Full-length IL-33 augments pulmonary fibrosis in an ST2- and Th2-independent, non-transcriptomic fashion.

Mature IL-33 (MIL33) acting through its receptor, ST2, is known to regulate fibrosis. The precursor, full-length IL-33 (FLIL33), may function differently from MIL33 and independently of ST2. Here we report that genetic deletion of either IL-33 or ST2 attenuates pulmonary fibrosis in the bleomycin model, as does Cre-induced IL-33 deficiency in response to either acute or chronic bleomycin challenge. However, adenovirus-mediated gene delivery of FLIL33, but not MIL33, to the lungs of either wild-type or ST2-deficient mice potentiates the profibrotic effect of bleomycin without inducing a Th2 phenotype. In cultured mouse lung cells, FLIL33 overexpression induces moderate and distinct transcriptomic changes compared with a robust response induced by MIL33, whereas ST2 deletion abrogates the effects of both IL-33 forms. Thus, FLIL33 may contribute to fibrosis in an ST2-independent, Th2-independent, non-transcriptomic fashion, suggesting that pharmacological targeting of both FLIL33 and MIL33 may prove efficacious in patients with pulmonary fibrosis.

Regulator of Cell Cycle Protein (RGCC/RGC-32) Protects against Pulmonary Fibrosis.

Some previous studies in tissue fibrosis have suggested a profibrotic contribution from elevated expression of a protein termed either RGCC (regulator of cell cycle) or RGC-32 (response gene to complement 32 protein). Our analysis of public gene expression datasets, by contrast, revealed a consistent decrease in RGCC mRNA levels in association with pulmonary fibrosis. Consistent with this observation, we found that stimulating primary adult human lung fibroblasts with transforming growth factor (TGF)-ß in cell cultures elevated collagen expression and simultaneously attenuated RGCC mRNA and protein levels. Moreover, overexpression of RGCC in cultured lung fibroblasts attenuated the stimulating effect of TGF-ß on collagen levels. Similar to humans with pulmonary fibrosis, the levels of RGCC were also decreased in vivo in lung tissues of wild-type mice challenged with bleomycin in both acute and chronic models. Mice with constitutive RGCC gene deletion accumulated more collagen in their lungs in response to chronic bleomycin challenge than did wild-type mice. RNA-Seq analyses of lung fibroblasts revealed that RGCC overexpression alone had a modest transcriptomic effect, but in combination with TGF-ß stimulation, induced notable transcriptomic changes that negated the effects of TGF-ß, including on extracellular matrix-related genes. At the level of intracellular signaling, RGCC overexpression delayed early TGF-ß-induced Smad2/3 phosphorylation, elevated the expression of total and phosphorylated antifibrotic mediator STAT1, and attenuated the expression of a profibrotic mediator STAT3. We conclude that RGCC plays a protective role in pulmonary fibrosis and that its decline permits collagen accumulation. Restoration of RGCC expression may have therapeutic potential in pulmonary fibrosis.

Full-length IL-33 regulates Smad3 phosphorylation and gene transcription in a distinctive AP2-dependent manner.

IL-33 has emerged as a central mediator of immune, inflammatory, and fibrotic responses. Many studies have focused on mature IL-33, but elevated expression of the precursor, full-length IL-33 (FLIL33), has also been implicated in a spectrum of diseases, including tissue fibrosis. We previously reported and now confirmed that overexpression of FLIL33 induced phosphorylation of the key profibrotic signaling mediator of TGF-ß, Smad3, in primary human lung fibroblasts from healthy donors and idiopathic pulmonary fibrosis patients. Presently, we demonstrate that FLIL33-induced Smad3 phosphorylation was not abrogated by anti-TGF-ß antibody but was abrogated by ALK5/TGFBR1-specific and Smad3-specific inhibition, indicating that FLIL33 effect was independent of TGF-ß but dependent on its receptor, TGFBR. Western blotting analyses revealed that FLIL33 overexpression increased levels, but did not affect subcellular distribution, of the AP2A1 and AP2B1 subunits of the adaptor protein complex 2 (AP2), a known TGFBR binding partner. siRNA-mediated inhibition of these subunits blocked FLIL33-induced Smad3 phosphorylation, whereas AP2 subunit overexpression induced Smad3 phosphorylation even in the absence of FLIL33. RNA-Seq transcriptomic analyses revealed that fibroblast stimulation with TGF-ß induced major changes in expression levels of numerous genes, whereas overexpression of FLIL33 induced modest expression changes in a small number of genes. Furthermore, qRT-PCR tests demonstrated that despite inducing Smad3 phosphorylation, FLIL33 did not induce collagen gene transcription and even mildly attenuated TGF-ß-induced levels of collagen I and III mRNAs. We conclude that FLIL33 induces Smad3 phosphorylation through a TGF-ß-independent but TGF-ß receptor- and AP2- dependent mechanism and has limited downstream transcriptomic consequences.

High-performance computing service for bioinformatics and data science.

Despite having an ideal setup in their labs for wet work, researchers often lack the computational infrastructure to analyze the magnitude of data that result from "-omics" experiments. In this innovative project, the library supports analysis of high-throughput data from global molecular profiling experiments by offering a high-performance computer with open source software along with expert bioinformationist support. The audience for this new service is faculty, staff, and students for whom using the university's large scale, CORE computational resources is not warranted because these resources exceed the needs of smaller projects. In the library's approach, users are empowered to analyze high-throughput data that they otherwise would not be able to on their own computers. To develop the project, the library's bioinformationist identified the ideal computing hardware and a group of open source bioinformatics software to provide analysis options for experimental data such as scientific images, sequence reads, and flow cytometry files. To close the loop between learning and practice, the bioinformationist developed self-guided learning materials and workshops or consultations on topics such as the National Center for Biotechnology Information's BLAST, Bioinformatics on the Cloud, and ImageJ. Researchers apply the data analysis techniques that they learned in the classroom in the library's ideal computing environment.

Mobilization of epithelial mesenchymal transition genes distinguishes active from inactive lesional tissue in patients with ulcerative colitis.

Ulcerative colitis (UC) is a chronic, relapsing and debilitating idiopathic inflammation, with variable and complex pathophysiologies. Our objective was to elucidate patterns of gene expression underlying the progression of UC disease. Single endoscopic pinch FFPE biopsies (n = 41) were sampled at both active and inactive stages at the same site in individual UC patients and compared with each other and with non-inflammatory bowel disease healthy controls. Gene expression results were validated by quantitative reverse transcriptase-PCR (QRT-PCR), and results at the protein level were validated by immunohistochemistry and western blot. Analysis of microarray results demonstrated that UC patients in remission display an intermediate gene expression phenotype between active UC patients and controls. It is clear that UC active site recovery does not revert fully back to a healthy control phenotype. Both UC active and inactive tissue displayed evidence, at both the gene expression and protein level, of a positive precancerous state as indicated by increases in the expression of Chitinase 3-Like-1, and the colorectal cancer metastasis marker MMP1. A key distinguishing feature between active and inactive UC, however, was the mobilization of marker genes and proteins for the Epithelial Mesenchymal Transition (EMT) pathway only in active UC. Analysis of the gene expression signatures associated with UC remission identified multiple pathways which appear to be permanently dysregulated in UC patients at formerly active sites in spite of clear histological recovery. Among these pathways, the EMT pathway was specifically up-regulated only in active UC emphasizing the potential for cancer progression in these patients.

Variation in spatial population structure in the Anopheles gambiae species complex.

Anopheles gambiae, Anopheles coluzzii, and Anopheles arabiensis are three of the most widespread vectors of malaria parasites, with geographical ranges stretching across wide swaths of Africa. Understanding the population structure of these closely related species, including the extent to which populations are connected by gene flow, is essential for understanding how vector control implemented in one location might indirectly affect vector populations in other locations. Here, we assessed the population structure of each species based on a combined data set of publicly available and newly processed whole-genome sequences. The data set included single nucleotide polymorphisms from whole genomes of 2,410 individual mosquitoes sampled from 128 locations across 19 African countries. We found that A. gambiae sampled from several countries in West and Central Africa showed low genetic differentiation from each other according to principal components analysis (PCA) and ADMIXTURE modeling. Using Estimated Effective Migration Surfaces (EEMS), we showed that this low genetic differentiation indicates high effective migration rates for A. gambiae across this region. Outside of this region, we found eight groups of sampling locations from Central, East, and Southern Africa for which A. gambiae showed higher genetic differentiation, and lower effective migration rates, between each other and the West/Central Africa group. These results indicate that the barriers to and corridors for migration between populations of A. gambiae differ across the geographical range of this malaria vector species. Using the same methods, we found higher genetic differentiation and lower migration rates between populations of A. coluzzii in West and Central Africa than for A. gambiae in the same region. In contrast, we found lower genetic differentiation and higher migration rates between populations of A. arabiensis in Tanzania, compared to A. gambiae in the same region. These differences between A. gambiae, A. coluzzii, and A. arabiensis indicate that migration barriers and corridors may vary, even between very closely related species. Overall, our results demonstrate that migration rates vary both within and between species of Anopheles mosquitoes, presumably based on species-specific responses to the ecological or environmental conditions that may impede or facilitate migration, and the geographical patterns of these conditions across the landscape. Together with previous findings, this study provides robust evidence that migration rates between populations of malaria vectors depend on the ecological context, which should be considered when planning surveillance of vector populations, monitoring for insecticide resistance, and evaluating interventions.

Eosinophils restrain humoral alloimmunity after lung transplantation.

While the function of many leukocytes in transplant biology has been well defined, the role of eosinophils is controversial and remains poorly explored. Conflicting data exist regarding eosinophils' role in alloimmunity. Due to their prevalence in the lung, and their defined role in other pulmonary pathologies such as asthma, we set out to explore the role of eosinophils in the long-term maintenance of the lung allograft. We noted that depletion of eosinophils results in the generation of donor-specific antibodies. Eosinophil depletion increased memory B cell, plasma cell, and antibody-secreting cell differentiation and resulted in de novo generation of follicular germinal centers. Germinal center formation depended on the expansion of CD4+Foxp3-Bcl6+CXCR5+PD-1+ T follicular helper (Tfh) cells, which increase in number after eosinophil depletion. Mechanistically, we demonstrate that eosinophils prevent Tfh cell generation by acting as the dominant source of IFN-γ in an established lung allograft, thus facilitating Th1 rather than Tfh polarization of naive CD4+ T cells. Our data thus describe what we believe is a unique and previously unknown role for eosinophils in maintaining allograft tolerance and suggest that indiscriminate administration of eosinophil-lytic corticosteroids for treatment of acute cellular rejection may inadvertently promote humoral alloimmunity.

Kinetics of mast cell, basophil, and oral food challenge responses in omalizumab-treated adults with peanut allergy.

BACKGROUND: Monoclonal antibodies directed at IgE demonstrate clinical efficacy in subjects with peanut allergy, but previous studies have not addressed the kinetics of the clinical response or the role of mast cells and basophils in the food-induced allergic response. OBJECTIVE: We sought to determine the kinetics of the clinical response to omalizumab and whether clinical improvement is associated with either mast cell or basophil suppression. METHODS: Subjects with peanut allergy were treated with omalizumab for 6 months and assessed for clinical and cellular responses. At baseline, subjects had a double-blind, placebo-controlled oral food challenge (OFC), skin prick test titration (SPTT), and basophil histamine release (BHR) to peanut. BHR was repeated at week 2 and then weekly until it decreased to less than 20% of baseline values. The OFCs and SPTTs were repeated after the BHR reduction (or at week 8 if BHR did not decrease) and again at 6 months. RESULTS: Fourteen subjects enrolled in the study. At the second food challenge, there was a significant increase in the threshold dose of peanut inducing allergic symptoms (80 to 6500 mg, P < .01). Peanut-induced BHR was either completely suppressed (n = 5) or 10-fold more allergen was required to induce maximal BHR (n = 9), and SPTT responses were not significantly changed from baseline. After 6 months of omalizumab, further changes in the OFC threshold dose or BHR were not observed, but a significant suppression in SPTTs was identified. CONCLUSIONS: The clinical response to omalizumab occurs early in treatment when the basophil, but not the mast cell, is suppressed, supporting a role for the basophil in acute food reactions.

RGC-32 Acts as a Hub to Regulate the Transcriptomic Changes Associated With Astrocyte Development and Reactive Astrocytosis.

Response Gene to Complement 32 (RGC-32) is an important mediator of the TGF-ß signaling pathway, and an increasing amount of evidence implicates this protein in regulating astrocyte biology. We showed recently that spinal cord astrocytes in mice lacking RGC-32 display an immature phenotype reminiscent of progenitors and radial glia, with an overall elongated morphology, increased proliferative capacity, and increased expression of progenitor markers when compared to their wild-type (WT) counterparts that make them incapable of undergoing reactive changes during the acute phase of experimental autoimmune encephalomyelitis (EAE). Here, in order to decipher the molecular networks underlying RGC-32's ability to regulate astrocytic maturation and reactivity, we performed next-generation sequencing of RNA from WT and RGC-32 knockout (KO) neonatal mouse brain astrocytes, either unstimulated or stimulated with the pleiotropic cytokine TGF-ß. Pathway enrichment analysis showed that RGC-32 is critical for the TGF-ß-induced up-regulation of transcripts encoding proteins involved in brain development and tissue remodeling, such as axonal guidance molecules, transcription factors, extracellular matrix (ECM)-related proteins, and proteoglycans. Our next-generation sequencing of RNA analysis also demonstrated that a lack of RGC-32 results in a significant induction of WD repeat and FYVE domain-containing protein 1 (Wdfy1) and stanniocalcin-1 (Stc1). Immunohistochemical analysis of spinal cords isolated from normal adult mice and mice with EAE at the peak of disease showed that RGC-32 is necessary for the in vivo expression of ephrin receptor type A7 in reactive astrocytes, and that the lack of RGC-32 results in a higher number of homeodomain-only protein homeobox (HOPX)+ and CD133+ radial glia cells. Collectively, these findings suggest that RGC-32 plays a major role in modulating the transcriptomic changes in astrocytes that ultimately lead to molecular programs involved in astrocytic differentiation and reactive changes during neuroinflammation.

J.Leonard Goldner Award 2008. Effect of extracorporeal shock wave therapy on cultured tenocytes.

BACKGROUND: Little has been reported about the biologic effect of shock waves on human normal or pathologic tendon tissue. We hypothesized that inflammatory cytokine and MMP production would be down-regulated by shock wave stimulation. MATERIALS AND METHODS: Diseased Achilles tendon tissue and healthy flexor hallucis longus tissue were used. Shock wave treatment was applied to cultured cells at 0.17 mJ/mm(2)energy 250, 500, 1000, and 2000 times. RESULTS: A dose-dependent decrease in cell viability was noted in cells receiving 1000 and 2000 shocks (86.0 +/- 5.6%, p = 0.01 and 72.4 +/- 8.9%, p = 0.001) as compared with the normal control. Cell count in the 500-shock group increased by 23.4% as compared with the control (p = 0.05). The concentration of MMP 1, 2, and 13 was higher in diseased tenocytes as compared with normal cells (p = 0.04, all comparisons). IL-6 levels were higher in the diseased tenocytes as compared with normal tenocytes (44.10 +/- 16.72 versus 0.21 +/- 0.55 ng/ml, (p < 0.05). IL-1 levels in normal cells increased (2.24 +/- 5.02 ng/ml to 9.31 +/- 6.85 ng/ml) after shock wave treatment (p = 0.04). In diseased tenocytes, levels of MMP-1 (1.12 +/- 0.23 to 0.75 +/- 0.24 ng/ml; p = 0.04) and MMP-13 (1.43 +/- 0.11 to 0.80 +/- 0.15 ng/ml; p = 0.04) were significantly decreased after shock wave treatment. The IL-6 level in diseased tenocytes was decreased (44.10 +/- 16.72 to 14.66 +/- 9.49 ng/ml) after shock wave treatment (p = 0.04). CONCLUSION: Higher levels of MMPs and ILs were found in human tendinopathy-affected tenocytes as compared with normal cells. ESWT decreased the expression of several MMPs and ILs. CLINICAL RELEVANCE: This mechanism may play an important role in shock wave treatment of tendinopathy clinically.

Imaging flow cytometry: A method for examining dynamic native FOXO1 localization in human lymphocytes.

While flow cytometry can reliably assess surface and intracellular marker expression within small cell populations, it does not provide any information on protein localization. Several key transcription factors (TF) downstream of lymphocyte surface receptors are regulated by nuclear versus cytoplasmic localization, and one such TF is Forkhead box O1 (FOXO1). FOXO1 integrates antigen-binding, co-receptor activation and metabolic signals in lymphocytes, leading to proliferation and differentiation. Importantly, the nuclear or cytoplasmic localization of FOXO1 is key for gene expression leading to different lymphocyte phenotypes. In effector lymphocytes (Teff), for example, lymphocyte receptor (TCR) signaling leads to an Akt-dependent phosphorylation of FOXO1. Phosphorylated FOXO1 is excluded from the nucleus, promoting proliferation and effector functions. In contrast, nuclear retention of FOXO1 is essential for early and late development of T and B cells and for the thymic development and stability of regulatory T cells. Given the critical role of FOXO1 localization as an indicator and determinant of function, quantification of FOXO1 cellular localization in human lymphocytes can help determine immune cell activation and activity in experimental and clinical scenarios. The standard method used to determine subcellular protein localization is the analysis of nuclear and cytoplasmic protein extracts by Western blotting (WB). However, available techniques, such as WB, are limited by a requirement for a large number of cells and inability to determine FOXO1 localization in individual cells or sub-populations. In contrast, a standardized method using an imaging flow cytometer (IFC) such as the Amnis ImagestreamX Mark II, would provide both qualitative, per-cell localization information, as well as quantitative data on gated sub-populations. To this end, we report the development and optimization of an IFC protocol to examine native FOXO1 localization in human lymphocytes. A human CD4+ lymphocyte line, HuT102, as well as primary human T cells, were assessed for dynamic FOXO1 localization after treatment with a lymphocyte receptor signaling mimic (PMA/Ionomycin). IFC nuclear translocation analysis permitted us to precisely quantify the alterations over time in nuclear and cytoplasmic localization of native FOXO1 on a per cell basis, including within specific, user-defined sub-populations of cells. For human lymphocytes, using IFC to assess and quantify dynamic FOXO1 localization allows the user to simultaneously study multiple lymphocyte subpopulations as well as to delineate differing effects of dynamic FOXO1 localization that may be lost when other available methods are used.

A novel method for assaying human regulatory T cell direct suppression of B cell effector function.

We have established a highly reproducible and reliable protocol for testing human regulatory T cell function in suppressing IgM production from an immature human B cell line. The autoreactive Ramos B cell line provides a stable reporter of B cell effector function that can be tested by a straight-forward IgM ELISA. Tregs from healthy volunteers display a range of ability for suppressing baseline IgM production in a contact- and death-independent manner. Having established the normal range for human Treg direct suppression of B cell effector function, it will now be possible to efficiently test Tregs from various autoimmune conditions in which B cell hyperactivity and secretion of auto-antibodies are a hallmark of disease.

Comparative analysis of gene expression in normal and degenerative human tendon cells: effects of cyclic strain.

BACKGROUND: Tendinopathy is a clinical problem for which treatment shows mixed results and treatment options are limited. Gene expression signatures early in the mechanotransduction pathway can accurately predict risk and correlate with different clinical outcomes. Studies aimed at elucidating the molecular mechanisms of tendinopathy have focused on small cohorts of genes that show an incomplete picture of the degeneration process. This study compared the effect of cyclic strain on gene expression in tendon cells from normal tendon and chronically painful areas of tendinopathy in 3 patients. METHODS: We measured a panel of mechanotransduction genes and cytoskeletal tensional balance with and without cyclic strain, which disrupts connective tissue synthetic-degradative equilibrium. Normal and degenerative tendons were obtained from patients undergoing surgery to treat chronic painful tendinopathy. A cyclic strain model was established to measure cytoskeletal tensional homeostasis. RESULTS: Prior to cyclic strain, the normal tendon cells exhibited varying patterns of elevated expression of 7 genes compared with degenerative tendon cells. In response to cyclic strain, gene expression of COL1A1, ITGA6, CTNNA1, and CLEC3B was up-regulated in normal tendon cells. Cyclic strain had no effect on degenerative tendon cells. Cyclic strain exacerbated the inhibition of protein synthesis in both cell types, especially in the degenerative tendon cells. CONCLUSION: Alterations in the pattern of gene expression are suggestive of a dynamic equilibrium between synthesis and degradation, whereby cell adhesion molecules are predominantly up-regulated to facilitate cellular reorientation in response to their altered functional environment. CLINICAL RELEVANCE: These data might have future applications, including the identification of markers for early diagnosis, targets for drug design, and indicators for treatment responsiveness and prognosis.

Interleukins 4 and 13 modulate gene expression and promote proliferation of primary human tenocytes.

BACKGROUND: Tendon disorders (tendinopathies) pose serious biomedical and socioeconomic problems. Despite diverse treatment approaches, the best treatment strategy remains unclear. Surgery remains the last resort because of the associated morbidity and inconsistent outcomes. We hypothesized that, similar to fibroblasts in various organs, tendon fibroblasts (tenocytes) might be responsive to stimulation with interleukins (ILs), particularly IL-4 and IL-13. These two cytokines share sequence homology, receptor chains and functional effects, including stimulation of fibrogenesis. It is unknown whether tenocytes are responsive to stimulation with IL-4 or IL-13. If true, local use of these cytokines might be used to facilitate tendon repair in patients with tendinopathies or used for tendon tissue-engineering approaches to facilitate tenocyte growth on scaffolds in culture. RESULTS: Tendon tissues that would normally be discarded were obtained during reconstructive surgery procedures performed for clinical indications. Primary tenocytes were derived from Achilles, posterior tibial, flexor digitorum longus and flexor hallucis longus tendon tissue samples. Reverse transcriptase quantitative PCR (RT-qPCR) experiments revealed that mRNAs for the receptor (R) chains IL-4Ralpha, IL-13Ralpha1 and IL-13Ralpha2, but not the common gamma-chain were present in all tested tendon tissues and in cultured tenocytes. Levels of IL-13R chain mRNAs were significantly higher than those of IL-4R mRNA. The cultures responded, in a dose-dependent fashion, to stimulation with recombinant human IL-4 or IL-13, by increasing proliferation rates 1.5 to 2.0-fold. The mRNA levels of 84 genes related to cell cycle regulation were measured by RT-qPCR after 6 h and 24 h of activation. The expression levels of several genes, notably CDK6 and CDKN2B changed more than twofold. In contrast to their effects on proliferation, stimulation with IL-4 or IL-13 had little if any effect on the levels of collagen mRNA or protein in cultured primary tenocytes. The mRNA levels of 84 other genes related to extracellular matrix and cell adhesion were also measured by RT-qPCR; expression of only five genes was consistently changed. CONCLUSIONS: Stimulation with IL-4 or IL-13 could be used to facilitate tendon repair in vivo or to aid in tendon tissue engineering, through stimulation of tenocyte proliferation.

Effect of bupivacaine on cultured tenocytes.

Proliferation of cultured human fibroblasts and other types of cells has been shown to be hindered by exposure to local anesthetics, which are widely used in musculoskeletal medicine for their use in regional anesthesia, selective nerve blocks, bursography, and brisement. We hypothesized that bupivacaine would decrease cell proliferation and production of extracellular matrix components collagen and proteoglycan in healthy human tenocytes in culture. Primary human tenocyte cultures were prepared from samples of normal tendons obtained from healthy tissue that would otherwise have been discarded during lower extremity tendon transfer surgery. Samples were obtained from 6 patients, 5 women and 1 man with an average age of 69 years (range, 17-73 years). Five flexor digitorum longus tendon samples and 1 peroneus longus tendon sample were used. Harvested tendon tissues (5 mm(3)) were used as explants for primary cell cultures. To measure the proliferative response to bupivacaine, seeded cells were exposed to saline control or to various concentrations of bupivacaine in 1% fetal bovine serum DMEM/F12 or 10% fetal bovine serum DMEM/F12. The 1% fetal bovine serum medium demonstrated the pure bupivacaine effect, and 10% fetal bovine serum more closely approximated the in vivo environment. Seeded cells were starved of fetal bovine serum for 12 hours before exposure to phosphate-buffered saline (control group) and 500 microM bupivacaine (experimental group). This concentration of bupivacaine was selected because it was found to significantly hinder proliferation in both the 1% and 10% fetal bovine serum groups in our proliferation assay. Tenocyte proliferation and extracellular matrix component production were significantly lower (Por=1 time points up to 6 days in bupivacaine-treated groups as compared with controls.