No abstract

Summary Sirtuins are NAD-dependent deacylases. Previous studies have established two important enzymatic intermediates in sirtuin-catalyzed deacylation, an alkylamidate intermediate I, which is then converted to a bicyclic intermediate II. However, how intermediate II is converted to products is unknown. Based on potent SIRT2-specific inhibitors we developed, here we report crystal structures of SIRT2 in complexes with a thiomyristoyl (TM) inhibitor and carba-NAD or NAD. Interestingly by soaking crystals with NAD, we capture a distinct covalent catalytic intermediate (III) that is different from the intermediates I and II. In this intermediate, the covalent bond between the S and the myristoyl carbonyl carbon is broken and we believe this intermediate III is the decomposition product of II in route to form the end products. MALDI-TOF data further support the intermediate III formation. This is the first time such an intermediate is captured by X-ray crystallography and provides more mechanistic insights into sirtuin-catalyzed reactions.

Lysine succinylation is a newly discovered posttranslational modification with distinctive physical properties. However, to date rarely have studies reported effectors capable of interpreting this modification on histones. Following our previous study of SIRT5 as an eraser of succinyl-lysine (Ksuc), here we identified the GAS41 YEATS domain as a reader of Ksuc on histones. Biochemical studies showed that the GAS41 YEATS domain presents significant binding affinity toward H3K122suc upon a protonated histidine residue. Furthermore, cellular studies showed that GAS41 had prominent interaction with H3K122suc on histones and also demonstrated the coenrichment of GAS41 and H3K122suc on the promoter. To investigate the binding mechanism, we solved the crystal structure of the YEATS domain of Yaf9, the GAS41 homolog, in complex with an H3K122suc peptide that demonstrated the presence of a salt bridge formed when a protonated histidine residue (His39) recognizes the carboxyl terminal of the succinyl group. We also solved the apo structure of GAS41 YEATS domain, in which the conserved His43 residue superimposes well with His39 in the Yaf9 structure. Our findings identified a reader of succinyl-lysine, and the binding mechanism will provide insight into the development of specific regulators targeting GAS41.

The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next‐generation sequencing and single‐cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.

Tumor-associated macrophages (TAMs) are correlated with the progression of prostatic adenocarcinoma (PCa). The mechanistic basis of this correlation and therapeutic strategies to target TAMs in PCa remain poorly defined. Here, single-cell RNA sequencing was used to profile the transcriptional landscape of TAMs in human PCa, leading to identification of a subset of macrophages characterized by dysregulation in transcriptional pathways associated with lipid metabolism. This subset of TAMs correlates positively with PCa progression and shorter disease-free survival and is characterized by an accumulation of lipids that is dependent on Marco. Mechanistically, cancer cell–derived IL-1β enhances Marco expression on macrophages, and reciprocally, cancer cell migration is promoted by CCL6 released by lipid-loaded TAMs. Moreover, administration of a high-fat diet to tumor-bearing mice raises the abundance of lipid-loaded TAMs. Finally, targeting lipid accumulation by Marco blockade hinders tumor growth and invasiveness and improves the efficacy of chemotherapy in models of PCa, pointing to combinatorial strategies that may influence patient outcomes.

People for and against direct-to-consumer (DTC) genomic tests are arguing around two issues: first, on whether an autonomy-based account can justify the tests; second, on whether the tests bring any personal utility. Bunnik et al, in an article published in this journal, were doubtful on the latter, especially in clinically irrelevant and uninterpretable sequences, and how far this claim could go in the justification. Here we argue that personal utility is inherent to DTC genomic tests and their results. We discuss Bunnik et al's account of personal utility and identify problems in its motivation and application. We then explore concepts like utility and entertainment which suggest that DTC genomic tests bring personal utility to their consumers, both in the motivation and the content of the tests. This points to an alternative account of personal utility which entails that entertainment value alone is adequate to justify DTC genomic tests, given appropriate strategies to communicate tests results with the consumers. It supports the autonomy-based justification of the test by showing that DTC genomic test itself stands as a valuable option and facilitates meaningful choice of the people.

Seasonal influenza is a primary public health burden in the USA and globally. Annual vaccination programs are designed on the basis of circulating influenza viral strains. However, the effectiveness of the seasonal influenza vaccine is highly variable between seasons and among individuals. A number of factors are known to influence vaccination effectiveness including age, sex, and comorbidities. Here, we sought to determine whether whole blood gene expression profiling prior to vaccination is informative about pre-existing immunological status and the immunological response to vaccine. We performed whole transcriptome analysis using RNA sequencing (RNAseq) of whole blood samples obtained prior to vaccination from 275 participants enrolled in an annual influenza vaccine trial. Serological status prior to vaccination and 28 days following vaccination was assessed using the hemagglutination inhibition assay (HAI) to define baseline immune status and the response to vaccination. We find evidence that genes with immunological functions are increased in expression in individuals with higher pre-existing immunity and in those individuals who mount a greater response to vaccination. Using a random forest model, we find that this set of genes can be used to predict vaccine response with a performance similar to a model that incorporates physiological and prior vaccination status alone. A model using both gene expression and physiological factors has the greatest predictive power demonstrating the potential utility of molecular profiling for enhancing prediction of vaccine response. Moreover, expression of genes that are associated with enhanced vaccination response may point to additional biological pathways that contribute to mounting a robust immunological response to the seasonal influenza vaccine.

Organoids can shed light on the dynamic interplay between complex tissues and rare cell types within a controlled microenvironment. Here, we developed gut organoid co-cultures with type-1 innate lymphoid cells (ILC1) to dissect the impact of their accumulation in inflamed intestines.We demonstrate for the first time that murine and human ILC1 secrete TGFβ1, driving expansion of CD44v6 + epithelial crypts. ILC1 additionally express MMP9 and drive gene signatures indicative of extracellular matrix remodelling. We therefore encapsulated human epithelial-mesenchymal intestinal organoids in MMP-sensitive, synthetic hydrogels designed to form efficient networks at low polymer concentrations. Harnessing this defined system, we demonstrate that ILC1 drive matrix softening and stiffening, which we suggest occurs through balanced matrix degradation and deposition. Our platform enabled us to elucidate previously undescribed interactions between ILC1 and their microenvironment, which suggest that they may exacerbate fibrosis and tumour growth when enriched in inflamed patient tissues. MainIntestinal epithelial cells (IEC) 1 interact with innate lymphoid cells (ILC) 2 to form a dynamic barrier between organisms and their environment. Together, they are capable of rapidly responding to danger and damage in an antigen non-specific manner. For instance, type-3 ILC3 secrete Interleukin-22 (IL-22, Il22 ) in response to extracellular pathogens, which promotes anti-microbial peptide secretion and proliferation of Lgr5 + CD44 + intestinal stem cells 3 .Conversely, type-1 ILC express Interferon-gamma (IFNγ, Ifng ) in response to intracellular pathogens, and are comprised of circulating natural killer (NK) cells and tissue resident helper-like ILC1 (ILC1), which are considered less cytotoxic than their NK-cell counterparts 4 .Notably, ILC1 accumulate in the inflamed intestines of Inflammatory Bowel Disease (IBD) patients 5 , however the nature of their subset-specific interactions with the epithelium has remained elusive. Understanding the impact of ILC1 enrichment could offer novel avenues for treating this complex disease, which is a pressing issue as only a third of patients respond to gold standard TNFα-blocking biologics 6 .Teasing apart the role of rare cell populations in multifactorial diseases is challenging, and redundant cytokine signalling pathways in vivo can obscure ILC-specific phenotypes. Thus, to explore the impact of ILC1 on IEC we developed a reductionist co-culture system with murine small intestine organoids (SIO) 7 . We unexpectedly found that ILC1-derived TGFβ1 induces p38γ activity to drive epithelial Cd44v6 expression and SIO proliferation. Pathway analysis of co-culture transcriptomes also predicted ILC1-driven matrisome remodelling, so we developed highly defined PEG-based hydrogels to quantitatively characterize the impact of ILC1 on matrix remodelling in a human iPSC-derived organoid model (HIO) 8 . We not only confirmed that IBD patient-derived ILC1 express TGFB1 and upregulate CD44v6, but also that they p...