Author contributions L.M.M. and S.K. conceived the project and designed the experiments. L.M.M., M.L., E.G. and R.M. curated patient samples. S.K. led data production and performed the experiments together with A.S.K., A.M. and L.M.M. G.X.Y.Z. provided healthy bone marrow and peripheral blood CITE-seq data. S.K. analyzed the scADT-seq data with contribution from B.P. M.R.C. performed data analysis. J.M.G. conceived the analytical workflows and performed the data analysis for scATAC-seq and scRNA-seq supervised by H.Y.C. and

DNA double strand breaks are generated by genotoxic agents and by cellular endonucleases as intermediates of several important physiologic processes. The cellular response to genotoxic DNA breaks includes the activation of transcriptional programs known primarily to regulate cell cycle checkpoints and cell survival1–5. DNA double strand breaks are generated in all developing lymphocytes during the assembly of antigen receptor genes, a process that is essential for normal lymphocyte development. Here we demonstrate that these physiologic DNA breaks activate a broad transcriptional program. This program transcends the canonical DNA double strand break response and includes many genes that regulate diverse cellular processes important for lymphocyte development. Moreover, the expression of several of these genes is regulated similarly in response to genotoxic DNA damage. Thus, physiologic DNA double strand breaks provide cues that can regulate cell-type-specific processes not directly involved in maintaining the integrity of the genome, and genotoxic DNA breaks could disrupt normal cellular functions by corrupting these processes.

A panel of variants with alanine substitutions in the small loop of anthrax toxin protective antigen domain 4 was created to determine individual amino acid residues critical for interactions with the cellular receptor and with a neutralizing monoclonal antibody, 14B7. Substituted protective antigen proteins were analyzed by cellular cytotoxicity assays, and their interactions with antibody were measured by plasmon surface resonance and analytical ultracentrifugation. Residue Asp 683 was the most critical for cell binding and toxicity, causing an ϳ1000-fold reduction in toxicity, but was not a large factor for interactions with 14B7. Substitutions in residues Tyr 681 , Asn 682 , and Pro 686 also reduced toxicity significantly, by 10 -100-fold. Of these, only Asn 682 and Pro 686 were also critical for interactions with 14B7. However, residues Lys 684 , Leu 685 , Leu 687 , and Tyr 688 were critical for 14B7 binding without greatly affecting toxicity. The K684A and L685A variants exhibited wild type levels of toxicity in cell culture assays; the L687A and Y688A variants were reduced only 1.5-and 5-fold, respectively.Bacillus anthracis secretes two toxins: edema toxin and lethal toxin. Each is composed of a common binding component, protective antigen (PA), 1 together with an enzymatic component, edema factor (EF), in the case of edema toxin and lethal factor (LF) in the case of lethal toxin (1-3). The current model for toxin entry into the cell illustrates the centrality of PA for toxin action. PA binds to cellular receptors, recently identified as splice variants of either tumor endothelial marker 8 (TEM8) (4 -6) or the closely related capillary morphogenesis protein 2 (CMG2) (7). Furin cleaves PA, releasing a 20-kDa fragment and leaving behind a 63-kDa portion (PA 63 ) capable of forming a heptamer, which has a newly exposed surface that binds . Heptamer complexes enter the endocytic pathway by receptor-mediated endocytosis (13), and upon acidification of the vesicle, the PA 63 heptamer undergoes a conformational change to form a pore through which EF and LF translocate into the cytoplasm (10, 11, 14 -16). Once in the cytoplasm, EF and LF exert their toxic effects.The PA protein can be divided into four domains based on its crystal structure, and functions can be attributed to the different domains based on mutational and biochemical analyses (16). Domain 1 (residues 1-258) contains the furin cleavage site as well as the hydrophobic portion of PA, which is exposed upon furin cleavage to allow EF and LF to bind (16,17). Several lines of evidence indicate that domain 2 (residues 259 -487) is involved in oligomerization and contains the loop that inserts into the membrane to form the channel through which the LF and EF enter the cytosol (16, 18 -20). Various amino acids in domain 3 (residues 488 -595) are necessary for oligomerization, and this has been the only function attributed to domain 3 to date (21,22). Domain 4 (residues 596 -735) is essential for binding to cellular receptor as indicated by several lines of...

Signaling initiated by hypoxia and insulin powerfully alters cellular metabolism. The protein stability of hypoxia-inducible factor-1 alpha (Hif-1α) and Hif-2α is regulated by three prolyl hydroxylase domain–containing protein isoforms (Phd1, Phd2 and Phd3). Insulin receptor substrate-2 (Irs2) is a critical mediator of the anabolic effects of insulin, and its decreased expression contributes to the pathophysiology of insulin resistance and diabetes1. Although Hif regulates many metabolic pathways2, it is unknown whether the Phd proteins regulate glucose and lipid metabolism in the liver. Here, we show that acute deletion of hepatic Phd3, also known as Egln3, improves insulin sensitivity and ameliorates diabetes by specifically stabilizing Hif-2α, which then increases Irs2 transcription and insulin-stimulated Akt activation. Hif-2α and Irs2 are both necessary for the improved insulin sensitivity, as knockdown of either molecule abrogates the beneficial effects of Phd3 knockout on glucose tolerance and insulin-stimulated Akt phosphorylation. Augmenting levels of Hif-2α through various combinations of Phd gene knockouts did not further improve hepatic metabolism and only added toxicity. Thus, isoform-specific inhibition of Phd3 could be exploited to treat type 2 diabetes without the toxicity that could occur with chronic inhibition of multiple Phd isoforms.

Insulin initiates diverse hepatic metabolic responses, including gluconeogenic suppression and induction of glycogen synthesis and lipogenesis1,2. The liver possesses a rich sinusoidal capillary network with increased hypoxia and decreased gluconeogenesis in the perivenous zone3. Here, diverse vascular endothelial growth factor (VEGF) inhibitors improved glucose tolerance in normal or diabetic db/db mice, potentiating hepatic insulin signaling, decreasing gluconeogenic gene expression, increasing glycogen storage and suppressing hepatic glucose production (HGP). VEGF inhibition induced hepatic hypoxia via sinusoidal vascular regression and sensitized liver insulin signaling through hypoxia inducible factor-2α (HIF-2α) stabilization. Notably, liver-specific constitutive activation of HIF-2α, but not HIF-1α, was sufficient to augment hepatic insulin signaling via direct and indirect induction of insulin receptor substrate 2 (IRS2), an essential insulin receptor adaptor protein4–6. Further, liver IRS2 was both necessary and sufficient to mediate HIF-2α and VEGF inhibition effects on glucose tolerance and hepatic insulin signaling. These results demonstrate an unsuspected intersection between HIF-2α–mediated hypoxic signaling and hepatic insulin action via IRS2 induction, which can be co-opted by VEGF inhibitors to modulate glucose metabolism. These studies also indicate distinct roles in hepatic metabolism for HIF-1α, which promotes glycolysis7–9, versus HIF-2α, which suppresses gluconeogenesis, and suggest novel treatment approaches for type 2 diabetes mellitus.

At critical times in development, cells are able to convert graded signals into discrete developmental outcomes; however, the mechanisms involved are poorly understood. During thymocyte development, cell fate is determined by signals originating from the α β T-cell receptor. Low-affinity/avidity interactions between the T-cell receptor and peptide-MHC complexes direct differentiation to the single-positive stage (positive selection), whereas highaffinity/avidity interactions induce death by apoptosis (negative selection) 1,2 . Here we show that mice deficient in both calcineurin and nuclear factor of activated T cells (NFAT)c2/c3 lack a population of preselection thymocytes with enhanced ability to activate the mitogen-activated protein kinase (Raf-MEK-ERK) pathway, and fail to undergo positive selection. This defect can be partially rescued with constitutively active Raf, indicating that calcineurin controls MAPK signalling. Analysis of mice deficient in both Bim (which is required for negative selection) and calcineurin revealed that calcineurin-induced ERK (extracellular signal-regulated kinase) sensitization is required for differentiation in response to 'weak' positive selecting signals but not Reprints and permissions information is available at www.nature.com/reprints.Correspondence and requests for materials should be addressed to G.R.C. (crabtree@stanford.edu). Supplementary Information is linked to the online version of the paper at www.nature.com/nature.Author Contributions E.M.G., M.M.W. and G.R.C. generated the hypotheses, designed the experiments and wrote the manuscript. E.M.G. performed the experiments and generated the figures. K.C.-B. generated the NFATc3 conditional knockout mice, maintained this line in the NFATc2-null background and contributed to the experiments in Fig. 4. A.N.R. and L.H. contributed to pilot experiments and experiments shown in Fig. 2 and Supplementary Fig. 8. J.R.N. generated the Cnb1 conditional knockout mice, conducted pilot experiments and contributed to experimental rationale. L.M. contributed to experiments shown in Supplementary Fig. 5. B.I. provided the Raf-CAAX transgenic mice. The calcineurin/NFAT 3,4 and the Raf-MEK-ERK 5-7 pathways have been shown to be required for positive selection of thymocytes but not for their negative selection. Calcineurin B1 (Cnb1)-deficient CD4 + CD8 + double-positive thymocytes lack calcineurin activity, fail to dephosphorylate NFATc transcription factors and are not positively selected (Fig. 1a and ref. 3). Cnb1-deficient thymocytes have normal phosphorylation of JNK (c-Jun N-terminal kinase), p38, protein kinase C-θ, protein kinase D and glycogen synthase kinase 3α after crosslinking of the T-cell receptor (TCR) (Fig.1band ref. 3). Actin polymerization and Ca 2+ influx were also normal in these cells ( Supplementary Fig. 2a, b). Collectively, these results indicated that Cnb1-deficient thymocytes did not have widespread signalling defects downstream of the TCR. However, Cnb1-deficient thymocytes showed a specific and sever...

Over the past decade, invention and adoption of novel multiplexing technologies for tissues have made increasing impacts in basic and translational research and, to a lesser degree, clinical medicine. Platforms capable of highly multiplexed immunohistochemistry or in situ RNA measurements promise evaluation of protein or RNA targets at levels of plex and sensitivity logs above traditional methods – all with preservation of spatial context. These methods promise objective biomarker quantification, markedly increased sensitivity, and single‐cell resolution. Increasingly, development of novel technologies is enabling multi‐omic interrogations with spatial correlation of RNA and protein expression profiles in the same sample. Such sophisticated methods will provide unprecedented insights into tissue biology, biomarker science, and, ultimately, patient health. However, this sophistication comes at significant cost, requiring extensive time, practical knowledge, and resources to implement. This review will describe the technical features, advantages, and limitations of currently available multiplexed immunohistochemistry and spatial transcriptomic platforms. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Langerhans cell histiocytosis is a proliferative disorder of neoplastic Langerhans cells with activating mutations in the Erk signaling pathway. TP53 and U2AF1 mutations have been implicated in other myelomonocytic malignancies and we hypothesized that mutations in these genes may cosegregate in LCH patients according to BRAF mutation status. Towards this end, we collected cases with a pathologic diagnosis of Langerhans cell histiocytosis from Stanford University Hospital. We analyzed the status of known pathogenic alleles in BRAF, ARAF, TP53, U2AF1, and MAP2K1 on formalin-fixed, paraffin-embedded tissue by direct sequencing. A total of 41 cases (71%) had a BRAFV600E allele detected by sequencing. MAP2K1 mutations were also detected in 5 cases: 3 of 17 (18%) cases with wild-type BRAF and 2 of 41 (5%) cases with BRAFV600E mutations (P=0.14). No cases contained the previously reported ARAF mutation, Q347_A348del. All 10 cases with TP53 mutations contained mutant BRAFV600E allele (P=0.021). Of the 11 cases with U2AF1 mutated, 9 of 41 cases co-occurred with BRAFV600E mutations (P=0.31) and 2 of 17 with wild-type BRAF. Interestingly, we do not find that somatic activating MAP2K1 mutations are mutually exclusive with BRAFV600E mutations as has been reported previously. Instead, our data suggests that MAP2K1 mutations may be present along with BRAF either at diagnosis or may be acquired during disease progression. Furthermore, we demonstrated that likely deleterious TP53 mutations correlate with BRAF mutational status and may play a role in the underlying pathogenesis.