Examination of Wnt signaling as a therapeutic target for pancreatic ductal adenocarcinoma (PDAC) using a pancreatic tumor organoid library (PTOL)

Pancreatic ductal adenocarcinoma (PDAC) presents at advanced stages and is refractory to most treatment modalities. Wnt signaling activation plays a critical role in proliferation and chemotherapeutic resistance. Minimal media conditions, growth factor dependency, and Wnt dependency were determined via Wnt inhibition for seven patient derived organoids (PDOs) derived from pancreatic tumor organoid libraries (PTOL). Organoids demonstrating response in vitro were assessed in vivo using patient-derived xenografts. Wnt (in)dependent gene signatures were identified for each organoid. Panc269 demonstrated a trend of reduced organoid growth when treated with ETC-159 in combination with paclitaxel or gemcitabine as compared with chemotherapy or ETC-159 alone. Panc320 demonstrated a more pronounced anti-proliferative effect in the combination of ETC-159 and paclitaxel but not with gemcitabine. Panc269 and Panc320 were implanted into nude mice and treated with ETC-159, paclitaxel, and gemcitabine as single agents and in combination. The combination of ETC-159 and paclitaxel demonstrated an anti-tumor effect greater than ETC-159 alone. Extent of combinatory treatment effect were observed to a lesser extent in the Panc320 xenograft. Wnt (in)dependent gene signatures of Panc269 and 320 were consistent with the phenotypes displayed. Gene expression of several key Wnt genes assessed via RT-PCR demonstrated notable fold change following treatment in vivo. Each pancreatic organoid demonstrated varied niche factor dependencies, providing an avenue for targeted therapy, supported through growth analysis following combinatory treatment of Wnt inhibitor and standard chemotherapy in vitro. The clinical utilization of this combinatory treatment modality in pancreatic cancer PDOs has thus far been supported in our patient-derived xenograft models treated with Wnt inhibitor plus paclitaxel or gemcitabine. Gene expression analysis suggests there are key Wnt genes that contribute to the Wnt (in)dependent phenotypes of pancreatic tumors, providing plausible mechanistic explanation for Wnt (in)dependency and susceptibility or resistance to treatment on the genotypic level.

MIG6 Mediates Adaptive and Acquired Resistance to ALK/ROS1 Fusion Kinase Inhibition through EGFR Bypass Signaling

Despite the initial benefit from tyrosine kinase inhibitors (TKI) targeting oncogenic ALK and ROS1 gene fusions in non-small cell lung cancer, complete responses are rare and resistance ultimately emerges from residual tumor cells. Although several acquired resistance mechanisms have been reported at the time of disease progression, adaptative resistance mechanisms that contribute to residual diseases before the outgrowth of tumor cells with acquired resistance are less clear. For the patients who have progressed after TKI treatments, but do not demonstrate ALK/ROS1 kinase mutations, there is a lack of biomarkers to guide effective treatments. Herein, we found that phosphorylation of MIG6, encoded by the ERRFI1 gene, was downregulated by ALK/ROS1 inhibitors as were mRNA levels, thus potentiating EGFR activity to support cell survival as an adaptive resistance mechanism. MIG6 downregulation was sustained following chronic exposure to ALK/ROS1 inhibitors to support the establishment of acquired resistance. A higher ratio of EGFR to MIG6 expression was found in ALK TKI-treated and ALK TKI-resistant tumors and correlated with the poor responsiveness to ALK/ROS1 inhibition in patient-derived cell lines. Furthermore, we identified and validated a MIG6 EGFR-binding domain truncation mutation in mediating resistance to ROS1 inhibitors but sensitivity to EGFR inhibitors. A MIG6 deletion was also found in a patient after progressing to ROS1 inhibition. Collectively, this study identifies MIG6 as a novel regulator for EGFR-mediated adaptive and acquired resistance to ALK/ROS1 inhibitors and suggests EGFR to MIG6 ratios and MIG6-damaging alterations as biomarkers to predict responsiveness to ALK/ROS1 and EGFR inhibitors.

Combination CDC-like kinase inhibition (CLK)/Dual-specificity tyrosine-regulated kinase (DYRK) and taxane therapy in CTNNB1-mutated endometrial cancer

SM08502 (cirtuvivint) is a novel pan CDC-like kinase (CLK) and Dual specificity tyrosine kinase (DYRK) inhibitor that targets mRNA splicing and is optimized for Wnt pathway inhibition. Previous evaluation of single agent CLK/DYRK inhibition (SM04690) demonstrated inhibition of tumor progression and β-catenin/TCF transcriptional activity in CTNNB1-mutant endometrial cancer (EC). In-vitro analysis of SM08502 similarly decreases Wnt transcriptional activity and cellular proliferation while increasing cellular apoptosis. SM08502 is an active single-agent therapy with IC50's in the nanomolar range for all EC cell lines evaluated. Combination of SM08502 with paclitaxel has synergistic effect in vitro, as demonstrated by Combination Index <1, and inhibits tumor progression in four endometrial cancer models (HEC265, Ishikawa, Ishikawa-S33Y, and SNGM). In our in vivo mouse models, Ishikawa demonstrated significantly lower tumor volumes of combination vs SM08502 alone (Repeated Measures one-way ANOVA, p = 0.04), but not vs paclitaxel alone. HEC265, SNGM, and Ishikawa-S33Y tumors all had significantly lower tumor volumes with combination SM08502 and paclitaxel compared to single-agent paclitaxel (Repeated Measures one-way ANOVA, p = 0.01, 0.004, and 0.0008, respectively) or single-agent SM08502 (Repeated Measures one-way ANOVA, p = 0.002, 0.005, and 0.01, respectively) alone. Mechanistically, treatment with SM08502 increases alternative splicing (AS) events compared to treatment with paclitaxel. AS regulation is an important post-transcriptional mechanism associated with the oncogenic process in many cancers, including EC. Results from these studies have led to a Phase I evaluation of this combination in recurrent EC.

Molecular networks in atopic mothers impact the risk of infant atopy

BACKGROUND

The prevalence of atopic diseases has increased with atopic dermatitis (AD) as the earliest manifestation. We assessed if molecular risk factors in atopic mothers influence their infants' susceptibility to an atopic disease.

METHODS

Pregnant women and their infants with (n = 174, high-risk) or without (n = 126, low-risk) parental atopy were enrolled in a prospective birth cohort. Global differentially methylated regions (DMRs) were determined in atopic (n = 92) and non-atopic (n = 82) mothers. Principal component analysis was used to predict atopy risk in children dependent on maternal atopy. Genome-wide transcriptomic analyses were performed in paired atopic (n = 20) and non-atopic (n = 15) mothers and cord blood. Integrative genomic analyses were conducted to define methylation-gene expression relationships.

RESULTS

Atopic dermatitis was more prevalent in high-risk compared to low-risk children by age 2. Differential methylation analyses identified 165 DMRs distinguishing atopic from non-atopic mothers. Inclusion of DMRs in addition to maternal atopy significantly increased the odds ratio to develop AD in children from 2.56 to 4.26. In atopic compared to non-atopic mothers, 139 differentially expressed genes (DEGs) were identified significantly enriched of genes within the interferon signaling pathway. Expression quantitative trait methylation analyses dependent on maternal atopy identified 29 DEGs controlled by 136 trans-acting methylation marks, some located near transcription factors. Differential expression for the same nine genes, including MX1 and IFI6 within the interferon pathway, was identified in atopic and non-atopic mothers and high-risk and low-risk children.

CONCLUSION

These data suggest that in utero epigenetic and transcriptomic mechanisms predominantly involving the interferon pathway may impact and predict the development of infant atopy.

Mapping Macrophage Polarization and Origin during the Progression of the Foreign Body Response to a Poly(ethylene glycol) Hydrogel Implant

Poly(ethylene glycol) (PEG) hydrogels hold promise for in vivo applications but induce a foreign body response (FBR). While macrophages are key in the FBR, many questions remain. This study investigates temporal changes in the transcriptome of implant-associated monocytes and macrophages. Proinflammatory pathways are upregulated in monocytes compared to control monocytes but subside by day 28. Macrophages are initially proinflammatory but shift to a profibrotic state by day 14, coinciding with fibrous capsule emergence. Next, this study assesses the origin of macrophages responsible for fibrous encapsulation using wildtype, C-C Motif Chemokine Receptor 2 (CCR2)^-/- mice that lack recruited macrophages, and Macrophage Fas-Induced Apoptosis (MaFIA) mice that enable macrophage ablation. Subpopulations of recruited and tissue-resident macrophages are identified. Fibrous encapsulation proceeds in CCR2^-/- mice similar to wildtype mice. However, studies in MaFIA mice indicate that macrophages are necessary for fibrous capsule formation. These findings suggest that macrophage origin impacts the FBR progression and provides evidence that tissue-resident macrophages and not the recruited macrophages may drive fibrosis in the FBR to PEG hydrogels. This study demonstrates that implant-associated monocytes and macrophages have temporally distinct transcriptomes in the FBR and that profibrotic pathways associated with macrophages may be enriched in tissue-resident macrophages.

Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens

Agrobacterium tumefaciens is a member of the Alphaproteobacteria that pathogenises plants and associates with biotic and abiotic surfaces via a single cellular pole. A. tumefaciens produces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using an A. tumefaciens derivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is composed of two genetically, chemically, and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing, and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each type. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific.

Prognostic accuracy of a peripheral blood transcriptome signature in chronic hypersensitivity pneumonitis

The prognostic value of peripheral blood mononuclear cell (PBMC) expression profiles, when used in patients with chronic hypersensitivity pneumonitis (CHP), as an adjunct to traditional clinical assessment is unknown. RNA-seq analysis on PBMC from 37 patients with CHP at initial presentation determined that (1) 74 differentially expressed transcripts at a 10% false discovery rate distinguished those with (n=10) and without (n=27) disease progression, defined as absolute FVC and/or diffusing capacity of the lungs for carbon monoxide (DLCO) decline of ≥10% and increased fibrosis on chest CT images within 24 months, and (2) classification models based on gene expression and clinical factors strongly outperform models based solely on clinical factors (baseline FVC%, DLCO% and chest CT fibrosis).

Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire

The CD4⁺ T cell response is critical to host protection against helminth infection. How this response varies across different hosts and tissues remains an important gap in our understanding. Using IL-4-reporter mice to identify responding CD4⁺ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4⁺ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. Antigen-reactivity of the broader repertoires was predicted to be shared across both tissues and individual mice. Transcriptome, trajectory, and chromatin accessibility analysis of lung and lymph-node repertoires revealed three unique but related populations of responding IL-4⁺ CD4⁺ T cells consistent with T follicular helper, T helper 2, and a transitional population sharing similarity with both populations. The shared antigen reactivity of lymph node and lung repertoires combined with the adoption of tissue-specific gene programs allows for the pairing of cellular and humoral responses critical to the orchestration of anti-helminth immunity.

Using various “omic” approaches, the CD4⁺ T cell receptor (TCR) repertoire was explored after primary helminth infection. Infection generated a broadly reactive and clonally diverse CD4⁺ T cell response with the most prevalent clonotypes and predicted antigen specificities residing in both the lung and lung-draining lymph nodes. Tissue-specific programming of responding CD4⁺ T cells directed the establishment of committed Tfh and Th2 cells, both critical for driving distinct hallmarks of type-2 inflammation. These datasets help to explore the diverse yet tissue-specific nature of anti-helminth immunity.

GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers

Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage-determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes.

Human and Mouse Transcriptome Profiling Identifies Cross-Species Homology in Pulmonary and Lymph Node Mononuclear Phagocytes

The mononuclear phagocyte (MP) system consists of macrophages, monocytes, and dendritic cells (DCs). MP subtypes play distinct functional roles in steady-state and inflammatory conditions. Although murine MPs are well characterized, their pulmonary and lymph node (LN) human homologs remain poorly understood. To address this gap, we have created a gene expression compendium across 24 distinct human and murine lung and LN MPs, along with human blood and murine spleen MPs, to serve as validation datasets. In-depth RNA sequencing identifies corresponding human-mouse MP subtypes and determines marker genes shared and divergent across species. Unexpectedly, only 13%-23% of the top 1,000 marker genes (i.e., genes not shared across species-specific MP subtypes) overlap in corresponding human-mouse MP counterparts. Lastly, CD88 in both species helps distinguish monocytes/macrophages from DCs. Our cross-species expression compendium serves as a resource for future translational studies to investigate beforehand whether pursuing specific MP subtypes or genes will prove fruitful.

BATF acts as an essential regulator of IL-25-responsive migratory ILC2 cell fate and function

A transitory, interleukin-25 (IL-25)-responsive, group 2 innate lymphoid cell (ILC2) subset induced during type 2 inflammation was recently identified as iILC2s. This study focuses on understanding the significance of this population in relation to tissue-resident nILC2s in the lung and intestine. RNA-sequencing and pathway analysis revealed the AP-1 superfamily transcription factor BATF (basic leucine zipper transcription factor, activating transcription factor-like) as a potential modulator of ILC2 cell fate. Infection of BATF-deficient mice with Nippostrongylus brasiliensis showed a selective defect in IL-25-mediated helminth clearance and a corresponding loss of iILC2s in the lung characterized as IL-17RB^high, KLRG1^high, BATF^high, and Arg1^low BATF deficiency selectively impaired iILC2s because it had no impact on tissue-resident nILC2 frequency or function. Pulmonary-associated iILC2s migrated to the lung after infection, where they represented an early source of IL-4 and IL-13. Although the composition of ILC2s in the small intestine was distinct from those in the lung, their frequency and IL-13 expression remained dependent on BATF, which was also required for optimal goblet and tuft cell hyperplasia. Findings support IL-25-responsive ILC2s as early sentinels of mucosal barrier integrity.

Comparative Profiling of the Immune System in Sarcoidosis via CITE-Seq and Flow Cytometry

CITE-Seq enables simultaneous single cell transcriptome and proteome analysis via combining single cell RNA-seq with oligo-labeled antibodies. Conventional techniques such as flow or mass cytometry have caveats including the number of epitopes accurately detected or an inability to recover samples for transcriptome analysis. These limitations are prohibitive for multivariate analysis of limited clinical samples. We developed a CITE-seq assay that enables comprehensive immune cell profiling of Sarcoidosis. Sarcoidosis is a granulomatous lung disease characterized by abnormal CD4+ T cell Th1 activity. However, the disease etiology and course are variable and the underlying molecular drivers remain unknown. The long-term goal of this study is to utilize CITE-seq to identify immune molecular pathways of Sarcoidosis pathogenesis. In our initial studies, we analyzed PBMC’s by CITE-seq vs. flow cytometry and observed similar cell profiles. However, the synergy of protein detection coupled with transcriptome analysis via CITE-seq enhanced cell subset identification vs. flow or scRNA-seq alone. We utilized CITE-seq in an ongoing longitudinal study of Sarcoidosis subjects to enhance resolution of the immune components contributing to disease. We compared CITE-seq to a flow cytometry panel analyzing the differential contributions of various CD4+ T cell lineages. The enhanced granularity provided by CITE-seq elucidated molecular pathways associated with disease pathogenesis. Thus, moving forward CITE-seq can provide the resolution and multivariate data collection required to identify the inflammatory drivers of Sarcoidosis.

IL-25-responsive migratory iILC2s require BATF and stably convert to tissue-resident nILC2s

Inflammatory ILC2s (iILC2s) are a transient subset of group-2 innate lymphoid cells that migrate to the lung shortly after helminth infection or IL-25 administration. Our recent findings identified the AP-1 factor BATF as the major transcriptional regulator required for iILC2 generation and function. Batf-deficient mice infected with the helminth Nippostrongylus brasiliensis display a selective defect in IL-25-mediated worm clearance and a loss of iILC2s but not nILC2s. This corresponds with the absence of early cytokine production by ILC2s in Batf-deficient mice, indicating the requirement of this transcription factor in ILC2 function. The fate of iILC2s is currently unknown as this subset of ILC2s is found only transiently in the lung following infection. Taking advantage of our finding that Arginase-1 (Arg1) expression can delineate tissue-resident nILC2 (Arg1+) and migratory iILC2 (Arg1−) populations, we used an Arg1 reporter mouse to address whether iILC2s could acquire an Arg1+ nILC2-like phenotype. Upon transfer into a congenic host, sorted Arg1− iILC2s acquired Arg1 expression and further adopted characteristics of nILC2s. These converted cells stably persisted after transfer indicating a potential long-term contribution of migratory iILC2s to the tissue-resident nILC2 pool in the lung.

Altered CD4+ T cell Transcriptional and Epigenetic Programming Define Changes in Sarcoidosis Disease Phenotypes

Sarcoidosis is an inflammatory disease, which is characterized by granulomas in the lungs, extrapulmonary inflammation, and can cause death by lung fibrosis. It is known that CD4+ T cell lung population increases in Sarcoidosis. However, the immunopathology remains unclear and no biomarker has been identified. Here we use RNA-seq to examine gene expression in CD4+ T cells of differential Sarcoidosis phenotypes and healthy donors. Our data showed that BATF, a Tfh inducer/key factor in Th17 differentiation was up-regulated while BCL6, a Th17 repressor is down-regulated in RNA-seq. IRF4 and BCL6 were identified as potential transcriptional upstream regulators using IPA. IL-4 and fibrosis related genes were differentially expressed with altered disease phenotype, indicating that type 2 immune response may participate in disease phenotype progression for development of fibrosis. In addition, we used ChIP-seq and ATAC-seq to examine genome-wide epigenetic histone signatures and global chromatin accessibility associated with Sarcoidosis phenotypes. TF binding-site analysis of ATAC-seq peaks revealed an enrichment of BATF binding motifs, highlighting the utility of integrating epigenetic and transcriptional signatures to suggest molecular drivers of Sarcoidosis. Our findings identified several potential immune related biomarkers and molecular mechanisms that may drive disease progression.

Linking environmental exposures to molecular regulation of inflammation via epigenetic histone signatures in an exacerbation prone pediatric asthma cohort

Environmental exposures, such as air pollution, are correlated with asthma susceptibility and airway inflammation. Epigenetic mechanisms can translate these exposures to regulation of molecular pathways that drive asthma pathogenesis. Indeed, specific epigenetic modifications have been linked to regulation of asthma-associated inflammation. Yet, there have been no studies linking environmental exposures to direct regulation of molecular mechanisms driving dysfunction of inflammation in pediatric asthma. Here we examined a cohort of exacerbation prone pediatric asthmatics tracking exposure through multiple air monitoring methods, including personalized vest monitors, stationary monitors, and Colorado DPHE monitors. We performed ChIP-seq examining histone modifications in PBMCs and integrated the epigenetic data with the environmental exposure data from the air pollution monitors. Our results statistically linked specific histone modifications in PBMCs to specific types of environmental exposures within the pediatric asthmatics. Annotation of these histone modifications to proximal genes identified a potential immune program regulating asthma inflammation. Concomitant examination of the PBMC transcriptome enabled functional analysis of epigenetic regulation of these immune genes. The resultant molecular profiles can be used to identify biomarkers for patient stratification and disease course prediction. Moreover, these studies identify a potential link between the molecular programming associated with environmental exposures and regulation of key biological pathways, which alter immune cell activity that ultimately can increase asthma exacerbation in children.

Clonal expansion of vaccine-elicited T cells is independent of aerobic glycolysis

In contrast to responses against infectious challenge, T cell responses induced via adjuvanted subunit vaccination are dependent on interleukin-27 (IL-27). We show that subunit vaccine-elicited cellular responses are also dependent on IL-15, again in contrast to the infectious response. Early expression of interferon regulatory factor 4 (IRF4) was compromised in either IL-27- or IL-15-deficient environments after vaccination but not infection. Because IRF4 facilitates metabolic support of proliferating cells via aerobic glycolysis, we expected this form of metabolic activity to be reduced in the absence of IL-27 or IL-15 signaling after vaccination. Instead, metabolic flux analysis indicated that vaccine-elicited T cells used only mitochondrial function to support their clonal expansion. Loss of IL-27 or IL-15 signaling during vaccination resulted in a reduction in mitochondrial function, with no corresponding increase in aerobic glycolysis. Consistent with these observations, the T cell response to vaccination was unaffected by in vivo treatment with the glycolytic inhibitor 2-deoxyglucose, whereas the response to viral challenge was markedly lowered. Collectively, our data identify IL-27 and IL-15 as critical to vaccine-elicited T cell responses because of their capacity to fuel clonal expansion through a mitochondrial metabolic program previously thought only capable of supporting quiescent naïve and memory T cells.

Dietary Lipids Differentially Shape Nonalcoholic Steatohepatitis Progression and the Transcriptome of Kupffer Cells and Infiltrating Macrophages

A crucial component of nonalcoholic fatty liver disease (NAFLD) pathogenesis is lipid stress, which may contribute to hepatic inflammation and activation of innate immunity in the liver. However, little is known regarding how dietary lipids, including fat and cholesterol, may facilitate innate immune activation in vivo. We hypothesized that dietary fat and cholesterol drive NAFLD progression to steatohepatitis and hepatic fibrosis by altering the transcription and phenotype of hepatic macrophages. This hypothesis was tested by using RNA-sequencing methods to characterize and analyze sort-purified hepatic macrophage populations that were isolated from mice fed diets with varying amounts of fat and cholesterol. The addition of cholesterol to a high-fat diet triggered hepatic pathology reminiscent of advanced nonalcoholic steatohepatitis (NASH) in humans characterized by signs of cholesterol dysregulation, generation of oxidized low-density lipoprotein, increased recruitment of hepatic macrophages, and significant fibrosis. RNA-sequencing analyses of hepatic macrophages in this model revealed that dietary cholesterol induced a tissue repair and regeneration phenotype in Kupffer cells (KCs) and recruited infiltrating macrophages to a greater degree than fat. Furthermore, comparison of diseased KCs and infiltrating macrophages revealed that these two macrophage subsets are transcriptionally diverse. Finally, direct stimulation of murine and human macrophages with oxidized low-density lipoprotein recapitulated some of the transcriptional changes observed in the RNA-sequencing study. These findings indicate that fat and cholesterol synergize to alter macrophage phenotype, and they also challenge the dogma that KCs are purely proinflammatory in NASH. Conclusion: This comprehensive view of macrophage populations in NASH indicates mechanisms by which cholesterol contributes to NASH progression and identifies potential therapeutic targets for this common disease.

CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis

Cell lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage and developmental stage-specific transcriptional programs. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in B cell progenitors in vivo, development of these cells is arrested at an early pro-B-like stage that is unresponsive to IL-7 receptor signaling and unable to efficiently complete V(D)J rearrangements at Igh loci. Our studies confirm that chromatin accessibility and transcription of thousands of gene loci are controlled dynamically by CHD4 during early B cell development. Strikingly, CHD4-deficient pro-B cells express transcripts of many non-B cell lineage genes, including genes that are characteristic of other hematopoietic lineages, neuronal cells, and the CNS, lung, pancreas, and other cell types. We conclude that CHD4 inhibits inappropriate transcription in pro-B cells. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.

BATF is an essential regulator of migratory ILC2 cell fate and function

A recently identified subset of group-2 innate lymphoid cells (ILC2s) migrates to mucosal tissues early during type-2 inflammation and is characterized by responsiveness to interleukin-25 and high expression of KLRG1. This study identifies the major transcriptional regulator required for their generation and function. RNA-sequencing and unbiased pathway analysis revealed the AP-1 transcription factor BATF as a potential modulator of ILC2 cell fate. Indeed, infection of BATF-deficient mice with the helminth N. brasiliensis showed a selective defect in IL-25-induced, ILC2-mediated worm clearance as well as a corresponding loss of IL17RB+ (IL-25 receptor) KLRG1high ILC2s in the lung. Moreover, these BATF-dependent migratory ILC2s serve as the major early source of IL-4 and IL-13 after infection. Interestingly, while the presence of KLRG1high ILC2s in the small intestine are unaffected by BATF-deficiency, their ability to produce IL-13 is significantly impacted. Defects in IL-13 expression by intestinal KLRG1high ILC2s corresponded with decreased goblet and tuft cell hyperplasia in BATF-deficient mice, supporting the critical role of these migratory ILC2s as early sentinels of mucosal barrier integrity.

TGF beta inhibits HGF, FGF7, and FGF10 expression in normal and IPF lung fibroblasts

TGF beta is a multifunctional cytokine that is important in the pathogenesis of pulmonary fibrosis. The ability of TGF beta to stimulate smooth muscle actin and extracellular matrix gene expression in fibroblasts is well established. In this report, we evaluated the effect of TGF beta on the expression of HGF, FGF7 (KGF), and FGF10, important growth and survival factors for the alveolar epithelium. These growth factors are important for maintaining type II cells and for restoration of the epithelium after lung injury. Under conditions of normal serum supplementation or serum withdrawal TGF beta inhibited fibroblast expression of HGF, FGF7, and FGF10. We confirmed these observations with genome wide RNA sequencing of the response of control and IPF fibroblasts to TGF beta. In general, gene expression in IPF fibroblasts was similar to control fibroblasts. Reduced expression of HGF, FGF7, and FGF10 is another means whereby TGF beta impairs epithelial healing and promotes fibrosis after lung injury.

Control of T cell development and function by Protein Arginine Methyltransferase 5

Temporally and spatially regulated gene expression is essential for the development of thymocytes and functional T cells. Gene transcription is controlled, in part, by reversible post-translational modifications (PTM) of histones by epigenetic regulators. In turn, histone PTMs are bound by reader proteins, which mediate transcriptional activation and repression. Together, PTMs and readers enhance or suppress the accessibility of DNA to sequence-specific DNA-binding proteins. Epigenetic mechanisms are often dysregulated in human diseases and are promising targets for cancer treatments and immunotherapy. One such candidate is Protein Arginine Methyltransferase 5 (PRMT5), a type II arginine methyltransferase. PRMT5 catalyzes symmetric dimethylation (Rme2s) of arginines on histones H2A, H3, and H4. Rme2s strongly correlates with transcriptional repression. However, the roles of PRMT5-dependent histone arginine methylation in thymocyte development and T cell activation are poorly understood. Dynamic expression of Prmt5 transcripts suggests that the methyltransferase modulates transcription at select stages in T lymphopoiesis. Previous studies employing hematopoietic system-wide depletion of Prmt5 detected reduced cellularity of T cell progenitor populations, but effects on thymocyte transcriptomes were not determined. Here, we describe consequences of the loss of PRMT5 on T cell progenitor stage-specific transcription. PRMT5 suppresses activities of key transcription factors by regulating DNA accessibility, which in turn prevents inappropriate transcription in thymocytes in vitro and in vivo. Together, our data support a role of PRMT5 as an essential ‘gatekeeper’ of T cell development and function.

Deletion of c-FLIP from CD11bhi Macrophages Prevents Development of Bleomycin-induced Lung Fibrosis

Idiopathic pulmonary fibrosis is a progressive lung disease with complex pathophysiology and fatal prognosis. Macrophages (MΦ) contribute to the development of lung fibrosis; however, the underlying mechanisms and specific MΦ subsets involved remain unclear. During lung injury, two subsets of lung MΦ coexist: Siglec-F^hi resident alveolar MΦ and a mixed population of CD11b^hi MΦ that primarily mature from immigrating monocytes. Using a novel inducible transgenic system driven by a fragment of the human CD68 promoter, we targeted deletion of the antiapoptotic protein cellular FADD-like IL-1β-converting enzyme-inhibitory protein (c-FLIP) to CD11b^hi MΦ. Upon loss of c-FLIP, CD11b^hi MΦ became susceptible to cell death. Using this system, we were able to show that eliminating CD11b^hi MΦ present 7-14 days after bleomycin injury was sufficient to protect mice from fibrosis. RNA-seq analysis of lung MΦ present during this time showed that CD11b^hi MΦ, but not Siglec-F^hi MΦ, expressed high levels of profibrotic chemokines and growth factors. Human MΦ from patients with idiopathic pulmonary fibrosis expressed many of the same profibrotic chemokines identified in murine CD11b^hi MΦ. Elimination of monocyte-derived MΦ may help in the treatment of fibrosis. We identify c-FLIP and the associated extrinsic cell death program as a potential pathway through which these profibrotic MΦ may be pharmacologically targeted.

The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor

Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.

Cell Origin Dictates Programming of Resident versus Recruited Macrophages during Acute Lung Injury

Two populations of alveolar macrophages (AMs) coexist in the inflamed lung: resident AMs that arise during embryogenesis, and recruited AMs that originate postnatally from circulating monocytes. The objective of this study was to determine whether origin or environment dictates the transcriptional, metabolic, and functional programming of these two ontologically distinct populations over the time course of acute inflammation. RNA sequencing demonstrated marked transcriptional differences between resident and recruited AMs affecting three main areas: proliferation, inflammatory signaling, and metabolism. Functional assays and metabolomic studies confirmed these differences and demonstrated that resident AMs proliferate locally and are governed by increased tricarboxylic acid cycle and amino acid metabolism. Conversely, recruited AMs produce inflammatory cytokines in association with increased glycolytic and arginine metabolism. Collectively, the data show that even though they coexist in the same environment, inflammatory macrophage subsets have distinct immunometabolic programs and perform specialized functions during inflammation that are associated with their cellular origin.

Glucocorticoid Receptor ChIP-Seq Identifies PLCD1 as a KLF15 Target that Represses Airway Smooth Muscle Hypertrophy

Glucocorticoids exert important therapeutic effects on airway smooth muscle (ASM), yet few direct targets of glucocorticoid signaling in ASM have been definitively identified. Here, we show that the transcription factor, Krüppel-like factor 15 (KLF15), is directly induced by glucocorticoids in primary human ASM, and that KLF15 represses ASM hypertrophy. We integrated transcriptome data from KLF15 overexpression with genome-wide analysis of RNA polymerase (RNAP) II and glucocorticoid receptor (GR) occupancy to identify phospholipase C delta 1 as both a KLF15-regulated gene and a novel repressor of ASM hypertrophy. Our chromatin immunoprecipitation sequencing data also allowed us to establish numerous direct transcriptional targets of GR in ASM. Genes with inducible GR occupancy and putative antiinflammatory properties included IRS2, APPL2, RAMP1, and MFGE8. Surprisingly, we also observed GR occupancy in the absence of supplemental ligand, including robust GR binding peaks within the IL11 and LIF loci. Detection of antibody-GR complexes at these areas was abrogated by dexamethasone treatment in association with reduced RNA polymerase II occupancy, suggesting that noncanonical pathways contribute to cytokine repression by glucocorticoids in ASM. Through defining GR interactions with chromatin on a genome-wide basis in ASM, our data also provide an important resource for future studies of GR in this therapeutically relevant cell type.

Three Unique Interstitial Macrophages in the Murine Lung at Steady State

The current paradigm in macrophage biology is that some tissues mainly contain macrophages from embryonic origin, such as microglia in the brain, whereas other tissues contain postnatal-derived macrophages, such as the gut. However, in the lung and in other organs, such as the skin, there are both embryonic and postnatal-derived macrophages. In this study, we demonstrate in the steady-state lung that the mononuclear phagocyte system is comprised of three newly identified interstitial macrophages (IMs), alveolar macrophages, dendritic cells, and few extravascular monocytes. We focused on similarities and differences between the three IM subtypes, specifically, their phenotype, location, transcriptional signature, phagocytic capacity, turnover, and lack of survival dependency on fractalkine receptor, CX₃CR1. Pulmonary IMs were located in the bronchial interstitium but not the alveolar interstitium. At the transcriptional level, all three IMs displayed a macrophage signature and phenotype. All IMs expressed MER proto-oncogene, tyrosine kinase, CD64, CD11b, and CX₃CR1, and were further distinguished by differences in cell surface protein expression of CD206, Lyve-1, CD11c, CCR2, and MHC class II, along with the absence of Ly6C, Ly6G, and Siglec F. Most intriguingly, in addition to the lung, similar phenotypic populations of IMs were observed in other nonlymphoid organs, perhaps highlighting conserved functions throughout the body. These findings promote future research to track four distinct pulmonary macrophages and decipher the division of labor that exists between them.

Three unique interstitial macrophages in the murine lung at steady state

Rationale

The current paradigm in macrophage biology is that some tissues mainly contain macrophages from embryonic origin such as microglia in the brain, while other tissues contain postnatal-derived macrophages, such as the gut. However, in the lung and in other organs such as the skin, there are both embryonic and postnatal-derived macrophages.

Objectives

In this study, we demonstrate in the steady-state lung that the mononuclear phagocyte system is comprised of three newly identified interstitial macrophages (IMs), alveolar macrophages (AMs), dendritic cells and few extravascular monocytes.

Methods

We focused on similarities and differences between the three IM subtypes, specifically, their phenotype, location, transcriptional signature, phagocytic capacity, turnover and lack of survival dependency on CX3CR1.

Measurements and Main Results

Pulmonary IMs were located in the bronchial interstitium but not the alveolar interstitium. At the transcriptional level, all three IMs displayed a macrophage signature. All IMs expressed MerTK+CD64+ CD11b+ CX CR1+ and were furthermore distinguished by differences in cell surface protein expression of CD206, Lyve-1, CD11c, CCR2 and MHCII, along with the absence of Ly6C, Ly6G, and Siglec F. Ex vivo analysis revealed that all three IMs were highly phagocytic compared to AMs. Finally, similar phenotypic populations of IMs were present in other non-lymphoid organs, suggesting that these IMs may not be unique to the lung.

Conclusions

These findings promote future research to track four distinct pulmonary macrophages and decipher the division of labor that exists between them.

Virtual memory T cells develop and mediate bystander protective immunity in an IL-15-dependent manner

Virtual memory cells (VM) are an antigen-specific, memory phenotype CD8 T-cell subset found in lymphoreplete, unchallenged mice. Previous studies indicated that VM cells were the result of homeostatic proliferation (HP) resembling the proliferation observed in a lymphopenic environment. Here we demonstrate that HP is ongoing in lymphoreplete mice, the degree of which is dictated by the number of naive CD8 T cells with a sufficiently high affinity for self-antigen interacting with peripheral IL-15. VM cell transcriptional profiles suggest a capacity to mediate protective immunity via antigen non-specific bystander killing, a function we show is dependent on IL-15. Finally, we show a VM-like population of human cells that accumulate with age and traffic to the liver, displaying phenotypic and functional attributes consistent with the bystander protective functions of VM cells identified in the mouse. These data identify developmental and functional attributes of VM cells, including their likely role in protective immunity.

Ly6C(+) monocyte efferocytosis and cross-presentation of cell-associated antigens

Recently it was shown that circulating Ly6C⁺ monocytes traffic from tissue to the draining lymph nodes (LNs) with minimal alteration in their overall phenotype. Furthermore, in the steady state, Ly6C⁺ monocytes are as abundant as classical dendritic cells (DCs) within the draining LNs, and even more abundant during inflammation. However, little is known about the functional roles of constitutively trafficking Ly6C⁺ monocytes. In this study we investigated whether Ly6C⁺ monocytes can efferocytose (acquire dying cells) and cross-present cell-associated antigen, a functional property particularly attributed to Batf3⁺ DCs. We demonstrated that Ly6C⁺ monocytes intrinsically efferocytose and cross-present cell-associated antigen to CD8⁺ T cells. In addition, efferocytosis was enhanced upon direct activation of the Ly6C⁺ monocytes through its corresponding TLRs, TLR4 and TLR7. However, only ligation of TLR7, and not TLR4, enhanced cross-presentation by Ly6C⁺ monocytes. Overall, this study outlines two functional roles, among others, that Ly6C⁺ monocytes have during an adaptive immune response.

Chromodomain helicase DNA-binding 4 is required for proliferation, distal VH rearrangements and developmental progression of B cell progenitors (HEM1P.221)

Chromodomain Helicase DNA-binding protein 4 (CHD4, or Mi-2β) is a catalytic core subunit of Nucleosome Remodeling and Deacetylase (NuRD) complexes, which regulate chromatin structure and transcription in lymphocytes. CHD4 activities include ATP-dependent mobilization of nucleosomes, DNA binding and binding to histone tails. Here, we investigated requirements for CHD4 in B cell development in a mouse model system. We utilized Chd4flox/flox:Cd79a-Cre (Chd4 cko) mice, which inactivate Chd4 genes selectively in early B cell progenitors. These mice confirmed that CHD4 is essential for B lymphopoiesis. Following the loss of CHD4 expression, B cell development is arrested at the pro-B cell stage. Peripheral B220+ cells were nearly absent. To address the basis of the observed developmental arrest, we measured effects of the lack of CHD4 on proliferation and Igh gene rearrangements. CHD4-deficient pro-B cells fail to proliferate in response to IL-7. Furthermore, pro-B cells lacking CHD4 complete proximal VH to DJH rearrangements, but rearrange distal VH segments only rarely. Overall, our data demonstrate that CHD4 and NuRD complexes are essential for multiple aspects of early B cell development, including V(D)J recombination, proliferation and survival of pro-B cells.

Virtual memory cells: a consequence of self-affinity-linked naïve CD8 T cell heterogeneity (LYM5P.703)

Memory phenotype (MP), CD44hi CD49dlo CD8 T cells are found in nearly all mice—lymphoreplete, pathogen naïve, and even TCR transgenics. The presence of MP was long thought to be due to environmental pathogen exposure (or, in the case of transgenics, heterologous immunity to same), but studies establishing the presence of these cells in germ-free mice suggested that this was not the case. These cells, dubbed Virtual Memory (VM), are of special relevance due to their increased effector functioning, and, in contrast to other MP CD8 T cells, develop in the periphery with a dependence on IL-15. Our recent studies have determined that VM cells develop in a manner reminiscent of lymphopenic homeostatic expansion, whereby the highest self-affinity T cells (as measured by CD5) interact with available IL-15 to turn into VM cells. This indicates that the naïve CD8 T cell pool is not as homogeneous as usually assumed, and RNA sequencing has further confirmed the heterogeneity of the CD8 naïve T cell pool (separated on CD5). The sequencing has further implicated VM cells in mediating CD8 bystander protection, and ongoing studies suggest that this is indeed the case, with the VM bystander effects being IL-15 dependent.

Regulation of toll-like receptor signaling by the SF3a mRNA splicing complex

The innate immune response plays a key role in fighting infection by activating inflammation and stimulating the adaptive immune response. However, chronic activation of innate immunity can contribute to the pathogenesis of many diseases with an inflammatory component. Thus, various negatively acting factors turn off innate immunity subsequent to its activation to ensure that inflammation is self-limiting and to prevent inflammatory disease. These negatively acting pathways include the production of inhibitory acting alternate proteins encoded by alternative mRNA splice forms of genes in Toll-like receptor (TLR) signaling pathways. We previously found that the SF3a mRNA splicing complex was required for a robust innate immune response; SF3a acts to promote inflammation in part by inhibiting the production of a negatively acting splice form of the TLR signaling adaptor MyD88. Here we inhibit SF3a1 using RNAi and subsequently perform an RNAseq study to identify the full complement of genes and splicing events regulated by SF3a in murine macrophages. Surprisingly, in macrophages, SF3a has significant preference for mRNA splicing events within innate immune signaling pathways compared with other biological pathways, thereby affecting the splicing of specific genes in the TLR signaling pathway to modulate the innate immune response.

Within minutes after we are exposed to pathogens, our bodies react with a rapid response known as the “innate immune response.” This arm of the immune response regulates the process of inflammation, in which various immune cells are recruited to sites of infection and are activated to produce a host of antimicrobial compounds. This response is critical to fight infection. However, this response, if it is activated too strongly or if it becomes chronic, can do damage and can contribute to numerous very common diseases ranging from atherosclerosis to asthma to cancer. Thus it is essential that this response be tightly regulated, turned on when we have an infection, and turned off when not needed. We are investigating a mechanism that helps turn off this response, to ensure that inflammation is limited to prevent inflammatory disease. This mechanism involves the production of alternate forms of RNAs and proteins that control inflammation. We have discovered that a protein known as SF3a1 can regulate the expression of these alternate inhibitory RNA forms and are investigating how to use this knowledge to better control inflammation.

Phosphorus limitation increases attachment in Agrobacterium tumefaciens and reveals a conditional functional redundancy in adhesin biosynthesis

Bacterial responses to phosphorus limitation, commonly inorganic phosphate (P(i)), are important survival mechanisms in a variety of environments. The two-component sensor kinase PhoR and its cognate response regulator PhoB are central to the P(i) limitation response of many bacteria and control the large Pho regulon. Limitation for P(i) significantly increased attachment and biofilm formation by the plant pathogen Agrobacterium tumefaciens, and this was driven by PhoB. Surprisingly, it was also found that both phoR and phoB were essential in A. tumefaciens. Expression of a plasmid-borne copy of the low affinity P(i) transporter (pit) from Sinorhizobium meliloti in A. tumefaciens abolished the phoB and phoR essentiality in A. tumefaciens and allowed direct demonstration of the requirement for this regulatory system in the biofilm response. Increased attachment under P(i) limitation required a unipolar polysaccharide (UPP) adhesin. Mutation of a polyisoprenylphosphate hexose-1-phosphate transferase (PHPT) called uppE abolished UPP production and prevented surface attachment under P(i)-replete conditions, but this was rescued under P(i) limitation, and this rescue required phoB. In low P(i) conditions, either uppE or a paralogous gene Atu0102 is functionally redundant, but only uppE functions in UPP synthesis and attachment when P(i) is replete. This conditional functional redundancy illustrates the influence of phosphorus availability on A. tumefaciens surface colonization.

Biofilm formation by plant-associated bacteria

Plants support a diverse array of bacteria, including parasites, mutualists, and commensals on and around their roots, in the vasculature, and on aerial tissues. These microbes have a profound influence on plant health and productivity. Bacteria physically interact with surfaces to form complex multicellular and often multispecies assemblies, including biofilms and smaller aggregates. There is growing appreciation that the intensity, duration, and outcome of plant-microbe interactions are significantly influenced by the conformation of adherent microbial populations. Biofilms on different tissues have unique properties, reflecting the prevailing conditions at those sites. Attachment is required for biofilm formation, and bacteria interact with plant tissues through adhesins including polysaccharides and surface proteins, with initial contact often mediated by active motility. Recognition between lectins and their cognate carbohydrates is a common means of specificity. Biofilm development and the resulting intimate interactions with plants often require cell-cell communication between colonizing bacteria.

Motility and chemotaxis in Agrobacterium tumefaciens surface attachment and biofilm formation

Bacterial motility mechanisms, including swimming, swarming, and twitching, are known to have important roles in biofilm formation, including colonization and the subsequent expansion into mature structured surface communities. Directed motility requires chemotaxis functions that are conserved among many bacterial species. The biofilm-forming plant pathogen Agrobacterium tumefaciens drives swimming motility by utilizing a small group of flagella localized to a single pole or the subpolar region of the cell. There is no evidence for twitching or swarming motility in A. tumefaciens. Site-specific deletion mutations that resulted in either aflagellate, flagellated but nonmotile, or flagellated but nonchemotactic A. tumefaciens derivatives were examined for biofilm formation under static and flowing conditions. Nonmotile mutants were significantly deficient in biofilm formation under static conditions. Under flowing conditions, however, the aflagellate mutant rapidly formed aberrantly dense, tall biofilms. In contrast, a nonmotile mutant with unpowered flagella was clearly debilitated for biofilm formation relative to the wild type. A nontumbling chemotaxis mutant was only weakly affected with regard to biofilm formation under nonflowing conditions but was notably compromised in flow, generating less adherent biomass than the wild type, with a more dispersed cellular arrangement. Extragenic suppressor mutants of the chemotaxis-impaired, straight-swimming phenotype were readily isolated from motility agar plates. These mutants regained tumbling at a frequency similar to that of the wild type. Despite this phenotype, biofilm formation by the suppressor mutants in static cultures was significantly deficient. Under flowing conditions, a representative suppressor mutant manifested a phenotype similar to yet distinct from that of its nonchemotactic parent.

Quorum sensing and motility mediate interactions between Pseudomonas aeruginosa and Agrobacterium tumefaciens in biofilm cocultures

In the environment, multiple microbial taxa typically coexist as communities, competing for resources and, often, physically associated within biofilms. A dual-species cocultivation model has been developed by using two ubiquitous and well studied microbes Pseudomonas aeruginosa (P.a.) and Agrobacterium tumefaciens (A.t.) as a tractable system to identify molecular mechanisms that underlie multispecies microbial associations. Several factors were found to influence coculture interactions. P.a. had a distinct growth-rate advantage in cocultures, increasing its relative abundance during planktonic and biofilm growth. P.a. also demonstrated a slight quorum-sensing-dependent increase in growth yield in liquid cocultures. P.a. dominated coculture biofilms, "blanketing" or burying immature A.t. microcolonies. P.a. flagellar and type IV pili mutant strains exhibited deficient blanketing and impaired competition in coculture biofilms, whereas, in planktonic coculture, these mutations had no effect on competition. In contrast, A.t. used motility to emigrate from coculture biofilms. In both planktonic and biofilm cocultures, A.t. remained viable for extended periods of time, coexisting with its more numerous competitor. These findings reveal that quorum-sensing-regulated functions and surface motility are important microbial competition factors for P.a. and that the outcome of competition and the relative contribution of different factors to competition are strongly influenced by the environment in which they occur.

Phosphorus limitation enhances biofilm formation of the plant pathogen Agrobacterium tumefaciens through the PhoR-PhoB regulatory system

The plant pathogen Agrobacterium tumefaciens forms architecturally complex biofilms on inert surfaces. Adherence of A. tumefaciens C58 was significantly enhanced under phosphate limitation compared to phosphate-replete conditions, despite slower overall growth under low-phosphate conditions. Replacement of Pi with sn-glycerol-3-phosphate and 2-aminoethylphosphonate yielded similar results. The increase in surface interactions under phosphate limitation was observed in both static culture and continuous-culture flow cells. Statistical analysis of confocal micrographs obtained from the flow cell biofilms revealed that phosphate limitation increased both the overall attached biomass and the surface coverage, whereas the maximum thickness of the biofilm was not affected. Functions encoded on the two large plasmids of A. tumefaciens C58, pTiC58 and pAtC58, were not required for the observed phosphate effect. The phosphate concentration at which increased attachment was observed triggered the phosphate limitation response, controlled in many bacteria by the two-component regulatory system PhoR-PhoB. The A. tumefaciens phoB and phoR orthologues could only be disrupted in the presence of plasmid-borne copies of the genes, suggesting that this regulatory system might be essential. Expression of the A. tumefaciens phoB gene from a tightly regulated inducible promoter, however, correlated with the amount of biofilm under both phosphate-limiting and nonlimiting conditions, demonstrating that components of the Pho regulon influence A. tumefaciens surface interactions.

Characterization of an S-layer glycoprotein produced in the course of S-layer variation of Bacillus stearothermophilus ATCC 12980 and sequencing and cloning of the sbsD gene encoding the protein moiety

The cell surface of Bacillus stearothermophilus ATCC 12980 is completely covered by an oblique lattice which consists of the S-layer protein SbsC. On SDS-polyacrylamide gels, the mature S-layer protein migrates as a single band with an apparent molecular mass of 122 kDa. During cultivation of B. stearothermophilus ATCC 12980 at 67 degrees C instead of 55 degrees C, a variant developed that had a secondary cell wall polymer identical to that of the wild-type strain, but it carried an S-layer glycoprotein that could be separated on SDS-polyacrylamide gels into four bands with apparent molecular masses of 92, 118, 150 and 175 kDa. After deglycosylation, only a single protein band with a molecular mass of 92 kDa remained. The complete nucleotide sequence encoding the protein moiety of this S-layer glycoprotein, termed SbsD, was established by PCR and inverse PCR. The sbsD gene of 2,709 bp is predicted to encode a protein of 96.2 kDa with a 30-amino-acid signal peptide. Within the 807 bp encoding the signal peptide and the N-terminal sequence (amino acids 31-269), different nucleotides for sbsD and sbsC were observed in 46 positions, but 70% of these mutations were silent, thus leading to a level of identity of 95% for the N-terminal parts. The level of identity of the remaining parts of SbsD and SbsC was below 10%, indicating that the lysine-, tyrosine- and arginine-rich N-terminal region in combination with a distinct type of secondary cell wall polymer remained conserved upon S-layer variation. The sbsD sequence encoding the mature S-layer protein cloned into the pET28a vector led to stable expression in Escherichia coli HMS174(DE3). This is the first example demonstrating that S-layer variation leads to the synthesis of an S-layer glycoprotein.

ISBst12, a novel type of insertion-sequence element causing loss of S-layer-gene expression in Bacillus stearothermophilus ATCC 12980

The cell surface of the surface layer (S-layer)-carrying strain of Bacillus stearothermophilus ATCC 12980 is completely covered with an oblique lattice composed of the S-layer protein SbsC. In the S-layer-deficient strain, theS-layer gene sbsC was still present but was interrupted by a novel type of insertion sequence (IS) element designated ISBst12. The insertion site was found to be located within the coding region of the sbsC gene, 199 bp downstream from the translation start of SbsC. ISBst12 is 1612 bp long, bounded by 16 bp imperfect inverted repeats and flanked by a directly repeated 8 bp target sequence. ISBst12 contains an ORF of 1446 bp and is predicted to encode a putative transposase of 482 aa with a calculated theoretical molecular mass of 55562 Da and an isoelectric point of 9.13. The putative transposase does not exhibit a typical DDE motif but displays aHis-Arg-Tyr triad characteristic of the active site of integrases from the bacteriophage lambda Int family. Furthermore, two overlapping leucine-zipper motifs were identified at the N-terminal part of the putative transposase. As revealed by Southern blotting, ISBst12 was present in multiple copies in the S-layer-deficient strain as well as in the S-layer-carrying strain. Northern blotting indicated that S-layer gene expression is already inhibited at the transcriptional level, since no sbsC-specific transcript could be identified in the S-layer-deficient strain. By using PCR, ISBst12 was also detected in B. stearothermophilus PV72/p6, in its oxygen-induced strain variant PV72/p2 and in the S-layer-deficient strain PV72/T5.