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Profiling changes to the global proteome in HEK293T cells in response to heat stress. (PMID: 34739326)

ABSTRACT: Here we have determined changes to the global proteome in response to heat stress. The abundance of individual proteins was compared between heat stressed and untreated control HEK293T cells in the presence of proteasome inhibition using quantitative proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ashutosh Mishra

LAB HEAD: J. Paul Taylor

PROVIDER: PXD069754 | Pride | 2025-10-22

REPOSITORIES: Pride

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			Action	DRS
	Tayl1grp_072619_diGGAbTMT_TMTchannel.txt	Txt
	Tayl1grp_072619_diGGAbTMT_nLC10p_F1.mzXML	Mzxml
	Tayl1grp_072619_diGGAbTMT_nLC10p_F1.raw	Raw
	Tayl1grp_072619_diGGAbTMT_nLC10p_F10.mzXML	Mzxml
	Tayl1grp_072619_diGGAbTMT_nLC10p_F10.raw	Raw

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Publications

Ubiquitination is essential for recovery of cellular activities after heat shock.

Maxwell Brian A BA Gwon Youngdae Y Mishra Ashutosh A Peng Junmin J Nakamura Haruko H Zhang Ke K Kim Hong Joo HJ Taylor J Paul JP

Science (New York, N.Y.) 20210601 6549

Eukaryotic cells respond to stress through adaptive programs that include reversible shutdown of key cellular processes, the formation of stress granules, and a global increase in ubiquitination. The primary function of this ubiquitination is thought to be for tagging damaged or misfolded proteins for degradation. Here, working in mammalian cultured cells, we found that different stresses elicited distinct ubiquitination patterns. For heat stress, ubiquitination targeted specific proteins associ ...[more]

PMID: 34739326

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Profiling changes to the global proteome in HEK293T cells in response to heat stress. Total Proteome TMT data PMID 34739326.

Project description:Here we have determined changes to the global proteome in response to heat stress. The abundance of individual proteins was compared between heat stressed and untreated control HEK293T cells in the presence of proteasome inhibition using quantitative proteomics.

2025-10-31 | PXD070122 | Pride

Profiling the stress-dependent ubiquitinome of HEK293T cells via TUBE-capture and spectral counting proteomics

Project description:Here we investigate changes to the ubiquitin conjugation profile in response to various types of cellular stress. Ubiquitinated proteins from HEK293T cells following stress treatments and compared to those in unstressed cells using TUBE-affinity captured and MS-spectral counting analysis. This work is associated with the Science paper published in 2021 (Maxwell et.al. Ubiquitination is essential for recovery of cellular activities after heat shock)

2025-10-17 | PXD069603 | Pride

UAG suppression in HEK293T cells

Project description:HEK293T cells, stably transfected with pyrrolysine UAG suppressor tRNA and aminoacyl tRNA synthetase, for the co-translational incorporation of Boc-protected lysine.

2020-02-24 | PXD016728 | Pride

Long non-coding Satellite III RNAs link the heat shock response and cell proliferation

Project description:Genomes of complex organisms encode a wide variety of long non-coding RNAs (lncRNAs) that regulate gene expression. In human cells exposed to heat stress, transcription of lncRNAs is highly induced from Satellite III sequences located primarily within locus 9q12. Expression of Sat III transcripts is dependent on heat shock factor 1, the master regulator of the heat shock response. Sat III transcripts serve as the backbone of specific subnuclear structures called nuclear Stress Bodies, nSBs. Despite being known for two decades, the function of nSBs and Sat III transcripts is unknown, which prompted us to conduct RNA profiling in human cells where Sat III transcripts were either intact or downregulated. Comparison of these cells revealed that under stress conditions, Sat III transcripts are involved in regulating a plethora of genes, including such associated with cell growth and protein homeostasis. Our results show that the presence of Sat III transcripts has a repressive effect on cell proliferation. We propose a model in which the inducible expression of Sat III transcripts restrains cell proliferation, allowing the cell to assess whether to grow or undergo apoptosis, and thereby suggesting a function for these lncRNAs in cell fate decisions and in restoring protein homeostasis. Total RNA from HEK293T cells transfected with siRNA against Satellite III transcripts or scrambled siRNA and heat shocked 1 h at 42Â°C , or heat shocked 1 h at 42 Â°C followed by recovery for 6 h, or left untreated was compared.

2015-12-31 | E-GEOD-58439 | biostudies-arrayexpress

Mouse hepatocyte conditioned media LC-MS/MS.

Project description:Hepatocyte caspase-8 is elevated in MASH and promotes fibrosis independently of apoptosis changes. To investigate how hepatocyte caspase-8 might drive liver fibrosis progression in MASH, we focused on activated hepatic stellate cells (HSCs), which are the primary source of collagen-producing myofibroblasts and central players in MASH fibrosis. To assess a potential link between hepatocyte caspase-8 and HSC activation, we used an ex vivo model where primary murine HSCs were cultured with conditioned media from siCasp8-treated or control primary hepatocytes. Supporting our hypothesis, HSC activation markers were reduced in HSCs exposed to conditioned media from Casp8-silenced AML12 hepatocytes compared to controls. To pinpoint caspase-8-dependent secretory proteins that could activate HSCs, we conducted LC-MS/MS on conditioned media from these cells, identifying secretory proteins reduced in Casp8-silenced AML12 hepatocytes.

2025-07-09 | PXD057540 | Pride

Transient Genotype-by-Environment Interactions in the Yeast Genomic Expression Response to Heat Shock

Project description:Microarray time courses followed the response of 5 yeast strains to heat shock. Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified. Keywords: Timecourse and single timepoint expression studies of stress response in yeast The genomic expression response to heat shock was measured in 5 different yeast strains over the course of 2 hours. Basal expression at 25C was also compared in 4 non-lab strains to the S288c refernce. All experiments were done in duplicate, for a total of 68 Samples.

2010-05-18 | E-GEOD-15147 | biostudies-arrayexpress

IRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development [expression array]

Project description:Interferon regulatory factor 4 (IRF4) is a master transcription factor required for the maturation of germinal center B cells that eventually develop into antibody secreting plasma cells and memory B cells. IRF4-deficient mice exhibit a profound reduction in serum immunoglobulin levels. In spite of wealth of the information relating to IRF4 and B cell biology, little is known about the intricate molecular details of the role of this transcription factor during B cell development. We therefore examined the genome-wide targets of IRF4 by ChIP-chip analysis in GC derived BL2 Burkittâs lymphoma cells. ChIP studies were further supplemented by whole genome expression analysis after shRNA-mediated knockdown of IRF4. Our study revealed that IRF4 regulates expression of genes important for a) BCR signaling b) antigen processing and presentation by MHC. In addition we found that IRF4 possibly in some way involved to regulate LTA, LTB and CXCR5 those involved in immune system development, particularly light zone development related genes such as FDC clustering regulating and IL21R and IL10 who are involved in B cell development.. On the other hand, IRF4 suppressesd genes in the oxidative phosphorylation pathway. Our findings illuminate hitherto unexplored roles of IRF4 in GC B cell development. BL2 Burkitt's lymphoma-derived B cells were infected with lentivirus expressing shRNA for IRF4 or control, and total RNA was subjected to Illumina BeadsExpression Arrays analysis.

2015-12-15 | E-GEOD-64269 | biostudies-arrayexpress

AP-MS analysis of IFIT1 and 5 interactions in interferon-stimulated human cells

Project description:This project sought to identify interactions of InterFeron Induced Tetratricopeptide repeat (IFIT) proteins 1 ad 5 in human cells. SILAC-labelled human HEK293T cells were transfected with FLAG-tagged human IFIT1 and IFIT5 pulldowns. After transfection, the cells were treated with human interferon 2-alpha and FLAG-immunoprecipitations performed to identify IFIT-binding proteins. Cells were then subject to LS/MS-MS analysis on a Orbitrap Fusion and data analysed in Maxquant v1.5.7.4

2018-03-16 | PXD007584 | Pride