Publications by authors named "Alejandro Fernandez-Woodbridge"

Article Synopsis
  • Molecular characterization has changed breast cancer research, offering a deep analysis of breast tumor proteomes and identifying different BC subtypes.
  • The study shows that poor-prognosis basal-like and luminal B tumors can be subdivided based on immune infiltration, indicating a need for improved classification.
  • It highlights the importance of protein quantification for better prognostic accuracy and identifies potential new immunotherapeutic targets from proteins linked to non-coding genomic regions.
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Article Synopsis
  • Subcellular localization is key to protein function, and this study offers a comprehensive analysis of protein localization across 12,418 genes in five cell lines using mass spectrometry.
  • The research uncovers insights on how alternative splicing, protein domains, and growth factors influence protein localization, revealing that most proteins have a primary subcellular location and that splicing has minimal impact on this aspect.
  • This work enhances our understanding of cellular architecture and is accessible to the public at www.subcellbarcode.org.
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Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation.

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Background & Aims: Adenocarcinomas of the pancreatobiliary system are currently classified by their primary anatomical location. In particular, the pathological diagnosis of intrahepatic cholangiocarcinoma is still considered as a diagnosis of exclusion of metastatic adenocarcinoma. Periampullary cancers have been previously classified according to the histological type of differentiation (pancreatobiliary, intestinal), but overlapping morphological features hinder their differential diagnosis.

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The p53-family member TAp73 is known to function as a tumor suppressor and regulates genomic integrity, cellular proliferation, and apoptosis; however, its role in tumor angiogenesis is poorly understood. Here we demonstrate that TAp73 regulates tumor angiogenesis through repression of proangiogenic and proinflammatory cytokines. Importantly, loss of TAp73 results in highly vascularized tumors, as well as an increase in vessel permeability resulting from disruption of vascular endothelial-cadherin junctions between endothelial cells.

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Current techniques for analyzing chromatin structures are hampered by either poor resolution at the individual cell level or the need for a large number of cells to obtain higher resolution. This is a major problem as it hampers our understanding of chromatin conformation in single cells and how these respond to environmental cues. Here we describe a new method, chromatin in situ proximity (ChrISP), which reproducibly scores for proximities between two different chromatin fibers in 3-D with a resolution of ~170Å in single cells.

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