In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

Pan, Fang; Wang, Xinjian; Yu, Xue; Liu, Mingqi; Zeng, Wenfeng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guoquan; Yao, Jun; Shen, Huali; Yang, Pengyuan

doi:10.18632/oncotarget.9737

Cited by 30 publications

(40 citation statements)

References 41 publications

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“…Overlap in glycosites from this study and two deglycoproteomic experiments were performed from Zielinska et al and Fang et al studies. 66,67 Gene ontology enrichment analysis was performed using DAVID 68 with a mouse brain proteome as the background. 69 The protein-glycan network, glycan co-occurrence networks, and glycosylation profiles for subcellular groups were created in R 3.2.2 using the igraph library, 70 and the arcplot were created with arcdiagram library (Sanchez, G. arcdiagram: Plot pretty arc diagrams.…”

Section: Discussionmentioning

confidence: 99%

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Riley

Hebert

Westphall

et al. 2019

Preprint

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Protein glycosylation is a highly important, yet a poorly understood protein post-translational modification. Thousands of possible glycan structures and compositions create potential for tremendous site heterogeneity and analytical challenge. A lack of suitable analytical methods for large-scale analyses of intact glycopeptides has ultimately limited our abilities to both address the degree of heterogeneity across the glycoproteome and to understand how it contributes biologically to complex systems. Here we show that N-glycoproteome site-specific microheterogeneity can be captured via large-scale glycopeptide profiling with methods enabled by activated ion electron transfer dissociation (AI-ETD), ultimately characterizing 1,545 Nglycosites (>5,600 unique N-glycopeptides) from mouse brain tissue. Moreover, we have used this large-scale glycoproteomic data to develop several new visualizations that will prove useful for analyzing intact glycopeptides in future studies. Our data reveal that N-glycosylation profiles can differ between subcellular regions and structural domains and that N-glycosite heterogeneity manifests in several different forms, including dramatic differences in glycosites on the same protein. MAIN TEXTAs insights into the role of glycosylation in health and disease continue to emerge, new technologies are required to improve the depth and breadth of glycoproteome analysis. [1][2][3][4] Especially needed are methods for intact glycopeptide analysisan approach that preserves biological context of the modification and enables understanding of proteome wide glycan heterogeneity. 5,6 The recent investment in glycoscience technology development made by the National Institutes of Health Common Fund program evince this importance and need. 7 Mass spectrometry (MS)-based methods are the premier approach to glycoproteome characterization.The bulk of our glycoproteome knowledge comes from methods that enzymatically cleave the glycan from the peptide and then sequence each molecular class separately. This approach has revealed a stunning diversity of hundreds of unique N-linked glycan structures that can decorate proteins. The specific residues that carried the modification can likewise be identified; however, the information of which glycan structures go on which sites is lost. For this reason, one cannot determine whether particular sites or classes of proteins have preference for one structure or another nor ultimately what the functional roles of the various glycans are. It is known that glycan heterogeneity can affect structure and function, such as binding specificities in immunoglobulins, 8,9 but the functional effects of heterogeneity across the glycoproteome remain largely uncharacterized.To gain a better understanding of glycan heterogeneity at a given site one can analyze intact glycopeptides. Similar to many other post-translational modifications (PTMs), glycopeptides require enrichment prior to analysis because of low stoichiometry and suppressed ionization efficiency compared to unmodified p...

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Section: Discussionmentioning

confidence: 99%

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Riley

Hebert

Westphall

et al. 2019

Preprint

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“…While glycans were shown to be specifically enriched in synapses 148, 149 , the intra-CNS expression of GP2 and GM-CSF in the developing or mature brain is still lacking. However, two recent MRI studies performed in CD patients demonstrated marked structural brain alterations 150, 151 that correlated with cognitive dysfunction 150 .…”

Section: The Cns Is a Major Source Of Superautoantigensmentioning

confidence: 99%

Evolution, immunity and the emergence of brain superautoantigens

Nataf¹

2017

F1000Res

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While some autoimmune disorders remain extremely rare, others largely predominate the epidemiology of human autoimmunity. Notably, these include psoriasis, diabetes, vitiligo, thyroiditis, rheumatoid arthritis and multiple sclerosis. Thus, despite the quasi-infinite number of "self" antigens that could theoretically trigger autoimmune responses, only a limited set of antigens, referred here as superautoantigens, induce pathogenic adaptive responses. Several lines of evidence reviewed in this paper indicate that, irrespective of the targeted organ (e.g. thyroid, pancreas, joints, brain or skin), a significant proportion of superautoantigens are highly expressed in the synaptic compartment of the central nervous system (CNS). Such an observation applies notably for GAD65, AchR, ribonucleoproteins, heat shock proteins, collagen IV, laminin, tyrosine hydroxylase and the acetylcholinesterase domain of thyroglobulin. It is also argued that cognitive alterations have been described in a number of autoimmune disorders, including psoriasis, rheumatoid arthritis, lupus, Crohn's disease and autoimmune thyroiditis. Finally, the present paper points out that a great majority of the "incidental" autoimmune conditions notably triggered by neoplasms, vaccinations or microbial infections are targeting the synaptic or myelin compartments. On this basis, the concept of an immunological homunculus, proposed by Irun Cohen more than 25 years ago, is extended here in a model where physiological autoimmunity against brain superautoantigens confers both: i) a crucial evolutionary-determined advantage via cognition-promoting autoimmunity; and ii) a major evolutionary-determined vulnerability, leading to the emergence of autoimmune disorders in Homo sapiens. Moreover, in this theoretical framework, the so called co-development/co-evolution model, both the development (at the scale of an individual) and evolution (at the scale of species) of the antibody and T-cell repertoires are coupled to those of the neural repertoires (i.e. the distinct neuronal populations and synaptic circuits supporting cognitive and sensorimotor functions). Clinical implications and future experimental insights are also presented and discussed.

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“…Given that both N - and O -linked CDGs present with abnormal development of other brain structures, and animal models with altered sialylation show distinct neurodevelopment defects, it is possible that the altered glycosylation we observe in JBTS10 patients may contribute to the formation of MTS. Recent work by Feng and colleagues to identify the N -glycoproteome in the mouse brain revealed that several key proteins for brain development are N -glycosylated [52]. …”

Section: Discussionmentioning

confidence: 99%

Abnormal glycosylation in Joubert syndrome type 10

Kane

Davids

Bond

et al. 2017

Cilia

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BackgroundThe discovery of disease pathogenesis requires systematic agnostic screening of multiple homeostatic processes that may become deregulated. We illustrate this principle in the evaluation and diagnosis of a 5-year-old boy with Joubert syndrome type 10 (JBTS10). He carried the OFD1 mutation p.Gln886Lysfs*2 (NM_003611.2: c.2656del) and manifested features of Joubert syndrome.MethodsWe integrated exome sequencing, MALDI-TOF mass spectrometry analyses of plasma and cultured dermal fibroblasts glycomes, and full clinical evaluation of the proband. Analyses of cilia formation and lectin staining were performed by immunofluorescence. Measurement of cellular nucleotide sugar levels was performed with high-performance anion-exchange chromatography with pulsed amperometric detection. Statistical analyses utilized the Student’s and Fisher’s exact t tests.ResultsGlycome analyses of plasma and cultured dermal fibroblasts identified abnormal N- and O-linked glycosylation profiles. These findings replicated in two unrelated males with OFD1 mutations. Cultured fibroblasts from affected individuals had a defect in ciliogenesis. The proband’s fibroblasts also had an abnormally elevated nuclear sialylation signature and increased total cellular levels of CMP-sialic acid. Ciliogenesis and each glycosylation anomaly were rescued by expression of wild-type OFD1.ConclusionsThe rescue of ciliogenesis and glycosylation upon reintroduction of WT OFD1 suggests that both contribute to the pathogenesis of JBTS10.Electronic supplementary materialThe online version of this article (doi:10.1186/s13630-017-0048-6) contains supplementary material, which is available to authorized users.

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In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

Cited by 30 publications

References 41 publications

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Evolution, immunity and the emergence of brain superautoantigens

Abnormal glycosylation in Joubert syndrome type 10

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