Chemoproteomic mapping of human milk oligosaccharide (HMO) interactions in cells

Hassan, Abdullah A.; Wozniak, Jacob M.; Vilen, Zak; Li, Weichao; Jadhav, Appaso Mahadev; Parker, Christopher G.; Huang, Mia L.

doi:10.1039/d2cb00176d

Cited by 7 publications

(4 citation statements)

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“…We defined proteins that were enriched in a UV-dependent manner [fold change (UV/no-UV ratio) > 4 with a p-value of <0.05] as potential target receptors for CXCL14. 39 MS-based analysis revealed that 26 and 27 cell-membrane proteins were significantly enriched by probe 10 and probe 11, respectively (Figures 4B,C and S16A). Of these cell-membrane receptors, 18 proteins were found to be captured by both probe 10 and 11 (Figure 4C), and C3a anaphylatoxin chemotactic receptor (C3AR1), B-cell differentiation antigen Cd72 (CD72), 4F2 cell-surface antigen heavy chain (SLC3A2), and low-density lipoprotein receptor-related protein 1 (LRP1) were identified as particularly enriched hits (Table 1).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Each MS-based experiment was performed in three independent biological replicates. We defined proteins that were enriched in a UV-dependent manner [fold change (UV/no-UV ratio) > 4 with a p -value of <0.05] as potential target receptors for CXCL14 . MS-based analysis revealed that 26 and 27 cell-membrane proteins were significantly enriched by probe 10 and probe 11 , respectively (Figures B,C and S16A).…”

Section: Results and Discussionmentioning

confidence: 99%

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Identification of Low-Density Lipoprotein Receptor-Related Protein 1 as a CXCL14 Receptor Using Chemically Synthesized Tetrafunctional Probes

Miyajima,

Tanegashima,

Naruse

et al. 2024

ACS Chem. Biol.

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CXCL14 is a primordial CXC-type chemokine that transports CpG oligodeoxynucleotides (ODN) into endosomes and lysosomes in dendritic cells, thereby leading to the activation of the Toll-like receptor 9 (TLR9)-mediated innate immune system. However, the underlying molecular mechanism by which the CXCL14-CpG ODN complex enters cells remains elusive. Herein, we describe the chemical synthesis of CXCL14-derived photoaffinity probes and their application to the identification of target receptors for CXCL14 using quantitative proteomics. By utilizing native chemical ligation and maleimide−thiol coupling chemistry, we synthesized site-specifically modified CXCL14-based photoaffinity probes that contain photoreactive 2-aryl-5-carboxytetrazole (ACT) and a hydrazine-labile cleavable linker. CXCL14-based probes were found to be capable of binding CpG ODN to immune cells, whose bioactivities were comparable to native CXCL14. Application of CXCL14-derived probes to quantitative proteomic experiments enabled the identification of dozens of target receptor candidates for CXCL14 in mouse macrophage-derived RAW264.7 cells, and we discovered that low-density lipoprotein receptorrelated protein 1 (LRP1) is a novel receptor for CXCL14 by competitive proteome profiling. We further showed that disruption of LRP1 affected the incorporation of the CXCL14-CpG ODN complex in the cells. Overall, this report highlights the power of synthetic CXCL14-derived photoaffinity probes combined with chemical proteomics to discover previously unidentified receptors for CXCL14, which could promote an understanding of the molecular functions of CXCL14 and the elaborate machinery of innate immune systems.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Results and Discussionmentioning

confidence: 99%

Identification of Low-Density Lipoprotein Receptor-Related Protein 1 as a CXCL14 Receptor Using Chemically Synthesized Tetrafunctional Probes

Miyajima,

Tanegashima,

Naruse

et al. 2024

ACS Chem. Biol.

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“…These soluble glycans, which are found in human breast milk, have been implicated in a variety of biological functions, including anti‐inflammatory and anti‐bacterial pathways [70] . To identify HMO counterreceptors, our group developed bifunctional probes mimicking the common HMOs, lactose, 2’fucosyl lactose, 3’sialyl lactose, and 6’sialyl lactose [71] . The probes contain both a photo‐activatable diazirine group to crosslink counterreceptors as well as an alkyne, allowing for the addition of azide‐containing reporter and enrichment tags via CuAAC.…”

Section: Functional Profiling Of Glycan‐processing or Glycan‐binding ...mentioning

confidence: 99%

“…[ 70 ] To identify HMO counterreceptors, our group developed bifunctional probes mimicking the common HMOs, lactose, 2’fucosyl lactose, 3’sialyl lactose, and 6’sialyl lactose. [ 71 ] The probes contain both a photoactivatable diazirine group to crosslink counterreceptors as well as an alkyne, allowing for the addition of azide-containing reporter and enrichment tags via CuAAC. By clicking a biotin group onto the probe post photocrosslinking, the probe-receptor complex can be enriched and analyzed by MS to identify putative binders of the HMO mimics in live cells.…”

Section: Functional Profiling Of Glycan-processing or Glycan-binding ...mentioning

confidence: 99%

(Glycan Binding) Activity‐Based Protein Profiling in Cells Enabled by Mass Spectrometry‐Based Proteomics

Vilen

Reeves

Huang

2023

Israel Journal of Chemistry

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The presence of glycan modifications at the cell surface and other locales positions them as key regulators of cell recognition and function. However, due to the complexity of glycosylation, the annotation of which proteins bear glycan modifications, which glycan patterns are present, and which proteins are capable of binding glycans is incomplete. Inspired by activity-based protein profiling to enrich for proteins in cells based on select characteristics, these endeavors have been greatly advanced by the development of appropriate glycan-binding and glycan-based probes. Here, we provide context for these three problems and describe how the capability of molecules to interact with glycans has enabled the assignment of proteins with specific glycan modifications or of proteins that bind glycans. Furthermore, we discuss how the integration of these probes with high resolution mass spectrometry-based technologies has greatly advanced glycoscience.

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Protein‐Metabolite Interactions: Discovery and Significance

Dixit

Kalia

2023

ChemBioChem

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Metabolites orchestrate cellular processes as either substrates, co-enzymes, inhibitors, or activators of cellular proteins such as enzymes and receptors. Although traditional biochemical and structural biology-based approaches have been successfully employed for the discovery of protein-metabolite interactions, they often fail to detect transient and low-affinity biomolecular relationships. Another limitation of these approaches is that they are performed under in vitro conditions lacking the physiological context. Recently developed mass spectrometrybased methodologies overcome both these shortcomings, and have resulted in the discovery of global protein-metabolite cellular interaction networks. Herein, we describe traditional and modern approaches for the discovery of protein-metabolite interactions, and discuss the impact of these discoveries on our understanding of cellular physiology and on drug development.

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Chemoproteomic mapping of human milk oligosaccharide (HMO) interactions in cells

Abstract: Human milk oligosaccharides (HMOs) are a family of unconjugated soluble glycans found in human breast milk that exhibit a myriad of biological activity.

Cited by 7 publications

References 50 publications

Identification of Low-Density Lipoprotein Receptor-Related Protein 1 as a CXCL14 Receptor Using Chemically Synthesized Tetrafunctional Probes

Identification of Low-Density Lipoprotein Receptor-Related Protein 1 as a CXCL14 Receptor Using Chemically Synthesized Tetrafunctional Probes

(Glycan Binding) Activity‐Based Protein Profiling in Cells Enabled by Mass Spectrometry‐Based Proteomics

Protein‐Metabolite Interactions: Discovery and Significance

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