A clonal expression biomarker associates with lung cancer mortality

An aim of molecular biomarkers is to stratify patients with cancer into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumor stage1. Transcriptomic intratumor heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types2,3,4,5,6. Here, we analyze multi-region whole-exome and RNA sequencing data for 156 tumor regions from 48 patients enrolled in the TRACERx study to explore and control for RNA-ITH in non-small cell lung cancer. We find that chromosomal instability is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumor sampling bias. To address this, we identify genes expressed homogeneously within individual tumors that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumor evolution. Clonal transcriptomic biomarkers overcome tumor sampling bias, associate with survival independent of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types

Wnt/β-Catenin Signaling Pathway Is a Direct Enhancer of Thyroid Transcription Factor-1 in Human Papillary Thyroid Carcinoma Cells

The Wnt/β-catenin signaling pathway is involved in the normal development of thyroid gland, but its disregulation provokes the appearance of several types of cancers, including papillary thyroid carcinomas (PTC) which are the most common thyroid tumours. The follow-up of PTC patients is based on the monitoring of serum thyroglobulin levels which is regulated by the thyroid transcription factor 1 (TTF-1): a tissue-specific transcription factor essential for the differentiation of the thyroid. We investigated whether the Wnt/β-catenin pathway might regulate TTF-1 expression in a human PTC model and examined the molecular mechanisms underlying this regulation. Immunofluorescence analysis, real time RT-PCR and Western blot studies revealed that TTF-1 as well as the major Wnt pathway components are co-expressed in TPC-1 cells and human PTC tumours. Knocking-down the Wnt/β-catenin components by siRNAs inhibited both TTF-1 transcript and protein expression, while mimicking the activation of Wnt signaling by lithium chloride induced TTF-1 gene and protein expression. Functional promoter studies and ChIP analysis showed that the Wnt/β-catenin pathway exerts its effect by means of the binding of β-catenin to TCF/LEF transcription factors on the level of an active TCF/LEF response element at [−798, −792 bp] in TTF-1 promoter. In conclusion, we demonstrated that the Wnt/β-catenin pathway is a direct and forward driver of the TTF-1 expression. The localization of TCF-4 and TTF-1 in the same area of PTC tissues might be of clinical relevance, and justifies further examination of these factors in the papillary thyroid cancers follow-up

The Influence of cis-Regulatory Elements on DNA Methylation Fidelity

It is now established that, as compared to normal cells, the cancer cell genome has an overall inverse distribution of DNA methylation (“methylome”), i.e., predominant hypomethylation and localized hypermethylation, within “CpG islands” (CGIs). Moreover, although cancer cells have reduced methylation “fidelity” and genomic instability, accurate maintenance of aberrant methylomes that underlie malignant phenotypes remains necessary. However, the mechanism(s) of cancer methylome maintenance remains largely unknown. Here, we assessed CGI methylation patterns propagated over 1, 3, and 5 divisions of A2780 ovarian cancer cells, concurrent with exposure to the DNA cross-linking chemotherapeutic cisplatin, and observed cell generation-successive increases in total hyper- and hypo-methylated CGIs. Empirical Bayesian modeling revealed five distinct modes of methylation propagation: (1) heritable (i.e., unchanged) high- methylation (1186 probe loci in CGI microarray); (2) heritable (i.e., unchanged) low-methylation (286 loci); (3) stochastic hypermethylation (i.e., progressively increased, 243 loci); (4) stochastic hypomethylation (i.e., progressively decreased, 247 loci); and (5) considerable “random” methylation (582 loci). These results support a “stochastic model” of DNA methylation equilibrium deriving from the efficiency of two distinct processes, methylation maintenance and de novo methylation. A role for cis-regulatory elements in methylation fidelity was also demonstrated by highly significant (p<2.2×10−5) enrichment of transcription factor binding sites in CGI probe loci showing heritably high (118 elements) and low (47 elements) methylation, and also in loci demonstrating stochastic hyper-(30 elements) and hypo-(31 elements) methylation. Notably, loci having “random” methylation heritability displayed nearly no enrichment. These results demonstrate an influence of cis-regulatory elements on the nonrandom propagation of both strictly heritable and stochastically heritable CGIs

The evolution of lung cancer and impact of subclonal selection in TRACERx

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource

Single-and Dual-Band Bandpass Filters Using Coupled Stepped-Impedance Resonators with Embedded Coupled-Lines

A pair of coupled stepped-impedance resonators and its use to build single-and dual-band bandpass filter (BPF) is presented. To that end, two symmetrical stepped-impedance resonators with two embedded coupled-line sections are used. The adopted resonators are coupled at the two open-ended edges. The first even-mode resonant mode can be suppressed or excited based on whether it is required to realize a single-or dual-band response. Sharp passband selectivity and stopband harmonic suppression are achieved due to the existence of multiple transmission zeros. For verification, single-and dual-band filters using the proposed resonator are designed, fabricated and tested. The experimental results show a passband of 2.34-2.62 GHz (centered at 2.45 GHz for WLAN system), less than 1.5 dB insertion loss for the single-band filter; the dual-band design has two passbands ranged from 2.28-2.67 GHz and 3.35-3.63 GHz with less than 1.2 dB insertion loss for WLAN and WiMAX systems

Holographic Prediction of Ground Multipath Parameters From Range Gain Patterns

A new technique is presented where the range gain pattern produced by ground multipath interference is considered as a hologram. The technique can be applied to both flat and spherical earth models. Field distribution at the transmitting antenna side is obtained by digital reconstruction from the range gain pattern. Transmitting antenna height and ground reflection coefficient can therefore be predicted. The technique is validated by calculated and measured range gain patterns, and the predicted values are in good agreement with actual ones

Holographic Prediction of Ray Parameters in Line-of-Sight Links Due to Tropospheric Multipath

Ducting in LOS radio links is investigated. A technique is proposed to estimate the number of refracted rays that could reach the receiver due to the presence of a duct, their angle of arrival and their relative amplitude in comparison to the direct ray

Modified Wideband Marchand Balun with Tunable Power Division Ratio and Constant Phase

A balun with a wide tunable power division ratio and constant phase across a wide frequency band is presented. The proposed design is a modification of the traditional Marchand balun with a varactor and series resistor loaded at the central point of the two connected pairs of coupled lines. The varactor is used to control the power division ratio at two output ports, whereas the resistor is used to stabilize the power division across a wide operational bandwidth. The achievable power division ratio and differential phase are investigated for different band ranges. A prototype is designed, fabricated, and tested. The results indicate a tuning power ratio range from 1:1 to 3.5:1 across 80% fractional bandwidth (1.2-2.8 GHz) with more than 10 dB return loss and less than 9 ° differential phase

A Compact Tunable Directional Coupler with Continuously Tuned Differential Phase

© 2001-2012 IEEE. A tunable directional coupler with outputs that have continuously tuned phase difference and constant magnitude is presented. The initial design is based on a 3-dB branch-line coupler with two arms having variable electrical lengths. To realize the variable-length lines, a novel concept of tunable phase shifting unit, which includes a pair of inductor-varactor loaded coupled lines, is proposed. By controlling the shifting phase of the two arms, the differential phase (i.e., the phase difference between the two output ports) can be tuned continuously. Explicit relation between the objective differential phase of the device and the required shifting phase of those units is analyzed and explained. To validate the design, a prototype is built, simulated, and tested. The experimental and predicted results agree well and show that the device can realize arbitrary and continuously tunable differential phase from 45° to 135°. The overall size of the design is only 0.18 λ{g} \times 0.24 λ{g} , which is extremely compact compared with using a cascaded coupler-phase shifters and is thus suitable for miniaturized wireless systems

Wideband Tunable In-Phase Power Divider Using Three-Line Coupled Structure

An in-phase power divider (PD) with a wide tuning range for the power division ratio across one octave bandwidth is presented. The device uses a quarter-wavelength three-line coupled structure with controllable coupling factors using two centrally connected varactors. One terminal of the central coupled line is connected to the input port, whereas its other terminal is grounded. The two coupled side lines are connected to the output ports, whereas an isolation resistor connects their other ends. The mode theory is used to analyze the performance and predict the initial dimensions. To validate the design, a prototype of dimensions 30 × 20 is built on Rogers RO6010 substrate and tested. The results indicate a tunable power division ratio from 1:1 to 1:2.4 with less than 0.5 dB additional insertion loss across the frequency band 0.7-1.4 GHz. The device has more than 10 dB return loss at all the ports and more than 15 dB isolation between the output ports. The two output signals are in-phase across the whole band with less than 8° differential phase imbalance