Introduction: TP53 mutant (mTP53) MDS and AML, accounting for 5-10% of de novo MDS and 25-30% of therapy related MDS (t-MDS), represent a distinct molecular cohort with inferior outcomes. ...Hypomethylating agents (HMA) are preferred treatments for patients (pts) with these mutations, although with CR rates of only 20-30% and median OS of 6-12 months. APR-246 is a novel, first-in-class small molecule that selectively induces apoptosis in mTP53 cancer cells through mutant p53 protein re-activation by restoring the wild-type conformation, with single agent activity in mTP53 AML. We report the planned, completed Phase 1b results of APR-246+ azacitidine (AZA) in mTP53 MDS/AML.
Methods: This is a multicenter Phase 1b/2 trial of APR-246+AZA in HMA naïve mTP53 MDS and oligoblastic AML (≤ 30% blasts) pts ≥ 18 years of age. Pts received APR-246 in a 3+3 dose escalation design (50, 75, 100 mg/kg lean body weight (equivalent to 4500mg fixed dose based on PK studies)) IV daily over 4 days in a lead-in phase (days -14 to -10) followed by the same dose of APR-246 (days 1-4) + AZA 75 mg/m2 SC/IV over 7 days (days 4-10 or 4-5 and 8-12) in 28 day cycles. The primary objective was to define safety and the recommended Phase 2 dose (RP2D), with AEs graded by CTCAE v4.03 and DLT assessment over 6 weeks. Secondary objectives included response by IWG 2006 criteria as well as serial next generation sequencing (NGS) and p53 IHC for evaluation of clonal suppression and remission depth as predictors of outcomes. For minimal residual disease (MRD) analysis, a custom target-capture NGS assay was developed using unique molecular Identifiers for error correction with a limit of detection of 0.1% with results validated by pt specific digital droplet PCR (ddPCR). Nanostring nCounter RNA expression analysis was conducted on a panel of 770 genes after the lead-in phase to assess transcriptional effects induced by APR-246.
Results: As of July 30, 2018, 12 pts (42% male; median age 66 years (39-73)) were enrolled. Three pts had AML-MRC and 9 had MDS; all pts had poor risk cytogenetics (17% poor, 83% very poor) and higher risk disease by IPSS-R (25% high, 75% very high). T-MDS occurred in 5 pts (42%) and 7 pts (58%) were transfusion-dependent at baseline. Median BM blasts were 9% (4-30). Eleven of 12 pts (92%) had a TP53 missense mutation in the DNA binding domain with multiple mutations in 4/12 pts (33%). For 9/12 pts (75%), TP53 was the sole mutation. Median time on study is 176 days (41-298) with 7 pts ongoing. Treatment (Tx) related AEs during the lead-in phase (all G1) included nausea (n=5), neuropathy (n=5), decreased appetite (n=2), and dizziness (n=2) which were all transient. Tx related AEs occurring in > 1 pt in the combination phase included nausea/vomiting (n=6), dizziness (n=3), headache (n=3), neuropathy (n=3), fall (n=2), pruritus (n=2), thrombocytopenia (n=6), neutropenia (n=5), and leukopenia (n=4); all G1/G2 except cytopenias (G3/G4). No DLTs have occurred to date.
Eleven of twelve pts were response evaluable with 1 pt discontinuing tx prior to 1st disease assessment (Fig 1A). ORR by IWG was 100% (11/11) with 9 CR (82%) and 2 marrow CR (mCR; 18%). Median time to first response was 70 days (4-91) and one CR patient achieved mCR and partial cytogenetic response after APR-246 lead-in prior to combination therapy. All CR pts had high p53 positivity by IHC at baseline (25-80%) which normalized on serial assessment with the 2mCR pts having <5% p53+ at baseline. Serial NGS with a variant allele frequency (VAF) cutoff of 5% was negative in 73% of patients (8/11). In NGS negative pts, MRD analysis, validated by ddPCR, was performed with a median VAF of 0.3% (0.1%-3.1%) at best molecular response. Enriched pathway analysis via Reactome following APR-246 lead-in phase showed transcriptional activation of p53 targets (FDR = 9.16E-09), including pathways involved in cell cycle arrest, apoptosis, DNA repair, and regulation of TP53 activity. At a median follow up of 7 months, the median OS or PFS has not been reached. In comparison to a internal historical cohort of 51 mTP53 MDS/AML treated with AZA alone, APR-246+AZA had a trend for improved OS (NR vs 7.6months; HR 0.30, P=0.07; Fig 1B).
Conclusions: APR-246+AZA combination is well tolerated in mTP53 MDS/AML. Responses have been achieved in all evaluable pts (82% CR) accompanied by deep molecular and durable remissions. The RP2D of APR-246 is a fixed dose of 4500mg days 1-4 in combination with AZA and phase 2 accrual has begun.
Display omitted
Sallman:Celgene: Research Funding, Speakers Bureau. Sweet:Agios: Consultancy; Phizer: Consultancy; Agios: Consultancy; BMS: Honoraria; Celgene: Honoraria, Speakers Bureau; Jazz: Speakers Bureau; Celgene: Honoraria, Speakers Bureau; BMS: Honoraria; Phizer: Consultancy; Novartis: Consultancy, Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau; Astellas: Consultancy; Jazz: Speakers Bureau; Astellas: Consultancy. Cluzeau:Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Pfizer: Speakers Bureau; Sanofi: Speakers Bureau; Menarini: Consultancy; Amgen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz Pharma: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Sekeres:Opsona: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Roboz:Orsenix: Consultancy; Cellectis: Research Funding; Eisai: Consultancy; Astex Pharmaceuticals: Consultancy; Argenx: Consultancy; Pfizer: Consultancy; Bayer: Consultancy; Eisai: Consultancy; Sandoz: Consultancy; Jazz Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Consultancy; Novartis: Consultancy; Pfizer: Consultancy; Otsuka: Consultancy; Bayer: Consultancy; Aphivena Therapeutics: Consultancy; Celltrion: Consultancy; Argenx: Consultancy; Celgene Corporation: Consultancy; Daiichi Sankyo: Consultancy; Celltrion: Consultancy; Sandoz: Consultancy; Astex Pharmaceuticals: Consultancy; Aphivena Therapeutics: Consultancy; Orsenix: Consultancy; Otsuka: Consultancy; Roche/Genentech: Consultancy; Roche/Genentech: Consultancy; Janssen Pharmaceuticals: Consultancy; Daiichi Sankyo: Consultancy; Novartis: Consultancy; AbbVie: Consultancy; Janssen Pharmaceuticals: Consultancy; Celgene Corporation: Consultancy; AbbVie: Consultancy; Cellectis: Research Funding. Bhagat:Genoptix: Employment. Tell:Aprea Therapeutics: Employment. Fenaux:Celgene: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Otsuka: Honoraria, Research Funding; Roche: Honoraria. List:Celgene: Research Funding. Komrokji:Novartis: Honoraria, Speakers Bureau; Celgene: Honoraria, Research Funding; Novartis: Honoraria, Speakers Bureau; Celgene: Honoraria, Research Funding; Novartis: Honoraria, Speakers Bureau; Novartis: Honoraria, Speakers Bureau.
Scientific access to spaceflight and especially the International Space Station has revealed that physiological adaptation to spaceflight is accompanied or enabled by changes in gene expression that ...significantly alter the transcriptome of cells in spaceflight. A wide range of experiments have shown that plant physiological adaptation to spaceflight involves gene expression changes that alter cell wall and other metabolisms. However, while transcriptome profiling aptly illuminates changes in gene expression that accompany spaceflight adaptation, mutation analysis is required to illuminate key elements required for that adaptation. Here we report how transcriptome profiling was used to gain insight into the spaceflight adaptation role of Altered response to gravity 1 (Arg1), a gene known to affect gravity responses in plants on Earth. The study compared expression profiles of cultured lines of Arabidopsis thaliana derived from wild-type (WT) cultivar Col-0 to profiles from a knock-out line deficient in the gene encoding ARG1 (ARG1 KO), both on the ground and in space. The cell lines were launched on SpaceX CRS-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC-17 spaceflight mission. The cultured cell lines were grown within 60 mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canisters (BRIC) hardware. Spaceflight samples were fixed on orbit. Differentially expressed genes were identified between the two environments (spaceflight and comparable ground controls) and the two genotypes (WT and ARG1 KO). Each genotype engaged unique genes during physiological adaptation to the spaceflight environment, with little overlap. Most of the genes altered in expression in spaceflight in WT cells were found to be Arg1-dependent, suggesting a major role for that gene in the physiological adaptation of undifferentiated cells to spaceflight. Key Words: ARG1-Spaceflight-Gene expression-Physiological adaptation-BRIC. Astrobiology 17, 1077-1111.
BackgroundThe majority of cancer patients remain refractory to existing cancer immunotherapies. Despite the growing evidence that dysregulated metabolism contributes to the exhaustion of ...tumor-infiltrating T lymphocytes (TILs) and the loss of their effector functions within the metabolically restricted tumor microenvironment (TME), actionable targets to rescue metabolic fitness and anti-tumor activity of TILs remain elusive.Memory T (TM) cells and TILs rely on fatty acid catabolism to preserve their effector functions due to nutrient competition for glucose with tumor cells. Therefore, enhancing fatty acid catabolism of TILs represents an attractive strategy to increase the efficacy of immunotherapies.Sirt2 is an NAD+ dependent histone deacetylase. We previously showed that upregulation of Sirt2 in human TILs negatively correlates with response to TIL therapy in advanced non-small cell lung cancer (NSCLC) and Sirt2 deficiency leads to hyper-reactive T cells with superior antitumor activity.MethodsSirt2 expression was analyzed by flow cytometry and Western blot. The role of Sirt2 in tumor immunity was studied using in vivo B16F10 tumor challenge models as well as ex vivo analysis including RNA-sequencing, CFSE proliferation assay, DAPI/AnnexinV staining, IFN-γ ELISpot assay, intracellular staining of effector molecules and LDH cytotoxicity assay on WT versus Sirt2KO T cells. Molecular partners of Sirt2 were identified using mass spectrometry (MS) and Co-immunoprecipitation analyses. The role of Sirt2 in T cell metabolism was investigated using seahorse bioanalyzer and LC-MS/MS Metabolomic profiling. AGK2, a Sirt2 selective inhibitor, was used for Sirt2 blockade in human T cells.ResultsSirt2 expression is upregulated during T cell activation, TM stage, and within the TME. Our molecular studies revealed that Sirt2 negatively impacts the acetylation status and the activity of the trifunctional protein, the key enzyme of fatty acid oxidation (FAO). Accordingly, Sirt2 deficiency enhanced FAO and metabolic fitness of activated T cells and mouse TILs isolated from B16F10 tumor nodules. As a consequence of enhanced FAO, Sirt2 deficient mice displayed increased accumulation of TM cells, which was associated with decreased apoptosis and increased survival after tumor challenge leading to superior tumor rejection. Most importantly, pharmacologic inhibition of Sirt2 in human TILs isolated from NSCLC patients enhanced their metabolic fitness and cytotoxic activity against their autologous tumor cells.ConclusionsOur findings indicate Sirt2 as a suppressor of T cell metabolism amenable to therapeutic targeting, and Sirt2 inhibition reprograms T cell metabolic fitness to optimally sustain their effector function within the hypoglycemic TME, thus, leading to an effective anti-tumor immune response.AcknowledgementsThis work was supported in part by K08 CA194273, ACS IRG-17-173-22, NCI Cancer Center Support Grant (P30-CA076292) and the Moffitt Foundation.
Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, ...20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in
,
,
, and
and CNA in
,
, and
compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in
and
were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents.
An effective PCR-based genomic walking approach is described to discover previously unknown flanking genomic DNA sequences from
Candidatus Liberibacter asiaticus, an unculturable, phloem-limited ...bacterium. Using this technique, 8564
bp of new DNA sequences were obtained from three genomic loci;
tufB-secE-nusG-rplKAJL-rpoBC gene cluster,
omp gene (outer membrane protein, Omp) and 16/23S rRNA gene in
Ca. L. asiaticus. These, together with publicly available
Ca. Liberibacter sequences, are clustered into five contigs and two singlets representing 24,477 non-redundant base pairs. BLAST annotation predicts 12 full-length genes, two partial genes and one pseudogene among these sequences. The sequences obtained in this study provide new genome information about
Ca. Liberibacter that will facilitate development of new genome-based detection tools. The technique described here can also be employed to acquire new genomic information for other unculturable or fastidious organisms for which available sequences are limited or for filling sequence gaps between known flanking genomic DNA sequences.
Abstract
Background
CD19 chimeric antigen receptor (CAR) T cell therapies have been successful in B cell malignancies. Recent reports about CD19 CAR T cell therapy in B-cell acute lymphoblastic ...leukemia suggest that the median event-free survival of children and young adult patients is longer than that of adult patients. Since the reason is unclear, we compared the functions of CAR-T derived from young or aged mice and also healthy human donors.
Methods
Young and aged B6 mice spleens (6-12 vs. ≥72 weeks) or young and aged human PBMCs (20-26 vs. 53-60 years) were used for mouse or human CAR-T preparation. 4 types of mouse CD19 CAR and 2 types of human CD19 CAR were evaluated in T cells.
Results
Aged mouse CAR-T predominates with CD8+ and effector-like phenotypes at the expense of CD4+ and memory-like phenotypes. Compared to young mouse CAR-T, aged mouse CAR-T exhibited superior cytotoxicity for mouse CD19+ artificial antigen presenting cell (aAPC). Using our immune competent in vivo murine model, aged mouse CAR-T was short-lived and expanded poorly despite superior in vitro cytotoxicity. RNA-Seq suggestes that young mouse CAR-T is advantageous for cell proliferation and regulation of cell differentiation whereas aged mouse CAR-T up-regulates gene expression pathways that regulate responses to stimulus and exocytosis. Furthermore, compared to mouse CAR-T, human CAR-T is complementary with immune phenotypes after human CD19+ aAPC stimulation.
Conclusions
Aged donor derived CAR-T exhibited enhanced effector functions but shorter persistence and less memory-like phenotypes. Our results suggest that the difference of clinical outcomes may be due to an age-dependent CAR-T cell phenotype that is reflected by its unique gene expression pattern, secretory profile, and/or transcription factor balance. In our future directions we are identifying potential methods to improve the function of aged donor derived CAR-T.
A β-glucosidase gene (bglA) from Butyrivibrio fibrisolvens H17c was cloned into the binary vector pGA482 under the control of the 35S Cauliflower Mosaic Virus (CaMV) promoter. A second construct was ...generated for accumulation of the bglA gene product in the vacuole of transformed tobacco plants. Reverse transcription - polymerase chain reaction analysis demonstrated that the bglA gene was expressed in 71% of cytosol-targeted and 67% of vacuole-targeted transgenic tobacco T^sub 1^ plants. T^sub 1^ transgenic plants (pGLU100 and pGLU200) exhibited elevated levels of free salicylic acid (SA) with a concomitant significant decrease in the level of glucosylsalicylic acid (GSA) compared to the untransformed tobacco plants and tobacco plants transformed with the empty vector (pGA482). Following inoculation with Tobacco Mosaic Virus (TMV), lesion area was 51% smaller in pGLU100 plants and 60% smaller in pGLU200 plants compared to inoculated untransformed and negative control plants.PUBLICATION ABSTRACT
Background: The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic ...information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae. Description: VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores approximately 320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of approximately 20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online informatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. Conclusion: The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website http://cropdisease.ars.usda.gov/vitis_at/main-page.htm.
PDF
![Expression of a [beta]-gluc...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0721-7714/small "Expression of a [beta]-glucosidase gene results in increased accumulation of salicylic acid in transgenic Nicotiana tabacum cv. Xanthi-nc NN genotype")
