Rab32 puts itaconate where it's needed: Myeloid cells can restrict the replication of intracellular bacterial pathogens such as Salmonella using a Rab family guanosine triphosphatase called Rab32. However, the underlying mechanisms remain unclear. Chen et al. report that Rab32 and its exchange factor, BLOC3, interact with aconitate decarboxylase 1 (IRG1). This complex enables the direct delivery of IRG1's antimicrobial product, itaconate, from the mitochondria to Salmonella -containing vacuoles. Itaconate concentrations in vacuoles correlated with bacterial survival, highlighting the biological relevance of this metabolite during infections. Similar findings in Escherichia coli –infected cells suggest that this is a more general phenomenon in which mitochondria and the Rab32 pathway play a critical role in antibacterial host defense. Science , this issue p. 450

Detailed observations of transcriptional, translational and post-translational events in the human brain are essential to improving our understanding of its development, function and vulnerability to disease. Here, we exploited label-free quantitative tandem mass-spectrometry to create an in-depth proteomic survey of regions of the postnatal human brain, ranging in age from early infancy to adulthood. Integration of protein data with existing matched whole-transcriptome sequencing (RNA-seq) from the BrainSpan project revealed varied patterns of protein–RNA relationships, with generally increased magnitudes of protein abundance differences between brain regions compared to RNA. Many of the differences amplified in protein data were reflective of cytoarchitectural and functional variation between brain regions. Comparing structurally similar cortical regions revealed significant differences in the abundances of receptor-associated and resident plasma membrane proteins that were not readily observed in the RNA expression data.

Dysregulation of several metabolite pathways, including branched-chain amino acids (BCAAs), are associated with Non-Alcoholic Fatty Liver Disease (NAFLD) and insulin resistance in adults, while studies in youth reported conflicting results. We explored whether, independently of obesity and insulin resistance, obese adolescents with NAFLD display a metabolomic signature consistent with disturbances in amino acid and lipid metabolism. A total of 180 plasma metabolites were measured by a targeted metabolomic approach in 78 obese adolescents with (n = 30) or without (n = 48) NAFLD assessed by magnetic resonance imaging (MRI). All subjects underwent an oral glucose tolerance test and subsets of patients underwent a two-step hyperinsulinemic-euglycemic clamp and/or a second MRI after a 2.2 ± 0.8-year follow-up. Adolescents with NAFLD had higher plasma levels of valine (p = 0.02), isoleucine (p = 0.03), tryptophan (p = 0.02), and lysine (p = 0.02) after adjustment for confounding factors. Circulating BCAAs were negatively correlated with peripheral and hepatic insulin sensitivity. Furthermore, higher baseline valine levels predicted an increase in hepatic fat content (HFF) at follow-up (p = 0.01). These results indicate that a dysregulation of BCAA metabolism characterizes obese adolescents with NAFLD independently of obesity and insulin resistance and predict an increase in hepatic fat content over time.

Processing of fish in aquaculture generates considerable amounts of by-products that remain underused and/or unexploited. We evaluated the nutritive content of fish by-products (head, gills, intestines, trimmings, bones, and skin) from meagre and gilthead sea bream fish species reared in Greece in order to estimate their nutritional value for future development of high added-value products. The proximate composition of the fish samples (total protein, total lipid, ash, moisture, and macro-element content) was determined using the Association of Official Analytical Chemists (AOAC) and International Organization for Standardization (ISO) official methods. The content of fatty acids was determined using capillary gas chromatography, and the protein profile was estimated employing scientific orbitrap mass spectrophotometer methodology. The nutrient composition of fish by-products presented fluctuations among the different by-products. Skin was the most significant protein source, trimmings and bones were high in calcium, and the head, intestines, and bones were a good source of lipids. The most abundant lipid acids found in by-products were oleic, palmitic, linoleic, and eicosenoic acids, whereas the most abundant proteins were adenosine triphosphate (ATP) synthase subunit epsilon, mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase, and mitochondrial cytochrome b-c1 complex subunit 8. These data suggest that by-products constitute valuable sources of nutrients and could therefore be exploited in accordance with the principles of a circular economy.

Parkinson’s disease (PD) is a prevalent neurodegenerative disorder, and recent evidence suggests that pathogenesis may be in part mediated by inflammatory processes, the molecular and cellular architectures of which are largely unknown. To identify and characterize selectively vulnerable brain cell populations in PD, we performed single-nucleus transcriptomics and unbiased proteomics to profile the prefrontal cortex from postmortem human brains of six individuals with late-stage PD and six age-matched controls. Analysis of nearly 80,000 nuclei led to the identification of eight major brain cell types, including elevated brain-resident T cells in PD, each with distinct transcriptional changes in agreement with the known genetics of PD. By analyzing Lewy body pathology in the same postmortem brain tissues, we found that α-synuclein pathology was inversely correlated with chaperone expression in excitatory neurons. Examining cell-cell interactions, we found a selective abatement of neuron-astrocyte interactions and enhanced neuroinflammation. Proteomic analyses of the same brains identified synaptic proteins in the prefrontal cortex that were preferentially down-regulated in PD. By comparing this single-cell PD dataset with a published analysis of similar brain regions in Alzheimer’s disease (AD), we found no common differentially expressed genes in neurons but identified many shared differentially expressed genes in glial cells, suggesting that the disease etiologies, especially in the context of neuronal vulnerability, in PD and AD are likely distinct.

Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons. This reporter marked excitatory synapses as measured by confocal microcopy and was targeted to the edge zone of the synaptic cleft as determined using 3D dSTORM super-resolution imaging. Proximity labeling with a membrane-impermeant biotin-phenol compound restricted labeling to the cell surface, and Label-Free Quantitation (LFQ) mass spectrometry combined with ratiometric HRP tagging of membrane vs. synaptic surface proteins was used to identify the proteomic content of excitatory clefts. Novel cleft candidates were identified, and Receptor-type tyrosine-protein phosphatase zeta was selected and successfully validated. This study supports the robust applicability of peroxidase-mediated proximity labeling for synaptic cleft proteomics and its potential for understanding synapse heterogeneity in health and changes in diseases such as psychiatric disorders and addiction.