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Integrative proteogenomics for differential expression and splicing variation in a DM1 mouse model
Mol Cell Proteomics. 2023 Nov 20:100683. doi: 10.1016/j.mcpro.2023.100683. Online ahead of print.ABSTRACTDysregulated mRNA splicing is involved in the pathogenesis of many diseases including cancer, neurodegenerative diseases, and muscular dystrophies such as myotonic dystrophy type 1 (DM1). Comprehensive assessment of dysregulated splicing on the transcriptome and proteome level has been methodologically challenging, and thus investigations have often been targeting only few genes. Here, we performed a large-scale coordinated transcriptomic and proteomic analysis to characterize a DM1 mouse model (HSALR) in comparison to ...
Source: Molecular and Cellular Proteomics : MCP - November 22, 2023 Category: Molecular Biology Authors: Elizaveta M Solovyeva Stephan Utzinger Alexandra Vissi ères Joanna Mitchelmore Erik Ahrn é Erwin Hermes Tania Poetsch Marie Ronco Michael Bidinosti Claudia Merkl Fabrizio C Serluca James Fessenden Ulrike Naumann Hans Voshol Angelika S Meyer Sebastian Ho Source Type: research

Glycan complexity and heterogeneity of glycoproteins in somatic extracts and secretome of the infective stage of the helminth Fasciola hepatica
This study opens many avenues to understand glycan biology of F. hepatica throughout its life-stages, as well as other helminth parasites, and allows us to probe the glycosylation of individual NEJs proteins in the search for innovative diagnostics and vaccines against fascioliasis.PMID:37993102 | DOI:10.1016/j.mcpro.2023.100684 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - November 22, 2023 Category: Molecular Biology Authors: Carolina De Marco Verissimo Krystyna Cwiklinski Jonas Nilsson Ekaterina Mirgorodskaya Chunsheng Jin Niclas G Karlsson John P Dalton Source Type: research

IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining
This study aims to build a repository of phosphosites with associated evidence in biomedical abstracts by applying deep learning-based natural language processing techniques (NLP). Our model for illuminating the dark phosphoproteome through PubMed mining (IDPpub) was generated by fine-tuning BioBERT using sentences containing protein substrates and phosphorylation site positions from 3000 abstracts. The IDPpub model was then used to extract phosphorylation sites from all abstracts in MEDLINE. The extracted proteins were normalized to gene symbols using NCBI gene query and sites were mapped to human UniProt sequences using ...
Source: Molecular and Cellular Proteomics : MCP - November 22, 2023 Category: Molecular Biology Authors: Sara R Savage Yaoyun Zhang Eric J Jaehnig Yuxing Liao Zhiao Shi Huy Anh Pham Hua Xu Bing Zhang Source Type: research

Influence of the Heme Nitric Oxide / Oxygen Binding Protein (H-NOX) on cell cycle regulation in Caulobacter crescentus
Mol Cell Proteomics. 2023 Nov 16:100679. doi: 10.1016/j.mcpro.2023.100679. Online ahead of print.ABSTRACTThe ability of an organism to respond to environmental changes is paramount to survival across a range of conditions. The bacterial Heme Nitric Oxide/Oxygen binding proteins (H-NOX) are a family of biofilm regulating gas sensors that enable bacteria to respond accordingly to the cytotoxic molecule nitric oxide (NO). By interacting with downstream signaling partners, H-NOX regulates the production of the bacterial secondary messenger c-di-GMP to influence biofilm formation. The aquatic organism Caulobacter crescentus has...
Source: Molecular and Cellular Proteomics : MCP - November 18, 2023 Category: Molecular Biology Authors: Cameron Lee-Lopez Shariful Islam Ady B Mel éndez Erik T Yukl Source Type: research

Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles
Mol Cell Proteomics. 2023 Nov 10:100678. doi: 10.1016/j.mcpro.2023.100678. Online ahead of print.ABSTRACTMicroglia are resident immune cells of the brain that play important roles in mediating inflammatory responses in several neurological diseases via direct and indirect mechanisms. One indirect mechanism may involve extracellular vesicle (EV) release, so that the molecular cargo transported by microglia-derived EVs can have functional effects by facilitating intercellular communication. The molecular composition of microglia-derived EVs, and how microglial activation states impacts EV composition and EV-mediated effects ...
Source: Molecular and Cellular Proteomics : MCP - November 12, 2023 Category: Molecular Biology Authors: Juliet V Santiago Aditya Natu Christina C Ramelow Sruti Rayaprolu Hailian Xiao Vishnu Kumar Prateek Kumar Nicholas T Seyfried Srikant Rangaraju Source Type: research

Synaptic involvement of the human amygdala in Parkinson's disease
Mol Cell Proteomics. 2023 Oct 27:100673. doi: 10.1016/j.mcpro.2023.100673. Online ahead of print.ABSTRACTα-Synuclein, a protein mostly present in presynaptic terminals, accumulates neuropathologically in Parkinson's disease in a 6-stage sequence and propagates in the nervous system in a prion-like manner through neurons and glia. In stage 3, the substantia nigra are affected, provoking motor symptoms, and the amygdaloid complex, leading to different nonmotor symptoms; from here synucleinopathy spreads to the temporal cortex and beyond. The expected increase in Parkinson's disease incidence accelerates the need for detecti...
Source: Molecular and Cellular Proteomics : MCP - November 10, 2023 Category: Molecular Biology Authors: Sandra Villar-Conde Veronica Astillero-Lopez Melania Gonzalez-Rodriguez Daniel Saiz-Sanchez Alino Martinez-Marcos Isabel Ubeda-Banon Alicia Flores-Cuadrado Source Type: research

Application of liquid-liquid extraction for N-terminal myristoylation proteomics
Mol Cell Proteomics. 2023 Nov 8:100677. doi: 10.1016/j.mcpro.2023.100677. Online ahead of print.ABSTRACTProteins can be modified by lipids in various ways, for example by myristoylation, palmitoylation, farnesylation, and geranylgeranylation-these processes are collectively referred to as lipidation. Current chemical proteomics using alkyne lipids has enabled the identification of lipidated protein candidates but does not identify endogenous lipidation sites and is not readily applicable to in vivo systems. Here, we introduce a proteomic methodology for global analysis of endogenous protein N-terminal myristoylation sites ...
Source: Molecular and Cellular Proteomics : MCP - November 10, 2023 Category: Molecular Biology Authors: Kazuya Tsumagari Yosuke Isobe Yasushi Ishihama Jun Seita Makoto Arita Koshi Imami Source Type: research