Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors

BACKGROUND: Breast cancer is the most commonly diagnosed cancer and second leading cancer death cause among females in the U.S.A. About 1 in 8 women in U.S will develop invasive breast cancer over the course of her lifetime. In 2013, 234,580 new invasive breast cancer cases are expected to occur in women within the US and approximately 64,640 non-invasive carcinomas in situ were diagnosed in 2013, most of which were ductal carcinoma in situ (DCIS). Along with technological advances, a wide variety of candidate biomarkers have been proposed for cancer diagnosis and prognosis, including DNA content and non-coding RNA. Current techniques for detecting DNA content abnormalities in formalin-fixed, paraffin-embedded (FFPE) tissue samples by flow cytometric analysis have used cells recovered from ≥50µm whole tissue sections. Here, in our first study, a novel core punch sampling method was investigated for assessing DNA content abnormalities and intratumoral heterogeneity in FFPE specimens. Secondly, long non-coding RNAs (lncRNAs) has been examined. LncRNA participates in a broad spectrum of biological activities by diverse mechanisms and its dysregulation is associated with tumorgenesis. Some lncRNAs may function as oncogenes (O) and others as tumor suppressor genes (TSG). To date, lncRNA has been investigated primarily by qRT-PCR and RNA sequencing. This study has examined the relationship of lncRNA expression patterns to breast tumor pathology by chromogenic in situ hybridization (CISH). METHODS: Firstly, FFPE breast carcinoma specimens were selectively targeted using 1.0 mm diameter punch needles. Extracted cores were assayed by flow cytometry using a modified-Headley method. Secondly, the lncRNA expression levels of 6 lncRNAs: HOTAIR, H19, KCNQ1OT1, MEG3, MALAT11 and Zfas1, was examined by RNAscope® CISH using FFPE breast tissue microarrays (TMAs) comprising normal adjacent epithelia (NA), DCIS, and invasive carcinoma (IC) from 46 patients. LncRNA associate polycomb complex protein EZH2 was evaluated by immunohistochemistry (IHC). LncRNA data was also compared to standard breast tumor data including ER, PR, Her2 and Ki67 IHC. SYSTAT version 11 statistical package was used to perform for all the tests. RESULTS: Following optimization experiments of the core punch flow cytometric approach, DNA index and percent S-phase fraction intratumoral heterogeneities were detected in 10/23 (44%) and 11/23 (47%) specimens respectively. The lncRNA CISH study utilized a TMA that contained 36 spots of NA breast tissues, 34 DCIS spots and 43 IC spots. HOTAIR CISH staining was significantly stronger in IC than DCIS (p CONCLUSION: Core-punching is an effective alternative to whole specimen sectioning and shows that macro-level genomic heterogeneity is common even within a single FFPE block. The interrelationship of DNA content heterogeneity to other forms of heterogeneity requires further study. RNAscope CISH supports bright-field microscopy investigations of lncRNA expression in FFPE tissue specimens. HOTAIR, H19 and KCNQ1OT1 may be potential breast cancer biomarkers, both HOTAIR and H19 may be a marker for DCIS at increased risk of progression to invasive cancer. HOTAIR, in particular, may be a predictor for invasive cancer grade

Comprehensive analysis of hypoxia-related genes for prognosis value, immune status, and therapy in osteosarcoma patients

Osteosarcoma is a common malignant bone tumor in children and adolescents. The overall survival of osteosarcoma patients is remarkably poor. Herein, we sought to establish a reliable risk prognostic model to predict the prognosis of osteosarcoma patients. Patients ’ RNA expression and corresponding clinical data were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus databases. A consensus clustering was conducted to uncover novel molecular subgroups based on 200 hypoxia-linked genes. A hypoxia-risk models were established by Cox regression analysis coupled with LASSO regression. Functional enrichment analysis, including Gene Ontology annotation and KEGG pathway analysis, were conducted to determine the associated mechanisms. Moreover, we explored relationships between the risk scores and age, gender, tumor microenvironment, and drug sensitivity by correlation analysis. We identified two molecular subgroups with significantly different survival rates and developed a risk model based on 12 genes. Survival analysis indicated that the high-risk osteosarcoma patients likely have a poor prognosis. The area under the curve (AUC) value showed the validity of our risk scoring model, and the nomogram indicates the model’s reliability. High-risk patients had lower Tfh cell infiltration and a lower stromal score. We determined the abnormal expression of three prognostic genes in osteosarcoma cells. Sunitinib can promote osteosarcoma cell apoptosis with down-regulation of KCNJ3 expression. In summary, the constructed hypoxia-related risk score model can assist clinicians during clinical practice for osteosarcoma prognosis management. Immune and drug sensitivity analysis can provide essential insights into subsequent mechanisms. KCNJ3 may be a valuable prognostic marker for osteosarcoma development

Aqueous Preparation of Platinum Nanoflowers on Three-Dimensional Graphene for Efficient Methanol Oxidation

A facile aqueous method to construct a platinum nanoflowers (PtNFs)/three-dimensional (3D) graphene electrode for electrochemical catalysis was demonstrated. PtNFs composed of thin Pt nanowires with the length of 6⁻16 nm and the diameter of 2⁻3 nm were prepared on 3D graphene foam as a growth template in the aqueous solution without any surfactant. The 3D graphene foam was used for patterning PtNFs and controlling their morphology. The fabricated PtNF/3D graphene electrode was applied for electrocatalytic methanol oxidation. Electrochemical measurements show that the PtNF/3D graphene electrode has higher electrocatalytic activity and better stability than commercial Pt-C modified glassy carbon electrode. It displays promising potential for applications in fuel cells

Additional file 2: of CircIBTK inhibits DNA demethylation and activation of AKT signaling pathway via miR-29b in peripheral blood mononuclear cells in systemic lupus erythematosus

Figure S1. a, b Statistical analysis of the cumulative densitometry data for western blot analysis of PTEN expression and AKT phosphorylation in PBMCs from HC transfected with miR-29b mimics. c, d Statistical analysis of the cumulative densitometry data for western blot analysis of PTEN expression and AKT phosphorylation in PBMCs from patients with SLE, transfected with miR-29b inhibitor. e, f Statistical analysis of the cumulative densitometry data for western blot analysis of PTEN/AKT signaling-related proteins in PBMCs from patients with SLE, transfected with miR-29b mimics, circIBTK expression plasmids, NC oligonucleotides or empty vector. g, h Statistical analysis of the cumulative densitometry data for western blot analysis of PTEN/AKT signaling-related proteins in PBMCs from HC transfected with miR-29b inhibitor, circIBTK siRNA or NC oligonucleotides. Three replicate experiments were performed. The cumulative densitometry data were compared using the paired Student’s t test and results were represented as mean ± SD (n = 3). *P < 0.05, **P < 0.01. (PDF 298 kb

Design, Fabrication and Characterization of a MEMS-Based Three-Dimensional Electric Field Sensor with Low Cross-Axis Coupling Interference

One of the major concerns in the development of three-dimensional (3D) electric field sensors (EFSs) is their susceptibility to cross-axis coupling interference. The output signal for each sensing axis of a 3D EFS is often coupled by electric field components from the two other orthogonal sensing axes. In this paper, a one-dimensional (1D) electric field sensor chip (EFSC) with low cross-axis coupling interference is presented. It is designed to be symmetrical, forming a pair of in-plane symmetrically-located sensing structures. Using a difference circuit, the 1D EFSC is capable of sensing parallel electric fields along symmetrical structures and eliminating cross-axis coupling interference, which is contrast to previously reported 1D EFSCs designed for perpendicular electric field component measurement. Thus, a 3D EFS with low cross-axis coupling interference can be realized using three proposed 1D EFSCs. This 3D EFS has the advantages of low cross-axis coupling interference, small size, and high integration. The testing and calibration systems of the proposed 3D EFS were developed. Experimental results show that in the range of 0–120 kV/m, cross-axis sensitivities are within 5.48%, and the total measurement errors of this 3D EFS are within 6.16%

Wafer-Level Vacuum-Packaged Electric Field Microsensor: Structure Design, Theoretical Model, Microfabrication, and Characterization

This paper proposes a novel wafer-level vacuum packaged electric field microsensor (EFM) featuring a high quality factor, low driving voltage, low noise, and low power consumption. The silicon-on-insulator (SOI) conductive handle layer was innovatively used as the sensing channel to transmit the external electric field to the surface of the sensitive structure, and the vacuum packaging was realized through anodic bonding between the SOI and glass-on-silicon (GOS). The fabrication process was designed and successfully realized, featured with a simplified process and highly efficient batch manufacturing, and the final chip size was only 5 × 5 mm. A theoretical model for the packaged device was set up. The influence of key parameters in the packaging structure on the output characteristics of the microsensor was analyzed on the basis of the proposed model. Experiments were conducted on the wafer-level vacuum-packaged EFM to characterize its performance. Experimental results show that, under the condition of applying 5 V DC driving voltage, the required AC driving voltage of the sensor was only 0.05 VP, and the feedthrough was only 4.2 mV. The quality factor was higher than 5000 and was maintained with no drop in the 50-day test. The vacuum in the chamber of the sensor was about 10 Pa. A sensitivity of 0.16 mV/(kV/m) was achieved within the electrostatic field range of 0–50 kV/m. The linearity of the microsensor was 1.62%, and the uncertainty was 4.42%

A Highly Sensitive and High-Resolution Resonant MEMS Electrostatic Field Microsensor Based on Electrostatic Stiffness Perturbation

This paper proposes a highly sensitive and high-resolution resonant MEMS electrostatic field sensor based on electrostatic stiffness perturbation, which uses resonant frequency as an output signal to eliminate the feedthrough interference from the driving voltage. The sensor is composed of a resonator, driving electrode, detection electrode, transition electrode, and electrostatic field sensing plate. The working principle is that when there is an electrostatic field, an induction charge will appear at the surface of the electrostatic field sensing plate and induce electrostatic stiffness on the resonator, which will cause a resonant frequency shift. The resonant frequency is used as the output signal of the microsensor. The characteristics of the electrostatic field sensor are analyzed with a theoretical model and verified by finite element simulation. A device prototype is fabricated based on the Silicon on Insulator (SOI) process and tested under vacuum conditions. The results indicate that the sensitivity of the sensor is 0.1384Hz/(kV/m) and the resolution is better than 10 V/m

A High Sensitivity Electric Field Microsensor Based on Torsional Resonance

This paper proposes a high sensitivity electric field microsensor (EFM) based on torsional resonance. The proposed microsensor adopts torsional shutter, which is composed of shielding electrodes and torsional beams. The movable shielding electrodes and the fixed sensing electrodes are fabricated on the same plane and interdigitally arranged. Push–pull electrostatic actuation method is employed to excite the torsional shutter. Simulation results proved that the torsional shutter has higher efficiency of charge induction. The optimization of structure parameters was conducted to improve its efficiency of charge induction further. A micromachining fabrication process was developed to fabricate the EFM. Experiments were conducted to characterize the EFM. A good linearity of 0.15% was achieved within an electrostatic field range of 0–50 kV/m, and the uncertainty was below 0.38% in the three roundtrip measurements. A high sensitivity of 4.82 mV/(kV/m) was achieved with the trans-resistance of 100 MΩ, which is improved by at least one order of magnitude compared with previously reported EFMs. The efficiency of charge induction for this microsensor reached 48.19 pA/(kV/m)

The effectiveness of chemotherapy for patients with pT3N0M0 renal pelvic urothelial carcinomas: An inverse probability of treatment weighting comparison using Surveillance, Epidemiology, and End Results data

Abstract Introduction Unlike the established evidence to use chemotherapy for urothelial carcinoma of the bladder, presently there are insufficient data to inform a recommendation on upper urinary tract urothelial carcinoma treatment. The prognosis for patients with stage T4 and positive lymph nodes is poor; however, primary tumors in the renal pelvis are associated with favorable prognoses compared to those located in the ureter. Our study aimed at investigating the effectiveness of chemotherapy in patients with pT3N0M0 renal pelvic urothelial carcinomas (RPUC) who have relative favorable prognosis. Methods Patients with pT3N0M0 tumors who underwent radical nephroureterectomy combined with bladder cuff excision between 2005 and 2014 and registered in the Surveillance, Epidemiology, and End Results database were eligible for inclusion (n = 939). Baseline characteristics between the chemotherapy and observation groups were controlled for with inverse probability of treatment weighting (IPTW)‐adjusted analysis. Results After the IPTW‐adjusted analysis, the 5‐year IPTW‐adjusted rates of overall survival (OS) for the chemotherapy and observation groups were 53.1% and 44.9%, respectively. The IPTW‐adjusted Kaplan‐Meier curves suggested that chemotherapy was associated with increased OS compared with observation (P = .028). In the IPTW‐adjusted Cox proportional hazards regression model, chemotherapy was associated with favorable survival benefits compared with observation (hazard ratio [HR] 0.71, 95% CI 0.52‐0.92, P = .031), and this was maintained after bootstrapping (HR 0.72, 95% CI 0.49‐0.93). Chemotherapy had a protective effect on OS benefits, which were found in a majority of the results of the subgroup analysis and were consistent with the main results (all P‐interactions > 0.05). Conclusion Chemotherapy may provide significant OS benefits for patients with pT3N0M0 RPUC. The results of our study could strengthen the evidence for using adjuvant chemotherapy in this rare group of patients