Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network

In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value >0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees >60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management.

[An analysis of four cases of misdiagnosed primary lymphocytic hypophysitis]

To improve the differential diagnosis of sellar region mass, 4 cases with sellar mass and misdiagnosed as lymphocytic hypophysitis (LYH) were reviewed retrospectively.The 4 patients (2 male and 2 female) aged 20-60 years old were all presented with symptoms of headache, polydipsia and polyuria.Biochemical studies confirmed the diagnoses of central diabetes insipidus and hypopituitarism.Head MRI scans showed LYH like image for all the cases, and, thus, high dose methylprednisolone pulse therapy (HDMPT) was applied to the patients.Their symptoms deteriorated and the sellar mass enlarged after a short period of partial improvement.Operations were performed in all the patients.Histology study showed craniopharyngioma with abscess, primary abscess, secondary hypophysitis caused by Wegener's granulomatosis, and germinoma with secondary hypophysitis, respectively.In conclusion, surgery or biopsy is necessary for those who presented with sellar region mass and was suspected to be with LYH, but with poor response or even worse after HDMPT.

Characterization of retroviral infectivity and superinfection resistance during retrovirus-mediated transduction of mammalian cells

Retroviral vectors including lentiviral vectors are commonly used tools to stably express transgenes or RNA molecules in mammalian cells. Their utilities are roughly divided into two categories, stable overexpression of transgenes and RNA molecules, which requires maximal transduction efficiency, or functional selection with retrovirus (RV)-based libraries, which takes advantage of retroviral superinfection resistance. However, the dynamic features of RV-mediated transduction are not well characterized. Here, we engineered two murine stem cell virus-based retroviral vectors expressing dual fluorescence proteins and antibiotic markers, and analyzed virion production efficiency and virion stability, dynamic infectivity and superinfection resistance in different cell types, and strategies to improve transduction efficiency. We found that the highest virion production occurred between 60 and 72 h after transfection. The stability of the collected virion supernatant decreased by >60% after 3 days in storage. We found that RV infectivity varied drastically in the tested human cancer lines, while low transduction efficiency was partially overcome with increased virus titer, prolonged infection duration and/or repeated infections. Furthermore, we demonstrated that RV receptors PIT1 and PIT2 were lowly expressed in the analyzed cells, and that PIT1 and/or PIT2 overexpression significantly improved transduction efficiency in certain cell lines. Thus, our findings provide resourceful information for the optimal conditions of retroviral-mediated gene delivery.

CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice

Despite the existence of various databases cataloging cancer drugs, there is an emerging need to support the development and application of personalized therapies, where an integrated understanding of the clinical factors and drug mechanism of action and its gene targets is necessary. We have developed CATTLE (CAncer Treatment Treasury with Linked Evidence), a comprehensive cancer drug knowledge base providing information across the complete spectrum of the drug life cycle. The CATTLE system collects relevant data from 22 heterogeneous databases, integrates them into a unified model centralized on drugs, and presents comprehensive drug information via an interactive web portal with a download function. A total of 2,323 unique cancer drugs are currently linked to rich information from these databases in CATTLE. Through two use cases, we demonstrate that CATTLE can be used in supporting both research and practice in personalized oncology.

Vascularization in Engineered Tissue Construct by Assembly of Cellular Patterned Micromodules and Degradable Microspheres

Tissue engineering aims to generate functional tissue constructs in which proper extracellular matrix (ECM) for cell survival and establishment of a vascular network are necessary. A modular approach via the assembly of modules mimicking the complex tissues' microarchitectural features and establishing a vascular network represents a promising strategy for fabricating larger and more complex tissue constructs. Herein, as a model for this modular tissue engineering, engineered bone-like constructs were developed by self-assembly of osteon-like modules and fast degradable gelatin microspheres. The collagen microspheres acting as osteon-like modules were developed by seeding human umbilical vein endothelial cells (HUVECs) onto collagen microspheres laden with human osteoblast-like cells (MG63) and collagenase. Both HUVECs and MG63 cells were well spatially patterned in the modules, and collagen as ECM well supported cell adhesion, spreading, and functional expression due to its native RGD domains and enzymatic degradation activity. The patterned modules facilitated both the cellular function expression of osteogenic MG63 cells and vasculogenic HUVECs; that is, the osteon-like units were successfully achieved. The assembly of the osteon-like modules and fast degradable gelatin microspheres promoted the vascularization, thus facilitating the osteogenic function expression. The study provides a highly efficient approach to engineering complex 3D tissues with micropatterned cell types and interconnected channels.

Aligned copper nanorod arrays for highly efficient generation of intense ultra-broadband THz pulses

We demonstrate an intense broadband terahertz (THz) source based on the interaction of relativistic-intensity femtosecond lasers with aligned copper nanorod array targets. For copper nanorod targets with a length of 5 μm, a maximum 13.8 times enhancement in the THz pulse energy (in ≤20 THz spectral range) is measured as compared to that with a thick plane copper target under the same laser conditions. A further increase in the nanorod length leads to a decrease in the THz pulse energy at medium frequencies (≤20 THz) and increase of the electromagnetic pulse energy in the high-frequency range (from 20–200 THz). For the latter, we measure a maximum energy enhancement of 28 times for the nanorod targets with a length of 60 μm. Particle-in-cell simulations reveal that THz pulses are mostly generated by coherent transition radiation of laser produced hot electrons, which are efficiently enhanced with the use of nanorod targets. Good agreement is found between the simulation and experimental results.

Efficacy and safety of basiliximab in liver transplantation for patients with hepatitis B virus-related diseases: a single centre study

AIMS

We aim to evaluate the efficacy and safety of basiliximab in liver transplantation (LT) for patients with hepatitis B virus-related diseases.

METHODS

A total of 268 patients with hepatitis B virus-related diseases undergoing LT were enrolled and divided into two groups according to the usage of basiliximab. Total survival, the survival of high-risk patients defined by the posttransplant model for predicting mortality, acute rejection rate, biochemical parameters and other follow-up data were compared between the two groups.

RESULTS

Group Bas was composed of 131 patients who received basiliximab, and Group Triple enrolled the other 137 patients who did not. Between the two groups, there was no significant difference in the cumulative survival of patients without hepatocellular carcinoma (HCC) or in the cumulative survival of patients with HCC. For patients with benign end-stage liver diseases, Group Bas had more patients with a high risk of short- and medium-term mortality than Group Triple (22.81% vs. 8.85%, p = 0.017), but the survival curves of the two groups were not significantly different. The 1-year incidence of acute rejection was lower in Group Bas, although the difference was not significant (8.75% vs. 15.33%, p > 0.05). In both Group Bas and Group Triple, the level of serum creatinine (Scr) at 1 week posttransplantation was significantly lower than pretransplantation (61.00 vs. 88.50 μmol/l, p < 0.001; 61.50 vs. 74.00 μmol/l, p < 0.001; respectively). There was a significant difference in the pretransplantation Scr between the two groups (88.50 vs. 74.00 μmol/l, p = 0.005), but the values of Scr decreased to the same level 1 week (61.00 vs. 61.50 μmol/l, p > 0.05) and 4 weeks (61.00 vs. 59.00 μmol/l, p > 0.05) after transplantation. Significantly fewer recipients in Group Bas experienced hepatitis B relapse than in Group Triple (2/131 vs. 13/137, p = 0.006).

CONCLUSIONS

A basiliximab-induced immunosuppressive protocol is a safe regimen that achieves similar survival without increasing the acute rejection rate for LT recipients with hepatitis B virus-related diseases. For patients with benign end-stage liver diseases, this regimen reduces medium-term mortality in high-risk patients. This regimen remarkably improves renal function in the first month after LT and is correlated with a decreased hepatitis B recurrence rate in adult patients after LT.

The microRNA-182-PDK4 axis regulates lung tumorigenesis by modulating pyruvate dehydrogenase and lipogenesis

Reprogrammed metabolism is one of the hallmarks of cancer. The dysregulation of glycolysis in cancer has been heavily studied. However, it remains largely unclear how other metabolic processes are regulated in cancer cells. Here we show that microRNA-182 (miR-182) suppresses pyruvate dehydrogenase (PDH) kinase 4 (PDK4) and promotes lung tumorigenesis. miR-182 is dysregulated and inversely correlated with PDK4 in human lung adenocarcinomas. The miR-182-PDK4 axis regulates lung cancer cell growth by modulating the activity of PDH, the gatekeeping enzyme of pyruvate flux into acetyl-CoA, and subsequently de novo lipogenesis of cancer cells. Suppression of lipogenesis by silencing ATP citrate lyase (ACLY) and fatty acid synthase (FASN) or by chemical inhibitors diminishes the effects of miR-182-PDK4 in tumor growth. Alteration of de novo lipogenesis also affects reactive oxygen species (ROS) production and the downstream JNK signaling pathway. Hence, our work suggests that the miR-182-PDK4 axis is a crucial regulator of cancer cell metabolism and a potential target for antitumor therapy.

[Microsurgical management of petroclival meningiomas combined trans-subtemporal and suboccipital retrosigmoid keyhole approach]

OBJECTIVE

With the development of modern skull base minimally invasive technology mature and neural radio surgery techniques, it is necessary to re-examine the therapeutic strategy for the treatment of petroclival meningiomas. To sum up the operative experience and methods in microsurgical resection of petroclival meningiomas by the combining trans-subtemporal and suboccipital retrosigmoid keyhole approach. To explore the minimally invasive operation approach of petroclival meningiomas, to raise the removal degree and to improve the postoperative result using this approach.

METHODS

The clinical data of the consecutive 21 patients with the petroclival meningiomas were reviewed retrospectively. The method, degree of tumor resection,techniques of the combining keyhole approach, Karnofsky performance score (KPS) before and after operation were also analyzed. The neuronavigation guided operation was performed in 9 cases, and 12 cases were operated in the neuroelectrophysiological monitoring.

RESULTS

Total excision of the tumor resection (Simpson, I-II levels) was conducted in 18 cases (85.7%, 18/21), and 3 patients underwent close resection (Simpson III level, 14.3%, 3/21). Postoperative three-dimensional CT showed good lock bone flap restoration; Postoperative pathology confirmed meningioma. Postoperative cranial nerve dysfunction or new original nerve dysfunction were aggravated in 5 cases (23.8%) , including transient trochlear nerve (3 cases), abducent nerve (1 case), and the motor branch of trigeminal nerve paralysis (1 case). Abducent nerve paralysis (1 case) appeared, with hearing impairment. After the 3-month follow-up, 11 cases had the same KPS aspreoperation, 7 cases improved, and 3 cases not improved. The KPS score was 77.14±23.12 on average, and there was no statistically significant difference compared with that before operation (P>0.05). The postoperative follow-up for half a year showed fluent speaking and writing in 19 cases (KPS 70 or higher), and general recovery in 2 cases (KPS<70). The postoperative follow-up for 3-29 months showed no tumor recurrence or progress.

CONCLUSION

The combining trans-subtemporal and suboccipital retrosigmoid keyhole approach is simple, safe, and minimally invasive, and an ideal operation approach of petroclival meningioma. To master the operation skills and the intraoperative matters needing attention in the operation, is favorable to improve the resection rate and curative effect.

Production of the 14 kDa trypsin inhibitor protein is important for maize resistance against Aspergillus flavus infection/aflatoxin accumulation

Maize (Zea mays L.) is one of the major crops susceptible to Aspergillus flavus Link ex. Fries infection and subsequent aflatoxin contamination. Previous studies found the production of an antifungal 14 kDa trypsin inhibitor (TI) was associated with maize aflatoxin resistance. To further investigate whether the TI plays any direct role in resistance, a TI gene silencing vector was constructed and transformed into maize. Mature kernels were produced from 66 transgenic lines representing 18 independent events. A final total of twelve lines representing four independent events were confirmed positive for transformation, five of which showed significant reduction (63 to 88%) in TI transcript abundance in seedling leaf tissue and seven of which showed significant TI protein reduction (39-85%) in mature kernels. Six of the seven silenced transgenic lines supported higher levels of aflatoxin production compared to negative controls. To further confirm the role of TI in field resistance to aflatoxin accumulation, DNA sequence polymorphisms from within the gene or linked simple sequence repeats were tested in four quantitative trait loci (QTL) mapping populations for QTL effect, and three QTL with log of the odds scores of 11, 4.5, and 3.0 and possibly caused by the TI protein encoding gene were found. Sequence polymorphisms were also tested for association to aflatoxin levels in an association mapping panel, and three single nucleotide polymorphisms were found associated with aflatoxin accumulation (P<0.01). The data from both RNAi and genetic mapping studies demonstrated that production of the TI in maize is important for its resistance to A. flavus infection and/or aflatoxin production.

Deletion of G-protein-coupled receptor 55 promotes obesity by reducing physical activity

BACKGROUND/OBJECTIVES

Cannabinoid receptor 1 (CB1) is the best-characterized cannabinoid receptor, and CB1 antagonists are used in clinical trials to treat obesity. Because of the wide range of CB1 functions, the side effects of CB1 antagonists pose serious concerns. G-protein-coupled receptor 55 (GPR55) is an atypical cannabinoid receptor, and its pharmacology and functions are distinct from CB1. GPR55 regulates neuropathic pain, gut, bone, immune functions and motor coordination. GPR55 is expressed in various brain regions and peripheral tissues. However, the roles of GPR55 in energy and glucose homeostasis are unknown. Here we have investigated the roles of GPR55 in energy balance and insulin sensitivity using GPR55-null mice (GPR55(-/-)).

METHODS

Body composition of the mice was measured by EchoMRI. Food intake, feeding behavior, energy expenditure and physical activity of GPR55(-/-) mice were determined by indirect calorimetry. Muscle function was assessed by forced treadmill running test. Insulin sensitivity was evaluated by glucose and insulin tolerance tests. Adipose inflammation was assessed by flow cytometry analysis of adipose tissue macrophages. The expression of inflammatory markers in adipose tissues and orexigenic/anorexigenic peptides in the hypothalamus was also analyzed by real-time PCR.

RESULTS

GPR55(-/-) mice had normal total energy intake and feeding pattern (i.e., no changes in meal size, meal number or feeding frequency). Intriguingly, whereas adult GPR55(-/-) mice only showed a modest increase in overall body weight, they exhibited significantly increased fat mass and insulin resistance. The spontaneous locomotor activity of GPR55(-/-) mice was dramatically decreased, whereas resting metabolic rate and non-shivering thermogenesis were unchanged. Moreover, GPR55(-/-) mice exhibited significantly decreased voluntary physical activity, showing reduced running distance on the running wheels, whereas muscle function appeared to be normal.

CONCLUSIONS

GPR55 has an important role in energy homeostasis. GPR55 ablation increases adiposity and insulin resistance by selectively decreasing physical activity, but not by altering feeding behavior as CB1.

[Microsurgical management of petroclival meningiomas combined trans-subtemporal and suboccipital retrosigmoid keyhole approach]

OBJECTIVE

With the development of modern skull base minimally invasive technology mature and neural radio surgery techniques, it is necessary to re-examine the therapeutic strategy for the treatment of petroclival meningiomas. To sum up the operative experience and methods in microsurgical resection of petroclival meningiomas by the combining trans-subtemporal and suboccipital retrosigmoid keyhole approach. To explore the minimally invasive operation approach of petroclival meningiomas, to raise the removal degree and to improve the postoperative result using this approach.

METHODS

The clinical data of the consecutive 21 patients with the petroclival meningiomas were reviewed retrospectively. The method, degree of tumor resection,techniques of the combining keyhole approach, Karnofsky performance score (KPS) before and after operation were also analyzed. The neuronavigation guided operation was performed in 9 cases, and 12 cases were operated in the neuroelectrophysiological monitoring.

RESULTS

Total excision of the tumor resection (Simpson, I-II levels) was conducted in 18 cases (85.7%, 18/21), and 3 patients underwent close resection (Simpson III level, 14.3%, 3/21). Postoperative three-dimensional CT showed good lock bone flap restoration; Postoperative pathology confirmed meningioma. Postoperative cranial nerve dysfunction or new original nerve dysfunction were aggravated in 5 cases (23.8%) , including transient trochlear nerve (3 cases), abducent nerve (1 case), and the motor branch of trigeminal nerve paralysis (1 case). Abducent nerve paralysis (1 case) appeared, with hearing impairment. After the 3-month follow-up, 11 cases had the same KPS aspreoperation, 7 cases improved, and 3 cases not improved. The KPS score was 77.14±23.12 on average, and there was no statistically significant difference compared with that before operation (P>0.05). The postoperative follow-up for half a year showed fluent speaking and writing in 19 cases (KPS 70 or higher), and general recovery in 2 cases (KPS<70). The postoperative follow-up for 3-29 months showed no tumor recurrence or progress.

CONCLUSION

The combining trans-subtemporal and suboccipital retrosigmoid keyhole approach is simple, safe, and minimally invasive, and an ideal operation approach of petroclival meningioma. To master the operation skills and the intraoperative matters needing attention in the operation, is favorable to improve the resection rate and curative effect.

Abstract P6-18-01: Novel genetic susceptibility loci for inflammatory breast cancer identified by whole exome sequencing

Background: Inflammatory breast cancer (IBC) is an extremely aggressive form of locally advanced breast cancer that affects approximately 5% of breast cancer patients. The prognosis of IBC patients is remarkably poor, with a three-year survival rate of approximately 30% compared to 60% for non-IBC breast cancer patients. The etiology of IBC is largely unknown. A few risk factors have been reported such as body mass index (BMI) and educational level. Prior evidence has also implicated genetic components in IBC etiology. For instance, the reported familial cases and racial incidence disparity of IBC patients, as well as the fact IBC patients typically have a younger age onset than non-IBC patients, all indicated the possible involvement of genetic factors. Nevertheless, as yet no genetic epidemiological study has been reported to evaluate IBC genetic predisposition.

Methods: To test the hypothesis that genetic variants and mutations may affect IBC susceptibility, we performed whole exome sequencing in a pilot case-control study that contained 70 IBC cases and 119 unrelated cancer-free controls. Sequencing data were de-multiplexed, filtered, assessed for various quality control metrics, mapped to reference genome and annotated. Comprehensive single variant-based, gene-centered, and pathway-based analyses were conducted to identify variants, genes, and pathways that may be involved in IBC predisposition.

Results: We obtained &gt; 50x on-target sequencing coverage of the whole exome in &gt; 90% of the patients. In single variant analysis, we identified six variants reaching genome-wide significance. Four variants were encoded by genes that have been implicated in breast cancer development including MALAT1, MAP3K9, POLR3B, and FIP1L1. Two variants were encoded by novel genes that have not been related to breast cancer, including CCDC30 and LINC01565. Two types of analyses based on a gene-centered strategy identified top genes such as SLC39A4, CDHR1, AP5Z1, GNB3, ITGA10, etc. However, possibly due to the limited sample size, none of these genes reached genome-wide significance. Ingenuity Pathway Analysis (IPA), using the complete list of significant genes identified by each of these analyses all reported "cancer" as the highest possible disorder associated with these genes, demonstrating the biological plausibility of our findings. Moreover, canonical pathways such as IL4 signaling, glycogen degradation, epithelial adherence junction signaling, and CCR3 signaling in eosinophils were among the top pathways that were found involved in IBC predisposition.

Conclusion: Overall, we provided novel preliminary evidence that genetic variants are potentially associated with the risk of developing IBC. We are currently conducting validation studies with larger sample sizes are warranted to confirm these findings and identify additional genetic susceptibility loci.

Citation Format: Ye Z, Li B, Wang C, Zhong X, Wei Q, Mu Z, Austin L, Jaslow R, Avery T, Palazzo J, Biederman L, Yang H, Cristofanilli M, IBC Inflammatory Breast Cancer International Consortium. Novel genetic susceptibility loci for inflammatory breast cancer identified by whole exome sequencing. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-18-01.

Neutral particles pushed or pulled by laser pulses

Acceleration of neutral particles is of great importance in many areas, such as controlled chemical reactions, atomic nanofabrication, and atom optics. Recent experimental studies have shown that pulsed lasers can be used to push neutral Rydberg atoms forward [Nature 461, 1261 (2009)10.1038/nature08481; Nat. Photonics 6, 386 (2012)10.1038/nphoton.2012.87]. Our simulation shows that pulsed lasers can also be used to pull Rydberg atoms back toward a light source. In particular, we proposed a method of using two laser pulses on a neutral atom, then selective operations on the neutral atom (pushing or pulling) can be performed by adjusting the delay time between the two laser pulses.

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence information to improve molecular-assisted markers to study C. nasus genetic diversity.

Ultra-sparse metasurface for high reflection of low-frequency sound based on artificial Mie resonances

Acoustic metamaterials offer great flexibility for manipulating sound waves and promise unprecedented functionality, ranging from transformation acoustics, super-resolution imaging to acoustic cloaking. However, the design of acoustic metamaterials with exciting functionality remains challenging with traditional approaches using classic acoustic elements such as Helmholtz resonators and membranes. Here we demonstrate an ultraslow-fluid-like particle with intense artificial Mie resonances for low-frequency airborne sound. Eigenstate analysis and effective parameter retrieval show two individual negative bands in the single-size unit cell, one of which exhibits a negative bulk modulus supported by the monopolar Mie resonance, whereas the other exhibits a negative mass density induced by the dipolar Mie resonance. The unique single-negative nature is used to develop an ultra-sparse subwavelength metasurface with high reflectance for low-frequency sound. We demonstrate a 0.15λ-thick, 15%-filling ratio metasurface with an insertion loss over 93.4%. The designed Mie resonators provide diverse routes to construct novel acoustic devices with versatile applications.