Single-Cell RNA-Sequencing in Glioma

Abstract

Purpose of Review

In this review, we seek to summarize the literature concerning the use of single-cell RNA-sequencing for CNS gliomas.

Recent Findings

Single-cell analysis has revealed complex tumor heterogeneity, subpopulations of proliferating stem-like cells and expanded our view of tumor microenvironment influence in the disease process.

Summary

Although bulk RNA-sequencing has guided our initial understanding of glioma genetics, this method does not accurately define the heterogeneous subpopulations found within these tumors. Single-cell techniques have appealing applications in cancer research, as diverse cell types and the tumor microenvironment have important implications in therapy. High cost and difficult protocols prevent widespread use of single-cell RNA-sequencing; however, continued innovation will improve accessibility and expand our of knowledge gliomas.

Comment on “Trivalent CAR T cells overcome interpatient antigenic variability in glioblastoma”

The authors of this study¹ should be commended on the important and complex undertaking of identifying multiple antigens for chimeric antigen receptor (CAR) T-cell therapy, which is one of several key limitations to the field. There are 2 levels of antigenic heterogeneity at play that require consideration—intrapatient variability, in which the existence of antigen-negative tumor cells may result in eventual recurrence, and interpatient variability, in which different expression patterns across all patients make identification of a single or "universal" therapeutic for treatment difficult, if not impossible. The authors state that by targeting 3 antigens: human epidermal growth factor receptor 2 (HER2), interleukin-13 receptor alpha 2 (IL13Rα2), and ephrin-A2 (EphA2) using a trivalent UCAR, they can "overcome intrapatient and interpatient variability" and that "trivalent T cells were able to approach killing in 100% of tumor cells in nearly all patients modeled." As investigators working in the field of immuno-oncology, we very much wish this to be the case; however, these conclusions are not supported by the data presented in the manuscript.

Effluent concentration and removal efficiency of nine heavy metals in secondary treatment plants in Shanghai, China

Abstract

Wastewater treatment plants (WWTPs) are the most common form of industrial and municipal wastewater control. To evaluate the performance of wastewater treatment and the potential risk of treated wastewater to aquatic life and human health, the influent and effluent concentrations of nine toxic metals were determined in 12 full-scale WWTPs in Shanghai, China. The performance was evaluated based on national standards for reclamation and aquatic criteria published by US EPA, and by comparison with other full-scale WWTPs in different countries. Potential sources of heavy metals were recognized using partial correlation analysis, hierarchical clustering, and principal component analysis (PCA). Results indicated significant treatment effect on As, Cd, Cr, Cu, Hg, Mn, Pb, and Zn. The removal efficiencies ranged from 92% (Cr) to 16.7% (Hg). The results indicated potential acute and/or chronic effect of Cu, Ni, Pb, and Zn on aquatic life and potential harmful effect of As and Mn on human health for the consumption of water and/or organism. The results of partial correlation analysis, hierarchical clustering based on cosine distance, and PCA, which were consistent with each other, suggested common source of Cd, Cr, Cu, and Pb and common source of As, Hg, Mn, Ni, and Zn. Hierarchical clustering based on Jaccard similarity suggested common source of Cd, Hg, and Ni, which was statistically proved by Fisher's exact test.

Wound outcomes in negative pressure dressings (wound) study – a randomised trial in lower limb skin cancer

The incidence of skin cancer in New Zealand is one of the highest in the world.1 Surgical excision is the mainstay of treatment for these lesions. While excision and primary closure is desirable, wounds in the lower limb are often too large or complex to obtain direct apposition and split thickness skin grafting is used to achieve wound closure without tissue tension.2,3 Grafting in the lower limb carries a high risk of failure. Over the years, various methods have been employed to reduce the risk of graft failure.

Exposure to 2,4-dichlorophenoxyacetic acid induced PPARβ-dependent disruption of glucose metabolism in HepG2 cells

Abstract

2,4-Dichlorophenoxyacetic acid is one of the most widely used herbicides. Its impact on health is increasingly attracting great attentions. This study aimed to investigate the effect of 2,4-dichlorophenoxyacetic acid on glucose metabolism in HepG2 cells and the underlying mechanism. After 24 h exposure to 2,4-dichlorophenoxyacetic acid, glycogen was measured by PAS staining and glucose by ELISA in HepG2 cells. The expression of genes involved in glucose metabolism was measured by real-time PCR, Western blotting, and immunofluorescence. HepG2 cells presented more extracellular glucose consumption and glycogen content after exposed to 2,4-dichlorophenoxyacetic acid. Expression of gluconeogenesis-related genes, FoxO1, and CREB is significantly elevated. Moreover, PPARβ was up-regulated dose-dependently. SiRNA knockdown of PPARβ completely rescued the increase of glycogen accumulation and glucose uptake, and the up-regulation of FOXO1 and CREB expression. Our findings propose novel mechanisms that 2,4-dichlorophenoxyacetic acid causes glucose metabolism dysfunction through PPARβ in HepG2 cells.

Bovine serum albumin binding study to erlotinib using surface plasmon resonance and molecular docking methods

Publication date: Available online 9 April 2018
Source:Journal of Photochemistry and Photobiology B: Biology
Author(s): Parvin Taghipour, Mostafa Zakariazadeh, Maryam Sharifi, Jafar Ezzati Nazhad Dolatabadi, Abolfazl Barzegar
Bovine serum albumin (BSA) is the most abundant protein in the blood circulation and it is commonly used for drug delivery in blood. Therefore, we study BSA interaction with erlotinib as an anticancer drug using surface plasmon resonance (SPR) and molecular modeling methods under physiological conditions (pH = 7.4). BSA immobilized on carboxymethyl dextran hydrogel Au chip (CMD) after activation with N-hydroxysuccinimide and N-ethyl-N-(3-diethylaminopropyl) carbodiimide and then the erlotinib binding to BSA at different concentrations was evaluated. Increasing of erlotinib concentration led to dose-response sensorgrams of BSA. The amount of equilibrium constant (KD) at 25 °C (4.25 × 10⁻⁹) showed the high affinity of erlotinib to BSA. Thermodynamic parameters were attained at four different temperatures. The positive value of enthalpy and entropy showed that hydrophobic forces play major role in the interaction of erlotinib with BSA. Besides, the positive value of Gibbs free energy demonstrated that the interaction of erlotinib with BSA was nonspontaneous and enthalpy driven and the complexion of drug were dependent on endothermic process. According to the molecular docking study, the most favorable binding sites of erlotinib on the BSA were subdomain IIIA and IB. Moreover, molecular docking study results showed that hydrogen binding has a role in intermolecular force that stabilize erlotinib–BSA complex.

Graphical abstract

Improved hypocrellin A production in Shiraia bambusicola by light-dark shift

Publication date: Available online 9 April 2018
Source:Journal of Photochemistry and Photobiology B: Biology
Author(s): Chun Xiao Sun, Yan Jun Ma, Jian Wen Wang
Hypocrellin A (HA) is a major bioactive perylenequinone from the fruiting body of Shiraia bambusicola used for the treatment of skin diseases and developed as a photodynamic therapy (PDT) agent against cancers and viruses. The mycelial culture of S. bambusicola under dark is a biotechnological alternative for HA production but with low yield. In this study, light and dark conditions were investigated to develop effective elicitation on HA production in the cultures. Our results showed the constant light at 200 lx stimulated HA production without any growth retardation of mycelia. A light/dark shift (24: 24 h) not only increased HA content in mycelia by 65%, but stimulated HA release into the medium with the highest total HA production 181.67 mg/L on day 8, about 73% increase over the dark control. Moreover, light/dark shifting induced the formation of smaller and more compact fungal pellets, suggesting a new effective strategy for large-scale production of HA in mycelium cultures. The light/dark shift up-regulated the expression levels of two reactive oxygen species (ROS) related genes including superoxide-generating NADPH oxidase (Nox) and cytochrome c peroxidase (CCP), and induced the generation of ROS. With the treatment of vitamin C, we found that ROS was involved in the up-regulated expression of key biosynthetical genes for hypocrellins and improved HA production. These results provide a basis for understanding the influence of light/dark shift on fungal metabolism and the application of a novel strategy for enhancing HA production in submerged Shiraia cultures.

Graphical abstract

Photochemical interaction of ascorbic acid and nicotinamide in aqueous solution: A kinetic study

Publication date: Available online 8 April 2018
Source:Journal of Photochemistry and Photobiology B: Biology
Author(s): Iqbal Ahmad, Muhammad Furqan Mobeen, Muhammad Ali Sheraz, Sofia Ahmed, Zubair Anwar, Ruby Saeed Shaikh, Imtiaz Hussain, Saiyed Muhammad Ali
The photodegradation of ascorbic acid (AH2) in the presence of nicotinamide (NA) at pH 2.0–12.0 has been studied using a 30 W UV radiation source. The reaction follows first-order kinetics and the values of apparent first-order rate constants (kobs) at 1 × 10⁻³ M NA concentration range from 1.17 (pH 2.0) to 3.61 × 10⁻³ min⁻¹ (pH 12.0). The values of these rate constants (k0) in the absence of NA range from 0.50 (pH 2.0) to 1.75 × 10⁻³ min⁻¹ (pH 12.0), indicating that the values of kobs for the photodegradation of AH2 in the presence of NA are about 2 fold compared to those of the AH2 alone. The second-order rate constants (k^') for the photochemical interaction of AH2 and NA are in the range of 0.67 (pH 2.0) and 1.86 × 10⁻³ M⁻¹ min⁻¹ (pH 12.0). The log k2-pH profile shows a gradual increase in the rate as a function of pH. This is due to the ionization of AH2 to give ascorbyl anions (AH⁻) which are more susceptible to photodegradation compared to the neutral molecule (AH2). NA appears to undergo photochemical interaction with AH2 during the reaction by acting as an electron acceptor to enhance its rate of photodegradation. The concentrations of AH2 and NA in degraded solutions have been determined by a two-component spectrometric method at 243 and 261 nm (pH 2.0) with a precision of ±2%. The method has been validated and the results are comparable to the HPLC method.

Graphical abstract

Mapping microbiology with scientometrics: help provide a clearer vision of microbiology research around the globe

An intraoperative fluoroscopic method to accurately measure the post-implantation position of pedicle screws

Abstract

Purpose

Pedicle screw malplacement, leading to neurological symptoms, vascular injury, and premature implant loosening, is not uncommon and difficult to reliably detect intraoperatively with current techniques. We propose a new intraoperative post-placement pedicle screw position assessment system that can therefore allow surgeons to correct breaches during the procedure. Our objectives were to assess the accuracy and robustness of this proposed screw location system and to compare its performance to that of 2D planar radiography.

Methods

The proposed system uses two intraoperative X-ray shots acquired with a standard fluoroscopic C-arm and processed using 2D/3D registration methods to provide a 3D visualization of the vertebra and screw superimposed on one another. Point digitization and CT imaging of the residual screw tunnel were used to assess accuracy in five synthetic lumbar vertebral models (10 screws in total). Additionally, the accuracy was evaluated with and without correcting for image distortion and for various screw lengths, screw materials, breach directions, and vertebral levels.

Results

The proposed method is capable of localizing the implanted screws with less than 2 mm of translational error (RMSE: 0.7 and 0.8 mm for the screw head and tip, respectively) and less than \(2.3^{\circ }\) angular error (RMSE: \(1.3^{\circ }\) ), with minimal change to the errors if image distortion is not corrected. Breaches and their anatomical locations were all correctly visualized and identified for a variety of screw lengths, screw materials, breach locations, and vertebral levels, demonstrating the robustness of this approach. In contrast, one breach, one non-breach, and the anatomical location of three screws were misclassified with 2D X-ray.

Conclusion

We have demonstrated an accurate and low-radiation technique for localizing pedicle screws post-implantation that requires only two X-rays. This intraoperative feedback of screw location and direction may allow the surgeon to correct malplaced screws intraoperatively, thereby reducing postoperative complications and reoperation rates.

Ongoing environmental monitoring and assessment of the long-term impacts of the February 2014 radiological release from the waste isolation pilot plant

Abstract

Three years ago, the Waste Isolation Pilot Plant (WIPP) experienced its first minor accident involving a radiological release. Late in the evening on February 14, 2014, a waste container in the repository underwent a chemical reaction that caused the container to overheat and breach, releasing its contents into the underground. Following a lengthy recovery process, the facility recently resumed waste disposal operations. The accident released significant levels of radioactivity into the disposal room and adjacent exhaust drifts, and although no one was present in the underground at the time of the release, a total of 22 workers tested positive for very low level of radiation, presumably from some of the radioactive material that was released above ground through a small leak in the HEPA filtration system. The dominant radionuclides released were ²⁴¹Am and ^{239 + 240}Pu in a ratio that matched the content of the drum from Los Alamos National Laboratory (LANL) that was eventually identified as the breached container. From the air particulate monitoring and plume modeling, it was concluded that the dose, at the nearest location accessible to the general public, from this radiation release event would have been less than 0.01 mSv (< 1 mrem/year). This level is well below the 0.1 mSv/year (10 mrem/year) regulatory limit for DOE facilities established by the US Environmental Protection Agency (EPA).

While no long-term impacts to public health or the environment are expected as a result of the WIPP radiation release, the limited ventilation and residual contamination levels in the underground are still a concern and pose a major challenge for the full recovery of WIPP. This article provides an up-to-date overview of environmental monitoring results through the WIPP recovery and an estimate of the long-term impacts of the accident on the natural and human environment.

Highlights from the Literature

Forthcoming Meetings

Linking inflammation and cancer: the unexpected SYK world

See the article by Moncayo et al pp. 621–631.

mTOR inhibition in glioblastoma: requiem for a dream?

See the article by Chinnaiyan et al, pp. 666–673.

Toward methylation-based classification of central nervous system tumors

Precise classification of nervous system tumors into coherent clinicopathologic entities is the necessary first step for the appropriate management of patients. While this has been traditionally performed by histopathology only, recent accelerations in our understanding of the molecular features of nervous system tumors have led to the integration of molecular characteristics into diagnostic criteria. The updated WHO 2016 classification of tumors of the central nervous system (CNS)¹ thus includes both histologic and molecular features—primarily mutational status of individual genes and copy number alterations—facilitating the precise diagnosis of CNS tumors. While this has led to increased objectivity and reproducibility, classification progress is still required, especially for rare and for poorly understood entities.

A new defense of trope content view of experience

Abstract

The idea that what we perceive are tropes (abstract particulars) is anything but new. In fact, it was one of the reasons why the ontology of tropes was postulated in the first place. Still, the claim that we perceive tropes is invariably and purely based on pre-philosophical intuitions or, indirectly, either as a supporting argument for the advantages of content view when compared to the relational view of experience, or as a supporting argument in favor of the irreducible subjective character of experience. In this paper, I take the content view for granted and argue in favor of what is herein referred to as the trope-content view of experience. My defense is a case of inference to the best explanation. The trope-content view can meet all reasonable desiderata on the experience and its content without assuming gaps or making the ad hoc assumption that there are different layers of content, or so shall I argue.

Multilevel Regression and Poststratification: A Modelling Approach to Estimating Population Quantities From Highly Selected Survey Samples

Abstract

Large-scale population health studies face increasing difficulties in recruiting representative samples of participants. Non-participation, item non-response and attrition, when follow-up is involved, often result in highly selected samples even in well-designed studies. We aimed to assess the potential value of multilevel regression and poststratification, a method previously used to successfully forecast US presidential election results, for addressing biases due to non-participation in the estimation of population descriptive quantities in large cohort studies. The investigation was performed as an extensive case study using a large national health survey of Australian males, the Ten to Men study. Analyses were performed in the Bayesian computational package RStan. Results showed greater consistency and precision across population subsets of varying sizes, when compared with estimates obtained using conventional survey sampling weights. Estimates for smaller population subsets exhibited a greater degree of shrinkage towards the national estimate. Multilevel regression and poststratification provides a promising analytic approach to addressing potential participation bias in the estimation of population descriptive quantities from large-scale health surveys and cohort studies.

Fractionation and leachability of Fe, Zn, Cu and Ni in the sludge from a sulphate-reducing bioreactor treating metal-bearing wastewater

Abstract

This work presents and discusses experimental results on the characterisation and metal leaching potential of a biogenic, metal-rich sulphidic sludge, generated in a sulphate-reducing bioreactor, operated to treat acidic synthetic solutions bearing Fe, Zn, Ni and Cu. The sustainability of the metal removal bioprocess strongly depends on the fate of the sludge. To propose appropriate management practices, a detailed characterisation of the sludge is necessary. The granulometry, chemical composition and mineralogy of the sludge were initially determined. The mobility of the metals was assessed via a modified Tessier experimental procedure. The leachability of the sludge metal content was determined via a standard compliance method (EN 12457-2) and experiments designed to evaluate the effect of pH and time on metal leaching from the sludge. The sludge metal content sums up to 69.5% dw, namely iron (14.8%), zinc (18.7%), nickel (17.7%) and copper (18.2%) and, based on the criteria set by European Union, the sludge is characterised as hazardous and inappropriate for landfilling without any pretreatment. The sludge consists mainly of very fine poorly crystalline aggregates of Fe, Zn, Cu and Ni sulphides. The fine grain size, the poorly crystalline structure and the oxidation of sulphide upon exposure to water/air render the high metal content of the sludge recoverable.

Effects of selected synthetic insecticides on the total and differential populations of circulating haemocytes in adults of the red cotton stainer bug Dysdercus koenigii (Fabricius) (Hemiptera: Pyrrhocoridae)

Abstract

Red cotton bug, Dysdercus koenigii (Hemiptera: Pyrrhocoridae), has become the major insect pest of various crops, including cotton, and thereby reducing the yield qualitatively and quantitatively and synthetic insecticides belonging to different groups are the major control agents for such insect pests. A laboratory experiment was carried out to evaluate the effect of different conventional insecticides, i.e., imidacloprid, deltamethrin, lambda cyhalothrin, gamma cyhalothrin and cyfluthirn on haemocytes of D. koenigii. The individuals were exposed to insecticides separately and data was recorded after 30 and 60 min of the exposure. The findings of current study depicted chlorpyrifos to be more effective and significant alterations in total haemocyte counts and differential haemocyte counts were observed in the cyfluthirn treated D. koenigii. In addition to this, cell structure was also disrupted as an immune response. Similar studies would also be helpful to understand the defence mechanisms of insects against the xenobiotics which will help to device efficient management tools for D. koenigii.

Arithmetic Judgements, First-Person Judgements and Immunity to Error Through Misidentification

Abstract

The paper explores the idea that some singular judgements about the natural numbers are immune to error through misidentification by pursuing a comparison between arithmetic judgements and first-person judgements. By doing so, the first part of the paper offers a conciliatory resolution of the Coliva-Pryor dispute about so-called "de re" and "which-object" misidentification. The second part of the paper draws some lessons about what it takes to explain immunity to error through misidentification. The lessons are: First, the so-called Simple Account (see Wright 2012) of which-object immunity to error through misidentification to the effect that a judgement is immune to this kind of error just in case its grounds do not feature any identification component fails. Secondly, wh-immunity can be explained by a Reference-Fixing Account to the effect that a judgement is immune to this kind of error just in case its grounds are constituted by the facts whereby the reference of the concept of the object which the judgement concerns is fixed. Thirdly, a suitable revision of the Simple Account explains the de re immunity of those arithmetic judgements which are not wh-immune. These three lessons point towards the general conclusion that there is no unifying explanation of de re and wh-immunity.

Targeted Methylation Sequencing of Plasma Cell-free DNA for Cancer Detection and Classification

Abstract

Background

Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.

Patients and methods

We developed a comprehensive methylation sequencing targeting 9,322 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we performed a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small cell lung cancer (NSCLC), breast cancer or melanoma and compared results to patients' outcomes.

Results

Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 vs. 85.29; p=0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 59 (86.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (76.3%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 vs. 4.4 months, p<0.001) and longer time to treatment failure (2.8 vs. 1.6 months, p=0.016).

Conclusions

Comprehensive targeted methylation sequencing of 9,322 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.