Abstract 4257: Integrated network analysis reveals potentially novel molecular pathways mechanism and therapeutic targets of pancreatic ductal adenocarcinoma

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human cancers and shows insensitivity towards many chemotherapeutic drugs and target-based drugs. There is an urgently need to identify PDAC disease mechanism and detect novelty drug targets. With the large availability of protein interaction networks and microarray data supported, to identify the disease essential genes that have biological significance for potential drug targets is a challenge issue still.

Methods: In this study, protein interaction network PathPPI, DrugBank targets and 374 transcriptome profiles from Gene Expression Omnibus (GEO) by Affymetrix HU 133 Plus 2.0 array test are collected. These microarray data includes 140 PDAC, 92 pancreatic cancer cell-line, 58 human normal pancreas tissues, and 72 patient original xenograft mouse. Based on these datasets, a novelty-integrated algorithm was developed for drug target prioritization by perturbed gene expression and network information. The integration network included data driven reconstruction network of gene regulatory (GRN) by Bayesian Network and protein interaction PathPPI network. The perturbed gene expression was refer to the differential expression genes of tumor verse adjacent normal. A novel hybrid method based on genetic algorithm (GA) is proposed to search the attractor with the maximum network perturbation for candidate drug targets in PDAC.These targets’ molecular mechanism was revealed further by network structure comparison of PDAC that is consistent with xerograph mouse model and cancer cells.

Results: Highly accordance 56 genes with high perturbation score both in mRNAs and protein-protein network were identified and recommended as candidate drug targets for PDAC, including 16 novel targets, such as PSMD2, EPOR and PSMB9. Fifty-four essential genes shown strong concordance among tumor-model, patient drive xenograft mouse and pancreatic cancer cell-line by systematically comparison. We identified 1375 dysregulated genes that enriched in 25 pathways in PDAC by Gene Set Enrichment Analysis, among which 244 genes played as hubs in reconstructed PDAC regulatory network.

Conclusion: In the study, we developed a global optimization-based inference of network perturbation to detect attractor for drug-target identification in PDAC tumors. The assembling Bayesian Network-based approach with protein-protein interaction provides a comprehensive information to observe energy transfer of gene perturbation in network to detect global optimum attractor for drug target selection.

Citation Format: Lijun Cheng, Enze Liu, Li Lang, Xiaolin Cheng, Xiaotian Kong, Korc Murray. Integrated network analysis reveals potentially novel molecular pathways mechanism and therapeutic targets of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4257.

Crystal structure of 5-(4-chlorophenyl)-3-(4-fluorophenyl)-1-phenyl-4,5-dihydro-1H-pyrazole, C21H16ClFN2

C21H16ClFN2, monoclinic, P21/c (no. 14), a = 20.286(4) Å, b = 5.3827(11) Å, c = 16.254(3) Å, β = 104.95(3)°, Z = 4, V = 1714.7(7) Å3, R gt(F) = 0.0548, wR ref(F 2) = 0.1199, T = 293(2) K.

The olfactory stimulation slows down the substance clearance in the extracellular space of the hippocampus in rat brain

Accelerating the clearance of toxin in the brain extracellular space (ECS) has grown a promising strategy for treating some central nervous system diseases. As oldest sensory system, we know little about the influence of olfaction on the brain, but preclinical studies such as treatment of neurological diseases through it are in the ascendant. This makes it important to clarify the effects of olfaction on brain ECS and interstitial fluid (ISF) drainage. In this study, the effect of olfactory stimulation (eugenol, EUG) on ISF flow in hippocampus and its association with aquaporin 4 (Aqp4) had been investigated. The results show that eugenol can significantly increase the activity of hippocampal neurons, but reduce the clearance and diffusion rates of Gd-DTPA and A-594 in hippocampus. Similarly, eugenol inhalation slows down the rate of Gd-DTPA in CSF entering the hippocampus and its clearance. And knockout of Aqp4 gene aggravated these processes. In vitro results showed that after Aqp4 gene silencing, astrocytes grew slowly, with significantly decreased cells number, less nuclei, atrophied bodies and shorter processes. These results concluded that olfactory stimulation can change the ECS structure of the hippocampus, slow down the ISF drainage, and improve the function of neurons, while Aqp4 plays important roles.

The effects of dihydroxyphenyl lactic acid on alleviating blood-brain barrier injury following subarachnoid hemorrhage in rats

BACKGROUND

In this study, the protective effects of 3,4-dihydroxyphenyl lactic acid (DLA) on blood-brain barrier (BBB) injury following subarachnoid hemorrhage (SAH) has been explored.

METHODS

Male Sprague-Dawley rats (weight 300-350 g) were used to establish the SAH model using the endovascular perforation method. The animals were randomly divided into four groups: sham (n = 40), SAH (n = 46), SAH + vehicle (n = 44), and SAH + DLA (n = 40) treatment groups. At 1 h after SAH, either DLA (10 mg/kg) or normal saline (vehicle) was administered by femoral vein injection. The effects of DLA on mortality, neurological function, brain water content, and BBB were observed. Additionally, immunohistochemistry and western blot techniques were applied to investigate the mechanism of action of DLA.

RESULTS

We found that the administration of DLA (10 mg/kg) following SAH could improve neurological functions, reduce brain water content, and maintain BBB integrity. The expression of pro-inflammatory and pro-apoptotic factors such as toll-like receptor 4 (TLR4), NF-κB (p-p65), tumor necrosis factor-α, p-p38 MAPK, p-p53, and caspase-3 were significantly increased after SAH. These same factors were markedly attenuated following treatment with DLA.

CONCLUSIONS

These findings showed that DLA can alleviate BBB injury following SAH through its anti-inflammatory and anti-apoptotic effects via suppression of TLR4 and its downstream NF-κB and p38 MAPK pathways.

Appendicular lean mass and fracture risk assessment: implications for FRAX® and sarcopenia

The vast majority of current sarcopenia definitions use DXA-derived appendicular lean mass (DXA ALM) as an approximation of muscle mass. However, there is increasing evidence that ALM is poorly predictive of incident fractures. In this editorial, we describe findings from several cohorts suggesting that DXA ALM gives only limited information on the risk of incident fracture, and that in the US MrOS, WHI and Health ABC cohorts, accounting for femoral neck bone mineral density may entirely remove ALM-fracture associations. These observations raise important questions about the role of DXA ALM both in sarcopenia definitions and as a potential input variable for FRAX. We conclude that DXA ALM is unlikely to be a useful addition to the FRAX tool, but that other means of estimating muscle mass, such as those derived from creatine dilution or peripheral quantitative CT, might offer more value for fracture risk assessment.

Structural and functional study for tRNA cleavage by Glycine o-phenanthroline CuII complex, [CuCl(phen)(gly)]∙4H2O

The o-phenanthroline gly Cu(II) complex, [CuCl(phen)(gly)]∙4H₂O 1, has been prepared and structurally characterized. The transfer RNA binding and degradation properties of complex 1 have been investigated by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE) and atomic force microscopy (AFM) methods. The results showed that 1 can efficiently cleave tRNA in the physiological conditions (pH 7.0, and 37 °C), and has a digestion coefficient nearly up to 100% within 75 h. AFM image for 1/RNA exhibited arrayed tandem repetitions of tRNA segments. This study is targeting the destruction of the high-order structures of genetic biomacromolecules which paves an important way to novel materials for the decontamination of microorganisms (e.g., bacteria and viruses).

Integration of genomic copy number variations and chemotherapy-response biomarkers in pediatric sarcoma

Background

While most pediatric sarcomas respond to front-line therapy, some bone sarcomas do not show radiographic response like soft-tissue sarcomas (rhabdomyosarccomas) but do show 90% necrosis. Though, new therapies are urgently needed to improve survival and quality of life in pediatric patients with sarcomas. Complex chromosomal aberrations such as amplifications and deletions of DNA sequences are frequently observed in pediatric sarcomas. Evaluation of copy number variations (CNVs) associated with pediatric sarcoma patients at the time of diagnosis or following therapy offers an opportunity to assess dysregulated molecular targets and signaling pathways that may drive sarcoma development, progression, or relapse. The objective of this study was to utilize publicly available data sets to identify potential predictive biomarkers of chemotherapeutic response in pediatric Osteosarcoma (OS), Rhabdomyosarcoma (RMS) and Ewing’s Sarcoma Family of Tumors (ESFTs) based on CNVs following chemotherapy (OS n = 117, RMS n = 64, ESFTs n = 25 tumor biopsies).

Methods

There were 206 CNV profiles derived from pediatric sarcoma biopsies collected from the public databases TARGET and NCBI-Gene Expression Omnibus (GEO). Through our comparative genomic analyses of OS, RMS, and ESFTs and 22,255 healthy individuals called from the Database of Genomic Variants (DGV), we identified CNVs (amplifications and deletions) pattern of genomic instability in these pediatric sarcomas. By integrating CNVs of Cancer Cell Line Encyclopedia (CCLE) identified in the pool of genes with drug-response data from sarcoma cell lines (n = 27) from Cancer Therapeutics Response Portal (CTRP) Version 2, potential predictive biomarkers of therapeutic response were identified.

Results

Genes associated with survival and/recurrence of these sarcomas with statistical significance were found on long arm of chromosome 8 and smaller aberrations were also identified at chromosomes 1q, 12q and x in OS, RMS, and ESFTs. A pool of 63 genes that harbored amplifications and/or deletions were frequently associated with recurrence across OS, RMS, and ESFTs. Correlation analysis of CNVs from CCLE with drug-response data of CTRP in 27 sarcoma cell lines, 33 CNVs out of 63 genes correlated with either sensitivity or resistance to 17 chemotherapies from which actionable CNV signatures such as IGF1R, MYC, MAPK1, ATF1, and MDM2 were identified. These CNV signatures could potentially be used to delineate patient populations that will respond versus those that will not respond to a particular chemotherapy.

Conclusions

The large-scale analyses of CNV-drug screening provides a platform to evaluate genetic alterations across aggressive pediatric sarcomas. Additionally, this study provides novel insights into the potential utilization of CNVs as not only prognostic but also as predictive biomarkers of therapeutic response. Information obtained in this study may help guide and prioritize patient-specific therapeutic options in pediatric bone and soft-tissue sarcomas.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0456-5) contains supplementary material, which is available to authorized users.

The roles of astrocyte in the brain pathologies following ischemic stroke

Aim: In this work, we systematically explored the physiological functions of astrocytes and their roles following ischemic stroke, additionally, the potential therapy strategy targeting the astrocytes was also discussed. Methods: This work searched the PubMed database (including MEDLINE) until 14 Feb 2018, and furthermore, the studies were identified through cross-referencing and by consulting the experts in this field. Results: This study indicated that the astrocytes can not only play harmful roles following ischemic stroke through release of inflammatory factors and formation of glial scar but also have protective effects through quenching glutamate excitotoxicity and maintaining the clearance function of glymphatic system in brain. Conclusion: Owing to their important roles in physiological functions of brain and in the pathological conditions following ischemic stroke, the astrocytes might be a potential but promising therapeutic target for treating the ischemic stroke in the future.