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Impact of azide metabolic glycoengineering and bioorthogonal click chemistry cell-cell tethering in adipose tissue-derived mesenchymal stromal cells

ABSTRACT: We report RNA sequencing data from adipose tissue-derived mesenchymal stromal cells (hASCs) functionalized via metabolic glycoengineering with pendant azide sialosides. Beyond the impact of this cell surface engineering on transcriptome, we explore the expression profiles of azide-hASCs covalently tethered to an interfacial glycosaminoglycan via bioorthogonal click chemistry and yielding a 3D multicellular construct. We find global gene expression changes in response to metabolic glycoengineering in 2D cell culture conditions as well as those arising from cell-to-cell tethering into 3D environments.

ORGANISM(S): Homo sapiens

PROVIDER: GSE231507 | GEO | 2024/04/15

REPOSITORIES: GEO

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Azide-containing amino acid modulation of cellular transcriptome and proteome composition – implications on click chemistry based secretome analysis

Project description:The analysis of the secretome provides important information on cellular communication and on the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, knowledge on the composition of the secretome plays an important role for diagnosis and therapy. Mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Azide-containing amino acid labeling in combination with click chemistry now facilitates this type of analysis without serum starvation. The modified amino acids, however, are less efficiently incorporated into newly synthesized proteins. Utilizing transcriptome and proteome analysis, we describe here in detail the effects of labeling cells with the methionine analog azidohomoalanin (AHA) on the modulation of gene expression and protein composition. We observe that 11% – 34% of the proteins detected in the secretome were affected by AHA labeling regarding their expression levels in the transcriptome and/or proteome. Performing gene ontology analyses, our results provide a detailed view on the AHA-based induction of cellular stress and apoptosis-related pathways and provide first insights on how this might affect the composition of the secretome on a global scale.

2023-07-05 | GSE211231 | GEO

Alkyne-azide "click" chemistry in designing nanocarriers for applications in biology.

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Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription

Project description:Transcription is the primary regulatory step in gene expression coordinating the coding and non-coding genomic regions across space and time. Divergent initiation of transcription from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity from cell populations. However, the lack of single-cell resolved view of active transcription has left fundamental questions in gene regulation unanswered. In this study, we present scGRO-seq - a single-cell nascent RNA sequencing assay using copper-catalyzed azide-alkyne cycloaddition - unveiling the coordinated regulation of dynamic transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription and provides estimates of burst size and frequency by directly quantifying transcribing RNA polymerases. It reveals the co-transcription of functionally related genes and leverages the transcription of replication-dependent non-polyadenylated histone genes to elucidate cell-cycle dynamics. The single-nucleotide spatiotemporal resolution of scGRO-seq characterizes networks of enhancers and genes and indicates the bursting of transcription at super-enhancers before the activation of burst from associated genes. Our method offers insights into the dynamic nature of transcription, functional architecture of the genome, and serves as a powerful tool to investigate the role of the non-coding genome in gene regulation.

2023-09-15 | GSE242176 | GEO

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Ecoli W3110_0.01 M sodium azide treatment vs untreated, timecourse

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2006-03-08 | GSE4372 | GEO

Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomics Studies

Project description:We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.

2024-01-12 | PXD043402 | Pride

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Enzymatic or in vivo installation of propargyl groups in combination with click chemistry enables enrichment and detection of methyltransferase target sites in RNA

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2018-02-21 | GSE109298 | GEO

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