Human skin specific long noncoding RNA HOXC13-AS regulates keratinocyte differentiation by inferfering with Golgi-ER retrograde transport
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ABSTRACT:
PROVIDER: PRJNA849206 | ENA |
REPOSITORIES: ENA
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Project description:In an RNAseq analysis, we have identified the HOXC13-AS significantly downregulated in wound biopsies and epidermal cells compared to skin counterparts. To study the genes regulated by HOXC13-AS, we transfected HOXC13-AS siRNA pool into human primary epidermal keratinocytes to knockdown HOXC13-AS and induced cell differentiation for 3 days by 1.5 mM calcium. We performed a global transcriptome analysis of keratinocytes upon the HOXC13-AS knockdown using Affymetrix arrays.
2022-06-15 | GSE206103 | GEO
Project description:Abnormal distribution of cellular cholesterol is associated with numerous diseases, including cardiovascular and neurodegenerative diseases. Regulated transport of cholesterol is critical for maintaining its proper distribution in the cell, yet the underlying mechanisms remain unclear. Here, we show that lipid transfer proteins, namely ORP9, OSBP, and GRAMD1s/Asters (GRAMD1a/GRAMD1b/GRAMD1c), control non-vesicular cholesterol transport at points of contact between the ER and the trans-Golgi network (TGN), thereby maintaining cellular cholesterol distribution. ORP9 localizes to the TGN via interaction between its tandem α-helices and ORP10/ORP11. ORP9 extracts PI4P from the TGN to prevent its overaccumulation and suppresses OSBP-mediated PI4P-driven cholesterol transport to the Golgi. By contrast, GRAMD1s transport excess cholesterol from the Golgi to the ER, thereby preventing its build-up. Cells lacking ORP9 exhibit accumulation of cholesterol at the Golgi, which is further enhanced by additional depletion of GRAMD1s with major accumulation in the plasma membrane. This is accompanied by chronic activation of the SREBP-2 signalling pathway. Our findings reveal the importance of regulated lipid transport at ER-Golgi contacts for maintaining cellular cholesterol distribution and homeostasis.
2023-09-24 | GSE240960 | GEO
Project description:The retrograde transport inhibitor Retro-2 has a protective effect on cells and in mice against Shiga-like toxins and ricin. Retro-2 causes toxin accumulation in early endosomes, and the relocalization of the Golgi SNARE protein syntaxin-5 to the endoplasmic reticulum. The molecular mechanisms by which this is achieved remain unknown. Here, we show that Retro-2 targets the endoplasmic reticulum exit site component Sec16A, affecting anterograde transport of syntaxin-5 from the endoplasmic reticulum to the Golgi. The formation of canonical SNARE complexes involving syntaxin-5 is not affected in Retro-2-treated cells. In contrast, the interaction of syntaxin-5 with a newly discovered binding partner, the retrograde trafficking chaperone GPP130, is abolished, and we show that GPP130 must indeed bind to syntaxin-5 to drive Shiga toxin transport from endosomes to the Golgi. We thereby identify Sec16A as a druggable target, and provide evidence for a non-SNARE function for syntaxin-5 in interaction with the retrograde cycling protein GPP130. a) Clickable Retro-2 pulldown. To identify protein target of Retro-2.1, providing the first steps to explain effects of Retro-2 on inhibition of STxB retrograde trafficking from endosomes to Golgi. b) GFP-STX5 pulldown. To find interactors of STX5, to build a hypothesis to explain the affect of Retro-2-inhibited anterograde trafficking of STX5 to Golgi, which in turn inhibits STxB retrograde transport from endosomes to Golgi. c) GFP-Sec16A pulldown. The aim of this proteomics assay is to show the effects of Retro-2 on the Sec16A interactome. Results show the differential effects of Retro-2 treatment on the Sec16A interactome, giving insight into the mechanism by which Retro-2, via Sec16A, specifically affects the anterograde trafficking of Syntaxin-5.
2020-02-24 | PXD015642 | Pride
Project description:Golgi biogenesis is a crucial cellular process, yet its study has been hindered by the lack of easy methods to induce massive production of new Golgi units. In this study, we optimized an enzyme inactivation approach to stimulate the formation of fully functional Golgi stacks. Massive Golgi biogenesis was achieved through DAB-mediated inactivation of preexisting Golgi structures in cells stably expressing the chimeric Golgi enzyme Mannosidase II fused with horse radish peroxidase (HRP). Within 10 to 18 hours post-Golgi inactivation, substantial number of cells regenerated new Golgi stacks capable of transporting various cargo proteins to their appropriate destinations. This functional and structural recovery of the Golgi in ManII-HRP cells offers an efficient system to study Golgi biogenesis and associated cellular responses. We further explored transcriptomic changes in ManII-HRP cells, discovering that the extensive biogenesis of Golgi membranes induces the transcriptional activation of numerous Golgi-associated genes. These genes encode proteins involved in diverse functions such as glycosylation, membrane tethering, and ion/sugar transport. The timing of this gene transactivation correlates with the restoration of Golgi cisternae architecture and trafficking capabilities, suggesting that this transcriptional response plays an integral role in the biogenesis of new Golgi units.
2026-05-13 | GSE288395 | GEO
Project description:Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, referred to as anterograde and retrograde IFT “trains”. Anterograde trains deliver cargoes from the cell to the ciliary tip, then remodel into retrograde trains for cargo export. We set out to understand how the structure of these trains changes at the tip, and thus how the same IFT complexes can perform opposing transport roles. We use cryo-electron tomography, subtomogram averaging and in-situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains, and compare with the known anterograde train structure. We show that the retrograde train is a two-fold symmetric polymer organised around a central thread of IFTA complexes. We conclude that the structural differences between anterograde and retrograde trains can only be achieved through de novo polymerisation of the retrograde train from individual IFTA/B complexes. Finally we describe how conformational changes to cargo binding sites allow for unidirectional cargo transport in a bidirectional system.
2024-08-21 | PXD049195 | JPOST Repository
Project description:Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, referred to as anterograde and retrograde IFT “trains”. Anterograde trains deliver cargoes from the cell to the ciliary tip, then remodel into retrograde trains for cargo export. We set out to understand how the structure of these trains changes at the tip, and thus how the same IFT complexes can perform opposing transport roles. We use cryo-electron tomography, subtomogram averaging and in-situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains, and compare with the known anterograde train structure. We show that the retrograde train is a two-fold symmetric polymer organised around a central thread of IFTA complexes. We conclude that the structural differences between anterograde and retrograde trains can only be achieved through de novo polymerisation of the retrograde train from individual IFTA/B complexes. Finally we describe how conformational changes to cargo binding sites allow for unidirectional cargo transport in a bidirectional system.
2024-08-21 | PXD049260 | JPOST Repository
Project description:Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo inside cilia. However, the mechanism of selective transport of cargo to cilia and entry across the diffusion barrier is not well understood. WDR35/IFT121 is a component of the IFT-A complex, best known for ciliary retrograde transport. Small Wdr35 mutant cilia are formed but fail to enrich in diverse classes of ciliary membrane proteins. Whilst the assembly of the IFT-B complex is unaffected, these exhibit retrograde trafficking defects in Wdr35 mutants. In contrast, the IFT-A peripheral components are degraded and core components remain stuck at the cilia base. The deep sequence homology and structural similarity of WDR35 and other IFT-As to the coatomer COPI proteins α and ß’, and accumulation of electron-light vesicles around Wdr35 mutant cilia, suggest that WDR35 is required to form coated vesicles delivering cargo from the Golgi necessary for cilia elongation. This is the first insitu proof towards a novel coatomer function for WDR35 and likely other IFT-A proteins in transporting ciliary membrane proteins from the Golgi.
2021-05-03 | PXD022652 | Pride
Project description: Not available
| S-EPMC10154349 | biostudies-literature
Project description:Regulation of cellular cholesterol distribution via non-vesicular lipid transport at ER-Golgi contact sites
| PRJNA1005938 | ENA
Project description:Androgen receptor (AR) plays an essential role in normal prostate development and prostate cancer (PCa) progression. To understand the role of AR at the single-cell level, we performed single-cell transcriptome analysis on PCa cells stimulated with androgen and antiandrogen to reconstruct the dynamic and direct AR transcriptional network. Our work reveals that androgen stimulates the ER and Golgi stress response , promoting secreting protein trafficking, and inhibiting cell apoptosis. Moreover, we identify an ER-to-Golgi protein vesicle-mediated transport gene signature essential for maximal androgen-mediated ER-Golgi trafficking, cell proliferation, and association with PCa prognosis and progression. Notably, we show that AR collaborates with CREB3L2, XXX, to coordinately promote ER-Golgi trafficking of Golgi enzyme Mannosidase II and PCa cell survival. Finally, we show the inhibition of the ER-Golgi transport process with Brefeldin A leads to tumor regression. Our study collectively reveals the heterogeneity of PCa cell transcriptional response to androgen stimulation, demonstrates a functional role for increased ER-Golgi trafficking process, and provides a mechanism for how the process is augmented in PCa as well as the potential of targeting may provide novel treatment strategies.
2021-10-10 | GSE165562 | GEO