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Cancer heterogeneity is a result of genetic mutations within the cancer cells. Their proliferation is not only driven by autocrine functions but also under the influence of cancer microenvironment, which consists of normal stromal cells such as infiltrating immune cells, cancer-associated fibroblasts, endothelial cells, pericytes, vascular and lymphatic channels. The relationship between cancer cells and cancer microenvironment is a critical one and we are just on the verge to understand it on a molecular level. Cancer microenvironment may serve as a selective force to modulate cancer cells to allow them to evolve into more aggressive clones with ability to invade the lymphatic or vascular channels to spread to regional lymph nodes and distant sites. It is important to understand these steps of cancer evolution within the cancer microenvironment towards invasion so that therapeutic strategies can be developed to control or stop these processes.

It is known, that the application of Forster Resonance Energy Transfer (FRET) between two dyes absorbing in different spectrum regions allows shifting of the excitation wavelength into the blue region. We investigated spectral properties and FRET between styryl (St) and squaraine (Sq) dyes to evaluate the possibility of using such FRET-pair to determine conformational changes in proteins. Spectral properties of St and Sq in polar (phosphate buffer), nonpolar (chloroform) solvents and in non-covalent complexes with BSA (bovine serum albumin) and HSA (human serum albumin) were studied. The effect of changes in protein conformation induced by urea solutions of various concentrations on the spectral properties of dyes and energy transfer efficiency was also studied. It was found that the polarity of the medium affects the fluorescent properties of dyes in different ways: styryl dye has a positive solvatofluorochromism, while the squaraine dye has the negative one. Both dyes show negative solvatochromism, and their quantum yields substantially increase in a less polar environment. Despite the spectral differences of the St-BSA and St-HSA complexes, their quantum yields are the same, and in case of squaraine dye the quantum yield for Sq-HSA is almost twice higher that for Sq-BSA. When the conformation of protein changes, the dyes go into the aqueous phase, as a result the intensity of their fluorescence decreases almost to the level of fluorescence of the free dye in phosphate buffer. There are two bands corresponding to the donor and acceptor in the fluorescence spectra of the double complexes St-BSA-Sq and St-HSA-Sq. The pair of styryl-squaraine dyes is differently sensitive to the conformation changes in these albumins caused by urea: the FRET efficiency for HSA changes by 11.5 times, while for BSA only by 2.1 times. Thus, the St–Sq pair has the ability to detect a change in the conformation of proteins, but the efficiency of the pair depends on the properties of the protein under study.

PURPOSE: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.METHODS: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.RESULTS: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.CONCLUSION: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

Background The reproducibility of gene expression measured by RNA sequencing (RNA-Seq) is dependent on the sequencing depth. While unmapped or non-exonic reads do not contribute to gene expression quantification, duplicate reads contribute to the quantification but are not informative for reproducibility. We show that mapped, exonic, non-duplicate (MEND) reads are a useful measure of reproducibility of RNA-Seq datasets used for gene expression analysis. Findings In bulk RNA-Seq datasets from 2,179 tumors in 48 cohorts, the fraction of reads that contribute to the reproducibility of gene expression analysis varies greatly. Unmapped reads constitute 1–77% of all reads (median [IQR], 3% [3–6%]); duplicate reads constitute 3–100% of mapped reads (median [IQR], 27% [13–43%]); and non-exonic reads constitute 4–97% of mapped, non-duplicate reads (median [IQR], 25% [16–37%]). MEND reads constitute 0–79% of total reads (median [IQR], 50% [30–61%]). Conclusions Because not all reads in an RNA-Seq dataset are informative for reproducibility of gene expression measurements and the fraction of reads that are informative varies, we propose reporting a dataset's sequencing depth in MEND reads, which definitively inform the reproducibility of gene expression, rather than total, mapped, or exonic reads. We provide a Docker image containing (i) the existing required tools (RSeQC, sambamba, and samblaster) and (ii) a custom script to calculate MEND reads from RNA-Seq data files. We recommend that all RNA-Seq gene expression experiments, sensitivity studies, and depth recommendations use MEND units for sequencing depth.

Group-living prey rely on social information such as alarm signals and other social cues to avoid predation. By definition, “signals” imply that a message is voluntarily directed at receivers (i.e., the audience), whereas “cues” are released incidentally regardless of the audience composition. Thus, audience effects can be used to differentiate between signals and cues when communication is difficult to observe or quantify. In at least two fish species, chemical disturbance cues are released during a predator attack to signal to familiar audiences about predation risk. Here, we examined whether audience composition affects disturbance cue release in wood frog (Lithobates sylvaticus) tadpoles to better understand the function of disturbance cues across aquatic prey. Groups of tadpoles underwent simulated predator attacks to obtain disturbance cues. The groups were either familiar and related, unfamiliar and related, familiar and unrelated, or unfamiliar and unrelated. To assess the relative potency of each cue, we used a behavioral bioassay design involving activity changes in independent tadpole receivers (unfamiliar and unrelated to the donors). If tadpoles use disturbance cues to signal related and/or familiar individuals, we predicted increased fright responses in receivers to cues obtained from those groups. However, we detected no effect of audience composition, indicating that tadpoles release similar disturbance cues regardless of audience kinship or familiarity. Nevertheless, disturbance cues evoked a consistent antipredator response in receivers indicating that these chemicals still act as reliable risk cues. Further comparative studies using audience effects are necessary to understand how disturbance cues have evolved across aquatic prey. When aquatic prey encounter predators and are frightened, they release chemicals known as “disturbance cues” into the water. These chemicals alert other prey nearby of potential danger. For example, wood frog tadpoles release disturbance cues when they are being chased by a predator. Tadpoles that smell the disturbance cues of other tadpoles are less likely to be eaten by predators. Since wood frog tadpoles are often found in shallow ponds filled with both familiar siblings as well as other tadpoles that are unfamiliar and unrelated, we wondered if tadpoles would produce more disturbance cues when familiar or related tadpoles were nearby. Here, we show that no matter who the audience members are, familiar siblings or not, tadpoles release disturbance cues that cause similar fright. This suggests that disturbance cues are not released differently depending on the audience in this species.

To protect the health of sows and gilts, significant investments are directed toward the development of vaccines against infectious agents that impact reproduction. We developed an intrauterine vaccine that can be delivered with semen during artificial insemination to induce mucosal immunity in the reproductive tract. An in vitro culture of uterine epithelial cells was used to select an adjuvant combination capable of recruiting antigen-presenting cells into the uterus. Adjuvant polyinosinic:polycytidylic acid (poly I:C), alone or in combination, induced expression of interferon gamma, tumor necrosis factor alpha, and select chemokines. A combination adjuvant consisting of poly I:C, host defense peptide and polyphosphazene (Triple Adjuvant; TriAdj), which previously was shown to induce robust mucosal and systemic humoral immunity when administered to the uterus in rabbits, was combined with boar semen to evaluate changes in localized gene expression and cellular recruitment, in vivo. Sows bred with semen plus TriAdj had decreased γδ T cells and monocytes in blood, however, no corresponding increase in the number of monocytes and macrophages was detected in the endometrium. Compared to sows bred with semen alone, sows bred with semen plus TriAdj showed increased CCL2 gene expression in the epithelial layer. These data suggest that the adjuvants may further augment a local immune response and, therefore, may be suitable for use in an intrauterine vaccine. When inactivated porcine parvovirus (PPV) formulated with the TriAdj was administered to the pig uterus during estrus along with semen, we observed induction of PPV antibodies in serum but only when the pigs were already primed with parenteral PPV vaccines. Recombinant protein vaccines and inactivated PPV vaccines administered to the pig uterus during breeding as a primary vaccine alone failed to induce significant humoral immunity. More trials need to be performed to clarify whether repeated intrauterine vaccination can trigger strong humoral immunity or whether the primary vaccine needs to be administered via a systemic route to promote a mucosal and systemic immune response.

Precision oncology has primarily relied on coding mutations as biomarkers of response to therapies. While transcriptome analysis can provide valuable information, incorporation into workflows has been difficult. For example, the relative rather than absolute gene expression level needs to be considered, requiring differential expression analysis across samples. However, expression programs related to the cell-of-origin and tumor microenvironment effects confound the search for cancer-specific expression changes. To address these challenges, we developed an unsupervised clustering approach for discovering differential pathway expression within cancer cohorts using gene expression measurements. The hydra approach uses a Dirichlet process mixture model to automatically detect multimodally distributed genes and expression signatures without the need for matched normal tissue. We demonstrate that the hydra approach is more sensitive than widely-used gene set enrichment approaches for detecting multimodal expression signatures. Application of the hydra analysis framework to small blue round cell tumors (including rhabdomyosarcoma, synovial sarcoma, neuroblastoma, Ewing sarcoma, and osteosarcoma) identified expression signatures associated with changes in the tumor microenvironment. The hydra approach also identified an association between ATRX deletions and elevated immune marker expression in high-risk neuroblastoma. Notably, hydra analysis of all small blue round cell tumors revealed similar subtypes, characterized by changes to infiltrating immune and stromal expression signatures., Author summary Pediatric cancers generally have few somatic mutations. To increase the number of actionable treatment leads, precision pediatric oncology initiatives also analyze tumor gene expression patterns. However, currently available approaches for gene expression data analysis in the clinical setting often use arbitrary thresholds for assessing overexpression and assume gene expression is normally distributed. These methods also rely on reference distributions of related cancer types or normal samples for assessing expression distributions. Often adequate normal samples are not available, and comparing matched cancer cohorts without accounting for subtype expression overestimates the uncertainty in the analysis. We developed a computational framework to automatically detect multimodal expression distributions within well-defined disease populations. Our analysis of small blue round cell tumors (including rhabdomyosarcoma, synovial sarcoma, neuroblastoma, Ewing sarcoma and osteosarcoma) discovered a significant number of multimodally expressed genes. Multimodally expressed genes were associated with proliferative signaling, extracellular matrix organization, and immune signaling pathways across cancer types. Expression signatures correlated with differences in patient outcomes for MYCN non-amplified neuroblastoma, osteosarcoma, and synovial sarcoma. The low mutation rate in pediatric cancers has led some to suggest that pediatric cancers are less immunogenic. However, our analysis suggests that immune infiltration can be identified across small blue round cell tumors. Thus, further research into modulating immune cells for patient benefit may be warranted.

Objective Introduction: Bloodstream infections (BSIs) are associated with high morbidity and mortality worldwide. However data of BSI from Ukraine are scarce. The aim: To obtain the first national estimates of the current incidence of BSI and antimicrobial resistance of responsible pathogens, and associated mortality in Ukraine. Patients and methods Materials and methods: A retrospective multicenter cohort study was conducted at the 14 hospitals of Ukraine between January 2013 to December 2015. Definitions of BSIs were adapted from the CDC. The identification and antimicrobial susceptibility of cultures were determined, using automated microbiology analyzer. Some antimicrobial susceptibility test used Kirby - Bauer antibiotic testing. Results Results: Among 20,544 patients, 3816 (18.6%) BSIs were observed. The rate of health care associated BSI was 92.4%. Death was reported in 68.4% BSI cases. The predominant pathogens were: Klebsiella pneumoniae (25.1%), Escherichia coli (17.5%), Staphylococcus aureus (9.9%), Pseudomonas aeruginosa (8.9%), and Acinetobacter spp.(8.5%). The overall proportion of extended spectrum beta-lactamase (ESBL) production among Enterobacteriaceae was 24.8% and of methicillin-resistance in S. aureus (MRSA) 38.2%. Vancomycin resistance was observwd in 9.2% of isolated enterococci (VRE). Carbapenem resistance was identified in 33.1% of P.aeruginosa isolates and 63.2% of A. baumannii isolates. Resistance to third-generation cephalosporins was observed in 14.2% K. pneumoniae and E.coli 55% isolates. Conclusion Conclusions: Healthcare-associated BSIs and antimicrobial resistance of responsible pathogens together with their associated impact on mortality, presents a significant burden to the Ukraine hospital system. Surveillance of BSIs may help to delineate the requirements for infection prevention and control.

The actual task of oncology is effective treatment of cancer while causing a minimum harm to the patient. The appearance of polymer nanomaterials and technologies launched new applications and approaches of delivery and release of anticancer drugs. The goal of work was to test ultra dispersed diamonds (UDDs) and onion-like carbon (OLCs) as new vehicles for delivery of antitumor drug (doxorubicin (DOX)) and specific antibodies to tumor receptors. Stable compounds of UDDs and OLCs with DOX were obtained. As results of work, an effectiveness of functionalization was 2.94 % w/w for OLC-DOX and 2.98 % w/w for UDD-DOX. Also, there was demonstrated that UDD-DOX and OLC-DOX constructs had dose-dependent cytotoxic effect on tumor cells in the presence of trypsin. The survival of adenocarcinoma cells reduced from 52 to 28 % in case of incubation with the UDD-DOX in concentrations from 8.4-2.5 to 670-20 μg/ml and from 72 to 30 % after incubation with OLC-DOX. Simultaneously, antibodies to epidermal growth factor maintained 75 % of the functional activity and specificity after matrix-assisted pulsed laser evaporation deposition. Thus, the conclusion has been made about the prospects of selected new methods and approaches for creating an antitumor agent with capabilities targeted delivery of drugs.

Epitopes are peptides that present on the surface of the cell and can be recognized by immune cells to initiate the immune response. Identification of neoepitopes – tumor-specific, MHC-bound epitopes recognized specifically by T-cells – is valuable for predicting response to immunotherapies, including checkpoint blockade therapies. Tumors with more neoepitopes tend to be more responsive to immune checkpoint therapies compared to tumors with fewer neoepitopes. ProTECT is a previously published computational method that uses Illumina whole genome and transcriptome sequencing data from tumor and matched normal tissues to identify neoepitopes. Tumor and normal whole genome sequencing data are used to infer a patient's HLA haplotypes, as well as annotate variants as either somatic or germline. While whole genome sequencing is comprehensive, it is quite costly and not available for many samples. Here we adapt ProTECT to use only tumor RNA sequencing data and HLA haplotype information available to the clinician to identify neoepitopes in a tumor sample. Prior to running ProTECT, we use the computational tools Opossum and Platypus for variant calling instead of Radia (which is designed for variant calling using both RNA and DNA sequencing data as input). To determine which variants are somatic and therefore could represent tumor neoepitopes, variants found in RNA are compared to a panel of normals, for example the Genome Aggregation Database (gnomAD; containing variants from 125,748 exome sequences and 15,708 whole-genome sequences). With the resulting somatic variants and the HLA type, ProTECT proceeds as usual, with translation of variants into proteins, MHC:Peptide binding predictions and neoepitope ranking. We find that high quality neoepitopes are identifiable using an RNA-only approach, when genomic data is absent. Future work will validate the sensitivity of our method by benchmarking it against the original ProTECT predictions in the TCGA Prostate Adenocarcinoma cohort. Citation Format: Drew Thompson, Olena M. Vaske, Arjun Rao, Holly C. Beale. Detecting neoepitopes from tumor RNA sequencing datasets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 176.

Wilms tumor is the most common childhood kidney cancer. 15% of patients with Wilms tumor have germline pathogenic variants in genes or regions such as WT1 or the 11p15 region. Variants in these regions can include structural or copy number alterations or alterations in methylation. In the majority of cases of Wilms tumor no known pathogenic variant could be found using the state-of-the-art technologies, including comprehensive approaches such as Illumina whole exome sequencing. One explanation for this is that such technologies have difficulties in detecting structural variants (SVs) in areas associated with repeat or low complexity sequence. In addition, Illumina technology does not immediately support direct methylation detection. Therefore, we hypothesized that analysis of bilateral Wilms tumor of unknown etiology using long-read sequencing could reveal molecular events of potential clinical interest. We performed in-depth genomic analysis on a whole blood DNA sample from a patient with a bilateral Wilms tumor. This patient had no significant family history of cancer, and previously tested negative for Beckwith-Wiedemann syndrome by methylation testing of the 11p15 region; clinical exome sequencing of the patient's germline detected no variants associated with Wilms tumors. We sequenced the genome at 40x depth using PromethION Nanopore sequencing. 29180 SVs (deletions or insertions larger than 30 base pairs) were detected using Sniffles and 26480 were detected with SVIM. Only SVs that were detected by both methods were considered for downstream analysis. Variants were annotated and filtered using a short-read catalog of SVs (gnomAD-SV), a long-read catalog, the Database of Genomic Variants catalog, and by comparison to 11 in-house genomes. We focused on SVs, copy number variants, and methylation events affecting genes previously associated with Wilms tumor. Our long-read sequencing approach detected compound heterozygotes using phased variant calls. A heterozygous missense mutation was identified in haplotype one, while a 300 base pair insertion in an ALU element was present in haplotype two. These two compound heterozygous variants overlap an exon of the OVCH2 gene, and the ALU element was not detected by the prior Illumina analysis. Additionally, we determined the frequency of methylation in CpG sites genomewide using nanopolish. Using a normal blood sample from an unrelated individual as a control, we searched for extreme differences across large and gene promoter regions. Hypermethylation in the promoter regions of genes in the 11p15.5 locus was observed in the patient as compared to the control. Hypomethylation in this region is associated with Beckwith-Wiedemann syndrome. In conclusion, nanopore technology is able to detect variants missed by Illumina sequencing, and has the potential to yield new findings of interest in a case of a child with suspected cancer predisposition syndrome. Citation Format: Allison R. Cheney, Jean Monlong, Holly C. Beale, Hugh Olsen, Ellen Towle Kephart, Katrina Learned, Shanna White, Julian A. Martinez-Agosto, Noah Federman, Mark Akeson, Miten Jain, Vivian Y. Chang, Olena M. Vaske. Long-read sequencing characterization of a patient with bilateral Wilms tumor of unknown etiology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 261.

Introduction: Leukemia is the most common cancer in children, accounting for approximately one third of all malignancies that occur in the pediatric age group. Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML) account for most leukemia diagnosed in this age group. While known markers for poor prognosis include higher age, higher white blood cell count at diagnosis and certain translocations, innovative approaches in tumor RNA sequencing (RNA-Seq) data analysis can discover novel prognostic factors that could be exploited for future therapeutic development in fusion-negative ALL and AML. Methods: To reveal gene expression signatures among fusion-negative leukemias, we used a novel unsupervised analysis model called Hydra. Hydra uses a Dirichlet process mixture model to detect multimodally expressed genes to use in characterizing clusters within cancer cohorts. This approach can detect subtle yet robust differences in gene expression without the reliance on reference normal RNA-Seq datasets. The Hydra model reveals clusters of the cancer cohort, and differences among these clusters can be investigated by finding enriched pathways via Gene Set Enrichment Analysis (GSEA). The cluster-specific enriched pathways can be used in conjunction with survival data to determine how certain pathways are associated with outcome. This analysis used publicly available data from the National Cancer Institute (NCI) Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database that was uniformly processed by the Treehouse Childhood Cancer Initiative. Results: First, 202 fusion-negative AML and fusion-negative B-cell precursor ALL samples were run through Hydra and five clusters were identified. These clusters had different enriched pathways, such as high mitochondrial activity, high cell proliferation, and high cell signaling. Though these are characteristics of all cancer cells, each cluster demonstrated that one pathway was most distinctive of those samples. Most clusters were differentiated by disease, however, one cluster with enriched heme metabolism and immunoglobulin pathways contained almost equal amounts of AML and ALL samples, suggesting that specific cohorts of AML and ALL patients had increased inflammatory response. Another cluster contained 72 AML samples and 4 ALL samples. The four ALL samples in this cluster showed lowered expression of CD19, a B-cell lineage immune marker, and elevated expression of CD14, a myeloid lineage immune marker. These ALL patients exhibited genomic characteristics of AML, which may suggest a more specialized treatment regimen. Discussion: Despite extensive characterization of pediatric high-risk leukemias using genomic approaches, there is ample opportunity to study RNA-Seq-derived gene expression profiles to help accurately diagnose and treat pediatric patients. Citation Format: Sneha S. Jariwala, Alfred Geoffrey Lyle, Jacob Pfeil, Lauren Sanders, Holly C. Beale, Ellen T. Kephart, Katrina Learned, Allison Cheney, Olena M. Vaske. Molecular classification of pediatric high-risk leukemias using expression profiles of multimodally expressed genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3033.

Synovial sarcoma (SS) is an aggressive soft-tissue malignancy, accounting for 10% of all soft-tissue sarcomas. These tumors can occur at any age but most often affect young adults and adolescents, developing deep in the distal extremities. The prognosis of SS tumors is poor, with a 5-year survival rate of 36-76%, a high rate of metastasis and few treatments. The purpose of this study was to identify novel overexpressed oncogenes that could serve as druggable targets for treating synovial sarcoma patients. We compared the RNA-Seq expression profiles of a cohort of 36 synovial sarcomas to our compendium of RNA-Seq expression data from 12,236 tumor samples (treehousegenomics.ucsc.edu) from pediatric and adult cancer patients. In comparing gene expression in the synovial sarcoma cohort samples against the compendium samples, gene expression outliers were defined as having expression above the gene-specific outlier threshold as defined by the Tukey's outlier method. Among the overexpression outliers, pathway enrichment analysis was used to identify common and druggable pathways, with implications for potential therapeutics for patients with SS. Our analysis identified the overexpression of members of the Sonic Hedgehog pathway in the majority of synovial sarcoma samples. For example, GLI1 expression exceeded the outlier threshold in 35 out of 36 samples. This pathway can be targeted by available small molecule inhibitors. Ongoing work focuses on evaluating the role of Sonic Hedgehog signaling in the pathogenesis of SS using pharmacological inhibition, CRISPRi studies in cell line models of the disease and nanopore sequencing. We currently have 4 patient-derived synovial sarcoma cell lines (HSSY-II, SYO-1, YAMATO, and ASKA) that we can grow in both adherent conditions and in 3D cell culture as sarcospheres. We detected the expression of the SYT-SSX fusion transcript in each of the cell lines by RT-PCR to confirm the cell lines maintained expression of the pathogenic fusion. This work has implications for using comparative tumor RNA-seq derived gene expression data for nominating novel druggable targets specific to synovial sarcoma tumors. Citation Format: Yvonne A. Vasquez, Jacob Pfeil, Letitia Mueller, Holly Beale, Alfred G. Lyle, Lauren Sanders, Katrina Learned, Ellen Kephart, Anouk van den Bout, Allison Cheney, Sahar Hosseinzadeh, Isabel Bjork, Sofie R. Salama, Olena Vaske. Identifying potential druggable targets for synovial sarcoma using comparative RNA-seq analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3035.

The turripeptide ubi3a was isolated from the venom of the marine gastropod Unedogemmula bisaya, family Turridae, by bioassay-guided purification; both native and synthetic ubi3a elicited prolonged tremors when injected intracranially into mice. The sequence of the peptide, DCCOCOAGAVRCRFACC-NH2 (O = 4-hydroxyproline) follows the framework III pattern for cysteines (CC–C–C–CC) in the M-superfamily of conopeptides. The three-dimensional structure determined by NMR spectroscopy indicated a disulfide connectivity that is not found in conopeptides with the cysteine framework III: C1–C4, C2–C6, C3–C5. The peptide inhibited the activity of the α9α10 nicotinic acetylcholine receptor with relatively low affinity (IC50, 10.2 μM). Initial Constellation Pharmacology data revealed an excitatory activity of ubi3a on a specific subset of mouse dorsal root ganglion neurons.

On the model of Cu-induced liver fibrosis, the relationship between the activity of prooxidant-antioxidant system, immune system parameters, liver morphology and several physiological parameters (body temperature and performance ability of the animals, taking into account their ages) was investigated. Classical biochemical, immunological, histological and physiological methods of investigation were used. The subjects of the study were male Wistar rats of 3-month (young) and 20-month (old) age. For the induction of liver fibrosis, experimental animals were successively injected with copper sulfate (three times at intervals of 24 hours at a dose corresponding to 33% of the lethal one). It was shown that after five days of sulfate copper administration inflammatory reactions in the liver, damage of the vessel epithelium, an increase in collagen content, and other morphological changes were detected. At this time, the content of lipid hydroperoxides in the liver and blood serum was increased, the activity of a number of antioxidant enzymes was reduced, and the activity of aconitase was two times less compared to values in the control group. These changes correlated with a decrease in the amount and activity of phagocytic cells in the blood of experimental animals. Inhibition of the general metabolism was accompanied by a decrease in body temperature, loss of body weight and performance ability. The relationship between a specific metabolic pattern in animals with Cu-induced fibrosis was age-dependent. The formed specific adaptive metabolic pattern is unstable, and in the future it can be realized in one of three possible adaptive strategies, the choice of which is influenced by age.

A comprehensive study of a typical steppe perennial Iris pumila L. were carried out in the central zone of the European part of this species’ range, namely in Ukraine. Intraspecific differentiation, population size and isolation degree and its consequences, the threat of human impact were analyzed, as well as ecological amplitude and genetic variation in ISSR markers and selected chloroplast regions were determined. The species was found to have a low intraspecific differentiation that indicates the uniformity of the gene pool in the studied part of the range. Moreover, the results of isolation assessment, population and ecological study of I. pumila confirm the potential risk of extinction. A considerable part of the species populations exist as separated patches of rare ecosystems, isolated from the nearest neighbours due to intense plowing of the steppe zone. The generative reproduction is rare. In contrast, ISSR analysis revealed comparably high genetic diversity in all the sampled populations. Furthermore, specific plastid haplotypes were demonstrated in some of them. The inconsistency between the results of population ecological study and the data of molecular genetic analysis indicates that the loss of genetic diversity in the species caused by habitat fragmentation and isolation under increasing anthropogenic pressure is likely to be slower than it would appear judging from the assessment of population parameters, which clearly show negative trends. This result also emphasizes the necessity for integrated approach to assessment of the extinction risk for particular species and careful analysis of all determinants of extinction.

BackgroundThe accuracy of gene expression as measured by RNA sequencing (RNA-Seq) is dependent on the amount of sequencing performed. However, some types of reads are not informative for determining this accuracy. Unmapped and non-exonic reads do not contribute to gene expression quantification. Duplicate reads can be the product of high gene expression or technical errors.FindingsWe surveyed bulk RNA-Seq datasets from 2179 tumors in 48 cohorts to determine the fractions of uninformative reads. Total sequence depth was 0.2-668 million reads (median (med.) 61 million; interquartile range (IQR) 53 million). Unmapped reads constitute 1-77% of all reads (med. 3%; IQR 3%); duplicate reads constitute 3-100% of mapped reads (med. 27%; IQR 30%); and non-exonic reads constitute 4-97% of mapped, non-duplicate reads (med. 25%; IQR 21%). Informative reads--Mapped, Exonic, Non-duplicate (MEND) reads--constitute 0-79% of total reads (med. 50%; IQR 31%). Further, we find that MEND read counts have a 0.22 Pearson correlation to the number of genes expressed above 1 Transcript Per Million, while total reads have a correlation of −0.05.ConclusionsSince the fraction of uninformative reads vary, we propose using only definitively informative reads, MEND reads, for the purposes of asserting the accuracy of gene expression measured in a bulk RNA-Seq experiment. We provide a Docker image containing 1) the existing required tools (RSeQC, sambamba and samblaster) and 2) a custom script. We recommend that all results, sensitivity studies and depth recommendations use MEND units.

Diffuse pediatric gliomas harboring a Histone H3 K27M mutation are significantly more aggressive than H3-wild type gliomas and demonstrate global hypomethylation at the K27 residue(1). As a result, these tumors show global aberrant gene expression, resulting in a primitive, stem-like proliferative cell population(2). Posterior fossa (PF) ependymomas, on the other hand, harbor few significantly recurrent somatic mutations, but PF-A and PF-B subgroups have been defined on the basis of epigenetic differences(3). Compared to PF-B, the PF-A subgroup demonstrates H3K27 hypomethylation, aberrant gene expression and aggressive tumor growth(4,5). We recently identified a set of long non-coding RNA (lncRNA) that are transiently expressed in early brain development(6), and hypothesized that H3K27M gliomas and PF-A ependymomas may share methylation-related dysregulation of long non-coding RNA (lncRNA) networks responsible for maintaining normal differentiation programs. Here we describe a network of regulatory lncRNA with increased expression in both H3K27M gliomas and PF-A ependymomas, as compared to H3-WT gliomas and PF-B ependymomas. We demonstrate that increased expression of this lncRNA network correlates with the over-expression of signaling pathways involved in maintaining a non-differentiated, proliferative phenotype and driving tumorigenesis. We hypothesize that in both H3K27M gliomas and PF-A ependymomas, aberrant global methylation may be driving lncRNA to activate and maintain stem-like states in early neural development, suggesting similarities in epigenetically driven, developmental origins for both tumor types. References: 1. Chan KM, Fang D, Gan H, et al. Genes Dev. 2013;27(9):985–90; 2. Filbin MG, Tirosh I, Hovestadt V, et al. Science. 2018;360(6386):331–5; 3. Witt H, Mack SC, Ryzhova M, et al. Cancer cell. 2011;20(2):143–57; 4. Bayliss J, Mukherjee P, Lu C, et al. Sci. Transl. Med. 2016;8(366):366ra161; 5. Mack SC, Witt H, Piro RM, et al. Nature. 2014;506(7489):445; 6. Field AR, Jacobs FM, Fiddes IT, et al. bioRxiv. 2017:232553.

The death rate from cancer and infectious diseases is still very high, therefore research in this area is extremely important and promising as in medical, so in economic point of view. Thus, potassium salt of tetrazolo[1,5- c ]quinazolin-5-thion was modified per alkylation by N -aryl(benzyl,heteryl)acetamides with proper confirmation of newly synthesized compounds’ structures by FT-IR, LC–MS, 1 H NMR and elemental analysis data. The substances were tested for bioluminescence inhibition against Photobacterium leiognathi Sh1 (5–50 μg/mL) to check their cytotoxicity. Then they were screened for antibacterial and antifungal activities (100 μg) against Escherichia coli , Staphylococcus aureus , Enterobacter aerogenes and Enterococcus faecalis , Pseudomonas aeruginosa , Klebsiella pneumoniae and Candida albicans . It was found that compounds 1.1 , 1.5 , 1.10 , 1.31 , 1.33 possessed light activity against K. pneumonia . The US National Cancer Institute (NCI) has chosen 19 compounds and screened them for ability to inhibit in 10 μM concentration 60 different human tumor cell lines. The LOX IMVI cell line of melanoma appeared to be the most sensitive one, and N -(6-methylbenzo[ d ]thiazol-2-yl)-2-(tetrazolo[1,5- c ]quinazolin-5-ylthio)acetamide ( 1.31 ) and N -(3-fluorobenzyl)-2-(tetrazolo[1,5- c ]quinazolin-5-ylthio)acetamide ( 1.19 ) exhibited high growth inhibition rate, and N -(6-methoxybenzo[ d ]thiazol-2-yl)-2-(tetrazolo[1,5- c ]quinazolin-5-ylthio)acetamide ( 1.32 ) showed lethal antitumor activity against it. The latter compound 1.32 showed the best anticancer results, also inhibiting growth of leukemia SR cell line, NCI-H460 of non-small cell lung cancer, KM12 of colon cancer and SF-295 of CNS cancer. The in silico molecular docking studies have predicted the affinity of the synthesized substances to the epidermal growth factor receptor (EGFR).

Mitochondria of mammalian cells contain multiple copies of mitochondrial (mt) DNA. Although mtDNA copy number can fluctuate dramatically depending on physiological and pathophysiologic conditions, the mechanisms regulating mitochondrial genome replication remain obscure. Hypoxia, like many other physiologic stimuli that promote growth, cell proliferation and mitochondrial biogenesis, uses reactive oxygen species as signaling molecules. Emerging evidence suggests that hypoxia-induced transcription of nuclear genes requires controlled DNA damage and repair in specific sequences in the promoter regions. Whether similar mechanisms are operative in mitochondria is unknown. Here we test the hypothesis that controlled oxidative DNA damage and repair in the D-loop region of the mitochondrial genome are required for mitochondrial DNA replication and transcription in hypoxia. We found that hypoxia had little impact on expression of mitochondrial proteins in pulmonary artery endothelial cells, but elevated mtDNA content. The increase in mtDNA copy number was accompanied by oxidative modifications in the D-loop region of the mitochondrial genome. To investigate the role of this sequence-specific oxidation of mitochondrial genome in mtDNA replication, we overexpressed mitochondria-targeted 8-oxoguanine glycosylase Ogg1 in rat pulmonary artery endothelial cells, enhancing the mtDNA repair capacity of transfected cells. Overexpression of Ogg1 resulted in suppression of hypoxia-induced mtDNA oxidation in the D-loop region and attenuation of hypoxia-induced mtDNA replication. Ogg1 overexpression also reduced binding of mitochondrial transcription factor A (TFAM) to both regulatory and coding regions of the mitochondrial genome without altering total abundance of TFAM in either control or hypoxic cells. These observations suggest that oxidative DNA modifications in the D-loop region during hypoxia are important for increased TFAM binding and ensuing replication of the mitochondrial genome.

We developed an experimental model of a cyclic feeding regime (CFR) that increased a lifespan in rats. The manifestations of oxidative stress and their interrelation with parameters of cell immunity were assessed in rats at CFR. It is shown that changes of body mass, liver mass and indexes of pro/antioxidant system after periods of starving—ad libitum nutrition at CFR diet in old animals were less pronounced than in young animals. The body mass loss of 30% in 14 days was accompanied by oxidative stress. Indexes of phagocytosis did not change, but activity of oxidase system of neutrophil was increased in 2 times. The response of metabolic and physiological systems on repeat starving—ad libitum nutrition cycles differs from the response to the initial cycle of CFR. This is interpreted as a change of adaptation strategy and the effect of metabolic memory, which influences the choice of organism strategy of adaptation for subsequent starving. The dynamics of change of the studied indexes in response to CFR was age-dependent. It was supposed that different answer to CFR in young and old animals is determined by the different amount of carbon and fat depots in young and old animals.

Introduction: There is strong experimental and clinical data to indicate the critical involvement of immune evasion in relapsed leukemia in children. A well-defined characteristic of refractory leukemia is the accumulation of genetic aberrations and mutations that may act as drivers or passengers in the process of tumor recurrence. Many of these mutations get translated into proteins that contain tumor-specific immune-stimulatory epitopes (neoantigens) that can elicit host antitumor immune responses. Although, in general, the mutation rate is lower in pediatric tumors, recent studies have shown that almost 90% of pediatric leukemias carry potentially actionable neoepitopes. In this study, we describe the results from a comprehensive experimental approach of neoantigen prediction coupled with antigen processing and HLA-binding prediction algorithms with in vitro validation assays for the generation of neoantigen vaccines against high-risk leukemias in children. Methods: DNA and RNA from leukemia cells and matched fibroblasts were obtained. Raw reads were aligned to human reference genome and somatic variants (SNVs) were called using Strelka v1.0.1441. RNA-seq data from leukemic cells were used to predict neoantigen expression levels resulting from SNVs using STAR (2.4.1)12 and Cufflinks v2.2.1. Normalized expression data were then cross-referenced with the list of SNVs to identify leukemia-specific mutant proteins. HLA typing for each sample was carried out from RNA-seq data using seq2HLA v2.2. Using the patient's HLA phenotype, we then used NetMHCons v1.1 to predict short peptides derived from leukemia-specific mutant proteins that will bind to autologous HLA Class I molecules. These 8/9-mers were filtered to predict a high likelihood of proteasomal or immune-proteasomal processing and transporter associated with antigen processing (TAP) using NetChop v3.1 and the immune epitope database (IEDB), respectively. The peptides identified were rank-ordered based on the composite immunogenicity score derived from MHC class I binding affinities, proteasomal processing and TCR binding predictions and synthesized accordingly. Peripheral blood derived dendritic cells (DCs) and CD8+ T-cells were isolated and expanded in culture with relevant cytokines. The DCs were pulsed with peptides and then co-cultured with CD8+ T-cells. After five days, the primed CD8+ T-Cells were separated, washed and exposed to the patient's leukemic cells at varying ratios and the leukemia specific CD8+ T-cell activation was quantified by IFN gamma secretion using ELISpot assays. Results: In the leukemia specimen studied, approximately 5% of all on-target germline mutations were found only in leukemic cells. Tumor mutational burden was, on average, 0.34 mut/Mb. Analysis of the highest ranking synthetic peptides (approximately 10 per leukemia sample) showed leukemia-specific activation of patient's T-cells as measured by the mean number of spots observed in ELISpot assays. For example, in patient one (15 year old male, high-risk ALL, one year off therapy), 14 individual short sequences were identified and corresponding peptides were synthesized. Among these, three peptides were not soluble and three peptides showed significant activity above controls. Maximum leukemia specific T-cell activation was noted with peptide #7 QQSALVLL (mean 135 ELISpots compared to 72 in controls, p Discussion: Completed data, including the vaccine peptide sequences and corresponding activities showed the feasibility of identifying pediatric leukemia neoantigen sequences in personalized mutational landscapes of these patients. In addition, we have provided an in vitro experimental approach to validate the potential of such vaccines in future clinical studies and this methodology can also be used to identify agents for effective combinations such as immune checkpoint inhibitors. A clinical trial using these strategies is in development for the treatment of high-risk leukemia in children. Disclosures No relevant conflicts of interest to declare.

The purpose of our study was to elucidate the molecular mechanisms by which the histone H3 K27M mutation drives tumorigenesis of pediatric gliomas. Though it has potential implications on the treatment of diffuse midline glioma as a disease driver, the timing, cell type of origin, and effect of the H3K27M mutation on early embryonic brain development are not fully characterized. Here, we performed differential expression analysis on a cohort of H3K27M and H3WT pediatric gliomas, revealing that genes in the epithelial-mesenchymal transition (EMT) pathway were significantly differentially expressed. SNAI1, the EMT master regulator, was significantly overexpressed in the H3K27M tumor cohort. Overall, pre-EMT genes were overexpressed in H3K27M tumors while post-EMT genes were underexpressed. We hypothesized that H3K27M may lead to gliomagenesis by stalling an EMT in early brain development and employed single-cell and bulk RNA sequencing data from cerebral organoids at multiple developmental timepoints to test this hypothesis. We observed that a long noncoding RNA (lncRNA) signature identified as transiently expressed in early brain development was preferentially expressed in H3K27M tumors. Cell type-specific lncRNA signatures had higher expression in H3K27M tumors for pre-EMT cell types, and higher expression in H3WT tumors for post-EMT cell types. Finally, t-SNE clustering of single-cell glioma RNA sequencing data with single-cell organoid data revealed transcriptional similarities between H3K27M and pre-EMT neural stem cells. In conclusion, we observed aberrant activity of the EMT in H3K27M gliomas. Our data suggest that the H3K27M mutation is associated with a pre-EMT cell phenotype, and that this mutation may cause EMT arrest or de-differentiation. Citation Format: Allison R. Cheney, Lauren M. Sanders, Lucas Seninge, Holly C. Beale, Ellen Towle Kephart, Jacob Pfeil, Katrina Learned, A. Geoffrey Lyle, Isabel Bjork, David Haussler, Sofie R. Salama, Olena M. Vaske. Candidate differentiation stall in epithelial mesenchymal transition in H3K27M diffuse midline glioma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B06.

Fragments of the mitochondrial genome released into the systemic circulation after mechanical trauma, termed mitochondrial DNA damage-associated molecular patterns (mtDNA DAMPs), are thought to mediate the systemic inflammatory response syndrome. The close association between circulating mtDNA DAMP levels and outcome in sepsis suggests that bacteria also might be a stimulus for mtDNA DAMP release. To test this hypothesis, we measured mtDNA DAMP abundance in medium perfusing isolated rat lungs challenged with an intratracheal instillation of 5 × 107 colony-forming units of Pseudomonas aeruginosa (strain 103; PA103). Intratracheal PA103 caused rapid accumulation of selected 200-bp sequences of the mitochondrial genome in rat lung perfusate accompanied by marked increases in both lung tissue oxidative mtDNA damage and in the vascular filtration coefficient ( Kf). Increases in lung tissue mtDNA damage, perfusate mtDNA DAMP abundance, and Kf were blocked by addition to the perfusion medium of a fusion protein targeting the DNA repair enzyme Ogg1 to mitochondria. Intra-arterial injection of mtDNA DAMPs prepared from rat liver mimicked the effect of PA103 on both Kf and lung mtDNA integrity. Effects of mtDNA and PA103 on Kf were also attenuated by an oligodeoxynucleotide inhibitor of Toll-like receptor 9 (TLR-9) by mitochondria-targeted Ogg1 and by addition of DNase1 to the perfusion medium. Collectively, these findings are consistent with a model wherein PA103 causes oxidative mtDNA damage leading to a feed-forward cycle of mtDNA DAMP formation and TLR-9-dependent mtDNA damage that culminates in acute lung injury.

The aim of the study was to develop the system of polymerase chain reaction (PCR)-based markers for the assessment of genetic diversity and population genetic studies of Gentiana lutea L. as well as to determine the utility of two indices of marker informativeness. The informativeness was determined for 40 PCR primers of different types (random amplified polymorphic DNA, inter simple sequence repeat, inter-retrotransposon amplified polymorphism, resistance gene analog polymorphism and conserved DNA-derived polymorphism markers) by evaluating discriminating power (DL) and resolving power (Rp) in a sample of 30 plants from two populations. Analysis of correlation between the index value and the number of differentiated pairs of genotypes in the given sample revealed that DL is more efficient than Rp; therefore, we selected primers based on the DL value. In total, 12 primers with the largest values of DL were chosen. Analysis of genetic relationship among 86 plants from six populations showed that the number of bands produced by the three of selected primers was sufficient to give average bootstrap support across six key nodes in the dendrogram higher than 85%, while using six of the primers resulted in average bootstrap value exceeding 99%. Thus, a minimal set of three to six selected primers are sufficient for a quick assessment of genetic diversity of G. lutea populations, depending on the sample size and degree of differentiation between populations, while the rest of the primers with DL values above 0.8 may be used for ecogenetic surveys. Preliminary results obtained with selected primers indicate the moderate level of genetic variation within the species and significant differentiation among individual populations.

Oxidative stress results in mtDNA damage and contributes to myocardial cell death. mtDNA repair enzymes are crucial for mtDNA repair and cell survival. We investigated a novel, mitochondria-targeted fusion protein (Exscien1-III) containing endonuclease III in myocardial ischemia-reperfusion injury and transverse aortic constriction (TAC)-induced heart failure. Male C57/BL6J mice (10–12 wk) were subjected to 45 min of myocardial ischemia and either 24 h or 4 wk of reperfusion. Exscien1-III (4 mg/kg ip) or vehicle was administered at the time of reperfusion. Male C57/BL6J mice were subjected to TAC, and Exscien1-III (4 mg/kg i.p) or vehicle was administered daily starting at 3 wk post-TAC and continued for 12 wk. Echocardiography was performed to assess left ventricular (LV) structure and function. Exscien1-III reduced myocardial infarct size ( P < 0.01) at 24 h of reperfusion and preserved LV ejection fraction at 4 wk postmyocardial ischemia. Exscien1-III attenuated TAC-induced LV dilation and dysfunction at 6–12 wk post-TAC ( P < 0.05). Exscien1-III reduced ( P < 0.05) cardiac hypertrophy and maladaptive remodeling after TAC. Assessment of cardiac mitochondria showed that Exscien1-III localized to mitochondria and increased mitochondrial antioxidant and reduced apoptotic markers. In conclusion, our results indicate that administration of Exscien1-III provides significant protection against myocardial ischemia and preserves myocardial structure and LV performance in the setting of heart failure. NEW & NOTEWORTHY Oxidative stress-induced mitochondrial DNA damage is a prominent feature in the pathogenesis of cardiovascular diseases. In the present study, we demonstrate the efficacy of a novel, mitochondria-targeted fusion protein that traffics endonuclease III specifically for mitochondrial DNA repair in two well-characterized murine models of cardiac injury and failure.

A new potential method of detecting the conformational changes in hydrophobic proteins such as bovine serum albumin (BSA) is introduced. The method is based on the change in the Forster resonance energy transfer (FRET) efficiency between protein-sensitive fluorescent probes. As compared to conventional FRET based methods, in this new approach the donor and acceptor dyes are not covalently linked to protein molecules. Performance of the new method is demonstrated using the protein-sensitive squaraine probes Square-634 (donor) and Square-685 (acceptor) to detect the urea-induced conformational changes of BSA. The FRET efficiency between these probes can be considered a more sensitive parameter to trace protein unfolding as compared to the changes in fluorescence intensity of each of these probes. Addition of urea followed by BSA unfolding causes a noticeable decrease in the emission intensities of these probes (factor of 5.6 for Square-634 and 3.0 for Square-685), and the FRET efficiency changes by a factor of up to 17. Compared to the conventional method the new approach therefore demonstrates to be a more sensitive way to detect the conformational changes in BSA.

Although studies in rat cultured pulmonary artery endothelial cells, perfused lungs, and intact mice support the concept that oxidative mitochondrial (mt) DNA damage triggers acute lung injury (ALI), it has not yet been determined whether enhanced mtDNA repair forestalls development of ALI and its progression to multiple organ system failure (MOSF). Accordingly, here we examined the effect of a fusion protein construct targeting the DNA glycosylase, Ogg1, to mitochondria in a rat model intra-tracheal Pseudomonas aeruginosa (strain 103; PA103)-induced ALI and MOSF. Relative to controls, animals given PA103 displayed increases in lung vascular filtration coefficient accompanied by transient lung tissue oxidative mtDNA damage and variable changes in mtDNA copy number without evidence of nuclear DNA damage. The approximate 40% of animals surviving 24 h after bacterial administration exhibited multiple organ dysfunction, manifest as increased serum and tissue-specific indices of kidney and liver failure, along with depressed heart rate and blood pressure. While administration of mt-targeted Ogg1 to control animals was innocuous, the active fusion protein, but not a DNA repair-deficient mutant, prevented bacteria-induced increases in lung tissue oxidative mtDNA damage, failed to alter mtDNA copy number, and attenuated lung endothelial barrier degradation. These changes were associated with suppression of liver, kidney, and cardiovascular dysfunction and with decreased 24 h mortality. Collectively, the present findings indicate that oxidative mtDNA damage to lung tissue initiates PA103-induced ALI and MOSF in rats.

Novel pH-sensitive, water-soluble, long-wavelength fluorescent norsquaraine dyes and their barbituric and dicyanomethylene derivatives were synthesized and investigated. Some of these dyes contain a carboxylic functionality that was converted into an NHS ester to facilitate bio-conjugation. The absorption and emission spectra, fluorescence quantum yields, lifetimes, polarization, and photostabilities were measured free in solution and after binding to bovine serum albumin (BSA) and compared to those of conventional squaraines and the norcyanine dye CypHer5. Contrary to squaraines, norsquaraines are pH-sensitive but almost unaffected by the interaction with proteins. These dyes can potentially be used as fluorescent labels for biomedical applications, in particular for protein labeling, polarization-based assays, cell-based and pH-sensing measurements.

Diffuse intrinsic pontine gliomas (DIPGs) are incurable pediatric brain tumors with an aggressive onset. Apart from irradiation, there are currently no effective therapies available for DIPG patients, who have a median survival time of less than one year. DIPG cells possess a mutation in histone H3 (H3K27M) that results in a reduction of H3K27 trimethylation and activation of oncogenic signaling pathways. We show that the H3K27M mutation induces RAS pathway signaling which is augmented by additional RAS activators including PDGFRA. We observed that the H3K27M mutation leads to silencing of GTPase-activating proteins, namely RASAL1, which when ectopically expressed, reduced proliferation and RAS activation. An siRNA screen of RAS pathway effectors identified ERK5, but not ERK1/2, as important for DIPG growth. Suppression of ERK5, which is highly expressed in DIPG, decreased DIPG cell proliferation and induced apoptosis both in vitro and in vivo. Mechanistically, we show that ERK5 directly activates and stabilizes the proto-oncogene MYC. ERK5 overexpression fully rescued ERK5-depleted cells and partial rescue was achieved by expression of ERK5 mutants lacking kinase activity or the transactivation domain (ΔTAD). However, no rescue was achieved with kinase-dead, ΔTAD double mutants. Additionally, ERK5 knockdown or treatment with ERK5 inhibitors significantly increased survival of mice intracranially engrafted with DIPG cells. TG02, a pan-CDK and ERK5 inhibitor currently in phase II trials for various cancers, was the most effective treatment, extending median survival time nearly two-fold. Collectively, our data demonstrate DIPG reliance on RAS and MYC activities, and in so doing reveal novel therapeutic targets for treating these tumors.

We investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

The novel heterocyclization of 5-(2-aminophenyl)-1H-tetrazole with potassium ethylxanthogenate or carbon disulfide was proposed. The potassium salt of the tetrazolo[1,5-c]quinazoline-5-thione was subsequently modified by alkylation with proper halogen derivatives to (tetrazolo[1,5-c]quinazolin-5-ylthio)alkyls, N,N-dialkylethylamines, 1-aryl-2-ethanones, 1-(alkyl)aryl-2-ethanols, carboxylic acids, and esters. The structures of all newly synthesized compounds were confirmed by FT-IR, UV-vis, LC-MS, (1)H, (13)C NMR, and elemental analysis data. The substances were screened for antibacterial and antifungal activities (100 μg) against Escherichia coli, Staphylococcus aureus, Enterobacter aerogenes, Entrococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Candida albicans. Preliminary bioluminescence inhibition tests against Photobacterium leiognathi Sh1 showed that substances 5.2-5.4, 6.1, 7.1 with ethanone or carboxylic acid substituents showed toxicity against bacteria cells. The substances chosen by the US National Cancer Institute (NCI) were screened for their ability to inhibit 60 different human tumor cell lines, where 2-(tetrazolo[1,5-c]quinazolin-5-ylthio)-1-(4-tolyl)ethanone (5.2), 3-(tetrazolo[1,5-c]quinazolin-5-ylthio)propanoic and related 3-metyl-butanoic acids (6.2, 6.3), and ethyl tetrazolo[1,5-c]quinazolin-5-ylthio)acetate (7.2) showed lethal antitumor activity (1.0 μM) against the acute lymphoblastic leukemia cell line (CCRF-CEM), and substances 5.2 and 6.3 exhibited moderate anticancer properties inhibiting growth of the leukemia MOLT-4 and HL06-(TB) cell lines. The moderate antitumor activity was demonstrated in 1-(2,5-dimethoxyphenyl)-2-(tetrazolo[1,5-c]quinazolin-5-ylthio)ethanone (5.4) against the CNS cancer cell line SNB-75. Comparing the docking mode of the Gefitinib and synthesised substances on the ATP binding site of EGFR, it could be assumed that these compounds might act in the same way. The results of the investigation could be considered as a useful base for future development of potent antimicrobials and antitumor agents among tetrazolo[1,5-c]quinazoline-5-thione S-derivatives.

Reactive oxygen species associated with hypoxic signaling in pulmonary arterial endothelial cells (PAECs) oxidatively modify specific nucleotides in the hypoxic response element (HRE) of the VEGF gene (FASEB J.19:387-394; 2005). In this study, we determined in PAECs if hypoxia caused genome-wide oxidative modifications or if they were restricted to the promoters of genes differentially regulated by hypoxia. Comet assays indicated that there were no differences between normoxic and hypoxic PAECs in terms of global DNA damage. However, a simple PCR-based method involving DNA amplification before and after treatment with formamidopyrimidine DNA glycosylase (Fpg), a bacterial DNA repair enzyme that cleaves at sites of purine base oxidation, revealed that hypoxia caused modifications in the HREs of the hypoxia-inducible VEGF, HO-1, and ET-1 genes which coincided with accumulation of their respective mRNA transcripts. Promoter sequences not involved with hypoxic induction and coding regions of these genes failed to display Fpg-sensitive sites. Oxidative modifications also were not detected in sequences of the hypoxia down-regulated ornithine decarboxylase and TFAM genes or the constitutively expressed beta-actin gene. These findings show that hypoxia-mediated oxidative DNA modifications cluster in functionally relevant promoter sequences in hypoxia-inducible genes and suggest that such oxidative modifications may be biologically significant.

Mitochondrial dysfunction underlies many processes in the development of atherosclerosis, including generation of reactive oxygen species, apoptosis, and inflammation. Oxidative mtDNA damage is a proximate cause of mitochondrial dysfunction and there is growing evidence that it can directly promote atherosclerosis. The mechanism of this action remains unclear, but may include initiation of apoptosis and inflammation by mtDNA oxidation. Previously, we have demonstrated protective role of mitochondria-targeted DNA glycosylase Ogg1 against oxidative stress and apoptosis in cell culture and against vascular injury in animal models. In the present study we tested the hypothesis that transgenic modulation of Ogg1 coordinately regulates atherogenesis in mice fed a high fat diet. Wild type (WT) mice, Ogg1 knock-out (KO) mice and KO mice transgenically overexpressing mitochondria-targeted Ogg1 (KO-Tg) were fed Western diet and analyzed for mtDNA damage and signs of atherogenesis. When compared to WT animals, KO mi...

Oxidant-induced death and dysfunction of pulmonary vascular cells play important roles in the evolution of acute lung injury. In pulmonary artery endothelial cells (PAECs), oxidant-mediated damage to mitochondrial DNA (mtDNA) seems to be critical in initiating cytotoxicity inasmuch as overexpression of the mitochondrially targeted human DNA repair enzyme, human Ogg1 (hOgg1), prevents both mtDNA damage and cell death (Dobson AW, Grishko V, LeDoux SP, Kelley MR, Wilson GL, and Gillespie MN. Am J Physiol Lung Cell Mol Physiol 283: L205–L210, 2002). The mechanism by which mtDNA damage leads to PAEC death is unknown, and the present study tested the specific hypothesis that enhanced mtDNA repair suppresses PAEC mitochondrial dysfunction and apoptosis evoked by xanthine oxidase (XO). PAECs transfected either with an adenoviral vector encoding hOgg1 linked to a mitochondrial targeting sequence or with empty vector were challenged with ascending doses of XO plus hypoxanthine. Quantitative Southern blot analyses revealed that, as expected, hOgg1 overexpression suppressed XO-induced mtDNA damage. Mitochondrial overexpression of hOgg1 also suppressed the XO-mediated loss of mitochondrial membrane potential. Importantly, hOgg1 overexpression attenuated XO-induced apoptosis as detected by suppression of caspase-3 activation, by reduced DNA fragmentation, and by a blunted appearance of condensed, fragmented nuclei. These observations suggest that mtDNA damage serves as a trigger for mitochondrial dysfunction and apoptosis in XO-treated PAECs.

The biological activity of Sambucus nigra bark lectin on Chinese hamster cells in vitro was investigated by comet-assay and cytotoxicity testing. Mitogenic properties at the concentrations 0.063-0.25 microg/ml (but not higher) were found, and the induction of DNA breaks at concentrations 0.5 microg/ml and higher is demonstrated. S. nigra bark lectin at mitogenic concentrations decreased the level of nickel-induced DNA damage. The character and mechanism of this lectin protective activity was probably related to the induction of DNA reparation in the cells, decreasing nickel uptake in cells, and non-specific binding of nickel ions by protein molecules.

Nicotinic acetylcholine receptors (nAChRs) containing the α9 subunit are expressed in a wide variety of non-neuronal tissues ranging from immune cells to breast carcinomas. The α9 subunit is able to assemble into a functional homomeric nAChR and also co-assemble with the α10 subunit into functional heteromeric nAChRs. Despite the increasing awareness of the important roles of this subunit in vertebrates, the study of human α9-containing nAChRs has been severely limited by difficulties in its expression in heterologous systems. In Xenopus laevis oocytes, functional expression of human α9α10 nAChRs is very low compared to that of rat α9α10 nAChRs. When oocytes were co-injected with cRNA of α9 and α10 subunits of human versus those of rat, oocytes with the rat α9 human α10 combination had an ∼-fold higher level of acetylcholine-gated currents (I(ACh)) than those with the human α9 rat α10 combination, suggesting difficulties with human α9 expression. When the ratio of injected human α9 cRNA to human α10 cRNA was increased from 1∶1 to 5∶1, I(ACh) increased 36-fold (from 142±23 nA to 5171±748 nA). Functional expression of human α9-containing receptors in oocytes was markedly improved by appending the 5'-untranslated region of alfalfa mosaic virus RNA4 to the 5'-leader sequence of the α9 subunit cRNA. This increased the functional expression of homomeric human α9 receptors by 70-fold (from 7±1 nA to 475±158 nA) and of human α9α10 heteromeric receptors by 80-fold (from 113±62 nA to 9192±1137 nA). These findings indicate the importance of the composition of the 5' untranslated leader sequence for expression of α9-containing nAChRs.

This study tested the hypothesis that oxidative mitochondrial-targeted DNA (mtDNA) damage triggered ventilator-induced lung injury (VILI). Control mice and mice infused with a fusion protein targeting the DNA repair enzyme, 8-oxoguanine-DNA glycosylase 1 (OGG1) to mitochondria were mechanically ventilated with a range of peak inflation pressures (PIP) for specified durations. In minimal VILI (1 h at 40 cmH2O PIP), lung total extravascular albumin space increased 2.8-fold even though neither lung wet/dry (W/D) weight ratios nor bronchoalveolar lavage (BAL) macrophage inflammatory protein (MIP)-2 or IL-6 failed to differ from nonventilated or low PIP controls. This increase in albumin space was attenuated by OGG1. Moderately severe VILI (2 h at 40 cmH2O PIP) produced a 25-fold increase in total extravascular albumin space, a 60% increase in W/D weight ratio and marked increases in BAL MIP-2 and IL-6, accompanied by oxidative mitochondrial DNA damage, as well as decreases in the total tissue glutathione (GSH) and GSH/GSSH ratio compared with nonventilated lungs. All of these injury indices were attenuated in OGG1-treated mice. At the highest level of VILI (2 h at 50 cmH2O PIP), OGG1 failed to protect against massive lung edema and BAL cytokines or against depletion of the tissue GSH pool. Interestingly, whereas untreated mice died before completing the 2-h protocol, OGG1-treated mice lived for the duration of observation. Thus mitochondrially targeted OGG1 prevented VILI over a range of ventilation times and pressures and enhanced survival in the most severely injured group. These findings support the concept that oxidative mtDNA damage caused by high PIP triggers induction of acute lung inflammation and injury.

In cultured pulmonary artery endothelial cells and other cell types, overexpression of mt-targeted DNA repair enzymes protects against oxidant-induced mitochondrial DNA (mtDNA) damage and cell death. Whether mtDNA integrity governs functional properties of the endothelium in the intact pulmonary circulation is unknown. Accordingly, the present study used isolated, buffer-perfused rat lungs to determine whether fusion proteins targeting 8-oxoguanine DNA glycosylase 1 (Ogg1) or endonuclease III (Endo III) to mitochondria attenuated mtDNA damage and vascular barrier dysfunction evoked by glucose oxidase (GOX)-generated hydrogen peroxide. We found that both Endo III and Ogg1 fusion proteins accumulated in lung cell mitochondria within 30 min of addition to the perfusion medium. Both constructs prevented GOX-induced increases in the vascular filtration coefficient. Although GOX-induced nuclear DNA damage could not be detected, quantitative Southern blot analysis revealed substantial GOX-induced oxidative mtDNA damage that was prevented by pretreatment with both fusion proteins. The Ogg1 construct also reversed preexisting GOX-induced vascular barrier dysfunction and oxidative mtDNA damage. Collectively, these findings support the ideas that mtDNA is a sentinel molecule governing lung vascular barrier responses to oxidant stress in the intact lung and that the mtDNA repair pathway could be a target for pharmacological intervention in oxidant lung injury.

Viktor M Pastukh1, Li Zhang2, Mykhaylo V Ruchko1, Olena Gorodnya1, Gina C Bardwell1, Rubin M Tuder2, Mark N Gillespie11Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL, USA; 2Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado at Denver, Aurora, CO, USAAbstract: Lung tissue from COPD patients displays oxidative DNA damage. The present study determined whether oxidative DNA damage was randomly distributed or whether it was localized in specific sequences in either the nuclear or mitochondrial genomes. The DNA damage-specific histone, gamma-H2AX, was detected immunohistochemically in alveolar wall cells in lung tissue from COPD patients but not control subjects. A PCR-based method was used to search for oxidized purine base products in selected 200 bp sequences in promoters and coding regions of the VEGF, TGF-β1, HO-1, Egr1, and β-actin genes while quantitative Southern blot analysis was used to detect oxidative damage to the mitochondrial genome in lung tissue from control subjects and COPD patients. Among the nuclear genes examined, oxidative damage was detected in only 1 sequence in lung tissue from COPD patients: the hypoxic response element (HRE) of the VEGF promoter. The content of VEGF mRNA also was reduced in COPD lung tissue. Mitochondrial DNA content was unaltered in COPD lung tissue, but there was a substantial increase in mitochondrial DNA strand breaks and/or abasic sites. These findings show that oxidative DNA damage in COPD lungs is prominent in the HRE of the VEGF promoter and in the mitochondrial genome and raise the intriguing possibility that genome and sequence-specific oxidative DNA damage could contribute to transcriptional dysregulation and cell fate decisions in COPD.Keywords: DNA damage, VEGF hypoxic response element, mtDNA, COPD

Emerging evidence suggests that mitochondrial (mt) DNA damage may be a trigger for apoptosis in oxidant challenged pulmonary artery endothelial cells (PAECs). Understanding the rate-limiting determinants of mtDNA repair may point to new targets for intervention in acute lung injury. The base excision repair (BER) pathway is the only pathway for oxidative damage repair in mtDNA. One of the key BER enzymes is Ogg1, which excises the base oxidation product, 8-oxoguanine. Previously we demonstrated that over-expression of mitochondrially-targeted Ogg1 in PAECs attenuated apoptosis induced by xanthine oxidase (XO) treatment. To test the idea that Ogg1 is a potentially rate-limiting BER determinant protecting cells from oxidant-mediated death, PAECs transfected with siRNA to Ogg1 were challenged with XO and the extent of mitochondrial and nuclear DNA damage was determined along with indices of apoptosis. Transfected cells demonstrated significantly reduced Ogg1 activity, which was accompanied by delayed repair of XO-induced mtDNA damage and linked to increased XO-mediated apoptosis. The nuclear genome was undamaged by XO in either control PAECs or cells depleted of Ogg1. These observations suggest that Ogg1 plays a critical and possibly rate-limiting role in defending PAECs from oxidant-induced apoptosis by limiting the persistence of oxidative damage in the mitochondrial genome.

We describe the photophysical properties of Seta-633, a commercially available near-infrared (NIR) dye, and its use as a fluorescent label to study the interaction between low-molecular-weight analytes and proteins using fluorescence lifetime as the readout parameter. In a model assay, we demonstrate that a biotinylated Seta-633 tracer binds to antibiotin with high specificity. Importantly, the lifetime of Seta-633-biotin increases about 1.8-fold upon binding to a specific antibody (antibiotin, MW = 160 kDa), while the titration with bovine serum albumin (BSA) or nonspecific antibody does not result in a noticeable change in lifetime. This behavior is contrary to that of fluorescent tracers like Cy5 or Alexa 647, which typically exhibit much smaller lifetime changes upon binding to antibodies.

Reactive oxygen species (ROS) generated in hypoxic pulmonary artery endothelial cells cause transient oxidative base modifications in the hypoxia-response element (HRE) of the VEGF gene that bear a conspicuous relationship to induction of VEGF mRNA expression (K.A. Ziel et al., FASEB J. 19, 387–394, 2005). If such base modifications are indeed linked to transcriptional regulation, then they should be detected in HRE sequences associated with transcriptionally active nucleosomes. Southern blot analysis of the VEGF HRE associated with nucleosome fractions prepared by micrococcal nuclease digestion indicated that hypoxia redistributed some HRE sequences from multinucleosomes to transcriptionally active mono- and dinucleosome fractions. A simple PCR method revealed that VEGF HRE sequences harboring oxidative base modifications were found exclusively in mononucleosomes. Inhibition of hypoxia-induced ROS generation with myxathiozol prevented formation of oxidative base modifications but not the redistribution of HRE sequences into mono- and dinucleosome fractions. The histone deacetylase inhibitor trichostatin A caused retention of HRE sequences in compacted nucleosome fractions and prevented formation of oxidative base modifications. These findings suggest that the hypoxia-induced oxidant stress directed at the VEGF HRE requires the sequence to be repositioned into mononucleosomes and support the prospect that oxidative modifications in this sequence are an important step in transcriptional activation.