Amino acid transport represents a druggable process for inhibiting human plasmacytoid dendritic cell activity during autoimmunity
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE157305 | GEO | 2022/04/07
REPOSITORIES: GEO
Similar Datasets
Project description:Amino acids (AA) support protein synthesis, and thus cell growth and proliferation. Specialized transporters mediate AA exchange across membranes and their regulation is critical for AA homeostasis. Here, we report that the DNA- and RNA-binding protein YBX3 regulates the expression of AA transporters. To investigate the functions of YBX3, we used a multiomics approach including proteomics, transcriptomics and metabolomics. We identified a subset of mRNAs that require YBX3 for de novo translation and are also bound to YBX3, including multiple solute carrier (SLC) AA transporters (SLC7A5, SLC3A2 and SLC1A3). We show that YBX3 stabilizes these SLC mRNAs and that the 3’UTR of SLC7A5 is necessary and sufficient for YBX3-mediated regulation. Further, YBX3 depletion results in diminished intracellular levels of SLC7A5/SLC3A2 substrate AA. Importantly, expression of an exogenous SLC7A5 not susceptible to YBX3 regulation restores AA levels. Thus, YBX3 is a key post-transcriptional regulator of large neutral AA import.
2022-03-01 | PXD007136 | Pride
Project description:Summary:
Amino acids (AA) support protein synthesis, and thus cell growth and proliferation. Specialized transporters mediate AA exchange across membranes and their regulation is critical for AA homeostasis. Here, we report that the DNA- and RNA-binding protein YBX3 regulates the expression of AA transporters. To investigate the functions of YBX3, we integrated proteomics and transcriptomics data with YBX3-RNA complex data to identify RNAs directly regulated by YBX3. The data revealed YBX3 as a versatile RNA-binding protein (RBP) that regulates as both a translational repressor and mRNA stabilizer. Among the direct YBX3 targets, we We identified two solute carrier (SLC) AA transporters (SLC7A5 and SLC3A2). We show that YBX3 stabilizes these SLC mRNAs and that the 3 UTR of SLC7A5 is necessary and sufficient for YBX3-mediated regulation. Further, YBX3 depletion results in diminished intracellular levels of SLC7A5/SLC3A2 substrates, large neutral AA. Importantly, expression of an exogenous SLC7A5 not susceptible to YBX3 regulation restores AA levels. Thus, YBX3 is a key post-transcriptional regulator of large neutral AA import.
2018-11-06 | MSV000083108 | MassIVE
Project description:This dataset consists of 29 raw MS files, acquired on Agilent 6550 iFunnel Q-TOF MS (Agilent Inc., Santa Clara, CA) mass spectrometer operated in DDA and target MS/MS mode.
Code for variants with additional NXS/T sites:
255I WTseq: (N365, N381, N424, N506)
256G N273A (+1 site)
257A N273A; N355D (+2 sites)
258F N355D; N492D (+2 sites)
259J N273A; N355D; N492D (+3 sites)
CJ1 D365N (-1 site)
CJ2 D381N (-1 site)
Cunjie Zhang did all the sample preparation, mass spectrometric acquisition and data analysis.
The files are associated with a manuscript submitted for publication by Cunjie Zhang et al. SLC3A2 (4F2hc, CD98) is a single-pass transmembrane glycoprotein and acts as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. Cancer cells often over-express SLC3A2, SLC7A5, SLC7A11 and the N-glycans branching, which support tumor progression by increasing mTOR signaling and mitigation of oxidative stress (ox-stress). Branched chain amino acids and mitigation of oxidative stress are also central to aging. Furthermore, the evolution of N-glycosylation sites on SLC3A adaptors and SLC7A transporters suggests a critical but poorly understood role for N-glycans. We have profiled the N-glycan structures at each site SLC3A2 (4F2hc, CD98) and analyzed their impact on trafficking, protein interactions, cellular AA balance and sensitivity to ox-stress.]
James W. Dennis is the corresponding author of the manuscript; James W. Dennis should be contacted for questions on this dataset DENNIS@lunenfeld.ca
This submission is associated with:
Figure 8
Figure S8
Table S6 Total N-glycans WT and SLC3A2 KO
| MSV000092985 | MassIVE
Project description:Deletion of Uhrf1 resulted in stage 1-specific defects during iNKT cell development. To investigate the molecular mechanism, we sorted WT and Uhrf1-KO stage 1 iNKT cells and performed RNA-seq. By comparing gene expression profile, we found metabolic defects in Uhrf1-KO stage 1 iNKT cells. The expression of CD71 (Tfrc), two subunits of CD98 (Slc3a2 and Slc7a5) and Glut3 (Slc2a3) was reduced in stage 1 iNKT cells. Besides, the downstream pathways of AKT-mTOR axis were significantly reduced. Collectively, our results suggest that Uhrf1 is required for iNKT cell development by regulating the Akt-mTOR signaling pathway. We first sorted WT and Uhrf1-KO stage 1 iNKT cells, extracted the mRNA and performed RNA-seq. We then analyzed the differentially expressed genes and performed KEGG pathway analysis. We used RT-PCR to verify the expression of the key nutrient related genes (Tfrc, Slc3a2, Slc7a5 and Slc2a3) and used flow cytometry to test the protein level of metabolic related molecules. Besides, we also analyzed the expression of genes of mTOR downstream pathways to demonstrate that Uhrf1 mediated AKt-mTOR axis regulates iNKT cell development.
2016-03-10 | E-GEOD-77941 | biostudies-arrayexpress
Project description:This dataset consists of 40 raw MS files, acquired on a TripleTOF 6600 (AB SCIEX, Concord, Ontario, Canada) mass spectrometer operated in data dependent acquisition (DDA) and SWATH mode.
Code for variants with additional NXS/T sites:
255I WTseq: (N365, N381, N424, N506)
256G N273A (+1 site)
257A N273A; N355D (+2 sites)
258F N355D; N492D (+2 sites)
259J N273A; N355D; N492D (+3 sites)
CJ1 D365N (-1 site)
CJ2 D381N (-1 site)
Cunjie Zhang did all the sample preparation, mass spectrometric acquisition and data analysis.
The files are associated with a manuscript submitted for publication by Cunjie Zhang et al. SLC3A2 (4F2hc, CD98) is a single-pass transmembrane glycoprotein and acts as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. Cancer cells often over-express SLC3A2, SLC7A5, SLC7A11 and the N-glycans branching, which support tumor progression by increasing mTOR signaling and mitigation of oxidative stress (ox-stress). Branched chain amino acids and mitigation of oxidative stress are also central to aging. Furthermore, the evolution of N-glycosylation sites on SLC3A adaptors and SLC7A transporters suggests a critical but poorly understood role for N-glycans. We have profiled the N-glycan structures at each site SLC3A2 (4F2hc, CD98) and analyzed their impact on trafficking, protein interactions, cellular AA balance and sensitivity to ox-stress.]
James W. Dennis is the corresponding author of the manuscript; James W. Dennis should be contacted for questions on this dataset DENNIS@lunenfeld.ca
This submission is associated with:
Figure 4
Figure 5
Table S4
| MSV000092989 | MassIVE
Project description:This dataset consists of 8 raw MS files, acquired on Agilent 6550 iFunnel Q-TOF MS (Agilent Inc., Santa Clara, CA) mass spectrometer operated in Data dependent acquisition (DDA) and target MS/MS mode.
Code for variants with additional NXS/T sites:
255I WTseq: (N365, N381, N424, N506)
256G N273A (+1 site)
257A N273A; N355D (+2 sites)
258F N355D; N492D (+2 sites)
259J N273A; N355D; N492D (+3 sites)
CJ1 D365N (-1 site)
CJ2 D381N (-1 site)
Cunjie Zhang did all the sample preparation, mass spectrometric acquisition and data analysis.
The files are associated with a manuscript submitted for publication by Cunjie Zhang et al. SLC3A2 (4F2hc, CD98) is a single-pass transmembrane glycoprotein and acts as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. Cancer cells often over-express SLC3A2, SLC7A5, SLC7A11 and the N-glycans branching, which support tumor progression by increasing mTOR signaling and mitigation of oxidative stress (ox-stress). Branched chain amino acids and mitigation of oxidative stress are also central to aging. Furthermore, the evolution of N-glycosylation sites on SLC3A adaptors and SLC7A transporters suggests a critical but poorly understood role for N-glycans. We have profiled the N-glycan structures at each site SLC3A2 (4F2hc, CD98) and analyzed their impact on trafficking, protein interactions, cellular AA balance and sensitivity to ox-stress.]
James W. Dennis is the corresponding author of the manuscript; James W. Dennis should be contacted for questions on this dataset DENNIS@lunenfeld.ca
This submission is associated with:
Figure S3
Table S2: Site-specific N-glycan SLC3A2 endogenous Figure S3 in the paper (in addition to this README file)
| MSV000092988 | MassIVE
Project description:This dataset consists of 57 raw MS files acquired on Agilent 6550 iFunnel Q-TOF MS (Agilent Inc., Santa Clara, CA) mass spectrometer operated in data dependent acquisition (DDA) and target MS/MS mode.
Code for variants with additional NXS/T sites:
255I WTseq: (N365, N381, N424, N506)
256G N273A (+1 site)
257A N273A; N355D (+2 sites)
258F N355D; N492D (+2 sites)
259J N273A; N355D; N492D (+3 sites)
CJ1 D365N (-1 site)
CJ2 D381N (-1 site)
Cunjie Zhang did all the sample preparation, mass spectrometric acquisition and data analysis.
The files are associated with a manuscript submitted for publication by Cunjie Zhang et al. SLC3A2 (4F2hc, CD98) is a single-pass transmembrane glycoprotein and acts as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. Cancer cells often over-express SLC3A2, SLC7A5, SLC7A11 and the N-glycans branching, which support tumor progression by increasing mTOR signaling and mitigation of oxidative stress (ox-stress). Branched chain amino acids and mitigation of oxidative stress are also central to aging. Furthermore, the evolution of N-glycosylation sites on SLC3A adaptors and SLC7A transporters suggests a critical but poorly understood role for N-glycans. We have profiled the N-glycan structures at each site SLC3A2 (4F2hc, CD98) and analyzed their impact on trafficking, protein interactions, cellular AA balance and sensitivity to ox-stress.
James W. Dennis is the corresponding author of the manuscript; James W. Dennis should be contacted for questions on this dataset DENNIS@lunenfeld.ca
This submission is associated with:
Figure 2
Figure S5
Table S1 Site-specific FLAG-SLC3A2 WTseq and variants
Table S3: Site-specific FLAG-SLC3A2_GlcNAc-supplement
| MSV000092980 | MassIVE
Project description:The intestine is the critical organ not only for processing and resorbing nutrients from ingested food but also for defending the organism from external stresses such as pathogens. These functions are mainly carried out by the epithelium which is constantly being self-renewed throughout adult life. Intestinal epithelial homeostasis is maintained through well-controlled cell proliferation of the stem cells and transient amplifying cells and the apoptotic degeneration of epithelial cells, mostly at or near the tip of the villi. Many genes and pathways have been found to influence intestinal epithelial cell proliferation. Among them is the mTORC1 signaling pathway, whose activation is known to increase cell proliferation. Here, we report the first intestinal epithelial specific knockout (IEC-KO) of an amino acid transporter capable of activating mTORC1. We show that the transporter, slc7a5, is highly expressed in the intestinal crypt and slc7a5 IEC-KO leads to expected reduction in mTORC1 signal in the crypt or even in intestinal organoids in vitro. Surprisingly, slc7a5 IEC-KO leads to increased proliferation of both transit amplifying cells and crypt base stem cells but a reduction in the secretory cells, particularly mature Paneth cells in the crypt base. Our scRNA-seq and electron microscopic analyses reveals that slc7a5 IEC-KO causes dedifferentiation of the Paneth cells, leading to drastically reduced secretory granules and lysozyme expression without affecting the overall Paneth cell number. We further show that slc7a5 IEC-KO mice are prone to induced colitis due to this loss of Paneth cell differentiation. We propose a model where slc7a5 regulates secretory cell differentiation to affect stem cell niche and/or inflammatory response to regulate cell proliferation in the crypts.
2024-04-24 | GSE216930 | GEO
Project description:BACKGROUND & AIMS- More frequent interaction of bacteria with the colonic epithelium is associated with ulcerative colitis (UC). The identities of all proteins which promote bacterial clearance in colonic epithelial cells are unknown. Previously, we discovered that dCAP-D3 (Chromosome Associated Protein-D3), regulates responses to bacterial infection. We examined whether CAP-D3 promotes bacterial clearance in human colonic epithelium. METHODS- Clearance of Salmonella or adherent-invasive Escherichia coli LF82 was assessed by gentamycin protection assays in HT-29 and Caco-2 cells expressing CAP-D3 shRNA. CAP-D3 levels in colonic epithelial cells from healthy and UC patient tissues were analyzed by immunoblot. RNA-sequencing identified bacterially-induced CAP-D3 target genes. The role of CAP-D3 target genes in bacterial clearance was analyzed by gentamycin protection assays, immunofluorescent staining, and by using pharmacologic inhibitors. RESULTS- CAP-D3 expression was reduced in colonic epithelial cells from UC patients with active disease. Reduction of CAP-D3 expression inhibited autophagy and decreased intracellular bacterial clearance. The components of the heterodimeric SLC7A5/SLC3A2 amino acid transporter were identified as CAP-D3 target genes; their levels increased in infected, CAP-D3 deficient cell lines and in cells from UC patients. In HT-29 cells, this resulted in earlier SLC7A5 recruitment to Salmonella-containing vacuoles, increased mTOR activity, and enhanced bacterial survival. Inhibition of SLC7A5/SLC3A2 or mTOR activity rescued the bacterial clearance defect in CAP-D3 deficient cells. CONCLUSIONS- CAP-D3 attenuates amino acid transporter transcription to promote bacterial autophagy in colon epithelial cells. CAP-D3 protein levels are decreased in patients with active UC, suggesting that CAP-D3 is a potential therapeutic target to restore mucosal homeostasis in UC patients. Three RNA samples from 3 independent experiments including timepoints taken at 0, 0.5 and 7 hours post-infection were analyzed on a bioanalyzer for quality; one of the 0.5 hour post-infection samples was excluded at this time due to poor RNA purity. Directional, cDNA libraries made from cellular mRNAs were generated from the other 8 samples and sequenced (paired-end sequencing of 100 bp reads) in the Genomics Core at the University of Chicago on an Illumina HiSeq2000.
2015-09-15 | E-GEOD-62520 | biostudies-arrayexpress
Project description:Obesity underpins the development of numerous chronic diseases such as type II diabetes mellitus. It is well established that obesity negatively alters immune cell frequencies and functions. Mucosal Associated Invariant T (MAIT) cells are a population of innate T cells, which we have previously reported are dysregulated in obesity, with altered circulating and adipose tissue frequencies and a reduction in their IFN-gamma production, which is a critical effector function of MAIT cells in host defence. Hence there is increased urgency to characterise the key molecular mechanisms that drive MAIT cell effector functions, and to identify those which are impaired in the obesity setting. In this study, we found that MAIT cells significantly upregulate their rates of glycolysis upon activation in an mTORC1 dependent manner and this is essential for MAIT cell IFN-g production. Furthermore, we show that mTORC1 activation is dependent on amino acid transport via SLC7A5. In obese patients, using RNA sequencing, Seahorse analysis and a series of in vitro experiments, we demonstrate that MAIT cells isolated from obese adults display defective glycolytic metabolism, mTORC1 signalling and SLC7A5 amino acid transport. Collectively our data details the intrinsic metabolic pathways controlling MAIT cell cytokine production and highlights mTORC1 as an important metabolic regulator that is impaired in obesity, leading to altered MAIT cell responses. We report on MAIT cells isolated from lean and obese adults
2019-04-16 | GSE126169 | GEO