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Article ; Online: Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique.

Choudhury, Feroza K / Premkumar, Viji / Zecha, Jana / Boyd, Jonathan / Gaynor, Andrew S / Guo, Zengli / Martin, Tom / Cimbro, Raffaello / Allman, Erik L / Hess, Sonja

Journal of proteome research

2024

Abstract: Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate specific cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we ... ...

Abstract	Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate specific cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and microfluidic chip-based sorting on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with larger shifts in proteostasis.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00773
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Article ; Online: Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling.

Zecha, Jana / Gabriel, Wassim / Spallek, Ria / Chang, Yun-Chien / Mergner, Julia / Wilhelm, Mathias / Bassermann, Florian / Kuster, Bernhard

Nature communications

2022 Volume 13, Issue 1, Page(s) 165

Abstract: Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labeling and mass spectrometry to measure the turnover of >120,000 peptidoforms ... ...

Abstract	Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labeling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we speculate that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We show examples of how the turnover data may give insights into unknown functions of PTMs and provide a freely accessible online tool that allows interrogation and visualisation of all turnover data. The SPOT methodology is applicable to many cell types and modifications, offering the potential to prioritize PTMs for future functional investigations.
MeSH term(s)	Acetylation ; B-Lymphocytes/cytology ; B-Lymphocytes/metabolism ; Cell Line, Tumor ; Half-Life ; HeLa Cells ; Humans ; Phosphorylation ; Protein Binding ; Protein Interaction Mapping ; Protein Processing, Post-Translational ; Protein Stability ; Proteins/genetics ; Proteins/metabolism ; Proteolysis ; Proteome/classification ; Proteome/genetics ; Proteome/metabolism ; Proteomics/methods ; Software ; Ubiquitination
Chemical Substances	Proteins ; Proteome
Language	English
Publishing date	2022-01-10
Publishing country	England
Document type	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/s41467-021-27639-0
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Article ; Online: Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling

Jana Zecha / Wassim Gabriel / Ria Spallek / Yun-Chien Chang / Julia Mergner / Mathias Wilhelm / Florian Bassermann / Bernhard Kuster

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 14

Abstract: Post-translational modifications (PTMs) can regulate cellular protein function but their global impact on protein turnover is largely unknown. Here, the authors develop proteomic workflows to profile PTM-resolved protein turnover and analyze the effects ... ...

Abstract	Post-translational modifications (PTMs) can regulate cellular protein function but their global impact on protein turnover is largely unknown. Here, the authors develop proteomic workflows to profile PTM-resolved protein turnover and analyze the effects of phosphorylation, acetylation and ubiquitination.
Keywords	Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests.

Ruprecht, Benjamin / Zecha, Jana / Zolg, Daniel P / Kuster, Bernhard

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

2017 Volume 1550, Page(s) 83–98

Abstract: Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun ... ...

Abstract	Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun digested proteomes. While a multitude of methods has been established for off-line peptide separation using HPLC columns, their use can be limited particularly when sample quantities are scarce. In this protocol, we describe an approach which combines high pH reversed-phase peptide separation into few fractions in StageTip micro-columns. This miniaturized sample preparation method enhances peptide recovery and hence improves sensitivity. This is particularly useful when working with limited sample amounts obtained from e.g., phosphopeptide enrichments or tissue biopsies. Essentially the same approach can also be applied for multiplexed analysis using tandem mass tags (TMT) and can be parallelized in order to deliver the required throughput. Here, we provide a step-by-step protocol for TMT6plex labeling of peptides, the construction of StageTips, sample fractionation and pooling schemes adjusted to different types of analytes, mass spectrometric sample measurement, and downstream data processing using MaxQuant. To illustrate the expected results using this protocol, we provide results from an unlabeled and a TMT6plex labeled phosphopeptide sample leading to the identification of >17,000 phosphopeptides in 8 h (Q Exactive HF) and >23,000 TMT6plex labeled phosphopeptides (Q Exactive Plus) in 12 h of measurement time. Importantly, this protocol is equally applicable to the fractionation of full proteome digests.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6747-6_8
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Book ; Online ; Thesis: Studying peptidoform-resolved proteome turnover

Zecha, Jana Verfasser] / [Küster, Bernhard [Akademischer Betreuer] / Küster, Bernhard [Gutachter] / Selbach, Matthias [Gutachter] / Bassermann, Florian [Gutachter]

2019

Author's details	Jana Zecha ; Gutachter: Bernhard Küster, Matthias Selbach, Florian Bassermann ; Betreuer: Bernhard Küster
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek der TU München
Publishing place	München
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics.

Zecha, Jana / Meng, Chen / Zolg, Daniel Paul / Samaras, Patroklos / Wilhelm, Mathias / Kuster, Bernhard

Molecular & cellular proteomics : MCP

2018 Volume 17, Issue 5, Page(s) 974–992

Abstract: The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. ... ...

Abstract	The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein properties and functions on protein stability in steady-state cells and uncovered that the high turnover of respiratory chain complex I proteins might be explained by oxidative stress.
MeSH term(s)	Enzyme Stability ; Half-Life ; HeLa Cells ; Humans ; Isotope Labeling ; NADH Dehydrogenase/metabolism ; Oxidative Stress/drug effects ; Peptides/metabolism ; Protein Biosynthesis ; Proteolysis ; Proteome/metabolism ; Proteomics/methods ; Reproducibility of Results
Chemical Substances	Peptides ; Proteome ; NADH Dehydrogenase (EC 1.6.99.3)
Language	English
Publishing date	2018-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.RA118.000583
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Article ; Online: The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma.

Paulmann, Carmen / Spallek, Ria / Karpiuk, Oleksandra / Heider, Michael / Schäffer, Isabell / Zecha, Jana / Klaeger, Susan / Walzik, Michaela / Öllinger, Rupert / Engleitner, Thomas / Wirth, Matthias / Keller, Ulrich / Krönke, Jan / Rudelius, Martina / Kossatz, Susanne / Rad, Roland / Kuster, Bernhard / Bassermann, Florian

The EMBO journal

2022 Volume 41, Issue 20, Page(s) e110871

Abstract: Deubiquitylases (DUBs) are therapeutically amenable components of the ubiquitin machinery that stabilize substrate proteins. Their inhibition can destabilize oncoproteins that may otherwise be undruggable. Here, we screened for DUB vulnerabilities in ... ...

Abstract	Deubiquitylases (DUBs) are therapeutically amenable components of the ubiquitin machinery that stabilize substrate proteins. Their inhibition can destabilize oncoproteins that may otherwise be undruggable. Here, we screened for DUB vulnerabilities in multiple myeloma, an incurable malignancy with dependency on the ubiquitin proteasome system and identified OTUD6B as an oncogene that drives the G1/S-transition. LIN28B, a suppressor of microRNA biogenesis, is specified as a bona fide cell cycle-specific substrate of OTUD6B. Stabilization of LIN28B drives MYC expression at G1/S, which in turn allows for rapid S-phase entry. Silencing OTUD6B or LIN28B inhibits multiple myeloma outgrowth in vivo and high OTUD6B expression evolves in patients that progress to symptomatic multiple myeloma and results in an adverse outcome of the disease. Thus, we link proteolytic ubiquitylation with post-transcriptional regulation and nominate OTUD6B as a potential mediator of the MGUS-multiple myeloma transition, a central regulator of MYC, and an actionable vulnerability in multiple myeloma and other tumors with an activated OTUD6B-LIN28B axis.
MeSH term(s)	Cell Cycle ; Cell Line, Tumor ; Endopeptidases/genetics ; Humans ; MicroRNAs/genetics ; Multiple Myeloma/genetics ; Proteasome Endopeptidase Complex/genetics ; Proto-Oncogene Proteins c-myc/genetics ; RNA-Binding Proteins/genetics ; Ubiquitins/metabolism
Chemical Substances	LIN28B protein, human ; MYC protein, human ; MicroRNAs ; Proto-Oncogene Proteins c-myc ; RNA-Binding Proteins ; Ubiquitins ; Endopeptidases (EC 3.4.-) ; OTUD6B protein, human (EC 3.4.-) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2022-09-05
Publishing country	England
Document type	Journal Article
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2022110871
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Zs.A 1808: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Functional expression of electrogenic sodium bicarbonate cotransporter 1 (NBCe1) in mouse cortical astrocytes is dependent on S255-257 and regulated by mTOR.

Khakipoor, Shokoufeh / Giannaki, Marina / Theparambil, Shefeeq M / Zecha, Jana / Küster, Bernhard / Heermann, Stephan / Deitmer, Joachim W / Roussa, Eleni

Glia

2019 Volume 67, Issue 12, Page(s) 2264–2278

Abstract: The electrogenic sodium bicarbonate cotransporter 1, NBCe1 (SLC4A4), is the major bicarbonate transporter expressed in astrocytes. It is highly sensitive for bicarbonate and the main regulator of intracellular, extracellular, and synaptic pH, thereby ... ...

Abstract	The electrogenic sodium bicarbonate cotransporter 1, NBCe1 (SLC4A4), is the major bicarbonate transporter expressed in astrocytes. It is highly sensitive for bicarbonate and the main regulator of intracellular, extracellular, and synaptic pH, thereby modulating neuronal excitability. However, despite these essential functions, the molecular mechanisms underlying NBCe1-mediated astrocytic response to extracellular pH changes are mostly unknown. Using primary mouse cortical astrocyte cultures, we investigated the effect of long-term extracellular metabolic alkalosis on regulation of NBCe1 and elucidated the underlying molecular mechanisms by immunoblotting, biotinylation of surface proteins, intracellular H
MeSH term(s)	Alkalosis/metabolism ; Alkalosis/pathology ; Animals ; Astrocytes/metabolism ; Cells, Cultured ; Cerebral Cortex/cytology ; Cerebral Cortex/metabolism ; Female ; Gene Expression ; HeLa Cells ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Phosphorylation/physiology ; Sodium-Bicarbonate Symporters/biosynthesis ; Sodium-Bicarbonate Symporters/genetics ; TOR Serine-Threonine Kinases/physiology
Chemical Substances	Sodium-Bicarbonate Symporters ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; mTOR protein, mouse (EC 2.7.1.1)
Language	English
Publishing date	2019-07-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	639414-0
ISSN	1098-1136 ; 0894-1491
ISSN (online)	1098-1136
ISSN	0894-1491
DOI	10.1002/glia.23682
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Article ; Online: TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach.

Zecha, Jana / Satpathy, Shankha / Kanashova, Tamara / Avanessian, Shayan C / Kane, M Harry / Clauser, Karl R / Mertins, Philipp / Carr, Steven A / Kuster, Bernhard

Molecular & cellular proteomics : MCP

2019 Volume 18, Issue 7, Page(s) 1468–1478

Abstract: Isobaric stable isotope labeling using, for example, tandem mass tags (TMTs) is increasingly being applied for large-scale proteomic studies. Experiments focusing on proteoform analysis in drug time course or perturbation studies or in large patient ... ...

Abstract	Isobaric stable isotope labeling using, for example, tandem mass tags (TMTs) is increasingly being applied for large-scale proteomic studies. Experiments focusing on proteoform analysis in drug time course or perturbation studies or in large patient cohorts greatly benefit from the reproducible quantification of single peptides across samples. However, such studies often require labeling of hundreds of micrograms of peptides such that the cost for labeling reagents represents a major contribution to the overall cost of an experiment. Here, we describe and evaluate a robust and cost-effective protocol for TMT labeling that reduces the quantity of required labeling reagent by a factor of eight and achieves complete labeling. Under- and overlabeling of peptides derived from complex digests of tissues and cell lines were systematically evaluated using peptide quantities of between 12.5 and 800 μg and TMT-to-peptide ratios (wt/wt) ranging from 8:1 to 1:2 at different TMT and peptide concentrations. When reaction volumes were reduced to maintain TMT and peptide concentrations of at least 10 mm and 2 g/l, respectively, TMT-to-peptide ratios as low as 1:1 (wt/wt) resulted in labeling efficiencies of > 99% and excellent intra- and interlaboratory reproducibility. The utility of the optimized protocol was further demonstrated in a deep-scale proteome and phosphoproteome analysis of patient-derived xenograft tumor tissue benchmarked against the labeling procedure recommended by the TMT vendor. Finally, we discuss the impact of labeling reaction parameters for N-hydroxysuccinimide ester-based chemistry and provide guidance on adopting efficient labeling protocols for different peptide quantities.
MeSH term(s)	Cost-Benefit Analysis ; HeLa Cells ; Humans ; Isotope Labeling/economics ; Jurkat Cells ; Mass Spectrometry ; Peptides/metabolism ; Proteome/metabolism ; Proteomics ; Reference Standards ; Reproducibility of Results
Chemical Substances	Peptides ; Proteome
Language	English
Publishing date	2019-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.TIR119.001385
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Article ; Online: A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines.

Ryan, Feargal J / Norton, Todd S / McCafferty, Conor / Blake, Stephen J / Stevens, Natalie E / James, Jane / Eden, Georgina L / Tee, Yee C / Benson, Saoirse C / Masavuli, Makutiro G / Yeow, Arthur E L / Abayasingam, Arunasingam / Agapiou, David / Stevens, Hannah / Zecha, Jana / Messina, Nicole L / Curtis, Nigel / Ignjatovic, Vera / Monagle, Paul /

Tran, Huyen / McFadyen, James D / Bull, Rowena A / Grubor-Bauk, Branka / Lynn, Miriam A / Botten, Rochelle / Barry, Simone E / Lynn, David J

Cell reports. Medicine

2023 Volume 4, Issue 3, Page(s) 100971

Abstract: Identifying the molecular mechanisms that promote optimal immune responses to coronavirus disease 2019 (COVID-19) vaccination is critical for future rational vaccine design. Here, we longitudinally profile innate and adaptive immune responses in 102 ... ...

Abstract	Identifying the molecular mechanisms that promote optimal immune responses to coronavirus disease 2019 (COVID-19) vaccination is critical for future rational vaccine design. Here, we longitudinally profile innate and adaptive immune responses in 102 adults after the first, second, and third doses of mRNA or adenovirus-vectored COVID-19 vaccines. Using a multi-omics approach, we identify key differences in the immune responses induced by ChAdOx1-S and BNT162b2 that correlate with antigen-specific antibody and T cell responses or vaccine reactogenicity. Unexpectedly, we observe that vaccination with ChAdOx1-S, but not BNT162b2, induces an adenoviral vector-specific memory response after the first dose, which correlates with the expression of proteins with roles in thrombosis with potential implications for thrombosis with thrombocytopenia syndrome (TTS), a rare but serious adverse event linked to adenovirus-vectored vaccines. The COVID-19 Vaccine Immune Responses Study thus represents a major resource that can be used to understand the immunogenicity and reactogenicity of these COVID-19 vaccines.
MeSH term(s)	Adult ; Humans ; Adenoviridae/genetics ; Antibodies ; BNT162 Vaccine ; COVID-19/prevention & control ; COVID-19 Vaccines/adverse effects ; RNA, Messenger/genetics ; Vaccines
Chemical Substances	Antibodies ; BNT162 Vaccine ; COVID-19 Vaccines ; RNA, Messenger ; Vaccines
Language	English
Publishing date	2023-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2023.100971
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