Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma.

Zhou Y, Ray PS, Zhu J, Stein F, Rettel M, Sekaran T, Sahadevan S, Perez-Perri JI, Roth EK, Myklebost O, Meza-Zepeda LA, von Deimling A, Fu C, Brosig AN, Boye K, Nathrath M, Blattmann C, Lehner B, Hentze MW, Kulozik AE

Nature communications, 2024

doi:10.1038/s41467-024-47031-y.

MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.

Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R

The EMBO journal, 2024

doi:10.1038/s44318-024-00063-y.

Trifunctional sphinganine: a new tool to dissect sphingolipid function.

Farley S, Stein F, Haberkant P, Tafesse FG, Schultz C

ACS chemical biology, 2024

doi:10.1021/acschembio.3c00554.

Macromolecular crowding in human tenocyte and skin fibroblast cultures: a comparative analysis.

Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI

Materials Today Bio, 2024

doi:10.1016/j.mtbio.2024.100977.

Comparative analysis of wild-type and chloroplast MCU-deficient plants reveals multiple consequences of chloroplast calcium handling under drought stress.

Corti F, Festa M, Stein F, Stevanato P, Siroka J, Navazio L, Vothknecht UC, Alboresi A, Novák O, Formentin E, Szabò I

Frontiers in plant science, 2023

doi:10.3389/fpls.2023.1228060.

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response.

Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers KJ, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D

Current biology : CB, 2023

doi:10.1016/j.cub.2023.12.021.

Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery.

McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S

Nucleic acids research, 2023

doi:10.1093/nar/gkad1211.

Flow in fetoplacental-like microvessels in vitro enhances perfusion, barrier function, and matrix stability.

Cherubini M, Erickson S, Padmanaban P, Haberkant P, Stein F, Beltran-Sastre V, Haase K

Science advances, 2023

doi:10.1126/sciadv.adj8540.

STPP-UP: an alternative method for drug target identification using protein thermal stability.

Zijlmans DW, Hernández-Quiles M, Jansen PWTC, Becher I, Stein F, Savitski MM, Vermeulen M

The Journal of biological chemistry, 2023

doi:10.1016/j.jbc.2023.105279.

A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates.

Mukhopadyay U, Levantovsky S, Gharbi S, Stein F, Behrends C, Bhogaraju S

bioRxiv, 2023

doi:10.1101/2023.09.04.556194.

RNA-binding proteins regulate post-transcriptional responses to TGF-β to coordinate function and mesenchymal activation of murine endothelial cells.

Wardman R, Keles M, Pachkiv I, Hemanna S, Grein S, Schwarz J, Stein F, Ola R, Dobreva G, Hentze MW, Heineke J

Arteriosclerosis, thrombosis, and vascular biology, 2023

doi:10.1161/atvbaha.123.319925.

Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins.

Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM

Life science alliance, 2023

doi:10.26508/lsa.202201805.

The RNA-binding protein landscapes differ between mammalian organs and cultured cells.

Perez-Perri JI, Ferring-Appel D, Huppertz I, Schwarzl T, Sahadevan S, Stein F, Rettel M, Galy B, Hentze MW

Nature communications, 2023

doi:10.1038/s41467-023-37494-w.

Independent human mesenchymal stromal cell-derived extracellular vesicle preparations differentially attenuate symptoms in an advanced murine graft-versus-host disease model.

Madel RJ, Börger V, Dittrich R, Bremer M, Tertel T, Phuong NNT, Baba HA, Kordelas L, Staubach S, Stein F, Haberkant P, Hackl M, Grillari R, Grillari J, Buer J, Horn PA, Westendorf AM, Brandau S, Kirschning CJ, Giebel B

Cytotherapy, 2023

doi:10.1016/j.jcyt.2023.03.008.

Redox proteomic profile of tirapazamine-resistant murine hepatoma cells.

Nemeikaitė-Čėnienė A, Haberkant P, Kučiauskas D, Stein F, Čėnas N

International journal of molecular sciences, 2023

doi:10.3390/ijms24076863.

Wnt/β-catenin signaling induces axial elasticity patterns of Hydra extracellular matrix.

Veschgini M, Suzuki R, Kling S, Petersen HO, Bergheim BG, Abuillan W, Linke P, Kaufmann S, Burghammer M, Engel U, Stein F, Özbek S, Holstein TW, Tanaka M

iScience, 2023

doi:10.1016/j.isci.2023.106416.

Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor.

Altuzar J, Notbohm J, Stein F, Haberkant P, Hempelmann P, Heybrock S, Worsch J, Saftig P, Höglinger D

Proceedings of the National Academy of Sciences of the United States of America, 2023

doi:10.1073/pnas.2213886120.

The membrane-associated protein 17 (MAP17) is upregulated in response to empagliflozin on top of RAS blockade in experimental diabetic nephropathy.

Vergara A, Llorens-Cebrià C, Martos N, Martínez-Díaz I, Stein F, Domínguez-Báez P, Molina-Van den Bosch M, Rettel M, Benito B, Bermejo S, Pieper MP, Jacobs C, Soler MJ

Clinical science (London, England : 1979), 2022

doi:10.1042/CS20220447.

Extended N-terminal acetyltransferase Naa50 in filamentous fungi adds to Naa50 diversity.

Weidenhausen J, Kopp J, Ruger-Herreros C, Stein F, Haberkant P, Lapouge K, Sinning I

International journal of molecular sciences, 2022

doi:10.3390/ijms231810805.

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, Monzon V, Pfalz B, Garcia-Santamarina S, Galardini M, Sueki A, Kobayashi C, Stein F, Bateman A, Zeller G, Savitski MM, Elfenbein JR, Andrews-Polymenis HL, Typas A

Nature, 2022

doi:10.1038/s41586-022-05091-4.

Protective signature of IFNγ-stimulated microglia relies on miR-124-3p regulation from the secretome released by mutant APP Swedish neuronal cells.

Garcia G, Fernandes A, Stein F, Brites D

Frontiers in pharmacology, 2022

doi:10.3389/fphar.2022.833066.

Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice.

Kallergi E, Daskalaki AD, Kolaxi A, Camus C, Ioannou E, Mercaldo V, Haberkant P, Stein F, Sidiropoulou K, Dalezios Y, Savitski MM, Bagni C, Choquet D, Hosy E, Nikoletopoulou V

Nature communications, 2022

doi:10.1038/s41467-022-28301-z.

CaMKK2 facilitates Golgi-associated vesicle trafficking to sustain cancer cell proliferation.

Stewart LM, Gerner L, Rettel M, Stein F, Burrows JF, Mills IG, Evergren E

Cell death & disease, 2021

doi:10.1038/s41419-021-04335-x.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P

Nature biotechnology, 2021

doi:10.1038/s41587-021-01051-x.

Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol.

Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM

The EMBO journal, 2021

doi:10.15252/embj.2021107913.

Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes.

Riechert E, Kmietczyk V, Stein F, Schwarzl T, Sekaran T, Jürgensen L, Kamuf-Schenk V, Varma E, Hofmann C, Rettel M, Gür K, Ölschläger J, Kühl F, Martin J, Ramirez-Pedraza M, Fernandez M, Doroudgar S, Méndez R, Katus HA, Hentze MW, Völkers M

Cell reports, 2021

doi:10.1016/j.celrep.2021.109100.

Global mapping of Salmonella enterica-host protein-protein interactions during infection.

Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A

Cell Host and Microbe, 2021

doi:10.1016/j.chom.2021.06.004.

Glucocorticoids exacerbate TGFß1 mediated fibrotic signalling in lung fibroblasts by inhibition of metalloproteinase expression and activity.

Khan MM, Zukowska-Kasprzyk J, Neumann B, Halavatyi A, Tischer C, Haberkant P, Stein F, Jung F, Landry J, Lewis J, Pepperkok R

ERJ open research, 2021

doi:10.1183/23120541.lsc-2021.33.

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes.

Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE

iScience, 2021

doi:10.1016/j.isci.2021.102389.

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM

Molecular systems biology, 2021

doi:10.15252/msb.202010188.

An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices.

Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R

The European respiratory journal, 2020

doi:10.1183/13993003.00221-2020.

Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals prognostic value of stroma signatures.

Karkampouna S, De Filippo MR, Ng CKY, Klima I, Zoni E, Spahn M, Stein F, Haberkant P, Thalmann GN, Kruithof de Julio M

Cancers, 2020

doi:10.3390/cancers12123786.

The functional proteome landscape of Escherichia coli.

Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM

Nature, 2020

doi:10.1038/s41586-020-3002-5.

Aggregation and disaggregation features of the human proteome.

Määttä TA, Rettel M, Sridharan S, Helm D, Kurzawa N, Stein F, Savitski MM

Molecular systems biology, 2020

doi:10.15252/msb.20209500.

Pseudo-RNA-binding domains mediate RNA structure specificity in Upstream of N-Ras.

Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Moojiman D, Benes V, Savitski MM, Gebauer F, Hennig J

2020

doi:10.1016/j.celrep.2020.107930.

Bacterial retrons encode tripartite toxin/antitoxin systems.

Bobonis J, Mateus A, Pfalz B, Garcia-Santamarina S, Galardini M, Kobayashi C, Stein F, Savitski MM, Elfenbein JR, Andrews-Poymenis H, Typas A

bioRxiv, 2020

doi:10.1101/2020.06.22.160168.

ACLY is the novel signaling target of PIP 2/PIP 3 and Lyn in acute myeloid leukemia.

Basappa J, Citir M, Zhang Q, Wang HY, Liu X, Melnikov O, Yahya H, Stein F, Muller R, Traynor-Kaplan A, Schultz C, Wasik MA, Ptasznik A

Heliyon, 2020

doi:10.1016/j.heliyon.2020.e03910.

Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins.

Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE

Nucleic acids research, 2020

doi:10.1093/nar/gkaa256.

Thermal proteome profiling for interrogating protein interactions.

Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM

Molecular systems biology, 2020

doi:10.15252/msb.20199232.

Systematic localization of Escherichia coli membrane proteins.

Sueki A, Stein F, Savitski MM, Selkrig J, Typas A

mSystems, 2020

doi:10.1128/mSystems.00808-19.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.

Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W

The EMBO journal, 2020

doi:10.15252/embj.2019102246.

Towards a systematic map of the functional role of protein phosphorylation.

Viéitez​ C​, Busby​ BP, Ochoa​ D​, Mateus​ A​, Galardini​ M​, Jawed​ A​, Memon​ D​, Potel​ CM​, Vonesch SC​, Tu​ CS, Shahraz​ M​, Stein​ F​, Steinmetz​ LM, Savitski​ MM, Typas A, Beltrao​ P

bioRxiv, 2019

doi:10.1101/872770.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P

Nature biotechnology, 2019

doi:10.1038/s41587-019-0344-3.

The Hsp90 isoforms from S. cerevisiae differ in structure, function and client range.

Girstmair H, Tippel F, Lopez A, Tych K, Stein F, Haberkant P, Schmid PWN, Helm D, Rief M, Sattler M, Buchner J

Nature communications, 2019

doi:10.1038/s41467-019-11518-w.

Monitoring cell-type-specific gene expression using ribosome profiling in vivo during cardiac hemodynamic stress.

Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Mauz V, Friedrich UA, Kramer G, Backs J, Dieterich C, Katus HA, Völkers M

Circulation research, 2019

doi:10.1161/CIRCRESAHA.119.314817.

Publisher Correction: Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology, 2019

doi:10.1038/s41556-019-0326-1.

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology, 2019

doi:10.1038/s41556-019-0294-5.

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation.

Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K

PloS one, 2019

doi:10.1371/journal.pone.0211180.

Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture.

Perez-Perri JI, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M, Brosig A, Hentze MW

Nature communications, 2018

doi:10.1038/s41467-018-06557-8.

A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation.

Hoffmann JE, Dziuba D, Stein F, Schultz C

Biochemistry, 2018

doi:10.1021/acs.biochem.8b00397.

Thermal proteome profiling in bacteria: probing protein state in vivo.

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM

Molecular systems biology, 2018

doi:10.15252/msb.20188242.

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma.

Jethwa A, Słabicki M, Hüllein J, Jentzsch M, Dalal V, Rabe S, Wagner L, Walther T, Klapper W, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T

Blood, 2018

doi:10.1182/blood-2017-09-806679.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell, 2018

doi:10.1016/j.cell.2018.03.053.

Author Correction: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications, 2018

doi:10.1038/s41467-018-04643-5.

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J

Metabolic engineering, 2018

doi:10.1016/j.ymben.2018.03.006.

Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications, 2018

doi:10.1038/s41467-018-04142-7.

A Ratiometric Sensor for Imaging Insulin Secretion in Single β Cells.

Schifferer M, Yushchenko DA, Stein F, Bolbat A, Schultz C

Cell chemical biology, 2017

doi:10.1016/j.chembiol.2017.03.001.

Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development

Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U, Aulehla A

Developmental cell, 2017

doi:10.1016/j.devcel.2017.01.015.

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.

Höglinger D, Nadler A, Haberkant P, Kirkpatrick J, Schifferer M, Stein F, Hauke S, Porter FD, Schultz C

Proceedings of the National Academy of Sciences of the United States of America, 2017

doi:10.1073/pnas.1611096114.

Reversible Chemical Dimerization by rCD1.

Schifferer M, Feng S, Stein F, Schultz C

Methods in enzymology, 2016

doi:10.1016/bs.mie.2016.10.035.

High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells.

Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmüller U, Schultz C

Cell chemical biology, 2016

doi:10.1016/j.chembiol.2016.11.008.

Bifunctional Sphingosine for Cell-Based Analysis of Protein-Sphingolipid Interactions.

Haberkant P, Stein F, Höglinger D, Gerl MJ, Brügger B, Van Veldhoven PP, Krijgsveld J, Gavin AC, Schultz C

ACS chemical biology, 2015

doi:10.1021/acschembio.5b00810.

Exclusive photorelease of signalling lipids at the plasma membrane.

Nadler A, Yushchenko DA, Müller R, Stein F, Feng S, Mulle C, Carta M, Schultz C

Nature communications, 2015

doi:10.1038/ncomms10056.

A single-cell model of PIP3 dynamics using chemical dimerization.

MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J

Bioorganic & medicinal chemistry, 2015

doi:10.1016/j.bmc.2015.04.074.

Reversible chemical dimerizer-induced recovery of PIP2 levels moves clathrin to the plasma membrane.

Schifferer M, Feng S, Stein F, Tischer C, Schultz C

Bioorganic & medicinal chemistry, 2015

doi:10.1016/j.bmc.2015.03.048.

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells

Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C

Angewandte Chemie (International ed. in English), 2014

doi:10.1002/anie.201402294.

FluoQ: a tool for rapid analysis of multiparameter fluorescence imaging data applied to oscillatory events

Stein F, Kress M, Reither S, Piljić A, Schultz C

ACS chemical biology, 2013

doi:10.1021/cb4003442.

The fatty acid composition of diacylglycerols determines local signaling patterns

Nadler A, Reither G, Feng S, Stein F, Reither S, Müller R, Schultz C

Angewandte Chemie (International ed. in English), 2013

doi:10.1002/anie.201301716.

Target-Activated Prodrugs (TAPs) for the autoregulated inhibition of MMP12

Cobos-Correa A, Stein F, Schultz C

ACS medicinal chemistry letters, 2012

doi:10.1021/ml3001193.

Synthesis of trifunctional cyclo-β-tripeptide templates.

Stein F, Mehmood T, Plass T, Zaidi JH, Diederichsen U

Beilstein Journal of Organic Chemistry, 2012

doi:10.3762/bjoc.8.180.