Sézary syndrome (SS) is an aggressive leukaemia of mature T cells with poor prognosis and limited options for targeted therapies. The comprehensive genetic alterations underlying the pathogenesis of ...SS are unknown. Here we integrate whole-genome sequencing (n=6), whole-exome sequencing (n=66) and array comparative genomic hybridization-based copy-number analysis (n=80) of primary SS samples. We identify previously unknown recurrent loss-of-function aberrations targeting members of the chromatin remodelling/histone modification and trithorax families, including ARID1A in which functional loss from nonsense and frameshift mutations and/or targeted deletions is observed in 40.3% of SS genomes. We also identify recurrent gain-of-function mutations targeting PLCG1 (9%) and JAK1, JAK3, STAT3 and STAT5B (JAK/STAT total ∼11%). Functional studies reveal sensitivity of JAK1-mutated primary SS cells to JAK inhibitor treatment. These results highlight the complex genomic landscape of SS and a role for inhibition of JAK/STAT pathways for the treatment of SS.
The immune system has evolved specialized cellular and molecular mechanisms for targeting and regulating immune responses at epithelial surfaces. Here we show that small intestinal intraepithelial ...lymphocytes and lamina propria lymphocytes migrate to thymus-expressed chemokine (TECK). This attraction is mediated by CC chemokine receptor (CCR)9, a chemoattractant receptor expressed at high levels by essentially all CD4(+) and CD8(+) T lymphocytes in the small intestine. Only a small subset of lymphocytes in the colon are CCR9(+), and lymphocytes from other tissues including tonsils, lung, inflamed liver, normal or inflamed skin, inflamed synovium and synovial fluid, breast milk, and seminal fluid are universally CCR9(-). TECK expression is also restricted to the small intestine: immunohistochemistry reveals that intense anti-TECK reactivity characterizes crypt epithelium in the jejunum and ileum, but not in other epithelia of the digestive tract (including stomach and colon), skin, lung, or salivary gland. These results imply a restricted role for lymphocyte CCR9 and its ligand TECK in the small intestine, and provide the first evidence for distinctive mechanisms of lymphocyte recruitment that may permit functional specialization of immune responses in different segments of the gastrointestinal tract. Selective expression of chemokines by differentiated epithelium may represent an important mechanism for targeting and specialization of immune responses.
CCR7, along with L-selectin and LFA-1, mediates homing of T cells to secondary lymphoid organs via high endothelial venules (HEV). CCR7 has also been implicated in microenvironmental positioning of ...lymphocytes within secondary lymphoid organs and in return of lymphocytes and dendritic cells to the lymph after passage through nonlymphoid tissues. We have generated mAbs to human CCR7, whose specificities correlate with functional migration of lymphocyte subsets to known CCR7 ligands. We find that CCR7 is expressed on the vast majority of peripheral blood T cells, including most cells that express adhesion molecules (cutaneous lymphocyte Ag alpha(4)beta(7) integrin) required for homing to nonlymphoid tissues. A subset of CD27(neg) memory CD4 T cells from human peripheral blood is greatly enriched in the CCR7(neg) population, as well as L-selectin(neg) cells, suggesting that these cells are incapable of homing to secondary lymphoid organs. Accordingly, CD27(neg) T cells are rare within tonsil, a representative secondary lymphoid organ. All resting T cells within secondary lymphoid organs express high levels of CCR7, but many activated cells lack CCR7. CCR7 loss in activated CD4 cells accompanies CXC chemokine receptor (CXCR)5 gain, suggesting that the reciprocal expression of these two receptors may contribute to differential positioning of resting vs activated cells within the organ. Lymphocytes isolated from nonlymphoid tissues (such as skin, lung, or intestine) contain many CD27(neg) cells lacking CCR7. The ratio of CD27(neg)/CCR7(neg) cells to CD27(pos)/CCR7(pos) cells varies from tissue to tissue, and may correlate with the number of cells actively engaged in Ag recognition within a given tissue.
The European Union (EU) Project Routes aimed to discover new routes in sludge stabilization treatments leading to high-quality digested sludge, suitable for land application. In order to investigate ...the impact of different enhanced sludge stabilization processes such as (a) thermophilic digestion integrated with thermal hydrolysis pretreatment (TT), (b) sonication before mesophilic/thermophilic digestion (UMT), and (c) sequential anaerobic/aerobic digestion (AA) on digested sludge quality, a broad class of conventional and emerging organic micropollutants as well as ecotoxicity was analyzed, extending the assessment beyond the parameters typically considered (i.e., stability index and heavy metals). The stability index was improved by adding aerobic posttreatment or by operating dual-stage process but not by pretreatment integration. Filterability was worsened by thermophilic digestion, either alone (TT) or coupled with mesophilic digestion (UMT). The concentrations of heavy metals, present in ranking order Zn > Cu > Pb > Cr ~ Ni > Cd > Hg, were always below the current legal requirements for use on land and were not removed during the processes. Removals of conventional and emerging organic pollutants were greatly enhanced by performing double-stage digestion (UMT and AA treatment) compared to a single-stage process as TT; the same trend was found as regards toxicity reduction. Overall, all the digested sludges exhibited toxicity to the soil bacterium Arthrobacter globiformis at concentrations about factor 100 higher than the usual application rate of sludge to soil in Europe. For earthworms, a safety margin of factor 30 was generally achieved for all the digested samples.
Abstract
Mucosae-associated epithelial chemokine (MEC) is a novel chemokine whose mRNA is most abundant in salivary gland, with strong expression in other mucosal sites, including colon, trachea, and ...mammary gland. MEC is constitutively expressed by epithelial cells; MEC mRNA is detected in cultured bronchial and mammary gland epithelial cell lines and in epithelia isolated from salivary gland and colon using laser capture microdissection, but not in the endothelial, hemolymphoid, or fibroblastic cell lines tested. Although MEC is poorly expressed in skin, its closest homologue is the keratinocyte-expressed cutaneous T cell-attracting chemokine (CTACK; CCL27), and MEC supports chemotaxis of transfected lymphoid cells expressing CCR10, a known CTACK receptor. In contrast to CTACK, however, MEC also supports migration through CCR3. Consistent with this, MEC attracts eosinophils in addition to memory lymphocyte subsets. These results suggest an important role for MEC in the physiology of extracutaneous epithelial tissues, including diverse mucosal organs.
Idiopathic pulmonary fibrosis (IPF)/usual interstitial pneumonia (UIP) is the severest form of idiopathic interstitial pneumonia for which therapeutic targets are needed. Surgical lung biopsy ...specimens from IPF/UIP patients exhibit focal expression of CC chemokine receptor (CCR) 7, but the identity of these CCR7-positive cells is unknown. The purpose of the present study was to examine the functional and signalling significance of CCR7 expression of primary fibroblasts grown from IPF/UIP and normal surgical lung biopsy specimens. Primary fibroblasts were cultured from surgical lung biopsy specimens from IPF/UIP and normal patients. Fibroblasts treated with or without CC chemokine ligand (CCL) 21 were analysed for functional, transcriptional and proteomic differences using immunocytochemical analysis, gene arrays, Taqman real-time PCR, and migration, proliferation and Western blot assays. CCR7 was expressed by IPF/UIP fibroblasts, but not normal fibroblasts. IPF/UIP fibroblasts, but not normal fibroblasts, showed significant migratory and proliferative responses when exposed to CCL21, which were inhibited by pertussis toxin or neutralising antibodies to CCR7. Exposure of IPF/UIP fibroblasts to CCL21 altered the phosphorylation status of mitogen-activated protein kinase kinase 1/2, extracellular signal-regulated kinase 1/2 and ribosomal S6 kinase (90 kDa) in these cells; this was abrogated by pertussis toxin or CCR7-specific small interfering RNA. Together, these data demonstrate that CC chemokine ligand 21 modulates the functional properties of idiopathic pulmonary fibrosis/usual interstitial pneumonia fibroblasts, but not normal fibroblasts.
Abstract
The detection and attribution of changes in precipitation characteristics relies on dense networks of rain gauges. In the United States, the COOP network is widely used for such studies even ...though there are reported inconsistencies due to changes in instruments and location, inadequate maintenance, dissimilar observation time, and the fact that measurements are made by a group of dedicated volunteers. Alternately, the Long-Term Agroecosystem Research (LTAR) network has been consistently and professionally measuring precipitation since the early 1930s. The purpose of this study is to compare changes in extreme daily precipitation characteristics during the warm season using paired rain gauges from the LTAR and COOP networks. The comparison, done at 12 LTAR sites located across the United States, shows underestimation and overestimation of daily precipitation totals at the COOP sites compared to the reference LTAR observations. However, the magnitude and direction of the differences are not linked to the underlying precipitation climatology of the sites. Precipitation indices that focus on extreme precipitation characteristics match closely between the two networks at most of the sites. Our results show consistency between the COOP and LTAR networks with precipitation extremes. It also indicates that despite the discrepancies at the daily time steps, the extreme precipitation observed by COOP rain gauges can be reliably used to characterize changes in the hydrologic cycle due to natural and human causes.
Severe forms of idiopathic interstitial pneumonia (IIP), such as usual interstitial pneumonia, can be impervious to modern steroid and immunosuppressive treatment regimens, thereby emphasizing the ...need for novel effective therapies. Consequently, research attention has been directed toward understanding the cytokine networks that may affect fibroblast activation and, hence, the progression of certain IIPs. This led us to investigate whether the specific targeting of resident lung cells responsive to IL-4 and IL-13 exerted a therapeutic effect in an experimental model of IIP, namely the bleomycin-induced model of pulmonary fibrosis. IL-4, IL-13, and their corresponding receptor subunits, IL-4Ralpha, IL-13Ralpha1, and IL-13Ralpha2, were maximally expressed at the mRNA and protein levels in whole lung samples on day 21 or 28 after an intratracheal bleomycin challenge. The intranasal administration of an IL-13 immunotoxin chimeric molecule (IL13-PE) from days 21-28, but not for 1-wk periods at earlier times, after bleomycin challenge had a significant therapeutic effect on histological and biochemical parameters of bleomycin-induced pulmonary fibrosis compared with the control group. The intranasal IL13-PE therapy significantly reduced the numbers of IL-4 and IL-13 receptor-positive mononuclear cells and macrophages and the levels of profibrotic cytokine and chemokine in the lungs of bleomycin-challenged mice on day 28. Thus, this study demonstrates that IL-4- and/or IL-13-binding cells are required for the maintenance of pulmonary fibrosis induced by bleomycin and highlights the importance of further investigation of antifibrotic therapeutics that target these cells during pulmonary fibrosis.
In situ measurements of ice crystal size distributions in tropical upper troposphere/lower stratosphere (UT/LS) clouds were performed during the SCOUT-AMMA campaign over West Africa in August 2006. ...The cloud properties were measured with a Forward Scattering Spectrometer Probe (FSSP-100) and a Cloud Imaging Probe (CIP) operated aboard the Russian high altitude research aircraft M-55 Geophysica with the mission base in Ouagadougou, Burkina Faso. A total of 117 ice particle size distributions were obtained from the measurements in the vicinity of Mesoscale Convective Systems (MCS). Two to four modal lognormal size distributions were fitted to the average size distributions for different potential temperature bins. The measurements showed proportionately more large ice particles compared to former measurements above maritime regions. With the help of trace gas measurements of NO, NOy, CO2, CO, and O3 and satellite images, clouds in young and aged MCS outflow were identified. These events were observed at altitudes of 11.0 km to 14.2 km corresponding to potential temperature levels of 346 K to 356 K. In a young outflow from a developing MCS ice crystal number concentrations of up to (8.3 ± 1.6) cm−3 and rimed ice particles with maximum dimensions exceeding 1.5 mm were found. A maximum ice water content of 0.05 g m−3 was observed and an effective radius of about 90 μm. In contrast the aged outflow events were more diluted and showed a maximum number concentration of 0.03 cm−3, an ice water content of 2.3 × 10−4 g m−3, an effective radius of about 18 μm, while the largest particles had a maximum dimension of 61 μm. Close to the tropopause subvisual cirrus were encountered four times at altitudes of 15 km to 16.4 km. The mean ice particle number concentration of these encounters was 0.01 cm−3 with maximum particle sizes of 130 μm, and the mean ice water content was about 1.4 × 10−4 g m−3. All known in situ measurements of subvisual tropopause cirrus are compared and an exponential fit on the size distributions is established for modelling purposes. A comparison of aerosol to ice crystal number concentrations, in order to obtain an estimate on how many ice particles may result from activation of the present aerosol, yielded low ratios for the subvisual cirrus cases of roughly one cloud particle per 30 000 aerosol particles, while for the MCS outflow cases this resulted in a high ratio of one cloud particle per 300 aerosol particles.
Processes occurring in the tropical upper troposphere (UT), the Tropical Transition Layer (TTL), and the lower stratosphere (LS) are of importance for the global climate, for stratospheric dynamics ...and air chemistry, and for their influence on the global distribution of water vapour, trace gases and aerosols. In this contribution we present aerosol and trace gas (in-situ) measurements from the tropical UT/LS over Southern Brazil, Northern Australia, and West Africa. The instruments were operated on board of the Russian high altitude research aircraft M-55 "Geophysica" and the DLR Falcon-20 during the campaigns TROCCINOX (Araçatuba, Brazil, February 2005), SCOUT-O3 (Darwin, Australia, December 2005), and SCOUT-AMMA (Ouagadougou, Burkina Faso, August 2006). The data cover submicron particle number densities and volatility from the COndensation PArticle counting System (COPAS), as well as relevant trace gases like N2O, ozone, and CO. We use these trace gas measurements to place the aerosol data into a broader atmospheric context. Also a juxtaposition of the submicron particle data with previous measurements over Costa Rica and other tropical locations between 1999 and 2007 (NASA DC-8 and NASA WB-57F) is provided. The submicron particle number densities, as a function of altitude, were found to be remarkably constant in the tropical UT/LS altitude band for the two decades after 1987. Thus, a parameterisation suitable for models can be extracted from these measurements. Compared to the average levels in the period between 1987 and 2007 a slight increase of particle abundances was found for 2005/2006 at altitudes with potential temperatures, Θ, above 430 K. The origins of this increase are unknown except for increases measured during SCOUT-AMMA. Here the eruption of the Soufrière Hills volcano in the Caribbean caused elevated particle mixing ratios. The vertical profiles from Northern hemispheric mid-latitudes between 1999 and 2006 also are compact enough to derive a parameterisation. The tropical profiles all show a broad maximum of particle mixing ratios (between Θ≈340 K and 390 K) which extends from below the TTL to above the thermal tropopause. Thus these particles are a "reservoir" for vertical transport into the stratosphere. The ratio of non-volatile particle number density to total particle number density was also measured by COPAS. The vertical profiles of this ratio have a maximum of 50% above 370 K over Australia and West Africa and a pronounced minimum directly below. Without detailed chemical composition measurements a reason for the increase of non-volatile particle fractions cannot yet be given. However, half of the particles from the tropical "reservoir" contain compounds other than sulphuric acid and water. Correlations of the measured aerosol mixing ratios with N2O and ozone exhibit compact relationships for the tropical data from SCOUT-AMMA, TROCCINOX, and SCOUT-O3. Correlations with CO are more scattered probably because of the connection to different pollution source regions. We provide additional data from the long distance transfer flights to the campaign sites in Brazil, Australia, and West-Africa. These were executed during a time window of 17 months within a period of relative volcanic quiescence. Thus the data represent a "snapshot picture" documenting the status of a significant part of the global UT/LS fine aerosol at low concentration levels 15 years after the last major (i.e., the 1991 Mount Pinatubo) eruption. The corresponding latitudinal distributions of the measured particle number densities are presented in this paper to provide data of the UT/LS background aerosol for modelling purposes.
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