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Article ; Online: Functional characterization of the human Cdk10/Cyclin Q complex.

Düster, Robert / Ji, Yanlong / Pan, Kuan-Ting / Urlaub, Henning / Geyer, Matthias

2022 Volume 12, Issue 3, Page(s) 210381

Abstract: Cyclin-dependent kinases (CDKs) are key players in cell cycle regulation and transcription. The CDK-family member Cdk10 is important for neural development and can act as a tumour suppressor, but the underlying molecular mechanisms are largely unknown. ... ...

Abstract	Cyclin-dependent kinases (CDKs) are key players in cell cycle regulation and transcription. The CDK-family member Cdk10 is important for neural development and can act as a tumour suppressor, but the underlying molecular mechanisms are largely unknown. Here, we provide an in-depth analysis of Cdk10 substrate specificity and function. Using recombinant Cdk10/CycQ protein complexes, we characterize RNA pol II CTD, c-MYC and RB1 as
MeSH term(s)	Cell Cycle ; Cell Division ; Cyclin-Dependent Kinases/genetics ; Cyclin-Dependent Kinases/metabolism ; Cyclins/metabolism ; Humans ; RNA Polymerase II/metabolism
Chemical Substances	CCNQ protein, human ; Cyclins ; CDK10 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2022-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.210381
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity.

Fang, Pan / Ji, Yanlong / Oellerich, Thomas / Urlaub, Henning / Pan, Kuan-Ting

International journal of molecular sciences

2022 Volume 23, Issue 3

Abstract: Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for ... ...

Abstract	Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
MeSH term(s)	Disease Progression ; Glycoproteins/analysis ; Humans ; Isotope Labeling ; Proteomics/methods ; Tandem Mass Spectrometry
Chemical Substances	Glycoproteins
Language	English
Publishing date	2022-01-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23031609
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Book ; Online ; Thesis: Quantitative N-glycoproteome, phosphoproteome and ubiquitinome analyses for studying B-cell receptor signaling in B-cell lymphoma

Ji, Yanlong [Verfasser] / Dötsch, Volker [Gutachter] / Oellerich, Thomas [Gutachter]

2021

Author's details	Yanlong Ji ; Gutachter: Volker Dötsch, Thomas Oellerich
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Johann Christian Senckenberg
Publishing place	Frankfurt am Main
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Functional genomics identifies N-acetyllactosamine extension of complex N-glycans as a mechanism to evade lysis by natural killer cells.

Zhuang, Xiaoxuan / Woods, James / Ji, Yanlong / Scheich, Sebastian / Mo, Fei / Rajagopalan, Sumati / Coulibaly, Zana A / Voss, Matthias / Urlaub, Henning / Staudt, Louis M / Pan, Kuan-Ting / Long, Eric O

Cell reports

2024 Volume 43, Issue 4, Page(s) 114105

Abstract: Natural killer (NK) cells are primary defenders against cancer precursors, but cancer cells can persist by evading immune surveillance. To investigate the genetic mechanisms underlying this evasion, we perform a genome-wide CRISPR screen using B ... ...

Abstract	Natural killer (NK) cells are primary defenders against cancer precursors, but cancer cells can persist by evading immune surveillance. To investigate the genetic mechanisms underlying this evasion, we perform a genome-wide CRISPR screen using B lymphoblastoid cells. SPPL3, a peptidase that cleaves glycosyltransferases in the Golgi, emerges as a top hit facilitating evasion from NK cytotoxicity. SPPL3-deleted cells accumulate glycosyltransferases and complex N-glycans, disrupting not only binding of ligands to NK receptors but also binding of rituximab, a CD20 antibody approved for treating B cell cancers. Notably, inhibiting N-glycan maturation restores receptor binding and sensitivity to NK cells. A secondary CRISPR screen in SPPL3-deficient cells identifies B3GNT2, a transferase-mediating poly-LacNAc extension, as crucial for resistance. Mass spectrometry confirms enrichment of N-glycans bearing poly-LacNAc upon SPPL3 loss. Collectively, our study shows the essential role of SPPL3 and poly-LacNAc in cancer immune evasion, suggesting a promising target for cancer treatment.
MeSH term(s)	Humans ; Polysaccharides/metabolism ; Killer Cells, Natural/metabolism ; Killer Cells, Natural/immunology ; Amino Sugars/metabolism ; Genomics/methods ; Rituximab/pharmacology ; Rituximab/metabolism ; Cell Line, Tumor
Chemical Substances	Polysaccharides ; Amino Sugars ; N-acetyllactosamine (3Y5B2K5OOK) ; Rituximab (4F4X42SYQ6)
Language	English
Publishing date	2024-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.114105
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Article ; Online: Relative Quantification of Phosphorylated and Glycosylated Peptides from the Same Sample Using Isobaric Chemical Labelling with a Two-Step Enrichment Strategy.

Silbern, Ivan / Fang, Pan / Ji, Yanlong / Christof, Lenz / Urlaub, Henning / Pan, Kuan-Ting

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2228, Page(s) 185–203

Abstract: Post-translational modifications (PTMs) are essential for the regulation of all cellular processes. The interplay of various PTMs on a single protein or different proteins comprises a complexity that we are far from understanding in its entirety. ... ...

Abstract	Post-translational modifications (PTMs) are essential for the regulation of all cellular processes. The interplay of various PTMs on a single protein or different proteins comprises a complexity that we are far from understanding in its entirety. Reliable strategies for the enrichment and accurate quantification of PTMs are needed to study as many PTMs on proteins as possible. In this protocol we present a liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based workflow that enables the enrichment and quantification of phosphorylated and N-glycosylated peptides from the same sample. After extraction and digestion of proteins, we label the peptides with stable isotope-coded tandem mass tags (TMTs) and enrich N-glycopeptides and phosphopeptides by using zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and titanium dioxide (TiO
MeSH term(s)	Animals ; Cell Line ; Chromatography, High Pressure Liquid ; Chromatography, Reverse-Phase ; Glycosylation ; Humans ; Isotope Labeling ; Phosphorylation ; Protein Processing, Post-Translational ; Proteins/analysis ; Proteomics ; Research Design ; Tandem Mass Spectrometry
Chemical Substances	Proteins
Language	English
Publishing date	2021-05-05
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1024-4_14
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Article: Evaluation and Optimization of High-Field Asymmetric Waveform Ion-Mobility Spectrometry for Multiplexed Quantitative Site-Specific N-Glycoproteomics

Fang, Pan / Ji, Yanlong / Silbern, Ivan / Viner, Rosa / Oellerich, Thomas / Pan, Kuan-Ting / Urlaub, Henning

Analytical chemistry. 2021 June 16, v. 93, no. 25

2021

Abstract: The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has been shown to improve the scope of bottom-up proteomics. The benefits of ... ...

Abstract	The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has been shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified immunoglobulin M (IgM) protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size, and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 methods provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass spectrometry-based qualitative and quantitative N-glycoproteomics.
Keywords	amino acid sequences ; analytical chemistry ; glycoproteomics ; glycosylation ; humans ; lymphoma ; mass spectrometry
Language	English
Dates of publication	2021-0616
Size	p. 8846-8855.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00802
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Quantitative Analysis of the Cardiac Phosphoproteome in Response to Acute β-Adrenergic Receptor Stimulation In Vivo.

Güran, Alican / Ji, Yanlong / Fang, Pan / Pan, Kuan-Ting / Urlaub, Henning / Avkiran, Metin / Lenz, Christof

International journal of molecular sciences

2021 Volume 22, Issue 22

Abstract: β-adrenergic receptor (β-AR) stimulation represents a major mechanism of modulating cardiac output. In spite of its fundamental importance, its molecular basis on the level of cell signalling has not been characterised in detail yet. We employed mass ... ...

Abstract	β-adrenergic receptor (β-AR) stimulation represents a major mechanism of modulating cardiac output. In spite of its fundamental importance, its molecular basis on the level of cell signalling has not been characterised in detail yet. We employed mass spectrometry-based proteome and phosphoproteome analysis using SuperSILAC (spike-in stable isotope labelling by amino acids in cell culture) standardization to generate a comprehensive map of acute phosphoproteome changes in mice upon administration of isoprenaline (ISO), a synthetic β-AR agonist that targets both β1-AR and β2-AR subtypes. Our data describe 8597 quantitated phosphopeptides corresponding to 10,164 known and novel phospho-events from 2975 proteins. In total, 197 of these phospho-events showed significantly altered phosphorylation, indicating an intricate signalling network activated in response to β-AR stimulation. In addition, we unexpectedly detected significant cardiac expression and ISO-induced fragmentation of junctophilin-1, a junctophilin isoform hitherto only thought to be expressed in skeletal muscle. Data are available via ProteomeXchange with identifier PXD025569.
MeSH term(s)	Adrenergic beta-Agonists/pharmacology ; Amino Acids ; Animals ; Heart/drug effects ; Humans ; Isoproterenol/pharmacology ; Membrane Proteins/antagonists & inhibitors ; Membrane Proteins/genetics ; Mice ; Myocardium/metabolism ; Myocardium/pathology ; Phosphoproteins/antagonists & inhibitors ; Phosphoproteins/genetics ; Phosphorylation/drug effects ; Proteome/drug effects ; Proteome/genetics ; Receptors, Adrenergic, beta/genetics ; Receptors, Adrenergic, beta-1/drug effects ; Receptors, Adrenergic, beta-1/genetics ; Receptors, Adrenergic, beta-2 ; Signal Transduction/drug effects
Chemical Substances	ADRB2 protein, human ; Adrenergic beta-Agonists ; Amino Acids ; Membrane Proteins ; Phosphoproteins ; Proteome ; Receptors, Adrenergic, beta ; Receptors, Adrenergic, beta-1 ; Receptors, Adrenergic, beta-2 ; junctophilin ; Isoproterenol (L628TT009W)
Language	English
Publishing date	2021-11-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222212584
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Article ; Online: Evaluation and Optimization of High-Field Asymmetric Waveform Ion-Mobility Spectrometry for Multiplexed Quantitative Site-Specific

Fang, Pan / Ji, Yanlong / Silbern, Ivan / Viner, Rosa / Oellerich, Thomas / Pan, Kuan-Ting / Urlaub, Henning

Analytical chemistry

2021

Abstract	The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has been shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative
Language	English
Publishing date	2021-06-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00802
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Article ; Online: Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B Cell Lymphoma.

Cancer discovery

2024

Abstract: Polatuzumab Vedotin (Pola-V) is an antibody-drug conjugate directed to the CD79B subunit of the B cell receptor (BCR). When combined with conventional immunochemotherapy, Pola-V improves outcomes in DLBCL. To identify determinants of Pola-V sensitivity, ... ...

Abstract	Polatuzumab Vedotin (Pola-V) is an antibody-drug conjugate directed to the CD79B subunit of the B cell receptor (BCR). When combined with conventional immunochemotherapy, Pola-V improves outcomes in DLBCL. To identify determinants of Pola-V sensitivity, we used CRISPR-Cas9 screening for genes that modulated Pola-V toxicity for lymphomas or the surface expression of its target, CD79B. Our results reveal the striking impact of CD79B glycosylation on Pola-V epitope availability on the lymphoma cell surface and on Pola-V toxicity. Genetic, pharmacological, and enzymatic approaches that remove sialic acid from N-linked glycans enhanced lymphoma killing by Pola-V. Pola-V toxicity was also modulated by KLHL6, an E3 ubiquitin ligase that is recurrently inactivated in germinal center derived lymphomas. We reveal how KLHL6 targets CD79B for degradation in normal and malignant germinal center B cells, thereby determining expression of the surface BCR complex. Our findings suggest precision medicine strategies to optimize Pola-V as a lymphoma therapeutic.
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-23-0802
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Article ; Online: A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics.

Fang, Pan / Ji, Yanlong / Silbern, Ivan / Doebele, Carmen / Ninov, Momchil / Lenz, Christof / Oellerich, Thomas / Pan, Kuan-Ting / Urlaub, Henning

Nature communications

2020 Volume 11, Issue 1, Page(s) 5268

Abstract: Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based ... ...

Abstract	Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification and quantification of intact glycopeptides in complex biological samples. PAC significantly reduces sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search, which increases the identification rates of glycopeptides by 22% compared with conventional strategies. We apply SugarQuant to identify and quantify more than 5,000 unique glycoforms in Burkitt's lymphoma cells, and determine site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.
MeSH term(s)	Burkitt Lymphoma/chemistry ; Burkitt Lymphoma/metabolism ; Glycopeptides/chemistry ; Glycosylation ; Humans ; Proteomics/methods ; Tandem Mass Spectrometry
Chemical Substances	Glycopeptides
Language	English
Publishing date	2020-10-19
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-19052-w
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