Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival

Watson, Joanne; Ferguson, Harriet R.; Brady, Rosie M.; Ferguson, Jennifer; Fullwood, Paul; Mo, Hanyi; Bexley, Katherine H.; Knight, David; Howell, Gareth; Schwartz, Jean-Marc; Smith, Michael P.; Francavilla, Chiara

doi:10.1038/s41467-022-34298-2

Cited by 12 publications

(19 citation statements)

References 99 publications

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“…Normally, when FGFR is triggered by FGF, a lot of pathways involved in many physiological activities, such as cell growth, cell migration, cell survival, angiogenesis, embryonic organ development, tissue repair, wound healing, and metabolism are activated. The event is caused by the auto‐phosphorylation of FGFR 43–47 . The FGFR family includes five genes, namely, FGFR1 , FGFR2 , FGFR3 , FGFR4 , and FGFR5 (FGFRL1) .…”

Section: Introductionmentioning

confidence: 99%

FGFR families: biological functions and therapeutic interventions in tumors

Liu,

Huang,

Yan

et al. 2023

MedComm

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There are five fibroblast growth factor receptors (FGFRs), namely, FGFR1–FGFR5. When FGFR binds to its ligand, namely, fibroblast growth factor (FGF), it dimerizes and autophosphorylates, thereby activating several key downstream pathways that play an important role in normal physiology, such as the Ras/Raf/mitogen‐activated protein kinase kinase/extracellular signal‐regulated kinase, phosphoinositide 3‐kinase (PI3K)/AKT, phospholipase C gamma/diacylglycerol/protein kinase c, and signal transducer and activator of transcription pathways. Furthermore, as an oncogene, FGFR genetic alterations were found in 7.1% of tumors, and these alterations include gene amplification, gene mutations, gene fusions or rearrangements. Therefore, FGFR amplification, mutations, rearrangements, or fusions are considered as potential biomarkers of FGFR therapeutic response for tyrosine kinase inhibitors (TKIs). However, it is worth noting that with increased use, resistance to TKIs inevitably develops, such as the well‐known gatekeeper mutations. Thus, overcoming the development of drug resistance becomes a serious problem. This review mainly outlines the FGFR family functions, related pathways, and therapeutic agents in tumors with the aim of obtaining better outcomes for cancer patients with FGFR changes. The information provided in this review may provide additional therapeutic ideas for tumor patients with FGFR abnormalities.

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Section: Introductionmentioning

confidence: 99%

FGFR families: biological functions and therapeutic interventions in tumors

Liu,

Huang,

Yan

et al. 2023

MedComm

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“…However, the shift in protein abundance profiles between organelles is more inclusive . Similarly, in image-based subcellular proteomics studies, detecting partial protein translocation between organelles is hard to address as only absolute translocations are imaged using complex classifiers (one fit score).…”

Section: Challenges In the Field Of Subcellular Proteomicsmentioning

confidence: 99%

Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology

Bhushan,

Nita-Lazar

2024

J. Proteome Res.

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The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.

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“…Alternatively, phosphoproteome profiling of a Dahl salt-sensitive rat model of HFpEF demonstrated extensive hyperphosphorylation of the sarcomeric subproteome, which was partially reversed following cardiosphere-derived cell therapy [96]. Moving forward, new frontiers for phosphoproteomic-based analyses include spatiotemporal profiling of dynamic phosphorylation events in the subcellular proteome through enzyme-catalyzed proximity labeling strategies followed by phospho-peptide enrichment [97,98].…”

Section: Phosphorylationmentioning

confidence: 99%

Multi‐omic analyses and network biology in cardiovascular disease

Reitz,

Kuzmanov,

Gramolini

2023

Proteomics

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Heart disease remains a leading cause of death in North America and worldwide. Despite advances in therapies, the chronic nature of cardiovascular diseases ultimately results in frequent hospitalizations and steady rates of mortality. Systems biology approaches have provided a new frontier toward unraveling the underlying mechanisms of cell, tissue, and organ dysfunction in disease. Mapping the complex networks of molecular functions across the genome, transcriptome, proteome, and metabolome has enormous potential to advance our understanding of cardiovascular disease, discover new disease biomarkers, and develop novel therapies. Computational workflows to interpret these data‐intensive analyses as well as integration between different levels of interrogation remain important challenges in the advancement and application of systems biology‐based analyses in cardiovascular research. This review will focus on summarizing the recent developments in network biology‐level profiling in the heart, with particular emphasis on modeling of human heart failure. We will provide new perspectives on integration between different levels of large “omics” datasets, including integration of gene regulatory networks, protein–protein interactions, signaling networks, and metabolic networks in the heart.

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Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival

Cited by 12 publications

References 99 publications

FGFR families: biological functions and therapeutic interventions in tumors

FGFR families: biological functions and therapeutic interventions in tumors

Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology

Multi‐omic analyses and network biology in cardiovascular disease

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