Labeling and identifying cell-specific proteomes in the mouse brain

Krogager, Toke P.; Ernst, Russell J.; Elliott, T. S. J.; Calò, Laura; Beránek, Václav; Ciabatti, Ernesto; Spillantini, Maria Grazia; Tripodi, Marco; Hastings, Michael H.; Chin, Jason W.

doi:10.1038/nbt.4056

Cited by 85 publications

(91 citation statements)

References 25 publications

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“…At wo-sided StudentsT -test was performed with af alse discovery rate (FDR) = 0.05 and S 0 = 1a st he statistical threshold, shown as curved lines in each plot. [17] Thep roteins that met this threshold were considered as specific ones.T he numbers of specific proteins are summarized in Figure 3b,a nd the complete protein list is provided in the Supporting Information.…”

Section: Resultsmentioning

confidence: 99%

Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling

et al. 2020

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Histone deacetylase (HDAC) is a major class of deacetylation enzymes. Many HDACs exist in large protein complexes in cells and their functions strongly depend on the complex composition. The identification of HDAC‐associated proteins is highly important in understanding their molecular mechanisms. Although affinity probes have been developed to study HDACs, they were mostly targeting the direct binder HDAC, while other proteins in the complex remain underexplored. We report a DNA‐based affinity labeling method capable of presenting different probe configurations without the need for preparing multiple probes. Using one binding probe, 9 probe configurations were created to profile HDAC complexes. Notably, this method identified indirect HDAC binders that may be inaccessible to traditional affinity probes, and it also revealed new biological implications for HDAC‐associated proteins. This study provided a simple and broadly applicable method for characterizing protein‐protein interactions.

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Section: Resultsmentioning

confidence: 99%

Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling

et al. 2020

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“…He described stochastic orthogonal recording of translation (SORT) for cell-type-specific tagging of proteomes to brain slices and the brains of live mice. [26] In this ActA to the extract-oil interface results in well-defined actin cortices. It turned out that the connectivity of the actin network, which she tuned by varying the amount of the actin cross-linker alpha-actinin, is the crucial parameter for the cortex dynamic behavior and its mechanical properties.…”

Section: Conference Reportmentioning

confidence: 95%

2018 International Symposium on Chemical Biology of the NCCR Chemical Biology Campus Biotech, Geneva 10.–12.01.2018

Kruse

Sugihara

2018

Chimia

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Ve ry recently, his group has also shown that another ER protein, TMEM24, alters its localization at ER-PM contacts reversibly, governed by phosphorylation and dephosphorylation in response to oscillations in cytosolic calcium. [2] A lipid-binding module in TMEM24 transports the phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] precursor phosphatidylinositol between bilayers, allowing replenishment of PI(4,5)P2 hydrolyzed during signaling. He concluded his talk with a remark that the membrane contact sites are an emerging field, where even a new journal was created recently, with many open questions remaining, which provides many scientific opportunities for young researchers. The second lecture of this first evening session was a Keynote lecture by Paul Wender (Stanford University, USA). A grand challenge in science and medicine is breaching biological barriers for the drug delivery, including plasma membranes, bacterialmembranes,algalcellwalls,mitochondrialmembranes, skin, gastrointestinal tract, and blood brain barriers. The general golden rule is that a drug molecule has to have just the right polarity (not too polar, not too non-polar) to cross hydrophobic membranes. That is why RNA delivery is notoriously difficult; RNA has a high number of negative charges. This is the current bottleneck to its enormous clinical potential. To overcome this challenge, the Wender and Waymouth groups have synthesized new carrier molecules, Charge-Altering Releasable Transporters (CARTs), which are highly cationic and complex the anionic mRNA yet are designed to convert to neutral entities after crossing the membranes thereby releasing mRNA. This collaboration has shown the efficiency of CARTs by delivering luc-mRNA into mice using this delivery system, which presented luminescence emission peaking after 4 h. [3] They have employed CARTs also in cancer immunotherapy. In non-published work, he showed that the mouse immune system can be trained by injecting mice with mRNA-CART complexes, which dramatically improved the ability of mice to combat cancers that are implanted afterwards. This amazing new technology can be used as a cancer vaccination and also for treating established tumors. His group has also developed a scalable synthesis of a natural compound Bryostatin [4] and its analogs for latent HIV infections. Current HIV therapy is chronic with cost, compliance, resistance and chemo exposure issues because the active virus is re-supplied by 'reservoir cells' with replication competent genomically encoded virus. Elimination of these reservoir cells in conjunction with current antiretroviral therapy could lead to HIV/AIDS eradication. Bryostatin and the analogs Wender's group synthesized, activate these reservoir cells, allowing for their elimination through cytopathic or immunotoxin effects and possibly eradication of disease. Bryostatin is today in clinical trials for cancer immunotherapy, Alzheimer's disease and HIV eradication. These collaborative and translational efforts show how Chemical Biology can truly make a change...

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“…11c). 133,134 Because of its high specificity and sufficiently fast reaction rate, the CuAAC has been used in a variety of applications such as the site-specific modification of proteins, cellular proteomic analysis (bioorthogonal non-canonical amino acid tagging, BONCAT) [135][136][137] and visualization of newly synthesized proteins (fluorescent non-canonical amino acid tagging, FUNCAT). 138,139 Strain-promoted azide-alkyne cycloaddition (SPAAC) provides a more powerful tool for modifying POIs without requiring exogenous ligands and toxic metal catalysts (Figs.…”

Section: Chemical Modification Of Proteins Using Uaas 3•1 Protein Modmentioning

confidence: 99%

Recent Progress in Chemical Modification of Proteins

Sakamoto

Hamachi

2018

ANAL. SCI.

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Chemical modification of proteins is important for creating a myriad of engineered proteins and for elucidating the function and dynamics of proteins in live cells. A wide variety of chemical protein modification methods have been developed and can be categorized into three classes: (i) modification of proteins using the reactivity of naturally occurring amino acids; (ii) modification by bioorthogonal reactions using unnatural amino acids, most of which can be siteselectively incorporated into proteins-of-interest using genetic codon expansion techniques; and (iii) recognition driven chemical modification, which is the only approach that allows modification of endogenous proteins without any genetic manipulation even under heavily crowded and multi-molecular conditions, as in live cells and organisms. All of these approaches have merits and limitations. In this review, we summarize these approaches and discuss their characteristics with respect to specificity, reaction rate and versatility.

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Labeling and identifying cell-specific proteomes in the mouse brain

Cited by 85 publications

References 25 publications

Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling

Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling

2018 International Symposium on Chemical Biology of the NCCR Chemical Biology Campus Biotech, Geneva 10.–12.01.2018

Recent Progress in Chemical Modification of Proteins

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