A framework for ultra-low-input spatial tissue proteomics

Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell function and heterogeneity in (patho)physiology. However, optimized workflows that preserve morphological information for phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected tissue are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low-input archival material. Benchmarking in murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions. Applied to human tonsil, we profiled 146 microregions including T and B lymphocyte niches and quantified cell-type-specific markers, cytokines, and transcription factors. These data also highlighted proteome dynamics within activated germinal centers, illuminating sites undergoing B cell proliferation and somatic hypermutation. This approach has broad implications in biomedicine, including early disease profiling and drug target and biomarker discovery. A record of this paper's transparent peer review process is included in the supplemental information.

Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma

Recent exome-wide studies discovered frequent somatic mutations in the epigenetic modifier ZNF217 in primary mediastinal B cell lymphoma (PMBCL) and related disorders. As functional consequences of ZNF217 alterations remain unknown, we comprehensively evaluated their impact in PMBCL. Targeted sequencing identified genetic lesions affecting ZNF217 in 33% of 157 PMBCL patients. Subsequent gene expression profiling (n = 120) revealed changes in cytokine and interferon signal transduction in ZNF217-aberrant PMBCL cases. In vitro, knockout of ZNF217 led to changes in chromatin accessibility interfering with binding motifs for crucial lymphoma-associated transcription factors. This led to disturbed expression of interferon-responsive and inflammation-associated genes, altered cell behavior, and aberrant differentiation. Mass spectrometry demonstrates that ZNF217 acts within a histone modifier complex containing LSD1, CoREST and HDAC and interferes with H3K4 methylation and H3K27 acetylation. Concluding, our data suggest non-catalytic activity of ZNF217, which directs histone modifier complex function and controls B cell differentiation-associated patterns of chromatin structure.

Static and dynamic light-scattering studies on micellar solutions of alkyldimethylbenzylammonium chlorides

Static (SLS) and dynamic (DLS) light-scattering techniques were applied to the study of the aggregation of dodecyl- (C12DBACl), tetradecyl- (C14DBACl), and hexadecyldimethylbenzylammonium (C16DBACl) chlorides in water and in 0.01 and 0.05 m NaCl aqueous solutions at 25 degrees C. Results of SLS measurements yielded critical micelle concentration (cmc) values for aqueous and NaCl solutions. The aggregation numbers of the micelles for the homologous surfactants are low but increase with chain length and ionic strength of the solution. Various patterns of changes of the diffusion coefficient, D, as a function of chain length, molality, and with ionic strength were found for the studied surfactants. Transformations in the structure of micelles of C14DBACl in 0.01 m NaCl occur at a concentration of surfactant of about 0.01 m. Such transformations, presumably due to rodlike structure, are the more extensive the higher the concentration of NaCl. The concentration of C16DBACl in 0.05 m NaCl covers the range where already repulsive interactions between micelles occur, as judged by the strongly negative slope of the D versus molality plot. To provide additional information on the suggested transformations, complementary viscosity measurements for C14DBACl in 0.01 m of NaCl have been performed.