A5005639182- Advanced Proteomics Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Advanced Biosensing Techniques and Applications
- Cancer-related Molecular Pathways
- Glioma Diagnosis and Treatment
- Cell Adhesion Molecules Research
- Glycosylation and Glycoproteins Research
- Immunotherapy and Immune Responses
- Single-cell and spatial transcriptomics
- Genetic factors in colorectal cancer
- Cancer Immunotherapy and Biomarkers
- Cancer-related gene regulation
- Nonmelanoma Skin Cancer Studies
- Radiomics and Machine Learning in Medical Imaging
- Cancer Cells and Metastasis
- RNA Research and Splicing
- Hedgehog Signaling Pathway Studies
- Colorectal Cancer Treatments and Studies
- Axon Guidance and Neuronal Signaling
- Cancer-related molecular mechanisms research
- Phagocytosis and Immune Regulation
Uppsala University
2015-2024
Science for Life Laboratory
2015-2024
Uppsala University Hospital
2008-2019
KTH Royal Institute of Technology
1995-2018
Sapienza University of Rome
2015
Leibniz Research Centre for Working Environment and Human Factors
2012-2014
TU Dortmund University
2012-2014
Memorial Hospital
2014
Zhongshan Hospital
2014
Miller Children's & Women's Hospital
2014
Resolving the molecular details of proteome variation in different tissues and organs human body will greatly increase our knowledge biology disease. Here, we present a map tissue based on an integrated omics approach that involves quantitative transcriptomics at organ level, combined with microarray–based immunohistochemistry, to achieve spatial localization proteins down single-cell level. Our tissue-based analysis detected more than 90% putative protein-coding genes. We used this explore...
Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies biology disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) classify tissue-specific genes representative set all major combined this antibody-based profiling same tissues. To present data, launch new version Human Protein Atlas that integrates RNA protein data corresponding ∼80% protein-coding access primary both on an individual...
Modeling the cancer transcriptome Recent initiatives such as The Cancer Genome Atlas have mapped genome-wide effect of individual genes on tumor growth. By unraveling genomic alterations in tumors, molecular subtypes cancers been identified, which is improving patient diagnostics and treatment. Uhlen et al. developed a computer-based modeling approach to examine different types nearly 8000 patients. They provide an open-access resource for exploring how expression specific influences...
Spatial structure of RNA expression RNA-seq and similar methods can record gene within among cells. Current typically lose positional information many require arduous single-cell isolation sequencing. Ståhl et al. have developed a way measuring the spatial distribution transcripts by annealing fixed brain or cancer tissue samples directly to bar-coded reverse transcriptase primers, performing transcription followed sequencing computational reconstruction, they do so for multiple genes....
Mapping the proteome Proteins function in context of their environment, so an understanding cellular processes requires a knowledge protein localization. Thul et al. used immunofluorescence microscopy to map 12,003 human proteins at single-cell level into 30 compartments and substructures (see Perspective by Horwitz Johnson). They validated results mass spectroscopy them model refine protein-protein interaction networks. The is highly spatiotemporally regulated. Many localize multiple...
Antibody-based proteomics provides a powerful approach for the functional study of human proteome involving systematic generation protein-specific affinity reagents. We used this strategy to construct comprehensive, antibody-based protein atlas expression and localization profiles in 48 normal tissues 20 different cancers. Here we report new publicly available database containing, first version, ∼400,000 high resolution images corresponding more than 700 antibodies toward proteins. Each...
Single-cell RNA analysis has been integrated with spatial protein profiling to create a single–cell type map of human tissues.
Tissue-based diagnostics and research is incessantly evolving with the development of new molecular tools. It has long been realized that immunohistochemistry can add an important level information on top morphology protein expression patterns in a cancer may yield crucial diagnostic prognostic information. We have generated immunohistochemistry-based map profiles normal tissues, cell lines. For each antibody, altogether 708 spots tissues cells are analysed resulting images data presented as...
Mapping the mammalian brain The diverse physiology of is reflected in its complex organization at regional, cellular, and subcellular levels. Sjöstedt et al. combined data—both newly acquired from other large-scale mapping projects—from transcriptomics, single-cell genomics, situ hybridization, antibody-based protein profiling to map molecular profiles human, pig, mouse brain. analysis consistent with a conserved basic architecture during evolution, but it does show differences regional gene...
Article18 February 2019Open Access Transparent process A deep proteome and transcriptome abundance atlas of 29 healthy human tissues Dongxue Wang orcid.org/0000-0002-4402-0690 Chair Proteomics Bioanalytics, Technische Universität München, Freising, Germany Search for more papers by this author Basak Eraslan Computational Biology, Department Informatics, Technical University Munich, Garching bei Biochemistry, Quantitative Biosciences Gene Center, Ludwig Maximilian Universität, Thomas Wieland...
Tumor associated macrophages (TAMs) are alternatively activated that enhance tumor progression by promoting cell invasion, migration and angiogenesis. TAMs have an anti-inflammatory function resembling M2 macrophages. CD163 is regarded as a highly specific monocyte/macrophage marker for In this study we evaluated the specificity of using macrophage TAM compared its prognostic value with more frequently used pan-macrophage CD68. We also analyzed localization CD163+ CD68+ myeloid cells in...
Abstract Background The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels and corresponding proteins. Therefore, to assess degrees this we compared profiles (determined using both cDNA- oligo-based microarrays) protein immunohistochemically tissue 1066 gene products 23 human cell lines. Results A high mean coefficient (0.52) was obtained from pairwise...
A blood cell protein-expression atlas Genome-wide analyses are increasingly providing resources for advances in basic and applied biomedical science. Uhlen et al. performed a global expression analysis of human types integrated this data with across all major tissues organs the protein atlas. This comprehensive compendium allows classification protein-coding genes regard to their tissue- cell-type distribution. Science , issue p. eaax9198
An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies the corresponding protein levels. Here, we have developed targeted proteomics approach set human non-secreted proteins based on parallel reaction monitoring measure, at steady-state conditions, absolute copy numbers across tissues and cell lines compared these with mRNA using transcriptomics. The study shows that do not correlate well unless gene-specific RNA-to-protein...
A database provides information on the relative abundances and locations of human proteins that are predicted to be secreted.
Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well predict prognosis and therapy response. So far, the value of these multigene signatures clinical practice is unclear, biologic importance individual genes difficult assess, published virtually do not overlap.Here, we describe a novel single institute cohort, including 196 non-small cancers (NSCLC) with information long-term follow-up. Gene array data were...
In this review, we present an update on the progress of Human Protein Atlas, with emphasis strategies for validating immunohistochemistry-based protein expression patterns and possibilities to extend map cancer research projects. The objectives underlying Atlas include (i) generation validated antibodies toward a major isoform all proteins encoded by human genome, (ii) creating information database in normal tissues, cells, cancer, (iii) utilizing generated data as tools identify clinically...
The special AT-rich sequence-binding protein 2 (SATB2), a nuclear matrix-associated transcription factor and epigenetic regulator, was identified as tissue type-specific when screening expression patterns in human normal cancer tissues using an antibody-based proteomics approach. In this respect, the SATB2 shows selective pattern of and, within cells epithelial lineages, is restricted to glandular lining lower gastrointestinal tract. primarily preserved colorectal origin, indicating that...
The testis' function is to produce haploid germ cells necessary for reproduction. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling characterize the molecular components of testis. Deep sequencing (RNA-Seq) normal human testicular tissue from seven individuals was performed and compared 26 other types. All 20 050 putative genes were classified into categories based on expression patterns. shows that testis most tissue-specific by...
A decade on from the completion of Human Genome, Protein Atlas, a multinational research project supported by non-profit Knut and Alice Wallenberg Foundation, recently launched (November 6, 2014) an open source tissue-based interactive map human proteome. team multidisciplinary researchers with expertise spanning biotechnology, information technology, medicine have used combination several 'omics technologies to proteins down single cell level, showing both restricted certain tissues—such as...