-
Genes Nov 2023Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For... (Review)
Review
Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. At the same time, protein content (and its post-translational status) largely determines the cell's state and behavior. Such a forced extrapolation of conclusions from the transcriptome to the proteome often seems unjustified. The ratios of "transcript-protein" pairs can vary by several orders of magnitude for different genes. As a rule, the correlation coefficient between transcriptome-proteome levels for different tissues does not exceed 0.3-0.5. Several characteristics determine the ratio between the content of mRNA and protein: among them, the rate of movement of the ribosome along the mRNA and the number of free ribosomes in the cell, the availability of tRNA, the secondary structure, and the localization of the transcript. The technical features of the experimental methods also significantly influence the levels of the transcript and protein of the corresponding gene on the outcome of the comparison. Given the above biological features and the performance of experimental and bioinformatic approaches, one may develop various models to predict proteomic profiles based on transcriptomic data. This review is devoted to the ability of RNA sequencing methods for protein abundance prediction.
Topics: Proteome; Proteomics; Gene Expression Profiling; Transcriptome; RNA, Messenger
PubMed: 38003008
DOI: 10.3390/genes14112065 -
Platelets Dec 2023Research into the natural aging process of platelets has garnered much research interest in recent years, and there have long been associations drawn between the... (Review)
Review
Research into the natural aging process of platelets has garnered much research interest in recent years, and there have long been associations drawn between the proportion of newly formed platelets in the circulation and the risk of thrombosis. However, these observations have largely been demonstrated in patient groups in which there may be underlying systemic changes that effect platelet function. Recent advances in technology have allowed in-depth analysis of differently aged platelets isolated from the peripheral blood of healthy individuals and have demonstrated that aged platelets, often referred to as senescent platelets, undergo extensive changes in the transcriptome and proteome. Ultimately, these changes result in platelets whose functions have deteriorated such that they cannot partake in hemostatic responses to the same extent as newly formed platelets. Here, we review transcriptomic and proteomic research in platelet aging in the context of health and how this research sheds light upon alterations in platelet structure and function.
Topics: Humans; Aged; Transcriptome; Proteome; Proteomics; Blood Platelets; Aging
PubMed: 37070955
DOI: 10.1080/09537104.2023.2200838 -
The EMBO Journal Dec 2023Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well as high-content...
Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well as high-content molecular profiling technologies. The current work adds to these approaches by providing a comprehensive and quantitative protein expression map of 13 anatomically distinct brain regions covering more than 11,000 proteins. This was enabled by the optimization, characterization, and implementation of a high-sensitivity and high-throughput microflow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable of analyzing more than 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material. Analysis of this proteomic resource highlighted brain region-enriched protein expression patterns and functional protein classes, protein localization differences between brain regions and individual markers for specific areas. To facilitate access to and ease further mining of the data by the scientific community, all data can be explored online in a purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de).
Topics: Humans; Chromatography, Liquid; Proteomics; Paraffin Embedding; Tandem Mass Spectrometry; Proteins; Brain; Proteome
PubMed: 37916885
DOI: 10.15252/embj.2023114665 -
Scientific Reports Sep 2023In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We...
In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG's capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.
Topics: Humans; Animals; Mice; Disease Models, Animal; Phosphatidylinositol 3-Kinases; Proteomics; TOR Serine-Threonine Kinases; Colonic Neoplasms; Phosphoproteins; Proteome; Streptococcus gallolyticus subspecies gallolyticus; Signal Transduction
PubMed: 37696912
DOI: 10.1038/s41598-023-41951-3 -
ELife Jan 2024Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and...
Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked to longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using deep proteomic profiling, we systemically profiled lysosome-associated proteins linked with four different longevity mechanisms. We discovered the lysosomal recruitment of AMP-activated protein kinase and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we further elucidated lysosomal heterogeneity across tissues as well as the increased enrichment of the Ragulator complex on Cystinosin-positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity across multiple scales and provides resources for understanding the contribution of lysosomal protein dynamics to signal transduction, organelle crosstalk, and organism longevity.
Topics: Proteomics; Lysosomes; Intracellular Membranes; Proteome; Signal Transduction
PubMed: 38240316
DOI: 10.7554/eLife.85214 -
Nature Communications Jul 2023African trypanosomes are dixenous eukaryotic parasites that impose a significant human and veterinary disease burden on sub-Saharan Africa. Diversity between species and...
African trypanosomes are dixenous eukaryotic parasites that impose a significant human and veterinary disease burden on sub-Saharan Africa. Diversity between species and life-cycle stages is concomitant with distinct host and tissue tropisms within this group. Here, the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, are mapped across two life-stages. The four resulting datasets provide evidence of expression of approximately 5500 proteins per cell-type. Over 2500 proteins per cell-type are classified to specific subcellular compartments, providing four comprehensive spatial proteomes. Comparative analysis reveals key routes of parasitic adaptation to different biological niches and provides insight into the molecular basis for diversity within and between these pathogen species.
Topics: Humans; Animals; Trypanosomiasis, African; Tsetse Flies; Proteome; Proteomics; Trypanosoma brucei brucei; Trypanosoma congolense
PubMed: 37479728
DOI: 10.1038/s41467-023-40125-z -
Journal of Proteome Research Aug 2023Thermal proteome profiling (TPP) provides a powerful approach to studying proteome-wide interactions of small therapeutic molecules and their target and off-target... (Comparative Study)
Comparative Study
Thermal proteome profiling (TPP) provides a powerful approach to studying proteome-wide interactions of small therapeutic molecules and their target and off-target proteins, complementing phenotypic-based drug screens. Detecting differences in thermal stability due to target engagement requires high quantitative accuracy and consistent detection. Isobaric tandem mass tags (TMTs) are used to multiplex samples and increase quantification precision in TPP analysis by data-dependent acquisition (DDA). However, advances in data-independent acquisition (DIA) can provide higher sensitivity and protein coverage with reduced costs and sample preparation steps. Herein, we explored the performance of different DIA-based label-free quantification approaches compared to TMT-DDA for thermal shift quantitation. Acute myeloid leukemia cells were treated with losmapimod, a known inhibitor of MAPK14 (p38α). Label-free DIA approaches, and particularly the library-free mode in DIA-NN, were comparable of TMT-DDA in their ability to detect target engagement of losmapimod with MAPK14 and one of its downstream targets, MAPKAPK3. Using DIA for thermal shift quantitation is a cost-effective alternative to labeled quantitation in the TPP pipeline.
Topics: Mass Spectrometry; Mitogen-Activated Protein Kinase 14; Proteome; Proteomics
PubMed: 37439223
DOI: 10.1021/acs.jproteome.3c00111 -
Molecular & Cellular Proteomics : MCP Sep 2023Myeloid-derived suppressor cells (MDSC) are a heterogeneous cell population of incompletely differentiated immune cells. They are known to suppress T cell activity and...
Myeloid-derived suppressor cells (MDSC) are a heterogeneous cell population of incompletely differentiated immune cells. They are known to suppress T cell activity and are implicated in multiple chronic diseases, which make them an attractive cell population for drug discovery. Here, we characterized the baseline proteomes and phospho-proteomes of mouse MDSC differentiated from a progenitor cell line to a depth of 7000 proteins and phosphorylation sites. We also validated the cellular system for drug discovery by recapitulating and identifying known and novel molecular responses to the well-studied MDSC drugs entinostat and mocetinostat. We established a high-throughput drug screening platform using a MDSC/T cell coculture system and assessed the effects of ∼21,000 small molecule compounds on T cell proliferation and IFN-γ secretion to identify novel MDSC modulator. The most promising candidates were validated in a human MDSC system, and subsequent proteomic experiments showed significant upregulation of several proteins associated with the reduction of reactive oxygen species (ROS). Proteome-wide solvent-induced protein stability assays identified Acyp1 and Cd74 as potential targets, and the ROS-reducing drug phenotype was validated by measuring ROS levels in cells in response to compound, suggesting a potential mode of action. We anticipate that the data and chemical tools developed in this study will be valuable for further research on MDSC and related drug discovery.
Topics: Mice; Humans; Animals; Myeloid-Derived Suppressor Cells; High-Throughput Screening Assays; Proteome; Proteomics; Reactive Oxygen Species
PubMed: 37586548
DOI: 10.1016/j.mcpro.2023.100632 -
Journal of the American Society For... Oct 2023Bacteria are orders of magnitude smaller than mammalian cells, and while single cell proteomics (SCP) currently detects and quantifies several thousands of proteins per...
Bacteria are orders of magnitude smaller than mammalian cells, and while single cell proteomics (SCP) currently detects and quantifies several thousands of proteins per mammalian cell, it is not clear whether conventional SCP methods will be suitable for bacteria. Here we report on the first successful attempt to detect proteins from individual bacteria, with validation of our findings by comparison with two bacteria samples and bulk proteomics data. Data are available via ProteomeXchange with the identifier PXD043473.
Topics: Bacteria; Escherichia coli; Proteome; Proteomics
PubMed: 37713396
DOI: 10.1021/jasms.3c00242 -
Molecular & Cellular Proteomics : MCP Aug 2023Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used...
Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; DO) labeling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from two individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of "older" less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
Topics: Humans; Muscular Dystrophy, Facioscapulohumeral; Proteome; Proteomics; Homeodomain Proteins; Myoblasts; Muscle, Skeletal
PubMed: 37353005
DOI: 10.1016/j.mcpro.2023.100605