Evidence of novel Treponema phylotypes implicated in contagious ovine digital dermatitis and association of treponemes with major lameness causing foot pathogens.

In this study 269 swabs collected from 254 ovine foot lesions and 15 apparently healthy ovine feet were screened by PCR for the presence of major lameness causing foot pathogens viz. Treponema species, D. nodosus, F. necrophorum and T. pyogenes with the presumption that ovine foot lesion positive for Treponema species alone or in association with other three pathogens were categorized as contagious ovine digital dermatitis (CODD). While samples positive for D. nodosus alone or its combination with F. necrophorum and T. pyogenes were considered as footrot (FR) and samples in which F. necrophorum or T. pyogenes was found either alone or in combination were considered as interdigital dermatitis (ID). The overall occurrence of Treponema sp. in ovine foot lesions was 48.0%, and ranged from 33 to 58%. In Treponema positive samples D. nodosus, F. necrophorum and T. pyogenes were present in 34 (27.4%), 66 (54.4%) and 84 (68.5%) in contrast to Treponema negative samples in which these were present in 15 (11.1%), 20 (14.12%) and 17 (12.6%) samples, respectively. The data signifies that Treponema sp. are significantly associated with these foot pathogens and their different combinations with Treponema sp. influence the severity of CODD lesion. The identification of Treponema phylotypes was done by sequencing the 16S rRNA gene fragment of ten representative samples. Out of ten sequences, four (Trep-2, Trep-4, Trep-7 and Trep-10) were identical to Treponema sp. phylotype 1 (PT1) that belongs to phylogroup T. refringens-like, one sequence (Trep-1) was genetically close (90% sequence homology) to Treponema brennaborense while five sequences (Trep-3, Trep-5, Trep-6, Trep-8 and Trep-9) matched with uncultured bacterium clones of treponemes forming separate monophyletic group in phylogenetic tree and could represent new digital dermatitis phylogroup presently containing five ovine specific phylotypes. This is the first report on the presence of Treponema phylotypes other than three digital dermatitis (DD) Treponema phylogroups viz. T. phagedenis-like, T. medium/T. vincentii-like, and T. pedis-like that are frequently detected in CODD lesions. Metagenomic analysis of two representative samples revealed the abundance of genus Treponema in CODD lesion while this genus was absent in swab collected from clinically healthy foot suggesting that it might play primary role in producing CODD. These findings may further aid in understanding the etiopathogenesis of CODD and could help to develop appropriate treatment and mitigation strategies to combat the disease.

Transcription and methylation analyses of preleukemic promyelocytes indicate a dual role for PML/RARA in leukemia initiation.

Acute promyelocytic leukemia is an aggressive malignancy characterized by the accumulation of promyelocytes in the bone marrow. PML/RARA is the primary abnormality implicated in this pathology, but the mechanisms by which this chimeric fusion protein initiates disease are incompletely understood. Identifying PML/RARA targets in vivo is critical for comprehending the road to pathogenesis. Utilizing a novel sorting strategy, we isolated highly purified promyelocyte populations from normal and young preleukemic animals, carried out microarray and methylation profiling analyses, and compared the results from the two groups of animals. Surprisingly, in the absence of secondary lesions, PML/RARA had an overall limited impact on both the transcriptome and methylome. Of interest, we did identify down-regulation of secondary and tertiary granule genes as the first step engaging the myeloid maturation block. Although initially not sufficient to arrest terminal granulopoiesis in vivo, such alterations set the stage for the later, complete differentiation block seen in leukemia. Further, gene set enrichment analysis revealed that PML/RARA promyelocytes exhibit a subtle increase in expression of cell cycle genes, and we show that this leads to both increased proliferation of these cells and expansion of the promyelocyte compartment. Importantly, this proliferation signature was absent from the poorly leukemogenic p50/RARA fusion model, implying a critical role for PML in the altered cell-cycle kinetics and ability to initiate leukemia. Thus, our findings challenge the predominant model in the field and we propose that PML/RARA initiates leukemia by subtly shifting cell fate decisions within the promyelocyte compartment.

Gene expression profile identifies tyrosine kinase c-Met as a targetable mediator of antiangiogenic therapy resistance.

PURPOSE: To identify mediators of glioblastoma antiangiogenic therapy resistance and target these mediators in xenografts. EXPERIMENTAL DESIGN: We conducted microarray analysis comparing bevacizumab-resistant glioblastomas (BRG) with pretreatment tumors from the same patients. We established novel xenograft models of antiangiogenic therapy resistance to target candidate resistance mediator(s). RESULTS: BRG microarray analysis revealed upregulation versus pretreatment of receptor tyrosine kinase c-Met, which underwent further investigation because of its prior biologic plausibility as a bevacizumab resistance mediator. BRGs exhibited increased hypoxia versus pretreatment in a manner correlating with their c-Met upregulation, increased c-Met phosphorylation, and increased phosphorylation of c-Met-activated focal adhesion kinase and STAT3. We developed 2 novel xenograft models of antiangiogenic therapy resistance. In the first model, serial bevacizumab treatment of an initially responsive xenograft generated a xenograft with acquired bevacizumab resistance, which exhibited upregulated c-Met expression versus pretreatment. In the second model, a BRG-derived xenograft maintained refractoriness to the MRI tumor vasculature alterations and survival-promoting effects of bevacizumab. Growth of this BRG-derived xenograft was inhibited by a c-Met inhibitor. Transducing these xenograft cells with c-Met short hairpin RNA inhibited their invasion and survival in hypoxia, disrupted their mesenchymal morphology, and converted them from bevacizumab-resistant to bevacizumab-responsive. Engineering bevacizumab-responsive cells to express constitutively active c-Met caused these cells to form bevacizumab-resistant xenografts. CONCLUSION: These findings support the role of c-Met in survival in hypoxia and invasion, features associated with antiangiogenic therapy resistance, and growth and therapeutic resistance of xenografts resistant to antiangiogenic therapy. Therapeutically targeting c-Met could prevent or overcome antiangiogenic therapy resistance.

Microarray analysis verifies two distinct phenotypes of glioblastomas resistant to antiangiogenic therapy.

PURPOSE: To identify mechanisms and mediators of resistance to antiangiogenic therapy in human glioblastoma. EXPERIMENTAL DESIGN: We carried out microarray gene expression analysis and immunohistochemistry comparing 21 recurrent glioblastomas progressing during antiangiogenic treatment with VEGF neutralizing antibody bevacizumab to paired pretreatment tumors from the same patients. RESULTS: Microarray analysis revealed that bevacizumab-resistant glioblastomas (BRG) had two clustering patterns defining subtypes that reflect radiographic growth patterns. Enhancing BRGs (EBRG) exhibited MRI enhancement, a long-established criterion for glioblastoma progression, and expressed mitogen-activated protein kinases, neural cell adhesion molecule-1 (NCAM-1), and aquaporin 4. Compared with their paired pretreatment tumors, EBRGs had unchanged vascularity and hypoxia, with increased proliferation. Nonenhancing BRGs (NBRG) exhibited minimal MRI enhancement but had FLAIR-bright expansion, a newer criterion for glioblastoma recurrence since the advent of antiangiogenic therapy, and expressed integrin α5, laminin, fibronectin1, and PDGFRß. NBRGs had less vascularity, more hypoxia, and unchanged proliferation than their paired pretreatment tumors. Primary NBRG cells exhibited more stellate morphology with a 3-fold increased shape factor and were nearly 4-fold more invasive in Matrigel chambers than primary cells from EBRGs or bevacizumab-naive glioblastomas (P < 0.05). CONCLUSION: Using microarray analysis, we found two resistance patterns during antiangiogenic therapy with distinct molecular profiles and radiographic growth patterns. These studies provide valuable biologic insight into the resistance that has limited antiangiogenic therapy to date.

Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer.

PURPOSE: Although liver resection is the primary curative therapy for patients with colorectal hepatic metastases, most patients have a recurrence. Identification of molecular markers that predict patients at highest risk for recurrence may help to target further therapy. EXPERIMENTAL DESIGN: Array-based comparative genomic hybridization was used to investigate the association of DNA copy number alterations with outcome in patients with colorectal liver metastasis resected with curative intent. DNA from 50 liver metastases was labeled and hybridized onto an array consisting of 2,463 bacterial artificial chromosome clones covering the entire genome. The total fraction of genome altered (FGA) in the metastases and the patient's clinical risk score (CRS) were calculated to identify independent prognostic factors for survival. RESULTS: An average of 30 +/- 14% of the genome was altered in the liver metastases (14% gained and 16% lost). As expected, a lower CRS was an independent predictor of overall survival (P = 0.03). In addition, a high FGA also was an independent predictor of survival (P = 0.01). The median survival time in patients with a low CRS (score 0-2) and a high (> or =20%) FGA was 38 months compared with 18 months in patients with a low CRS and a low FGA. Supervised analyses, using Prediction Analysis of Microarrays and Significance Analysis of Microarrays, identified a set of clones, predominantly located on chromosomes 7 and 20, which best predicted survival. CONCLUSIONS: Both FGA and CRS are independent predictors of survival in patients with resected hepatic colorectal cancer metastases. The greater the FGA, the more likely the patient is to survive.

Fully automatic quantification of microarray image data.

DNA microarrays are now widely used to measure expression levels and DNA copy number in biological samples. Ratios of relative abundance of nucleic acids are derived from images of regular arrays of spots containing target genetic material to which fluorescently labeled samples are hybridized. Whereas there are a number of methods in use for the quantification of images, many of the software systems in wide use either encourage or require extensive human interaction at the level of individual spots on arrays. We present a fully automatic system for microarray image quantification. The system automatically locates both subarray grids and individual spots, requiring no user identification of any image coordinates. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. We present a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying the pixels in each spot, the system yields more accurate estimates of ratios than systems assuming spot circularity. The software, called, runs on Windows platforms and is available free of charge for academic use.

Stimulation of anti-influenza cytolytic T lymphocytes by a synthetic peptide of the influenza hemagglutinin can be modulated by at least three independent helper factors.

Secondary murine anti-influenza cytolytic T lymphocytes (CTL) could be induced in vitro by the chemically synthesized peptide HA1(181-204), corresponding to amino acids 181-204 of the hemagglutinin molecule of influenza strain A/Japan/305/57. This stimulation required the addition of exogenous helper factors, termed CHFP, which could be obtained from supernatant fluids of the WEHI-3 cell line or spleen cells stimulated by either concanavalin A or Sendai virus. Because the activities from these three sources could reflect different molecules, they were referred to as CHFPW, CHFPC, and CHFPS, respectively. When CHFPS was fractionated by using reverse-phase high performance liquid chromatography (HPLC), the CHFP activity was found to elute at two hydrophobicities. The more hydrophilic factor(s) was designated CHFPS1, while the more hydrophobic factor(s) was called CHFPS2. Similarly, CHFPW could be separated into more hydrophilic (CHFPW1) and more hydrophobic (CHFPW2) molecules. In contrast, CHFPC molecules eluted at only one hydrophobicity (CHFPC1). Based on HPLC characteristics, CHFPS1, CHFPW1, and CHFPC1 all could reflect the same molecule. That molecule could be interleukin 3 (IL 3), because IL 3, purified to homogeneity, was also found to function in the CHFP assay. In contrast, CHFPW2 and CHFPS2 had different hydrophobicities. Therefore, a possibility exists that there are a minimum number of three factors functional in the CHFP assay: IL 3, CHFPW2, and CHFPS2. Based on HPLC separations, CHFPS2 represents a molecule distinct from biochemically characterized cytokines implicated previously in the generation of CTL:CHF, CSF, interferon, and interleukins 1, 2, and 3. The killer cells stimulated are both virus-specific and H-2-restricted as is characteristic of CTL.

Cytolytic T lymphocyte and antibody responses to synthetic peptides of influenza virus hemagglutinin.

Two peptides corresponding to HA1(181-204) and HA2(103-123) of the A/Japan/305/57 influenza virus hemagglutinin (HA) were chemically synthesized by solid-phase methods and were tested for their ability to generate murine secondary anti-influenza cytolytic T lymphocytes (CTL) in vitro and to bind monoclonal anti-HA antibodies. Peptide HA1(181-204) could only generate CTL in the presence of helper factors contained in supernatant fluids from either Concanavalin A-stimulated mouse spleen cultures or WEHI-3 cells grown in vitro. Peptide HA2(103-123) stimulated the induction of anti-influenza CTL independent of helper factors, but the stimulation was also greatly increased if helper factors were added. A 10-fold molar excess of peptide HA2(103-123) was required to obtain optimal CTL activation over the quantities required in the HA1(181-204) system. This molar ratio remained unchanged, even in the presence of helper factors. Induction of influenza-specific CTL was antigen-dependent in both systems, even though some killing of noninfected target cells was also occasionally observed. Our results suggest that synthetic peptides can be recognized as antigenic determinants in the generation of H-2-restricted anti-viral CTL capable of killing appropriately infected target cells. The inability of peptide HA1(181-204) to generate sufficient help for CTL development suggests that certain regions of the HA can be recognized by CTL precursors, but not by all of the required helper cells. Peptide HA1(181-204) also reacted with three monoclonal anti-HA antibodies as well as mouse anti-influenza (A/Japan/305/57) immune sera. This antibody reactivity suggests the possibility of a shared antigenic epitope or region between T and B cells, and therefore provides new insight in our understanding of viral antigenicity.

A helper factor needed for the generation of mouse cytolytic T lymphocytes is made by tumor cell lines, cloned T cells, and spleen cells exposed to a variety of stimuli.

A helper factor termed cytolytic T lymphocyte helper factor (CHF) that is needed for the generation of allospecific mouse cytolytic T lymphocytes (CTL) in vitro was produced by mouse spleen cells 3 to 4 days after the time when interleukin 2 (IL 2) had reached its maximal production. These kinetics were observed by stimulation of immune spleen cells with allogeneic tumor or spleen cells, with Sendai or influenza viral peptides, with virus infected cells, or with concanavalin A (Con A). CHF produced by rat spleen cells was able to help in the generation of mouse CTL, indicating that this cytokine was not restricted genetically. CHF could also be made by WEHI-3 and EL4 cell lines, as well as cloned cytolytic and helper T cells. The production of CHF by WEHI-3 cells argues that CHF is not IL 2. In addition, if CHF was not present early in the in vitro stimulation no CTL were generated, suggesting that CHF participated in the activation of CTL precursors. The addition of IL 2-containing conditioned medium to the CHF assay resulted in no substantial CTL generation, although significant cellular proliferation was observed. In contrast, CHF-containing conditioned medium allowed the generation of CTL in the absence of the same level of proliferation.

Chromatographic separation from known cytokines of a helper factor necessary for the generation of murine cytolytic T lymphocytes.

A helper factor (CHF) necessary for the generation of primary allospecific CTL using BALB/c (H-2d) responder spleen cell and x-irradiated RDM4 (H-2k) stimulator tumor cells was obtained from cultures of mouse spleen cells stimulated for the production of secondary anti-Sendai virus CTL and fractionated by gel filtration chromatography to obtain a 30,000 m.w. species (CHF30). DEAE-cellulose chromatography separated CHF activity from the majority of interleukin 1 (IL 1), interleukin 2 (IL 2), granulocyte-macrophage colony-stimulating factor (CSF), and interferon (IFN). Interleukin 3 (IL 3) and CHF co-eluted when this procedure was used. Reverse-phase high performance liquid chromatography (HPLC) of CHF30 with a variety of elution conditions allowed the separation of CHF activity from IL 1, IL 2, IL 3, CSF, and IFN. IL 3 and CSF in the CHF30 preparation were stable at 80 degrees C for more than an hour, whereas CHF activity decreased rapidly during the first 10 min of incubation. Trypsin treatment of the same material showed that CHF activity was resistant to digestion for 40 min, whereas IL 3 and CSF lost most of their activities during the first 5 min of incubation. These results indicate that CHF activity is mediated by molecules biologically and biochemically distinct from the well characterized cytokines.