Array-based protein technologies are emerging for basic biological research, molecular diagnostics and therapeutic development with the potential of providing parallel functional analysis of hundreds or perhaps hundreds of thousands of proteins simultaneously. Array-based methods are becoming prevalent within proteomics research due to the desire to analyze proteins in an analogous format to that of the DNA microarray. Novel protein biochips are under development in academic laboratories and emerging biotechnology companies to advance the pace and scope of scientific discovery. This review will define array-based proteomics, its current applications and future directions, as well as examine the challenges and limitations of this projected billion dollar industry.
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Spatial omics-based machine learning algorithms for the early detection of hepatocellular carcinoma.
Commun Med (Lond)
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Medical University of South Carolina, Department of Cell and Molecular Pharmacology, Charleston, SC, 29425, USA.
Background: Worldwide, hepatocellular carcinoma (HCC) is the second most lethal cancer, although early-stage HCC is amenable to curative treatment and can facilitate long-term survival. Early detection has proved difficult, as proteomics, transcriptomics, and genomics have been unable to discover suitable biomarkers.
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December 2024
Unité de Technologies Chimiques et Biologiques pour la Santé - UTCBS, Faculté de Pharmacie de Paris, Université Paris Cité, CNRS UMR 8258, Inserm U1267, 75006 Paris, France.
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Division of Biomedical Research & Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Iwate, Japan. Electronic address:
Despite of massive emergence of molecular targeting drugs, the mainstay of advanced gastric cancer (GC) therapy is DNA-damaging drugs. Using a reverse-phase protein array-based proteogenomic analysis of a panel of 8 GC cell lines, we identified genetic alterations and signaling pathways, potentially associated with resistance to DNA-damaging drugs, including 5-fluorouracil (5FU), cisplatin, and etoposide. Resistance to cisplatin and etoposide, but not 5FU, was negatively associated with global copy number loss, vimentin expression, and caspase activity, which are considered hallmarks of previously established EMT subtype.
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NPJ Precis Oncol
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Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, USA.
Recent trials have shown the efficacy of trastuzumab deruxtecan (T-DXd) in HER2-negative patients, but there is not yet a way to identify which patients will best respond, especially with the inability of current HER2 IHC and FISH assays to accurately determine HER2 expression in the unamplified setting. Here, we present a heavily pre-treated patient with triple-negative breast cancer (HER2 IHC 0 who had a complete response to T-DXd. In this case, we used a CLIA-certified reverse-phase protein array-based proteomic assay (RPPA) to determine that the patient had moderate HER2 protein expression (HER2 2+, 42%) and activation (HER2 1+, 23%).
View Article and Find Full Text PDFA review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis.
Funct Integr Genomics
August 2024
Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, 02115, USA.
Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results.
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