Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.

Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.

Identification of a regeneration-organizing cell in the Xenopus tail.

Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.

Correlation of B7-H3 with androgen receptor, immune pathways and poor outcome in prostate cancer: an expression-based analysis.

BACKGROUND: B7-H3 (CD276), part of the B7 superfamily of immune checkpoint molecules, has been shown to have an immunomodulatory role. Its regulation, receptor and mechanism of action remain unclear. B7-H3 protein expression correlates with prostate cancer outcomes, and humanized monoclonal antibodies (that is, enoblituzumab) are currently being investigated for therapeutic use. Here we used genomic expression data to examine the relationship between B7-H3 mRNA expression and prostate cancer. METHODS: Prostatectomy tissue from 2781 patients were profiled using the Affymetrix HuEx 1.0 ST microarray. Pairwise comparisons were used to identify significant associations between B7-H3 expression and clinicopathologic variables, and survival analyses were used to evaluate the prognostic significance of B7-H3. Pearson's correlation analyses were performed to assess the relationship of B7-H3 expression with molecular subtypes and individual transcripts. Androgen receptor (AR) occupancy at the B7-H3 locus was determined using chromatin immunoprecipitation (ChIP), and androgen-dependent expression changes in B7-H3 was evaluated by quantitative reverse transcription PCR in LNCaP cell lines. Oncomine was queried to evaluate B7-H3 expression in metastatic disease. RESULTS: B7-H3 mRNA expression was positively associated with higher Gleason score (P<0.001), tumor stage (P<0.001), and castrate resistant metastatic disease (P<0.0001). High B7-H3 expression correlated with the development of metastasis and prostate cancer specific mortality, but this was not significant on multi-variable analysis. B7-H3 expression correlated with ERG-positive disease (r=0.99) and AR expression (r=0.36). ChIP revealed an AR-binding site upstream of B7-H3, and the presence of androgens decreased B7-H3 expression in LNCaP suggesting potential direct AR regulation. Gene set enrichment analysis demonstrated an association of B7-H3 with androgen signaling as well as immune regulatory pathways. CONCLUSIONS: Higher B7-H3 expression correlates with Gleason grade, prostate cancer stage and poor oncologic outcomes in prostatectomy cohorts. B7-H3 expression appears to be related to androgen signaling as well as the immune reactome.

Nested case-control study: hepatocellular carcinoma risk after hepatitis B surface antigen seroclearance.

BACKGROUND: Hepatocellular carcinoma (HCC) risk after resolving chronic hepatitis B virus (HBV) infection is unclear. AIM: To compare HCC risk between Alaska Native (AN) patients with and without hepatitis B surface antigen (HBsAg) seroclearance. METHODS: We selected persons with (case-patients) and without (control-patients) HBsAg seroclearance from a cohort of 1346 chronically HBV-infected AN patients followed during 1982-2013. We attempted to match two control-patients/case-patient on sex, HBV genotype, and age. Person-years of follow-up for case-patients began on the date of HBsAg resolution and for control-patients began on the date equivalent to the cohort entry date plus the years of HBsAg duration for their corresponding case-patient. We compared HCC risk using a Cox proportional hazards model. RESULTS: The 238 case-patients (4 with HCC) and 435 control-patients (9 with HCC) were similar in age [P-value (P) = 0.30], sex (P = 0.53) and HBV genotype (P = 0.99). Case-patients had longer person-years of follow-up than control-patients (11.7 vs. 10.1 years; P = 0.04). The HCC rate/100 000 persons was similar between case- (132) and control-patients (178; P = 0.65). The adjusted hazard ratio comparing case- and control-patients was similar for HCC [0.7; 95% confidence interval (CI): 0.2-2.4], increased for each 1-year increment for age (1.1; CI: 1.0-1.1; P < 0.01), and was greater if the initial HBeAg was positive (3.5; CI: 1.1-11.0; P = 0.03). CONCLUSIONS: Hepatitis B surface antigen seroclearance was not associated with reduced HCC risk; the HCC risk estimates are limited by wide 95% confidence intervals. Persons meeting HCC surveillance indications prior to HBsAg seroclearance could benefit from continued surveillance after seroclearance.

Fermionic superradiance in a transversely pumped optical cavity.

Following the experimental realization of Dicke superradiance in Bose gases coupled to cavity light fields, we investigate the behavior of ultracold fermions in a transversely pumped cavity. We focus on the equilibrium phase diagram of spinless fermions coupled to a single cavity mode and establish a zero temperature transition to a superradiant state. In contrast to the bosonic case, Pauli blocking leads to lattice commensuration effects that influence self-organization in the cavity light field. This includes a sequence of discontinuous transitions with increasing atomic density and tricritical superradiance. We discuss the implications for experiment.

Incidence of diabetes mellitus in a population-based cohort of persons with chronic hepatitis B virus infection.

To investigate the effect of hepatitis B virus (HBV) infection on the development of diabetes mellitus (DM), we compared DM incidence and characteristics of Alaska Native persons with and without HBV infection. From 1990 to 2010, there were 52 incident DM cases among 1309 persons with infection vs 4557 DM cases among 85 698 persons without infection (log-rank test, P = 0.20). Compared to infected persons without DM, those with DM were significantly older (57.0 vs 47.4 years, P < 0.001) and had higher body mass index (34.5 vs 28.4 kg/m(2) , P < 0.001). Genotype, immune active disease and the presence of cirrhosis were not associated with DM. In this population-based cohort with over 20 years of follow-up, there was no effect of HBV infection on DM development.

Holographic superfluids and the dynamics of symmetry breaking.

We explore the far-from-equilibrium response of a holographic superfluid using the AdS/CFT correspondence. We establish the dynamical phase diagram corresponding to quantum quenches of the order parameter source field. We find three distinct regimes of behavior that are related to the spectrum of black hole quasinormal modes. These correspond to damped oscillations of the order parameter and to overdamped approaches to the superfluid and normal states. The presence of three regimes, which includes an emergent dynamical temperature scale, is argued to occur more generally in time-reversal-invariant systems that display continuous symmetry breaking.

Genetic diversity of hepatitis B virus genotypes B6, D and F among circumpolar indigenous individuals.

Hepatitis B virus (HBV) infection is highly prevalent in circumpolar indigenous peoples. However, the clinical outcome is extremely variable, such that while hepatocellular carcinoma (HCC) is uncommon in Canadian Inuit, the incidence of HCC is slightly higher in Greenlanders than in Danes, and it is especially high in Alaskan Native people infected with HBV genotypes F (HBV/F) and C (HBV/C). These differences may be associated with the genomic variability of the predominant HBV genotype in each group. The purpose of this study was to determine the rate, nature and regional susceptibility of HBV genomic mutations among circumpolar indigenous individuals. Paired serum samples, separated by 5-6 years, were analysed from Canadian and Greenlandic Inuit infected with HBV genotype B6 (HBV/B6) and HBV/D, respectively, and from Alaskan Native people infected with HBV/F, each having subsequently developed HCC. Phylogenetic and mutational analyses were performed on full-genome sequences, and the dynamic evolution within the quasispecies population of each patient group was determined by clonal analysis of the non-overlapping core coding region. Mutations associated with severe outcomes predominated in HBV/F, mostly within the precore/core and PreS1 region. HBV/B6 genomes exhibited higher diversity compared to HBV/D and HBV/F, particularly within the core coding region. Thus, differing mutational profiles and genetic variability were observed among different HBV genotypes predominating in circumpolar indigenous patients. The unusual observation of persistently high genetic variability with HBV/B6 despite clinical inactivity could be due to the evolution of a host-pathogen balance, but other possible factors also need to be explored.

Ising deconfinement transition between Feshbach-resonant superfluids.

We investigate the phase diagram of bosons interacting via Feshbach-resonant pairing interactions in a one-dimensional lattice. Using large scale density matrix renormalization group and field theory techniques we explore the atomic and molecular correlations in this low-dimensional setting. We provide compelling evidence for an Ising deconfinement transition occurring between distinct superfluids and extract the Ising order parameter and correlation length of this unusual superfluid transition. This is supported by results for the entanglement entropy which reveal both the location of the transition and critical Ising degrees of freedom on the phase boundary.

Collective dynamics of Bose-Einstein condensates in optical cavities.

Experiments on Bose-Einstein condensates in optical cavities have observed a coherent state of the matter-light system-superradiance. The nature of these experiments demands consideration of collective dynamics. Including cavity leakage and the backreaction of the cavity field on the condensate, we find a rich phase diagram including multiphase coexistence regions, and persistent optomechanical oscillations. The proximity of the phase boundaries results in a critical slowing down of the decay of many-body oscillations, which can be enhanced by large cavity loss.

A potential tumor suppressor role for Hic1 in breast cancer through transcriptional repression of ephrin-A1.

The tumor suppressor gene hypermethylated in cancer 1 (HIC1), which encodes a transcriptional repressor, is epigenetically inactivated in various human cancers. In this study, we show that HIC1 is a direct transcriptional repressor of the gene encoding ephrin-A1, a cell surface ligand implicated in the pathogenesis of epithelial cancers. We also show that mouse embryos lacking both Hic1 alleles manifest developmental defects spatially associated with the misexpression of ephrin-A1, and that overexpression of ephrin-A1 is a feature of tumors arising in Hic1 heterozygous mice in which the remaining wild-type allele is epigenetically silenced. In breast cancer, we find that ephrin-A1 expression is common in vivo, but that in cell culture, expression of the EphA receptors is predominant. Restoration of HIC1 function in breast cancer cells leads to a reduction in tumor growth in vivo, an effect that can be partially rescued by co-overexpression of ephrin-A1. Interestingly, overexpression of ephrin-A1 in vitro triggers downregulation of EphA2 and EphA4 levels, resulting in an expression pattern similar to that seen in vivo. We conclude that Hic1 spatially restricts ephrin-A1 expression in development, and that upregulated expression of ephrin-A1 resulting from epigenetic silencing of HIC1 in cancer cells may be an important mechanism in epithelial malignancy.

Polaritons and pairing phenomena in Bose-Hubbard mixtures.

Motivated by recent experiments on cold atomic gases in ultrahigh finesse optical cavities, we consider the two-band Bose-Hubbard model coupled to quantum light. Photoexcitation promotes carriers between the bands, and we study the interplay between Mott insulating behavior and superfluidity. The model displays a U(1)xU(1) symmetry which supports the coexistence of Mott insulating and superfluid phases and yields a rich phase diagram with multicritical points. This symmetry is shared by several other problems of current experimental interest, including two-component Bose gases in optical lattices and the bosonic BEC-BCS crossover for atom-molecule mixtures induced by a Feshbach resonance. We corroborate our findings by numerical simulations.

Inhomogeneous magnetic phases: a Fulde-Ferrell-Larkin-Ovchinnikov-like phase in Sr3Ru2O7.

The phase diagram of Sr3Ru2O7 contains a metamagnetic transition that bifurcates to enclose an anomalous phase with intriguing properties--a large resistivity with anisotropy that breaks the crystal-lattice symmetry. We propose that this is a magnetic analogue of the spatially inhomogeneous superconducting Fulde-Ferrel-Larkin-Ovchinnikov state. We show-through a Ginzburg-Landau expansion where the magnetization transverse to the applied field can become spatially inhomogeneous-that a Stoner model with electronic band dispersion can reproduce this phase diagram and transport behavior.

Repulsive atomic gas in a harmonic trap on the border of itinerant ferromagnetism.

Alongside superfluidity, itinerant (Stoner) ferromagnetism remains one of the most well-characterized phases of correlated Fermi systems. A recent experiment has reported the first evidence for novel phase behavior on the repulsive side of the Feshbach resonance in a two-component ultracold Fermi gas. By adapting recent theoretical studies to the atomic trap geometry, we show that an adiabatic ferromagnetic transition would take place at a weaker interaction strength than is observed in experiment. This discrepancy motivates a simple nonequilibrium theory that takes account of the dynamics of magnetic defects and three-body losses. The formalism developed displays good quantitative agreement with experiment.

Inhomogeneous phase formation on the border of itinerant ferromagnetism.

A variety of analytical techniques suggest that quantum fluctuations lead to a fundamental instability of the Fermi liquid that drives ferromagnetic transitions first order at low temperatures. We present both analytical and numerical evidence that, driven by the same quantum fluctuations, this first order transition is preempted by the formation of an inhomogeneous magnetic phase. This occurs in a manner that is closely analogous to the formation of the inhomogeneous superconducting Fulde-Ferrel-Larkin-Ovchinnikov state. We derive these results from a field-theoretical approach supplemented with numerical quantum Monte Carlo simulations.

Feshbach resonance in optical lattices and the quantum Ising model.

Motivated by experiments on heteronuclear Feshbach resonances in Bose mixtures, we investigate s-wave pairing of two species of bosons in an optical lattice. The zero temperature phase diagram supports a rich array of superfluid and Mott phases and a network of quantum critical points. This topology reveals an underlying structure that is succinctly captured by a two-component Landau theory. Within the second Mott lobe we establish a quantum phase transition described by the paradigmatic longitudinal and transverse field Ising model. This is confirmed by exact diagonalization of the 1D bosonic Hamiltonian. We also find this transition in the homonuclear case.

Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer.

Cancer cells differentiate along specific lineages that largely determine their clinical and biologic behavior. Distinct cancer phenotypes from different cells and organs likely result from unique gene expression repertoires established in the embryo and maintained after malignant transformation. We used comprehensive gene expression analysis to examine this concept in the prostate, an organ with a tractable developmental program and a high propensity for cancer. We focused on gene expression in the murine prostate rudiment at three time points during the first 48 h of exposure to androgen, which initiates proliferation and invasion of prostate epithelial buds into surrounding urogenital sinus mesenchyme. Here, we show that androgen exposure regulates genes previously implicated in prostate carcinogenesis comprising pathways for the phosphatase and tensin homolog (PTEN), fibroblast growth factor (FGF)/mitogen-activated protein kinase (MAPK), and Wnt signaling along with cellular programs regulating such 'hallmarks' of cancer as angiogenesis, apoptosis, migration and proliferation. We found statistically significant evidence for novel androgen-induced gene regulation events that establish and/or maintain prostate cell fate. These include modulation of gene expression through microRNAs, expression of specific transcription factors, and regulation of their predicted targets. By querying public gene expression databases from other tissues, we found that rather than generally characterizing androgen exposure or epithelial budding, the early prostate development program more closely resembles the program for human prostate cancer. Most importantly, early androgen-regulated genes and functional themes associated with prostate development were highly enriched in contrasts between increasingly lethal forms of prostate cancer, confirming a 'reactivation' of embryonic pathways for proliferation and invasion in prostate cancer progression. Among the genes with the most significant links to the development and cancer, we highlight coordinate induction of the transcription factor Sox9 and suppression of the proapoptotic phospholipid-binding protein Annexin A1 that link early prostate development to early prostate carcinogenesis. These results credential early prostate development as a reliable and valid model system for the investigation of genes and pathways that drive prostate cancer.

Severity of post-ERCP pancreatitis directly proportional to the invasiveness of endoscopic intervention: a pilot study in a canine model.

BACKGROUND AND STUDY AIMS: Pancreatitis complicates 1% - 22% of endoscopic retrograde cholangiopancreatography procedures. The study aims were to develop a reproducible animal model of post-ERCP pancreatitis (PEP), and investigate the impact of endoscopic technique on severity of PEP. PATIENTS AND METHODS: ERCP was carried out in six male hound dogs. Pancreatitis was induced by one of three escalating methods: 1) pancreatic acinarization with 20 - 30 mL of contrast; 2) acinarization + ductal balloon occlusion + sphincterotomy; 3) acinarization + intraductal synthetic bile injection + ductal balloon occlusion + sphincterotomy. Dogs 5 and 6 received a pancreatic stent. Necropsy was performed on postoperative day 5. All pancreatic specimens were graded by two blinded pathologists according to a validated scoring system. All dogs were compared with three control dogs. RESULTS: Dogs 1 - 4 developed clinical pancreatitis and hyperamylasemia (11 736 vs. 722 U/L, P = 0.02). Total injury scores were significantly elevated compared with controls (6.85 vs. 1.06, P = 0.004). There was significant increase in acinar cell necrosis (0.86 vs. 0.06, P = < 0.001), and all other categories (except fibrosis) demonstrated elevated injury scores . Dogs 5 and 6 developed clinical pancreatitis without significant hyperamylasemia; total injury scores were elevated compared with controls (4.83 vs. 1.06, P = 0.01), but lower than in Dogs 1 - 4 (4.83 vs. 6.85, P = 0.25). There was escalating severity of pancreatic injury from Dogs 1 to 4 correlating with the method of endoscopic injury used. CONCLUSION: Severity of PEP is directly proportional to invasiveness of endoscopic intervention. Pancreatic acinarization, even without balloon occlusion and sphincterotomy, can be used as a reliable animal model for future studies investigating therapy and prevention of disease.

Polarized Fermi condensates with unequal masses: tuning the tricritical point.

We consider a two-component atomic Fermi gas within a mean-field, single-channel model, where both the mass and population of each component are unequal. We show that the tricritical point at zero temperature evolves smoothly from the BEC to BCS side of the resonance as a function of mass ratio r. We find that the interior gap state proposed by Liu and Wilczek is always unstable to phase separation, while the breached pair state with one Fermi surface for the excess fermions exhibits differences in its density of states and pair correlation functions depending on which side of the resonance it lies. Finally, we show that, when r greater, similar 3.95, the finite-temperature phase diagram of trapped gases at unitarity becomes topologically distinct from the equal mass system.