News | IMPRS for Molecules of Life

Publication of IMPRS-LS student Jonathan Swietlik

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Swietlik, J.J., Bärthel, S., Falcomatà, C., Fink, D., Sinha, A., Cheng, J., Ebner, S., Landgraf, P., Dieterich, D.C., Daub, H., Saur, D., and Meissner, F.
(IMPRS-LS students are in bold)
Nat Commun, 2023, 14, 2642.
doi: 10.1038/s41467-023-38171-8

Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation

Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.

Publication of IMPRS-LS student Anna Baptist

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Baptist, A.V., and Heuer-Jungemann, A.
ACS Omega, 2023, 8, 18225-18233.
doi: 10.1021/acsomega.3c01680

Lyophilization Reduces Aggregation of Three-Dimensional DNA Origami at High Concentrations

Although for many purposes, low concentrations of DNA origami are sufficient, certain applications such as cryo electron microscopy, measurements involving small-angle X-ray scattering, or in vivo applications require high DNA origami concentrations of >200 nM. This is achievable by ultrafiltration or polyethylene glycol precipitation but often at the expense of increasing structural aggregation due to prolonged centrifugation and final redispersion in low buffer volumes. Here, we show that lyophilization and subsequent redispersion in low buffer volumes can achieve high concentrations of DNA origami while drastically reducing aggregation due to initially very low DNA origami concentrations in low salt buffers. We demonstrate this for four structurally different types of three-dimensional DNA origami. All of these structures exhibit different aggregation behaviors at high concentrations (tip-to-tip stacking, side-to-side binding, or structural interlocking), which can be drastically reduced by dispersion in larger volumes of a low salt buffer and subsequent lyophilization. Finally, we show that this procedure can also be applied to silicified DNA origami to achieve high concentrations with low aggregation. We thus find that lyophilization is not only a tool for long-term storage of biomolecules but also an excellent way for up-concentrating while maintaining well-dispersed solutions of DNA origami.

Graduation of Sabine Helmrath

Congratulations on your PhD!

Sabine Helmrath

Deciphering the role of Roquin RNA-binding proteins in late B cell development

RG: Marc Schmidt-Supprian

Graduation of Anika Reifschneider

Congratulations on your PhD!

Anika Reifschneider

Lysosomal dysfunction and microglial hyperactivation in models of progranulin deficiency

RG: Christian Haass

Graduation of Martin Fernholz

Congratulations on your PhD!

Martin Fernholz

A search for functional connectivity rules in the visual thalamus and hippocampus

RG: Tobias Bonhoeffer

Publication of IMPRS-LS student Jakob Bader

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Bader, J.M., Albrecht, V., and Mann, M.
(IMPRS-LS students are in bold)
Mol Cell Proteomics, 2023, 100577.
doi: 10.1016/j.mcpro.2023.100577

MS-based proteomics of body fluids: The end of the beginning

Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.

Publication of IMPRS-LS student Leonie Zeitler

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Zeitler, L., and Murray, P.J.
J Biol Chem, 2023, 104827.
doi: 10.1016/j.jbc.2023.104827

IL4i1 and IDO1: oxidases that control a tryptophan metabolic nexus in cancer

Regulated tryptophan metabolism by immune cells has been associated with the promotion of tolerance and poor outcomes in cancer. The main focus of research has centered on local tryptophan depletion by IDO1, an intracellular heme-dependent oxidase that converts tryptophan to formyl-kynurenine. This is the first step of a complex pathway supplying metabolites for de novo NAD⁺ biosynthesis, 1-carbon metabolism and a myriad of kynurenine derivatives, of which several act as agonists of the arylhydrocarbon receptor (AhR). Thus, cells that express IDO1 deplete tryptophan while generating downstream metabolites. We now know that another enzyme, the secreted L-amino acid oxidase IL4i1, also generates bioactive metabolites from tryptophan. In tumor microenvironments, IL4i1 and IDO1 have overlapping expression patterns, especially in myeloid cells, suggesting the two enzymes control a network of tryptophan-specific metabolic events. New findings about IL4i1 and IDO1 have shown that both enzymes generate a suite of metabolites that suppress the oxidative cell death ferroptosis. Thus, within inflammatory environments, IL4i1 and IDO1 simultaneously control essential amino acid depletion, AhR activation, suppression of ferroptosis and biosynthesis of key metabolic intermediates. Here, we summarize the recent advances in this field, focusing on IDO1 and IL4i1 in cancer. We speculate that while inhibition of IDO1 remains a viable adjuvant therapy for solid tumors, the overlapping effects of IL4i1 must be accounted for, as potentially both enzymes may need to be inhibited at the same time to produce positive effects in cancer therapy.

Graduation of Alja Podgornik