Congratulations on your PhD!
Alexandra Eklund
Novel peptide probes for super-resolution microscopy and optimized DNA origami for cellular applications
RG: Ralf Jungmann
News
Congratulations on your PhD!
Hiranmay Girish Joag
A tool to selectively eliminate newly formed dendritic spines
RG: Tobias Bonhoeffer
Rosenberger, F.A.#, Thielert, M.#, and Mann, M.
(#equal contribution)
Nat Methods, 2023, 20, 320-323
doi: 10.1038/s41592-023-01771-9
Making single-cell proteomics biologically relevant
Recent technological advances in mass spectrometry promise to add single-cell proteomics to the biologist’s toolbox. Here we discuss the current status and what is needed for this exciting technology to lead to biological insight — alone or as a complement to other omics technologies.
Congratulations on your PhD!
Shachar Sherman
Genetic programming of the visual forebrain in the absence of retinal input
RG: Herwig Baier
Ugur, E., de la Porte, A., Qin, W., Bultmann, S., Ivanova, A., Drukker, M., Mann, M., Wierer, M., and Leonhardt, H.
Nucleic Acids Res, 2023, online ahead of print.
doi: 10.1093/nar/gkad058
The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) and analyzed chromatome reorganizations during major phases of pluripotency. This enabled us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the ground, formative and primed pluripotency states, and to pinpoint the specific binding and rearrangement of regulatory components. These comprehensive datasets combined with extensive analyses identified phase-specific factors like QSER1 and JADE1/2/3 and provide a detailed foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency. The technical advances reported here can be readily applied to other models in development and disease.
Weickert, P.#, Li, H.Y.#, Götz, M.J., Dürauer, S., Yaneva, D., Zhao, S., Cordes, J., Acampora, A.C., Forne, I., Imhof, A., and Stingele, J.
(IMPRS-LS students are in bold) #equal contribution
Nat Commun, 2023, 14, 352.
doi: 10.1038/s41467-023-35988-1
SPRTN patient variants cause global-genome DNA-protein crosslink repair defects
DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.
Martinsried. The 2023 Louis-Jeantet Prize for Medicine will be awarded jointly to Brenda Schulman, Director at the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich, and Ivan Ðikić, Director of the Faculty of Biochemistry II at Goethe University in Frankfurt am Main. The Louis-Jeantet Prize, awarded annually to promote European research, is amongst the most prestigious awards for biomedical research. Today, on January 24, 2023, it has been officially announced that this year's Prize will go to the scientists, Brenda Schulman and Ivan Ðikić for their outstanding scientific contributions to our understanding of the function of the protein ubiquitin and its mechanisms in cells.
"I am incredibly grateful for this award, made all the more special by sharing it with my close friend and colleague Ivan Ðikić. I am indebted to all the members of my lab over the years, to our collaborators, and to the wonderful community of colleagues in the ubiquitin field. I look forward to investing these research funds to make new scientific discoveries that we hope will provide opportunities to mitigate human disease" says Brenda Schulman, 2023 Louis-Jeantet Laureate.
Ubiquitin is a rather small protein, yet it plays a key role in cellular health. Ubiquitin is attached to other proteins in a process known as "ubiquitylation", which ensures that various processes in our cells occur in the right order. Similarly, when building a house, for example, it is important to first lay a solid foundation, then put up the roof. Ubiquitin would basically control that the heavy roof beams are not set without a strong foundation. Many processes therefore rely on ubiquitylation. Dysfunction contributes to numerous common diseases, such as for example cancer and infections.
Eklund, A.S., and Jungmann, R.
Small, 2023, e2206347.
doi: 10.1002/smll.202206347
Optimized Coiled-Coil Interactions for Multiplexed Peptide-PAINT
Super-resolution microscopy has revolutionized how researchers characterize samples in the life sciences in the last decades. Amongst methods employing single-molecule localization microscopy, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a relatively easy-to-implement method that uses the programmable and repetitive binding of dye-labeled DNA imager strands to their respective docking strands. Recently developed Peptide-PAINT replaces the interaction of oligonucleotides by short coiled-coil peptide sequences leading to an improved labeling scheme by reducing linkage errors to target proteins. However, only one coiled-coil pair is currently available for Peptide-PAINT, preventing multiplexed imaging. In this study, the initial Peptide-PAINT E/K coil is improved by modifying its length for optimized binding kinetics leading to improved localization precisions. Additionally, an orthogonal P3/P4 coil pair is introduced, enabling 2-plex Peptide-PAINT imaging and benchmarking its performance and orthogonality using single-molecule and DNA origami assays. Finally, the P3/P4 peptide pair is used to image the human epidermal growth factor receptors 2 (ErbB2/Her2) in 2D and 3D at the single receptor level using genetically encoded peptide tags.
Congratulations on your PhD!
Andrew Behrens
Development of mim-tRNAseq for global and quantitative profiling of cellular tRNA pools by high-throughput sequencing
RG: Danny Nedialkova
Bader, J.M., Deigendesch, N., Misch, M., Mann, M., Koch, A., and Meissner, F.
Cell Rep Med, 2023, 4, 100877.
doi: 10.1016/j.xcrm.2022.100877
High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.