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HEK293T cell proteome abundance (WT vs NUFIP1 knock-out). Related to Supplementary Table 5 from An et al (2020)

ABSTRACT: HEK293T cells proteome comparison with or without NUFIP1 deletion. TMT channels 128n, 128c, 130c, 131n and 131c were not used for this analysis.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Alban Ordureau

LAB HEAD: Wade Harper

PROVIDER: PXD017858 | Pride | 2020-04-30

REPOSITORIES: Pride

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			Action	DRS
	HA-8-41.msf	Msf
	HA-8-41_01.raw	Raw
	HA-8-41_02.raw	Raw
	HA-8-41_03.raw	Raw
	HA-8-41_04.raw	Raw

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Publications

Systematic quantitative analysis of ribosome inventory during nutrient stress.

An Heeseon H Ordureau Alban A Körner Maria M Paulo Joao A JA Harper J Wade JW

Nature 20200701 7815

Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysin ...[more]

PMID: 32612236

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Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase

Project description:O-GlcNAc transferase (OGT), found in the nucleus and cytoplasm of all mammalian cell types, is essential for cell proliferation. Why OGT is required for cell growth is not known. OGT performs two enzymatic reactions in the same active site. In one, it glycosylates thousands of different proteins, and in the other, it proteolytically cleaves another essential protein involved in gene expression. Deconvoluting OGT’s myriad cellular roles has been challenging because genetic deletion is lethal; complementation methods have not been established. Here, we developed approaches to replace endogenous OGT with separation-of-function variants to investigate the importance of OGT’s enzymatic activities for cell viability. Using genetic complementation, we found that OGT’s glycosyltransferase function is required for cell growth but its protease function is dispensable. We next used complementation to construct a cell line with degron-tagged wild-type OGT. When OGT was degraded to very low levels, cells stopped proliferating but remained viable. Adding back catalytically-inactive OGT rescued growth. Therefore, OGT has an essential noncatalytic role that is necessary for cell proliferation. By developing a method to quantify how OGT’s catalytic and noncatalytic activities affect protein abundance, we found that OGT’s noncatalytic functions often affect different proteins from its catalytic functions. Proteins involved in oxidative phosphorylation and the actin cytoskeleton were especially impacted by the noncatalytic functions. We conclude that OGT integrates both catalytic and noncatalytic functions to control cell physiology.

2021-09-09 | PXD022654 | Pride

Proteogenomic Network Analysis of Context-Specific KRAS Signaling In Mouse-to-Human Cross-Species Translation

Project description:The highest frequencies of KRAS mutations occur in colorectal carcinoma (CRC) and pancreatic ductal adenocarcinoma (PDAC). Therapeutically targeting downstream pathways mediating oncogenic properties of KRAS mutant cancers is limited by an incomplete understanding of the contextual cues modulating the signaling output of activated KRAS. We performed mass spectrometry on mouse tissues expressing wild-type or mutant KRAS to determine how tissue context and genetic background modulate oncogenic signaling. Mutant KRAS dramatically altered the proteomes and phosphoproteomes of pre-neoplastic and neoplastic colons and pancreases in a largely context-specific manner. We developed an approach to humanize the mouse networks with data from human cancer and identified genes within the CRC and PDAC networks synthetically lethal with mutant KRAS. Our studies demonstrate the context-dependent plasticity of oncogenic signaling, identify non-canonical mediators of KRAS oncogenicity within the KRAS-regulated signaling network, and demonstrate how statistical integration of mouse and human datasets can reveal cross-species therapeutic insights.

2019-06-28 | PXD013922 | Pride

HEK293T cell proteome remodeling upon Torin1 treatment or amino acid withdraw in WT and RPS3-Halo knock-in cells with or without NUFIP1 deletion. Related to Supplementary Table 5 from An et al (2020)

Project description:HEK293T proteome (single shot) with knock-in or not for RPS3-Halo and Knock out or not for NUFIP1. Cells were treated or not with Torin1 or deprived of amino acids.

2020-04-30 | PXD017851 | Pride

HEK293T cell degradome (pulse chase) time course (5h, 10, 15h) analysis upon Torin1 treatment. Related to Supplementary Table 3 from An et al (2020)

Project description:HEK293T Azidohomoalanine (AHA) Pulse Chase (degradome) time course experiment, were cells from various genetic background (WT, ATG7-/-, RB1CC1-/-) are treated or not with Torin1 for 5h, 10h or 15h. Samples are Biotin-click, and streptavidin enriched, digested and labeled with TMTpro 16plex.

2020-04-30 | PXD018158 | Pride

HEK293T cell translatome analysis upon 6-MP treatment. Related to Supplementary Table 6 from An et al (2020)

Project description:HEK293T cells were treated with 6-MP and harvested at various time point (6, 9 and 18h). Translatome was measure by Azidohomoalanine (AHA) incorporation, Biotin-click, and streptavidin enrichment.

2020-04-30 | PXD017860 | Pride

HCT116 cell proteome remodeling upon Torin1 treatment or amino acid withdraw. Related to Supplementary Table 1 from An et al (2020)

Project description:HCT116 cells with various genotype (WT, ATCG5 KO, RB1CC1 KO), treated with Torin1 or amino acid withdraw. TMT 11 plex single shot.

2020-07-13 | PXD017853 | Pride

HEK293T cell degradome (pulse chase) analysis upon 12h Torin1 treatment. Related to Supplementary Table 3 from An et al (2020)

Project description:HEK293T Azidohomoalanine (AHA) Pulse Chase (degradome) experiment, were cells from various genetic background (WT, ATG7-/-, RB1CC1-/-) are treated or not with Torin1 for 12h. Samples are Biotin-click, and streptavidin enriched.

2020-04-30 | PXD017857 | Pride

HEK293 cell proteome remodeling upon Torin1 treatment or amino acid withdraw. Related to Supplementary Table 1 from An et al (2020)

Project description:HEK293 cells with two genotype (WT or ATCG5 KO), treated with Torin1 or amino acid withdraw. TMT 11 plex.

2020-07-12 | PXD017852 | Pride

HEK293T cell proteome remodeling upon 6-MP treatment. Related to Supplementary Table 6 from An et al (2020)

Project description:Total proteome abundance measurement after 24h 6-MP treatment in WT or ATG5 KO HEK293T cells. Channels 128n, 128c, 129n, 129c are not used for this analysis.

2020-04-30 | PXD017859 | Pride

HEK293T cell translatome analysis upon Torin1 treatment or single amino acid withdrawal. Related to Supplementary Table 2 from An et al (2020)

Project description:HEK293T subject to Torin1 treatment or amino acid withdraw dataset and translatome analysis was determined using Azidohomoalanine (AHA) incorportation, Biotin-click, and streptavidin enrichment. TMT 10plex labelling was used. Three genotypes, WT (24 fractions), ATG7 KO (HA-9-53-1 single shot), RB1CC1 KO (HA-9-53-2 single shot).

2020-04-30 | PXD018252 | Pride