all literature mentionsSoftware for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsA quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.
View all literature mentionsCell line MS-5 [Mouse bone marrow] is a Stromal cell line with a species of origin Mus musculus
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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