Mutant PIK3CA is a targetable driver alteration in histiocytic neoplasms

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm characterized by the accumulation of clonal mononuclear phagocyte system cells expressing CD1a and CD207. In the past decade, molecular profiling of LCH as well as other histiocytic neoplasms demonstrated that these diseases are driven by MAPK activating alterations, with somatic BRAFV600E mutations in >50% of patients with LCH, and clinical inhibition of MAPK signaling has demonstrated remarkable clinical efficacy. At the same time, activating alterations in kinase-encoding genes, such as PIK3CA, ALK, RET, and CSF1R, which can activate mitogenic pathways independent from the MAPK pathway, have been reported in a subset of histiocytic neoplasms with anecdotal evidence of successful targeted treatment of histiocytoses harboring driver alterations in RET, ALK, and CSF1R. However, evidence supporting the biological consequences of expression of PIK3CA mutations in hematopoietic cells has been lacking, and whether targeted inhibition of PI3K is clinically efficacious in histiocytic neoplasms is unknown. Here, we provide evidence that activating mutations in PIK3CA can drive histiocytic neoplasms in vivo using a conditional knockin mouse expressing mutant PIK3CAH1047R in monocyte/dendritic cell progenitors. In parallel, we demonstrate successful treatment of PIK3CA-mutated, multisystemic LCH using alpelisib, an inhibitor of the alpha catalytic subunit of PI3K. Alpelisib demonstrated a tolerable safety profile at a dose of 750 mg per week and clinical and metabolic complete remission in a patient with PIK3CA-mutated LCH. These data demonstrate PIK3CA as a targetable noncanonical driver of LCH and underscore the importance of mutational analysis-based personalized treatment in histiocytic neoplasms.

Replication-attenuated r3LCMV vectors potentiate tumor control via IFN-I

Viral vectors are being used for the treatment of cancer. Yet their efficacy varies among tumors and their use poses challenges in immunosuppressed patients, underscoring the need for alternatives. We report striking antitumoral effects by a nonlytic viral vector based on attenuated lymphocytic choriomeningitis virus (r3LCMV). We show in multiple tumor models that injection of tumor-bearing mice with this novel vector results in improved tumor control and survival. Importantly, r3LCMV also improved tumor control in immunodeficient Rag1-/- mice. Single cell RNA-Seq analyses, antibody blockade experiments, and KO models revealed a critical role for host IFN-I in the antitumoral efficacy of r3LCMV vectors. Collectively, these data demonstrate potent antitumoral effects by a replication-attenuated LCMV vector and unveil mechanisms underlying its antitumoral efficacy.

Improved control of SARS-CoV-2 by treatment with a nucleocapsid-specific monoclonal antibody

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein is the main antigen in all approved COVID-19 vaccines and is also the only target for monoclonal antibody (mAb) therapies. Immune responses to other viral antigens are generated after SARS-CoV-2 infection, but their contribution to the antiviral response remains unclear. Here, we interrogated whether nucleocapsid-specific antibodies can improve protection against SARS-CoV-2. We first immunized mice with a nucleocapsid-based vaccine and then transferred sera from these mice into naive mice, followed by challenge with SARS-CoV-2. We show that mice that received nucleocapsid-specific sera or a nucleocapsid-specific mAb exhibited enhanced control of SARS-CoV-2. Nucleocapsid-specific antibodies elicited NK-mediated, antibody-dependent cellular cytotoxicity (ADCC) against infected cells. To our knowledge, these findings provide the first demonstration in the coronavirus literature that antibody responses specific to the nucleocapsid protein can improve viral clearance, providing a rationale for the clinical evaluation of nucleocapsid-based mAb therapies to treat COVID-19.

Adoptive B cell therapy for chronic viral infection

T cell-based therapies have been widely explored for the treatment of cancer and chronic infection, but B cell-based therapies have remained largely unexplored. To study the effect of B cell therapy, we adoptively transferred virus-specific B cells into mice that were chronically infected with lymphocytic choriomeningitis virus (LCMV). Adoptive transfer of virus-specific B cells resulted in increase in antibody titers and reduction of viral loads. Importantly, the efficacy of B cell therapy was partly dependent on antibody effector functions, and was improved by co-transferring virus-specific CD4 T cells. These findings provide a proof-of-concept that adoptive B cell therapy can be effective for the treatment of chronic infections, but provision of virus-specific CD4 T cells may be critical for optimal virus neutralization.

Interrogating Adaptive Immunity Using LCMV

In this invited article, we explain technical aspects of the lymphocytic choriomeningitis virus (LCMV) system, providing an update of a prior contribution by Matthias von Herrath and J. Lindsay Whitton. We provide an explanation of the LCMV infection models, highlighting the importance of selecting an appropriate route and viral strain. We also describe how to quantify virus-specific immune responses, followed by an explanation of useful transgenic systems. Specifically, our article will focus on the following protocols. © 2020 Wiley Periodicals LLC. Basic Protocol 1: LCMV infection routes in mice Support Protocol 1: Preparation of LCMV stocks ASSAYS TO MEASURE LCMV TITERS Support Protocol 2: Plaque assay Support Protocol 3: Immunofluorescence focus assay (IFA) to measure LCMV titer MEASUREMENT OF T CELL AND B CELL RESPONSES TO LCMV INFECTION Basic Protocol 2: Triple tetramer staining for detection of LCMV-specific CD8 T cells Basic Protocol 3: Intracellular cytokine staining (ICS) for detection of LCMV-specific T cells Basic Protocol 4: Enumeration of direct ex vivo LCMV-specific antibody-secreting cells (ASC) Basic Protocol 5: Limiting dilution assay (LDA) for detection of LCMV-specific memory B cells Basic Protocol 6: ELISA for quantification of LCMV-specific IgG antibody Support Protocol 4: Preparation of splenic lymphocytes Support Protocol 5: Making BHK21-LCMV lysate Basic Protocol 7: Challenge models TRANSGENIC MODELS Basic Protocol 8: Transfer of P14 cells to interrogate the role of IFN-I on CD8 T cell responses Basic Protocol 9: Comparing the expansion of naïve versus memory CD4 T cells following chronic viral challenge.

Adoptive B cell therapy improves viral control during a chronic viral infection

T cell-based therapies have been explored for the treatment of cancer and chronic infection. However, B cell-based therapies have remained largely understudied. To evaluate the antiviral effect of adoptive B cell therapy, we adoptively transferred virus-specific B cells into mice that were chronically infected with lymphocytic choriomeningitis virus (LCMV). This resulted in a significant increase in antibody titers and reduction of viral loads. Interestingly, blockade of the IFN-I pathway using IFNAR1 blocking antibodies abrogated the antiviral effect of adoptive B cell therapy, suggesting that IFN-I signaling is necessary to control infection after adoptive B cell therapy. These findings provide a proof-of-concept that adoptive B cell therapy can be effective for the treatment of chronic infections.

Blockade of IFN-I improves adaptive immune responses and immune coverage after vaccination

IFN-I is a main innate antiviral defense critical for the activation of adaptive immunity. However, we hypothesized that acute viral clearance by IFN-I could limit antigen availability following initial antigen encounter, which could in turn, reduce the priming of the adaptive immune system. To test this hypothesis, we immunized mice with different vaccines or acute viruses together with a low dose of an IFN-I receptor-blocking antibody to induce a short-term abrogation of IFN-I signaling. This resulted in transient increase in antigen levels followed by antigen clearance. Importantly, short-term IFN-I blockade during coronavirus, flavivirus, rhabdovirus, or arenavirus immunization resulted in a potent improvement of adaptive immune responses, which conferred improved protection following future re-infections. Short-term IFN-I modulation also improved immune coverage elicited by viral vaccines or acute viral infections. In particular, administration of an HIV-1 vaccine together with the IFN-I blocker generated highly cross-reactive antibody responses against other HIV-1 clades; and similarly, immunization with a mouse coronavirus (MHV) together with the IFN-I blocker generated more cross-reactive antibody responses against other related coronaviruses, including SARS CoV-2. These data demonstrate a novel mechanism by which innate immunity modulates the magnitude and breadth of adaptive immune responses, providing insights for rational vaccine design.

Early type I IFN blockade improves the efficacy of viral vaccines

Type I interferons (IFN-I) are a major antiviral defense and are critical for the activation of the adaptive immune system. However, early viral clearance by IFN-I could limit antigen availability, which could in turn impinge upon the priming of the adaptive immune system. In this study, we hypothesized that transient IFN-I blockade could increase antigen presentation after acute viral infection. To test this hypothesis, we infected mice with viruses coadministered with a single dose of IFN-I receptor–blocking antibody to induce a short-term blockade of the IFN-I pathway. This resulted in a transient “spike” in antigen levels, followed by rapid antigen clearance. Interestingly, short-term IFN-I blockade after coronavirus, flavivirus, rhabdovirus, or arenavirus infection induced a long-lasting enhancement of immunological memory that conferred improved protection upon subsequent reinfections. Short-term IFN-I blockade also improved the efficacy of viral vaccines. These findings demonstrate a novel mechanism by which IFN-I regulate immunological memory and provide insights for rational vaccine design.

Muscarinic acetylcholine receptor regulates self-renewal of early erythroid progenitors

Adult stem and progenitor cells are uniquely capable of self-renewal, and targeting this process represents a potential therapeutic opportunity. The early erythroid progenitor, burst-forming unit erythroid (BFU-E), has substantial self-renewal potential and serves as a key cell type for the treatment of anemias. However, our understanding of mechanisms underlying BFU-E self-renewal is extremely limited. Here, we found that the muscarinic acetylcholine receptor, cholinergic receptor, muscarinic 4 (CHRM4), pathway regulates BFU-E self-renewal and that pharmacological inhibition of CHRM4 corrects anemias of myelodysplastic syndrome (MDS), aging, and hemolysis. Genetic down-regulation of CHRM4 or pharmacologic inhibition of CHRM4 using the selective antagonist PD102807 promoted BFU-E self-renewal, whereas deletion of Chrm4 increased erythroid cell production under stress conditions in vivo. Moreover, muscarinic acetylcholine receptor antagonists corrected anemias in mouse models of MDS, aging, and hemolysis in vivo, extending the survival of mice with MDS relative to that of controls. The effects of muscarinic receptor antagonism on promoting expansion of BFU-Es were mediated by cyclic AMP induction of the transcription factor CREB, whose targets up-regulated key regulators of BFU-E self-renewal. On the basis of these data, we propose a model of hematopoietic progenitor self-renewal through a cholinergic-mediated "hematopoietic reflex" and identify muscarinic acetylcholine receptor antagonists as potential therapies for anemias associated with MDS, aging, and hemolysis.

Early IFN-I limits virus-specific immunity

Type I interferons (IFN-I) play a major role in the innate immune response. These cytokines are induced within hours of infection, conferring rapid protection before the onset of adaptive immunity. IFN-I are also critical for the priming of adaptive immune responses, but it is not clear if early antiviral restriction by IFN-I can also limit the amount of antigen available to prime the adaptive immune system. Here we demonstrate that reinforcement of IFN-I signaling early after viral immunization limits the priming of adaptive immunity, whereas blocking IFN-I signaling improves adaptive immunity and enhances subsequent host protection following viral re-infection. Paradoxically, short-term blockade of IFN-I improved the efficacy of clinically approved vaccines, such as the yellow fever virus vaccine (YFV-17D) and the smallpox virus vaccine, as well as experimental HIV vaccines in mice. Short-term blockade of IFN-I also improved immune responses following acute viral infections, such as those with Zika virus, lymphocytic choriomeningitis virus (LCMV), and vesicular stomatitis virus (VSV). This unexpected adjuvant effect of blocking early IFN-I responses was associated with a hyperacute increase in antigen availability, which could not be recapitulated by increasing the dose of the virus inoculum. The improvement of virus-specific immunity following acute IFN-I blockade was mechanistically due to an increase in antigen presentation and costimulation. These findings warrant a re-evaluation of the immunoregulatory roles of IFN-I during immune memory differentiation, which may provide a framework for rational vaccine design.

Viral vaccines improve PD-1 therapy against cancer

Programmed cell death-1 (PD-1) therapy is effective against various types of cancer. However, only 30% of cancers respond to PD-1 therapy, highlighting the need to further improve its efficacy. In this study, we interrogated whether one could exploit the immunostimulatory properties of viral vaccines to enhance PD-1 therapy in a B16 melanoma model that is poorly responsive to PD-1 therapy. Immunization of tumor-bearing mice with clinically approved viral vaccines, such as the smallpox virus vaccine and the yellow fever virus vaccine (YFV-17D), resulted in an unprecedented improvement of PD-1 therapy. This synergistic effect on PD-1 therapy was more potent upon a secondary immunization, suggesting a positive effect of recruiting pre-existent immune memory to the tumor microenvironment. Interestingly, co-administration of viral vaccines together with PD-1 therapy did not increase tumor-specific CD8 T cell responses relative to PD-1 therapy alone. Mechanistically, the adjuvant effect of viral vaccines on PD-1 therapy seems to be dependent on innate immune responses. These findings may be important for improving the efficacy of checkpoint-based immunotherapies by exploiting the immunogenicity of viral vaccines. Altogether, our data suggest that viral vaccines could be repurposed as immunotherapy adjuvants, and that the beneficial effects of viral vaccines on PD-1 therapy can be further improved by repetitive boosting of bystander immunity.

R21 AI132848-01A1 (NIAID); IRG-15-173-21 (ACS), and the Lurie Cancer Center.

TLR4 signaling improves PD-1 blockade therapy during chronic viral infection

CD8 T cells are necessary for the elimination of intracellular pathogens, but during chronic viral infections, CD8 T cells become exhausted and unable to control the persistent infection. Programmed cell death-1 (PD-1) blockade therapies have been shown to improve CD8 T cell responses during chronic viral infections. These therapies have been licensed to treat cancers in humans, but they have not yet been licensed to treat chronic viral infections because limited benefit is seen in pre-clinical animal models of chronic infection. In the present study, we investigated whether TLR4 triggering could improve PD-1 therapy during a chronic viral infection. Using the model of chronic lymphocytic choriomeningitis virus (LCMV) infection in mice, we show that TLR4 triggering with sublethal doses of lipopolysaccharide (LPS) followed by PD-1 blockade results in superior improvement in circulating virus-specific CD8 T cell responses, relative to PD-1 blockade alone. Moreover, we show that the synergy between LPS and PD-1 blockade is dependent on B7 costimulation and mediated by a dendritic cell (DC) intrinsic mechanism. Systemic LPS administration may have safety concerns, motivating us to devise a safer regimen. We show that ex vivo activation of DCs with LPS, followed by adoptive DC transfer, results in a similar potentiation of PD-1 therapy without inducing wasting disease. In summary, our data demonstrate a previously unidentified role for LPS/TLR4 signaling in modulating the host response to PD-1 therapy. These findings may be important for developing novel checkpoint therapies against chronic viral infection.

Although PD-1 therapies have revolutionized cancer treatment, these therapies have not yet been licensed to treat chronic viral infections. This is because limited benefit is seen in pre-clinical models of chronic viral infection. Interestingly, recent reports in cancer models have suggested that certain microbes can affect the efficacy of PD-1 therapies, but the specific microbial products that modulate host responses to therapy remain unknown. We utilized a model of chronic viral infection to evaluate if bacterial lipopolysaccharide (LPS), a major constituent of the microbiome, influences the efficacy of PD-1 therapy. Interestingly, we demonstrate that TLR4 triggering with low doses of LPS combined with PD-1 blockade induced a synergistic rescue of exhausted virus-specific CD8 T cell responses. Moreover, we demonstrate that adoptive transfer of LPS-activated DCs also results in similar improvement of PD-1 therapy without inducing overt immunopathology. Mechanistically, the synergy was DC-intrinsic, IFN-I independent, and B7/CD28 dependent. Taken together, our data may be important for understanding how components of the microbiome modulate the efficacy of PD-1 therapy, and may result in novel combined regimens for treating chronic viral infections.

The Dietary Supplement Chondroitin-4-Sulfate Exhibits Oncogene-Specific Pro-tumor Effects on BRAF V600E Melanoma Cells

Dietary supplements such as vitamins and minerals are widely used in the hope of improving health but may have unidentified risks and side effects. In particular, a pathogenic link between dietary supplements and specific oncogenes remains unknown. Here we report that chondroitin-4-sulfate (CHSA), a natural glycosaminoglycan approved as a dietary supplement used for osteoarthritis, selectively promotes the tumor growth potential of BRAF V600E-expressing human melanoma cells in patient- and cell line-derived xenograft mice and confers resistance to BRAF inhibitors. Mechanistically, chondroitin sulfate glucuronyltransferase (CSGlcA-T) signals through its product CHSA to enhance casein kinase 2 (CK2)-PTEN binding and consequent phosphorylation and inhibition of PTEN, which requires CHSA chains and is essential to sustain AKT activation in BRAF V600E-expressing melanoma cells. However, this CHSA-dependent PTEN inhibition is dispensable in cancer cells expressing mutant NRAS or PI3KCA, which directly activate the PI3K-AKT pathway. These results suggest that dietary supplements may exhibit oncogene-dependent pro-tumor effects.

Oncogenic TRK fusions are amenable to inhibition in hematologic malignancies

Rearrangements involving the neurotrophic receptor kinase genes (NTRK1, NTRK2, and NTRK3; hereafter referred to as TRK) produce oncogenic fusions in a wide variety of cancers in adults and children. Although TRK fusions occur in fewer than 1% of all solid tumors, inhibition of TRK results in profound therapeutic responses, resulting in Breakthrough Therapy FDA approval of the TRK inhibitor larotrectinib for adult and pediatric patients with solid tumors, regardless of histology. In contrast to solid tumors, the frequency of TRK fusions and the clinical effects of targeting TRK in hematologic malignancies are unknown. Here, through an evaluation for TRK fusions across more than 7,000 patients with hematologic malignancies, we identified TRK fusions in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), histiocytosis, multiple myeloma, and dendritic cell neoplasms. Although TRK fusions occurred in only 0.1% of patients (8 of 7,311 patients), they conferred responsiveness to TRK inhibition in vitro and in vivo in a patient-derived xenograft and a corresponding AML patient with ETV6-NTRK2 fusion. These data identify that despite their individual rarity, collectively, TRK fusions are present in a wide variety of hematologic malignancies and predict clinically significant therapeutic responses to TRK inhibition.

Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations

Mutations affecting RNA splicing factors are the most common genetic alterations in myelodysplastic syndrome (MDS) patients and occur in a mutually exclusive manner. The basis for the mutual exclusivity of these mutations and how they contribute to MDS is not well understood. Here we report that although different spliceosome gene mutations impart distinct effects on splicing, they are negatively selected for when co-expressed due to aberrant splicing and downregulation of regulators of hematopoietic stem cell survival and quiescence. In addition to this synthetic lethal interaction, mutations in the splicing factors SF3B1 and SRSF2 share convergent effects on aberrant splicing of mRNAs that promote nuclear factor κB signaling. These data identify shared consequences of splicing-factor mutations and the basis for their mutual exclusivity.

Abstract 5500: KMT2C directs estrogen receptor activity in normal and transformed mammary cells

Estrogen receptor alpha (ERα) is a ligand-activated nuclear receptor that regulates proliferation and differentiation in mammary epithelial cells. ERα activity is likely dependent on the actions of pioneer factors and H3K4 methyltransferases which can establish a genomic landscape permissive for ERα binding. Here, we identify the H3K4 methyltransferase KMT2C as essential for ERα activity in mammary gland development and ER+ breast cancer growth. KMT2C suppression decreases estrogen-dependent gene expression and causes H3K4me1 loss at ERα target gene enhancers. Consequently, KMT2C loss selectively suppresses estrogen-driven breast cancer proliferation. Moreover, mammary-specific Kmt2c knockout mice have defects in pubertal ductal formation similar to Esr1 deficient mice. Although KMT2C loss disrupts estrogen-driven proliferation, it conversely promotes tumor outgrowth under hormone-depleted conditions. Consistent with this, gene expression signatures of KMT2C loss are associated with poor outcomes. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples mammary phenotypes from hormone availability.

Citation Format: Kinisha Gala, Amit Sinha, Francisco Sanchez-Vega, Young Rock Chung, James Hseih, Michael Berger, Nikolaus Schultz, Alessandro Pastore, Omar Abdel-Wahab, Sarat Chandarlapaty. KMT2C directs estrogen receptor activity in normal and transformed mammary cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5500. doi:10.1158/1538-7445.AM2017-5500

Prevention of Dietary-Fat-Fueled Ketogenesis Attenuates BRAF V600E Tumor Growth

Lifestyle factors, including diet, play an important role in the survival of cancer patients. However, the molecular mechanisms underlying pathogenic links between diet and particular oncogenic mutations in human cancers remain unclear. We recently reported that the ketone body acetoacetate selectively enhances BRAF V600E mutant-dependent MEK1 activation in human cancers. Here we show that a high-fat ketogenic diet increased serum levels of acetoacetate, leading to enhanced tumor growth potential of BRAF V600E-expressing human melanoma cells in xenograft mice. Treatment with hypolipidemic agents to lower circulating acetoacetate levels or an inhibitory homolog of acetoacetate, dehydroacetic acid, to antagonize acetoacetate-BRAF V600E binding attenuated BRAF V600E tumor growth. These findings reveal a signaling basis underlying a pathogenic role of dietary fat in BRAF V600E-expressing melanoma, providing insights into the design of conceptualized "precision diets" that may prevent or delay tumor progression based on an individual's specific oncogenic mutation profile.

Targeting Mutant BRAF in Relapsed or Refractory Hairy-Cell Leukemia

BACKGROUND

BRAF V600E is the genetic lesion underlying hairy-cell leukemia. We assessed the safety and activity of the oral BRAF inhibitor vemurafenib in patients with hairy-cell leukemia that had relapsed after treatment with a purine analogue or who had disease that was refractory to purine analogues.

METHODS

We conducted two phase 2, single-group, multicenter studies of vemurafenib (at a dose of 960 mg twice daily)--one in Italy and one in the United States. The therapy was administered for a median of 16 weeks in the Italian study and 18 weeks in the U.S. study. Primary end points were the complete response rate (in the Italian trial) and the overall response rate (in the U.S. trial). Enrollment was completed (28 patients) in the Italian trial in April 2013 and is still open (26 of 36 planned patients) in the U.S. trial.

RESULTS

The overall response rates were 96% (25 of 26 patients who could be evaluated) after a median of 8 weeks in the Italian study and 100% (24 of 24) after a median of 12 weeks in the U.S. study. The rates of complete response were 35% (9 of 26 patients) and 42% (10 of 24) in the two trials, respectively. In the Italian trial, after a median follow-up of 23 months, the median relapse-free survival was 19 months among patients with a complete response and 6 months among those with a partial response; the median treatment-free survival was 25 months and 18 months, respectively. In the U.S. trial, at 1 year, the progression-free survival rate was 73% and the overall survival rate was 91%. Drug-related adverse events were usually of grade 1 or 2, and the events most frequently leading to dose reductions were rash and arthralgia or arthritis. Secondary cutaneous tumors (treated with simple excision) developed in 7 of 50 patients. The frequent persistence of phosphorylated ERK-positive leukemic cells in bone marrow at the end of treatment suggests bypass reactivation of MEK and ERK as a resistance mechanism.

CONCLUSIONS

A short oral course of vemurafenib was highly effective in patients with relapsed or refractory hairy-cell leukemia. (Funded by the Associazione Italiana per la Ricerca sul Cancro and others; EudraCT number, 2011-005487-13; ClinicalTrials.gov number NCT01711632.).

Abstract IA36: SRSF2 mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference

Spliceosomal mutations account for the most frequent class of mutations in patients with myelodysplastic syndromes, yet the mechanism by which these mutations perform their driver function is not well understood. Given the genetic heterogeneity of primary patient samples, we generated a model for conditional expression of the commonly occurring SRSF2P95H mutation from the endogenous murine locus of Srsf2 and compared expression of the Srsf2P95H mutation with genetic inactivation of 0, 1 or 2 copies of Srsf2.

Mx1-cre Srsf2P95H/wildtype mice exhibited significant morphologic dysplasia, leukopenia, macrocytic anemia, and preserved bone marrow (BM) cellularity as early as 2 weeks after mutation expression. Moreover, Mx1-cre Srsf2P95H/wildtype mice exhibited an increase in hematopoietic stem/progenitor cells (HSPCs) with an increase in lineage-negative Sca1+ c-Kit+ cells (LSK cells) in S-phase and early apoptosis. In competitive transplantation, Srsf2P95H mice HPSCs were expanded in the BM at 16 weeks post-transplantation despite having a reduced contribution to peripheral blood chimerism. In contrast, mice with homozygous deletion of Srsf2 exhibited anemia and leukopenia due to BM aplasia with striking loss of HSPCs. Collectively, these data show that Srsf2 is required for hematopoiesis, while mutations in Srsf2 provide a competitive advantage at the level of HSPCs but impair differentiation into mature circulating blood elements.

Next, to identify transcriptional alterations caused by SRSF2 mutations, we performed deep RNA-seq on sorted HSPC populations from wildtype and Srsf2P95H mice, stable K562 cell lines ectopically expressing an empty vector or a single allele of SRSF2 (WT, P95H, P95L, P95R), as well as primary CMML and AML patient samples. We quantified global changes in splicing of ~125,000 alternative splicing events and ~160,000 constitutive splice junctions associated with SRSF2 mutations in these datasets. Intersection of differentially spliced genes in primary murine HSPC, CMML, and AML samples identified 75 genes that were differentially spliced in association with SRSF2 mutations in murine HSPCs and at least one primary patient cohort. Many of the genes that were differentially spliced in SRSF2 mutant cells participate in biological processes of known importance in myeloid malignancies. For example, a cassette exon of EZH2 that alters the reading frame inducing nonsense-mediated decay was promoted by SRSF2 mutations. We next sought to determine how SRSF2 mutations alter SRSF2's normal role in RNA splicing. As SRSF2 recognizes exonic splicing enhancer (ESE) elements within the pre-mRNA to promote exon recognition, we hypothesized that SRSF2 mutations might alter its normal sequence-specific activity. To test this, we performed an ab initio motif identification screen to identify motifs that were enriched or depleted in cassette exons promoted versus repressed in primary Srsf2P95H cells relative to wildtype. This analysis identified CCAG and GGTG as the most enriched and depleted consensus motifs, respectively. A recent solution structure of SRSF2 in complex with RNA revealed that SRSF2 normally recognizes the motifs CCNG and GGNG equally well. Analysis of the spatial distribution of CCNG and GGNG motifs across genomic loci containing cassette exons that were promoted or repressed in association with SRSF2 mutations revealed that CCNG and GGNG were respectively enriched and depleted specifically over the cassette exons, that were differentially spliced in association with SRSF2 mutations. Together, our data indicate that mutant SRSF2 drives widespread changes in splicing due to alterations in its sequence-specific recognition of exonic splicing enhancers.

The biological as well as molecular data here identify an effect of the SRSF2P95H mutation distinct from haploinsufficient or complete loss of SRSF2 and reveal that mutations in SRSF2 alter ESE preference to contribute to key aspects of MDS.

Citation Format: Eunhee Kim, Janine O. Ilagan, Stanley Lee, Aravind Ramakrishnan, Young Rock Chung, Jean-Baptiste Micol, Michele E. Murphy, Min-Kyung Kim, Ahmad S. Zebari, Silvia Buonamici, Peter Smith, H. Joachim Deeg, Camille Lobry, Iannis Aifantis, Robert K. Bradley, Omar Abdel-Wahab. SRSF2 mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr IA36.

SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition

Mutations affecting spliceosomal proteins are the most common mutations in patients with myelodysplastic syndromes (MDS), but their role in MDS pathogenesis has not been delineated. Here we report that mutations affecting the splicing factor SRSF2 directly impair hematopoietic differentiation in vivo, which is not due to SRSF2 loss of function. By contrast, SRSF2 mutations alter SRSF2's normal sequence-specific RNA binding activity, thereby altering the recognition of specific exonic splicing enhancer motifs to drive recurrent mis-splicing of key hematopoietic regulators. This includes SRSF2 mutation-dependent splicing of EZH2, which triggers nonsense-mediated decay, which, in turn, results in impaired hematopoietic differentiation. These data provide a mechanistic link between a mutant spliceosomal protein, alterations in the splicing of key regulators, and impaired hematopoiesis.

Hematopoietic stem cell origin of BRAFV600E mutations in hairy cell leukemia

Hairy cell leukemia (HCL) is a chronic lymphoproliferative disorder characterized by somatic BRAFV600E mutations. The malignant cell in HCL has immunophenotypic features of a mature B cell, but no normal counterpart along the continuum of developing B lymphocytes has been delineated as the cell of origin. We find that the BRAFV600E mutation is present in hematopoietic stem cells (HSCs) in HCL patients, and that these patients exhibit marked alterations in hematopoietic stem/progenitor cell (HSPC) frequencies. Quantitative sequencing analysis revealed a mean BRAFV600E-mutant allele frequency of 4.97% in HSCs from HCL patients. Moreover, transplantation of BRAFV600E-mutant HSCs from an HCL patient into immunodeficient mice resulted in stable engraftment of BRAFV600E-mutant human hematopoietic cells, revealing the functional self-renewal capacity of HCL HSCs. Consistent with the human genetic data, expression of BRafV600E in murine HSPCs resulted in a lethal hematopoietic disorder characterized by splenomegaly, anemia, thrombocytopenia, increased circulating soluble CD25, and increased clonogenic capacity of B lineage cells-all classic features of human HCL. In contrast, restricting expression of BRafV600E to the mature B cell compartment did not result in disease. Treatment of HCL patients with vemurafenib, an inhibitor of mutated BRAF, resulted in normalization of HSPC frequencies and increased myeloid and erythroid output from HSPCs. These findings link the pathogenesis of HCL to somatic mutations that arise in HSPCs and further suggest that chronic lymphoid malignancies may be initiated by aberrant HSCs.

Cytomorphological characteristics of low-grade papillary urothelial carcinoma for differential diagnosis from benign papillary urothelial lesions: logistic regression analysis in SurePath(™) liquid-based voided urine cytology

OBJECTIVE

The diagnosis of low-grade papillary urothelial carcinoma (LGPUC) in urine cytology specimens is challenging because of its subtle, minimally atypical findings. Furthermore, as SurePath(™) liquid-based cytology (LBC) is becoming a widely used method in urine cytology, the inevitable cytomorphological alterations resulting from this technique call for new morphological diagnostic criteria in LGPUC.

METHODS

Logistic regression analysis was carried out on SurePath slides from surgically proven voided urine specimens. The study was designed to include a test set (n = 141) and a validation set (n = 61), and evaluated significant discriminative parameters between LGPUC and benign papillary urothelial neoplasm (BPUN).

RESULTS

Of the seven cytological findings that were found to have statistical significance in univariate analysis, five were found to be independent variables: loss of polarity of papillaroid clusters, irregular contours, absence of columnar cells, hobnail features and hyperchromasia. These independent variables had an area under the curve (AUC) of 0.781.

CONCLUSIONS

The distinctive cytological criteria identified above may prove to be helpful in cases in which other conventional criteria for LGPUC are insufficient for diagnosis.

Prospective blinded study of BRAFV600E mutation detection in cell-free DNA of patients with systemic histiocytic disorders

Patients with Langerhans cell histiocytosis (LCH) and Erdheim-Chester disease (ECD) have a high frequency of BRAF(V600E) mutations and respond to RAF inhibitors. However, detection of mutations in tissue biopsies is particularly challenging in histiocytoses due to low tumor content and stromal contamination. We applied a droplet-digital PCR assay for quantitative detection of the BRAF(V600E) mutation in plasma and urine cell-free (cf) DNA and performed a prospective, blinded study in 30 patients with ECD/LCH. There was 100% concordance between tissue and urinary cfDNA genotype in treatment-naïve samples. cfDNA analysis facilitated identification of previously undescribed KRAS(G12S)-mutant ECD and dynamically tracked disease burden in patients treated with a variety of therapies. These results indicate that cfDNA BRAF(V600E) mutational analysis in plasma and urine provides a convenient and reliable method of detecting mutational status and can serve as a noninvasive biomarker to monitor response to therapy in LCH and ECD.

SIGNIFICANCE

Patients with BRAF(V600E)-mutant histiocytic disorders have remarkable responses to RAF inhibition, but mutation detection in tissue in these disorders is challenging. Here, we identify that analysis of plasma and urinary cfDNA provides a reliable method to detect the BRAF(V600E) mutation and monitor response to therapy in these disorders.

Abstract 3140: Context specific effects of the BRAFV600E mutation on hematopoiesis identifies novel models of BRAF mutant hematopoietic disorders

BRAFV600E mutations have recently been identified in nearly 100% of patients with the chronic lymphoproliferative disorder hairy cell leukemia (HCL), as well as a small percentage of patients with the plasma cell malignancy multiple myeloma. Despite extensive knowledge regarding the functional effects of BRAFV600E expression in epithelial tissues, very little is understood about the role of the BRAFV600E mutation in hematopoietic transformation. We therefore utilized a conditional BRafV600E murine model crossed with Mx1-cre, Vav-cre, Cd19-cre, and Cγ1-cre transgenic mice to delineate the effects of mutant BRaf expression in pre-natal and post-natal hematopoietic stem and progenitor cells (HSPCs), B-lineage cells, and germinal center B cells respectively. We also investigated the origin of the BRAFV600E mutation in HCL patient bone marrow samples using prospective isolation of sorted HSPC populations followed by quantitative sequencing for the BRAFV600E mutation.

Surprisingly, we identified the presence of the BRAFV600E mutation in long-term hematopoietic stem cells of HCL patients, and we also observed marked alterations in HSPC frequencies. Consistent with the human genetic data, expression of BRafV600E in HSPCs of mice resulted in a lethal transplantable hematopoietic disorder characterized by splenomegaly, anemia, thrombocytopenia, increased circulating soluble CD25, and increased clonogenic capacity of B-lineage cells- all classic features of human HCL. In contrast, restricting expression of BRafV600E to B-lineage cells did not result in disease even up to 1.5 years of age.

We next assessed the effects of the BRafV600E mutation on HSPC self-renewal and lineage specification. We plated whole BM cells from Mx1-cre BRafV600E mice in methylcellulose containing myeloid/erythroid cytokines or lymphopoietic cytokes (IL-7). BRafV600E cells demonstrated impaired colony formation in myeloid/erythroid conditions. However, BRafV600E HSPCs exhibited limitless replating capacity when plated in the presence of IL-7, indicating that the BRAF mutation induces aberrant B lineage cell self-renewal. A clear competitive advantage was also seen with competitive transplantation of BRafV600E BM cells, identifying an increase in HSPC self-renewal associated with the BRAF mutation.

Data from the murine models studied here and characterization of the BM compartment in HCL patients suggest that the cytopenias seen in HCL patients are due in part to HSPC-intrinsic effects of the BRAFV600E mutation on erythropoiesis, megakarypoiesis, and myelopoiesis. Moreover, these data suggest that the use of therapies targeting MAP-kinase signaling in HCL may lead to durable remissions not only through effects on mature leukemic cells, but also through targeted inhibition of signaling and survival in mutant HSPCs.

Citation Format: Eunhee Kim, Stephen S. Chung, Jae H. Park, Young Rock Chung, Piro Lito, Julie Feldstein, Wenhuo Hu, Wendy Beguilin, Sebastien Monette, Cihangir Duy, Raajit Rampal, Leon Telis, Minal Patel, Min Kyung Kim, Ari M. Melnick, Neal Rosen, Martin S. Tallman, Christopher Y. Park, Omar Abdel-Wahab. Context specific effects of the BRAFV600E mutation on hematopoiesis identifies novel models of BRAF mutant hematopoietic disorders. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3140. doi:10.1158/1538-7445.AM2014-3140

Femoral bone marrow aspiration in live mice

Serial sampling of the cellular composition of bone marrow (BM) is a routine procedure critical to clinical hematology. This protocol describes a detailed step-by-step technical procedure for an analogous procedure in live mice which allows for serial characterization of cells present in the BM. This procedure facilitates studies aimed to detect the presence of exogenously administered cells within the BM of mice as would be done in xenograft studies for instance. Moreover, this procedure allows for the retrieval and characterization of cells enriched in the BM such as hematopoietic stem and progenitor cells (HSPCs) without sacrifice of mice. Given that the cellular composition of peripheral blood is not necessarily reflective of proportions and types of stem and progenitor cells present in the marrow, procedures which provide access to this compartment without requiring termination of the mice are very helpful. The use of femoral bone marrow aspiration is illustrated here for cytological analysis of marrow cells, flow cytometric characterization of the hematopoietic stem/progenitor compartment, and culture of sorted HSPCs obtained by femoral BM aspiration compared with conventional marrow harvest.

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo

Loss of Asxl1 results in myelodysplastic syndrome, whereas concomitant deletion of Tet2 restores HSC self-renewal and triggers a more severe disease phenotype distinct from that seen in single-gene knockout mice.

Somatic Addition of Sex Combs Like 1 (ASXL1) mutations occur in 10–30% of patients with myeloid malignancies, most commonly in myelodysplastic syndromes (MDSs), and are associated with adverse outcome. Germline ASXL1 mutations occur in patients with Bohring-Opitz syndrome. Here, we show that constitutive loss of Asxl1 results in developmental abnormalities, including anophthalmia, microcephaly, cleft palates, and mandibular malformations. In contrast, hematopoietic-specific deletion of Asxl1 results in progressive, multilineage cytopenias and dysplasia in the context of increased numbers of hematopoietic stem/progenitor cells, characteristic features of human MDS. Serial transplantation of Asxl1-null hematopoietic cells results in a lethal myeloid disorder at a shorter latency than primary Asxl1 knockout (KO) mice. Asxl1 deletion reduces hematopoietic stem cell self-renewal, which is restored by concomitant deletion of Tet2, a gene commonly co-mutated with ASXL1 in MDS patients. Moreover, compound Asxl1/Tet2 deletion results in an MDS phenotype with hastened death compared with single-gene KO mice. Asxl1 loss results in a global reduction of H3K27 trimethylation and dysregulated expression of known regulators of hematopoiesis. RNA-Seq/ChIP-Seq analyses of Asxl1 in hematopoietic cells identify a subset of differentially expressed genes as direct targets of Asxl1. These findings underscore the importance of Asxl1 in Polycomb group function, development, and hematopoiesis.

Abstract A09: Coordinate regulation of chromatin state by JAK2 and ASXL1 mutations in myeloid malignancies

Myeloproliferative neoplasms (MPNs) are clonal myeloid malignancies which are initiated by somatic mutations in hematopoietic stem and progenitor cells. Of the classic MPNs, the disease myelofibrosis (MF) is characterized by the shortest median survival as well as progressive anemia, splenomegaly, and constitutional symptoms. Somatic JAK2V617F mutations are observed in approximately 60% of MF patients; however, murine studies have shown that JAK2V617F mutations are not sufficient to induce MF in the absence of additional mutations. Notably, the most common mutations that co-occur with JAK2V617F in MF are in the polycomb gene Additional Sex Combs Like-1 (ASXL1). Importantly, ASXL1 mutations are the strongest predictor of poor overall survival in MF. Given the role of ASXL1 mutations in MF pathogenesis and outcome, we hypothesized that loss of ASXL1 and JAK2V617F would collaborate to modulate epigenetic regulation and facilitate hematopoietic disease transformation. Previous studies have shown that JAK2V617F can translocate to the nucleus and phosphorylate histone H3 on tyrosine 41 (H3Y41), allowing for regulation of specific target genes including JAK2 itself. We used RNA interference to knock down ASXL1 in two JAK2V617F-mutant leukemic cell lines, SET2 and UKE1, which revealed that global and locus-specific H3Y41 phosphorylation levels increased after ASXL1 silencing leading to increased expression of JAK2/H3Y41 target genes. To evaluate whether H3Y41 levels were changed in vivo as well, we crossed a Jak2V617F knock-in mouse to our Asxl1 hematopoietic conditional knockout allele. Heterozygous expression of Jak2V617F and heterozygous deletion of Asxl1 driven by Vav-Cre hastened myeloid expansion and decreased overall survival in primary mice consistent with in vivo cooperativity between Jak2V617F and Asxl1. Multiparameter flow cytometric staining revealed that Vav+ Jak2V617F/+ Asxl1f/+ mice have an expansion of immature erythrocytes in their bone marrow as compared to Vav+ Jak2V617F/+ mice, suggestive of impaired hematopoietic differentiation, which was more severe in Vav+ Jak2V617 VF/+ Asxl1 f/f mice. We then used the Mx1-Cre transgene to induce Jak2V617F and delete Asxl1 in the adult hematopoietic compartment. Mx1-Cre+ Jak2V617F/+ Asxl1f/f mice developed severe, progressive anemia, erythroid precursor expansion in the peripheral blood, bone marrow and spleen, and increased disease burden in primary mice and serially transplanted mice. Importantly, mice expressing Jak2V617F/+ and concomitant Asxl1 loss/haploinsufficency have increased Jak2 protein expression, and increased elevated expression of H3Y41 target genes consistent with coordinate dysregulation of chromatin state by JAK2V617F and ASXL1 loss. These findings suggest ASXL1 loss contributes to myeloid transformation in part through modulation of H3Y41 phosphorylation levels, leading to amplified JAK2 expression, increased JAK-STAT signaling, and disease progression.

Citation Format: Lindsay M. LaFave, Young Rock Chung, Matt Keller, Maria Kleppe, Ann Mullally, Omar Abdel-Wahab, Ross L. Levine. Coordinate regulation of chromatin state by JAK2 and ASXL1 mutations in myeloid malignancies. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A09.

EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation

The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B cells and targeted by somatic mutations in B cell lymphomas. Here, we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B cell differentiation. Somatic mutations reinforce these physiological effects through enhanced silencing of EZH2 targets. Conditional expression of mutant EZH2 in mice induces GC hyperplasia and accelerated lymphomagenesis in cooperation with BCL2. GC B cell (GCB)-type diffuse large B cell lymphomas (DLBCLs) are mostly addicted to EZH2 but not the more differentiated activated B cell (ABC)-type DLBCLs, thus clarifying the therapeutic scope of EZH2 targeting.

Progression of RAS-mutant leukemia during RAF inhibitor treatment

Vemurafenib, a selective RAF inhibitor, extends survival among patients with BRAF V600E-mutant melanoma. Vemurafenib inhibits ERK signaling in BRAF V600E-mutant cells but activates ERK signaling in BRAF wild-type cells. This paradoxical activation of ERK signaling is the mechanistic basis for the development of RAS-mutant squamous-cell skin cancers in patients treated with RAF inhibitors. We report the accelerated growth of a previously unsuspected RAS-mutant leukemia in a patient with melanoma who was receiving vemurafenib. Exposure to vemurafenib induced hyperactivation of ERK signaling and proliferation of the leukemic cell population, an effect that was reversed on drug withdrawal.

Epigenetic alterations in hematopoietic malignancies

Gene discovery efforts in patients with hematopoietic malignancies have brought to the forefront a series of mutations in genes thought to be involved in the epigenetic regulation of gene transcription. These mutations occur in genes known, or suspected, to play a role in modifying cytosine nucleotides on DNA and/or altering the state of histone modifications. Genes such as ASXL1, DNMT3A, EZH2, IDH1/2, MLL1, and TET2 all have been shown to be mutated and/or translocated in patients with myeloid malignancies. Intriguingly, many of the alterations affecting DNA cytosine modifications in myeloid malignancies (mutations in DNMT3A, IDH1/2, and TET2) have also been found in patients with T-cell lymphomas, and EZH2 mutations appear to be critical in T-cell acute lymphoblastic leukemia development as well. In addition, the discovery of frequent mutations in CREBBP, EP300, EZH2, and MLL2 in B-cell lymphomas suggests that epigenetic alterations play a critical role in lymphomagenesis. The purpose of this review is to present functional evidence of how alterations in these epigenetic modifiers promote hematopoietic transformation. The conclusions drawn from these data are valuable in understanding biological mechanisms and potential therapeutic targets.

ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression

Recurrent somatic ASXL1 mutations occur in patients with myelodysplastic syndrome, myeloproliferative neoplasms, and acute myeloid leukemia, and are associated with adverse outcome. Despite the genetic and clinical data implicating ASXL1 mutations in myeloid malignancies, the mechanisms of transformation by ASXL1 mutations are not understood. Here, we identify that ASXL1 mutations result in loss of polycomb repressive complex 2 (PRC2)-mediated histone H3 lysine 27 (H3K27) tri-methylation. Through integration of microarray data with genome-wide histone modification ChIP-Seq data, we identify targets of ASXL1 repression, including the posterior HOXA cluster that is known to contribute to myeloid transformation. We demonstrate that ASXL1 associates with the PRC2, and that loss of ASXL1 in vivo collaborates with NRASG12D to promote myeloid leukemogenesis.

Cloning of a Family 11 Xylanase Gene from Bacillus amyloliquefaciens CH51 Isolated from Cheonggukjang

Bacillus amyloliquefaciens CH51, an isolate from cheonggukjang, Korean fermented soyfood, secretes several enzymes into culture medium. A gene encoding 19 kDa xylanase was cloned by PCR. Sequencing showed that the gene encoded a glycohydrolase family 11 xylanase and named xynA. xynAHis, xynA with additional codons for his-tag, was overexpressed in Escherichia coli BL21(DE3) using pET-26b(+). XynAHis was purified using HisTrap affinity column. Km and Vmax of XynAHis were 0.363 mg/ml and 701.1 μmol/min/mg, respectively with birchwood xylan as a substrate. The optimum pH and temperature were pH 4 and 25 °C, respectively. When xynA was introduced into Bacillus subtilis WB600, active XynA was secreted into culture medium.

Expression of exo-polygalacturonases in Botrytis cinerea

The pathogenic fungus, Botrytis cinerea, causing gray mold disease in a variety of plant species, secretes at least four polygalacturonases (PGs), cell wall degrading enzymes. Among them, we prepared polyclonal antibody against purified 66-kDa exo-PG in rabbit. Immunoblot analysis revealed that the antibody recognized two exo-PGs, 66 kDa and 70 kDa in molecular mass, secreted from B. cinerea cultured in the medium containing citrus pectin as a carbon source. By immunohistochemical analysis, the expression of exo-PGs was identified in cucumber leaves inoculated with spores of B. cinerea. The exo-PGs were observed 9 h after inoculation, and the amount of exo-PGs increased with time in the leaves. The exo-PGs were induced by polygalacturonic acid as well as its monomer, galacturonic acid, in vitro. The expression of 66-kDa exo-PG (exo-PG I) increased with time of culture, while 70-kDa exo-PG (exo-PG II) was transiently expressed soon after the start of culture. Therefore, exo-PGs might play an important role in pathogenesis at an early stage of infection as well as in tissue maceration of host plant.

Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound

A bacterial strain, YC300T, that produces an iturin-like antifungal antibiotic was isolated from compost and identified as member of the genus Paenibacillus. Gram reaction of the strain was variable depending upon growth stages and culture media. Three different types of colonies were developed on tryptic soy agar. The organism was facultatively anaerobic and grew at 50 degrees C. The DNA G+C content was 54 mol % and anteiso-C15:0 was the major fatty acid. A 0.9 kb fragment was produced by PCR amplification of strain YC300T DNA using primers PAEN515F and 1377R. Levels of 16S rDNA similarity between strain YC300T and other Paenibacillus species were between 89.8 and 94.8%. Phylogenetically, strain YC300T formed a significant monophyletic clade with Paenibacillus validus. It is clear from polyphasic evidence that the isolate should be classified as Paenibacillus koreensis sp. nov., the type strain of which is YC300T (= KCTC 2393T, KCCM 40903T).

Kitasatospora cheerisanensis sp. nov., a new species of the genus Kitasatospora that produces an antifungal agent

An actinomycete, strain YC75T, which produced bafilomycin-like antifungal compounds, was identified as a member of the genus Kitasatospora on the basis of morphological and chemotaxonomic characteristics. The strain produced the aerial and fragmenting vegetative mycelia consisting of straight chains of 20 or more smooth-surfaced spores. Submerged spores were formed in tryptic soy broth. No soluble pigments were formed. Whole-cell hydrolysates contained glucose and mannose, but not galactose. The 16S rDNA sequence of YC75T was compared with those of the other representative kitasatosporae and streptomycetes. Strain YC75T formed a significant monophyletic clade with Kitasatospora phosalacinea. The levels of DNA relatedness between strain YC75T and representatives of the genus Kitasatospora ranged from 16 to 59% including K. phosalacinea (28 and 40%). It is clear from polyphasic evidence that the isolate should be classified as Kitasatospora cheerisanensis sp. nov., whose type strain is YC75T (= KCTC 2395T). The presence of galactose in whole-cell hydrolysates may not be a stable chemical marker for the genus Kitasatospora.

Biological control of fusarium wilt of cucumber by chitinolytic bacteria

ABSTRACT Two chitinolytic bacterial strains, Paenibacillus sp. 300 and Streptomyces sp. 385, suppressed Fusarium wilt of cucumber (Cucumis sativus) caused by Fusarium oxysporum f. sp. cucumerinum in nonsterile, soilless potting medium. A mixture of the two strains in a ratio of 1:1 or 4:1 gave significantly (P < 0.05) better control of the disease than each of the strains used individually or than mixtures in other ratios. Several formulations were tested, and a zeolite-based, chitosan-amended formulation (ZAC) provided the best protection against the disease. Dose-response studies indicated that the threshold dose of 6 g of formulation per kilogram of potting medium was required for significant (P < 0.001) suppression of the disease. This dose was optimum for maintaining high rhizosphere population densities of chitinolytic bacteria (log 8.1 to log 9.3 CFU/g dry weight of potting medium), which were required for the control of Fusarium wilt. The ZAC formulation was suppressive when added to pathogen-infested medium 15 days before planting cucumber seeds. The formulation also provided good control when stored for 6 months at room temperature or at 4 degrees C. Chitinase and beta-1,3-glucanase enzymes were produced when the strains were grown in the presence of colloidal chitin as the sole carbon source. Partial purification of the chitinases, followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and activity staining, revealed the presence of five bands with molecular masses of 65, 62, 59, 55, and 52 kDa in the case of Paenibacillus sp. 300; and three bands with molecular masses of 52, 38, and 33 kDa in the case of Streptomyces sp. 385. Incubation of cell walls of F. oxysporum f. sp. cucumerinum with partially purified enzyme fractions led to the release of N-acetyl-D-glucosamine (NAGA). NAGA content was considerably greater when pooled enzyme fractions (64 to 67) from Paenibacillus sp. were used, because they contained high beta-1,3-glucanase activity in addition to chitinase activity. Suppression of Fusarium wilt of cucumber by a combination of these two bacteria may involve the action of these hydrolytic enzymes.

Identification of putative phosphoinositide-specific phospholipase C genes in filamentous fungi

Five putative phosphoinositide-specific phospholipases C (PLC) genes were identified in three species of filamentous fungi. Using polymerase chain reaction with degenerate oligonucleotide primers, gene fragments encoding amino acid sequences homologous to PLCs of mammals and other organisms were amplified: one sequence from Botryotinia fuckeliana, one from Aspergillus nidulans, and three from Neurospora crassa. The molecular cloning and sequencing of a putative PLC gene (BCPLC1) from B. fuckeliana showed that it encoded a polypeptide containing X and Y domains, the two conserved regions found in all known PLCs. The hypothetical gene product of BCPLC1 was of delta type in its primary structural organization. The identification of three PLC genes in N. crassa shows that multiple PLC isozymes also occur in microbial eukaryotes.

Isolation and characterization of a benomyl-resistant form of beta-tubulin-encoding gene from the phytopathogenic fungus Botryotinia fuckeliana

As an initial step to develop a DNA-mediated transformation system using benomyl resistance as a dominant selectable marker in the phytopathogenic fungus Botryotinia fuckeliana (anamorph, Botrytis cinerea), we have constructed a phage lambda genomic DNA library of a benomyl-resistant strain 91T-1, and a beta-tubulin-encoding gene benA was isolated, cloned and sequenced. Southern blot analysis suggested that a single copy of benA is present in the genome of B. fuckeliana. The benA gene is composed of seven exons which are separated by six introns of 52 to 135 bp. The intron consensus sequences are similar to those of other fungal genes. The deduced amino acid sequence (447 amino acid residues) is highly homologous to those of other fungal beta-tubulin-encoding genes. Comparison of the sequences around codons 198 and 200 in benomyl-resistant and sensitive strains revealed that the benAHR allele from the benomyl-resistant strain 91T-1 contained a mutation at codon 198 from GAG (Glu) to GCG (Ala), which has been correlated with high resistance to benzimidazole fungicides including benomyl in various filamentous fungi.