This article reviews recent developments in the formulation and application of biodescriptors to characterize proteomics maps. Such biodescriptors can be derived by applying techniques from discrete mathematics (graph theory, linear algebra and information theory). This review focuses on the development of biodescriptors for proteomics maps derived from 2D gel electrophoresis. Preliminary results demonstrated that such descriptors have a reasonable ability to differentiate between proteomics patterns that result from exposure to closely related individual chemicals and complex mixtures, such as the jet fuel JP-8. Further research is required to evaluate the utility of these proteomics-based biodescriptors for drug discovery and predictive toxicology.
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Nat Methods
January 2025
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
The phenotypic and functional states of cells are modulated by a complex interactive molecular hierarchy of multiple omics layers, involving the genome, epigenome, transcriptome, proteome and metabolome. Spatial omics approaches have enabled the study of these layers in tissue context but are often limited to one or two modalities, offering an incomplete view of cellular identity. Here we present spatial-Mux-seq, a multimodal spatial technology that allows simultaneous profiling of five different modalities: two histone modifications, chromatin accessibility, whole transcriptome and a panel of proteins at tissue scale and cellular level in a spatially resolved manner.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the "Belt and Road", College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Influenza A viruses (IAVs) are highly contagious pathogens that cause zoonotic disease with limited availability of antiviral therapies, presenting ongoing challenges to both public health and the livestock industry. Unveiling host proteins that are crucial to the IAV life cycle can help clarify mechanisms of viral replication and identify potential targets for developing alternative host-directed therapies. Using a four-dimensional (4D), label-free methodology coupled with bioinformatics analysis, we analyzed the expression patterns of cellular proteins that changed following H9N2 virus infection.
View Article and Find Full Text PDFNPJ Breast Cancer
January 2025
Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
Cancer disrupts intratumoral innate-adaptive immune crosstalk, but how the systemic immune landscape evolves during breast cancer progression remains unclear. We profiled circulating immune cells in stage I-III and stage IV triple-negative breast cancer (TNBC) patients and healthy donors (HDs). Metastatic TNBC (mTNBC) patients had reduced T cells, dendritic cells, and differentiated B cells compared to non-metastatic TNBC patients and HDs, partly linked to prior chemotherapy.
View Article and Find Full Text PDFBMC Bioinformatics
January 2025
Department of Applied Computer Science, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada.
Background: Comprehensively mapping the hierarchical structure of breast cancer protein communities and identifying potential biomarkers from them is a promising way for breast cancer research. Existing approaches are subjective and fail to take information from protein sequences into consideration. Deep learning can automatically learn features from protein sequences and protein-protein interactions for hierarchical clustering.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Crop Science, Chungbuk National University, Cheongju-si, 28644, Republic of Korea.
Glyphosate (Gly) is a widely used herbicide for weed control in agriculture, but it can also adversely affect crops by impairing growth, reducing yield, and disrupting nutrient uptake, while inducing toxicity. Therefore, adopting integrated eco-friendly approaches and understanding the mechanisms of glyphosate tolerance in plants is crucial, as these areas remain underexplored. This study provides proteome insights into Si-mediated improvement of Gly-toxicity tolerance in Brassica napus.
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