Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH-MS data, a st...
Source: Molecular Systems Biology - August 13, 2018 Category: Molecular Biology Authors: Ludwig, C., Gillet, L., Rosenberger, G., Amon, S., Collins, B. C., Aebersold, R. Tags: Genome-Scale & Integrative Biology, Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics Reviews Source Type: research
Tumor-stroma interactions differentially alter drug sensitivity based on the origin of stromal cells
Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large-scale coculture assay optimized to measure drug-induced cell death, we identify tumor–stroma interactions that modulate drug sensitivity. Our data show that the chemo-insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these ...
Source: Molecular Systems Biology - August 6, 2018 Category: Molecular Biology Authors: Landry, B. D., Leete, T., Richards, R., Cruz-Gordillo, P., Schwartz, H. R., Honeywell, M. E., Ren, G., Schwartz, A. D., Peyton, S. R., Lee, M. J. Tags: Cancer, Genome-Scale & Integrative Biology Articles Source Type: research
Metabolic oscillations on the circadian time scale in Drosophila cells lacking clock genes
Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 h. Current models propose that transcriptional feedback loops are the primary mechanism for the generation of circadian oscillations. Within this framework, Drosophila S2 cells are regarded as "non-rhythmic" cells, as they do not express several canonical circadian components. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products, and in particular metabo...
Source: Molecular Systems Biology - August 2, 2018 Category: Molecular Biology Authors: Rey, G., Milev, N. B., Valekunja, U. K., Ch, R., Ray, S., Silva Dos Santos, M., Nagy, A. D., Antrobus, R., MacRae, J. I., Reddy, A. B. Tags: Genome-Scale & Integrative Biology, Metabolism, Quantitative Biology & Dynamical Systems Articles Source Type: research
Structured Methods for reproducible science
Detailed and accurate documentation of the reagents, tools and methods used in a study is key for reproducible science. However, the information provided in the Materials and Methods section is not always sufficiently detailed to allow for the adoption of methodologies across laboratories. Substantial time and effort, as well as extensive correspondence with the authors of a published paper, is often required in order to obtain all the relevant information related to a particular technique. Even after following a trail of references that frequently lead to a paper published decades ago, it is sometimes impossible to find a...
Source: Molecular Systems Biology - July 24, 2018 Category: Molecular Biology Authors: Polychronidou, M. Tags: Editorial Source Type: research
Two protein/protein interaction assays in one go
Discovering and characterizing protein–protein interactions (PPIs) that contribute to cellular homeostasis, development, and disease is a key priority in proteomics. Numerous assays for protein–protein interactions have been developed, but each one comes with its own strengths, weaknesses, and false-positive/false-negative rates. Therefore, it seems rather intuitive that combining multiple assays is beneficial for robust and reliable discovery of interactions. Along those lines, in their recent study, W.er and colleagues (Trepte et al, 2018) combined two complementary and quantitative interaction assays in...
Source: Molecular Systems Biology - July 18, 2018 Category: Molecular Biology Authors: Taipale, M. Tags: Genome-Scale & Integrative Biology, Methods & Resources, Network Biology News [amp ] Views Source Type: research
Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C
In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact...
Source: Molecular Systems Biology - July 16, 2018 Category: Molecular Biology Authors: Muller, H., Scolari, V. F., Agier, N., Piazza, A., Thierry, A., Mercy, G., Descorps-Declere, S., Lazar-Stefanita, L., Espeli, O., Llorente, B., Fischer, G., Mozziconacci, J., Koszul, R. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Methods & Resources Articles Source Type: research
LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells
Information on protein–protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double-readout bioluminescence-based two-hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence-based co-precipitation (LuC). The double-readout procedure detects interactions with higher...
Source: Molecular Systems Biology - July 11, 2018 Category: Molecular Biology Authors: Trepte, P., Kruse, S., Kostova, S., Hoffmann, S., Buntru, A., Tempelmeier, A., Secker, C., Diez, L., Schulz, A., Klockmeier, K., Zenkner, M., Golusik, S., Rau, K., Schnoegl, S., Garner, C. C., Wanker, E. E. Tags: Genome-Scale & Integrative Biology, Methods & Resources, Network Biology Source Type: research
Thermal proteome profiling in bacteria: probing protein state in vivo
In conclusion, we demonstrate that TPP can be used in bacteria to probe protein complex architecture, metabolic pathways, and intracellular drug target engagement. (Source: Molecular Systems Biology)
Source: Molecular Systems Biology - July 6, 2018 Category: Molecular Biology Authors: Mateus, A., Bobonis, J., Kurzawa, N., Stein, F., Helm, D., Hevler, J., Typas, A., Savitski, M. M. Tags: Genome-Scale & Integrative Biology, Microbiology, Virology & Host Pathogen Interaction, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research
Quantifying compartment-associated variations of protein abundance in proteomics data
Quantitative mass spectrometry enables to monitor the abundance of thousands of proteins across biological conditions. Currently, most data analysis approaches rely on the assumption that the majority of the observed proteins remain unchanged across compared samples. Thus, gross morphological differences between cell states, deriving from, e.g., differences in size or number of organelles, are often not taken into account. Here, we analyzed multiple published datasets and frequently observed that proteins associated with a particular cellular compartment collectively increase or decrease in their abundance between conditio...
Source: Molecular Systems Biology - July 2, 2018 Category: Molecular Biology Authors: Parca, L., Beck, M., Bork, P., Ori, A. Tags: Genome-Scale & Integrative Biology, Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics Source Type: research
Integrative multi-omics analysis of intestinal organoid differentiation
Intestinal organoids accurately recapitulate epithelial homeostasis in vivo, thereby representing a powerful in vitro system to investigate lineage specification and cellular differentiation. Here, we applied a multi-omics framework on stem cell-enriched and stem cell-depleted mouse intestinal organoids to obtain a holistic view of the molecular mechanisms that drive differential gene expression during adult intestinal stem cell differentiation. Our data revealed a global rewiring of the transcriptome and proteome between intestinal stem cells and enterocytes, with the majority of dynamic protein expression being...
Source: Molecular Systems Biology - June 26, 2018 Category: Molecular Biology Authors: Lindeboom, R. G., van Voorthuijsen, L., Oost, K. C., Rodriguez-Colman, M. J., Luna-Velez, M. V., Furlan, C., Baraille, F., Jansen, P. W., Ribeiro, A., Burgering, B. M., Snippert, H. J., Vermeulen, M. Tags: Development & Differentiation, Genome-Scale & Integrative Biology, Stem Cells Articles Source Type: research
Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli
Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image-based quantitative screen of the single-gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division. Functional analyses, together with high-dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionall...
Source: Molecular Systems Biology - June 25, 2018 Category: Molecular Biology Authors: Campos, M., Govers, S. K., Irnov, I., Dobihal, G. S., Cornet, F., Jacobs-Wagner, C. Tags: Genome-Scale & Integrative Biology, Methods & Resources, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research
Pairing off: a bottom-up approach to the human gut microbiome
The human gut microbiome has been implicated in a variety of health outcomes, and extensive research has aimed to understand its composition and function, primarily via metagenomic analyses. An examination of how the microbiome develops and interacts through interspecies competition and cooperation has been lacking so far. In their recent work, Venturelli et al (2018) build a synthetic gut community and accurately predict its dynamics with a simple network of pairwise interactions. (Source: Molecular Systems Biology)
Source: Molecular Systems Biology - June 21, 2018 Category: Molecular Biology Authors: Abreu, C., Ortiz Lopez, A., Gore, J. Tags: Microbiology, Virology & Host Pathogen Interaction, Quantitative Biology & Dynamical Systems, Synthetic Biology & Biotechnology News [amp ] Views Source Type: research
Deciphering microbial interactions in synthetic human gut microbiome communities
The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological driver...
Source: Molecular Systems Biology - June 21, 2018 Category: Molecular Biology Authors: Venturelli, O. S., Carr, A. C., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S., Northen, T., Arkin, A. P. Tags: Microbiology, Virology & Host Pathogen Interaction, Quantitative Biology & Dynamical Systems, Synthetic Biology & Biotechnology Articles Source Type: research
Multi-Omics Factor Analysis--a framework for unsupervised integration of multi-omics data sets
We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities. The learnt factors enable a variety of downstream analyses, including identification of sample subgroups, data imputation and the detection of outlier samples. We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profile...
Source: Molecular Systems Biology - June 20, 2018 Category: Molecular Biology Authors: Argelaguet, R., Velten, B., Arnol, D., Dietrich, S., Zenz, T., Marioni, J. C., Buettner, F., Huber, W., Stegle, O. Tags: Computational Biology, Genome-Scale & Integrative Biology, Methods & Resources Source Type: research
Computer-aided biochemical programming of synthetic microreactors as diagnostic devices
(Source: Molecular Systems Biology)
Source: Molecular Systems Biology - June 1, 2018 Category: Molecular Biology Authors: Courbet, A., Amar, P., Fages, F., Renard, E., Molina, F. Tags: Corrigendum Source Type: research
