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Funder: Max Williamson Fund, Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.

Previous studies studying mis-splicing mutations were based on exome data and thus our current knowledge is largely limited to exons and the canonical splice sites. To comprehensively characterise intronic mis-splicing mutations, we analysed 1134 pan-cancer whole genomes and transcriptomes together with 3022 normal control samples. The ratio-based splicing analysis resulted in 678 somatic intronic mutations, with 46% residing in deep introns. Among the 309 deep intronic single nucleotide variants, 245 altered core splicing codes, with 38% activating cryptic splice sites, 12% activating cryptic polypyrimidine tracts, and 36% and 12% disrupting authentic polypyrimidine tracts and branchpoints, respectively. All the intronic cryptic splice sites were created at pre-existing GT/AG dinucleotides or by GC-to-GT conversion. Notably, 85 deep intronic mutations indicated gain of splicing enhancers or loss of splicing silencers. We found that 64 tumour suppressors were affected by intronic mutations and blood cancers showed higher proportion of deep intronic mutations. In particular, a telomere maintenance gene, POT1, was recurrently mis-spliced by deep intronic mutations in blood cancers. We validated a pseudoexon activation involving a splicing silencer in POT1 by CRISPR/Cas9. Our results shed light on previously unappreciated mechanisms by which noncoding mutations acting on splicing codes in deep introns contribute to tumourigenesis.

Background It is crucial to unravel molecular determinants of responses to immune checkpoint blockade (ICB) therapy because only a small subset of advanced non-small cell lung cancer (NSCLC) patients responds to ICB therapy. Previous studies were concentrated on genomic and transcriptomic markers (e.g., mutation burden and immune gene expression). However, these markers are not sufficient to accurately predict a response to ICB therapy. Results Here, we analyzed DNA methylomes of 141 advanced NSCLC samples subjected to ICB therapy (i.e., anti-programmed death-1) from two independent cohorts (60 and 81 patients from our and IDIBELL cohorts). Integrative analysis of patients with matched transcriptome data in our cohort (n = 28) at pathway level revealed significant overlaps between promoter hypermethylation and transcriptional repression in nonresponders relative to responders. Fifteen immune-related pathways, including interferon signaling, were identified to be enriched for both hypermethylation and repression. We built a reliable prognostic risk model based on eight genes using LASSO model and successfully validated the model in independent cohorts. Furthermore, we found 30 survival-associated molecular interaction networks, in which two or three hypermethylated genes showed significant mutual exclusion across nonresponders. Conclusions Our study demonstrates that methylation patterns can provide insight into molecular determinants underlying the clinical benefit of ICB therapy.

Neoantigen burden is regarded as a fundamental determinant of response to immunotherapy. However, its predictive value remains in question because some tumours with high neoantigen load show resistance. Here, we investigate our patient cohort together with a public cohort by our algorithms for the modelling of peptide-MHC binding and inter-cohort genomic prediction of therapeutic resistance. We first attempt to predict MHC-binding peptides at high accuracy with convolutional neural networks. Our prediction outperforms previous methods in > 70% of test cases. We then develop a classifier that can predict resistance from functional mutations. The predictive genes are involved in immune response and EGFR signalling, whereas their mutation patterns reflect positive selection. When integrated with our neoantigen profiling, these anti-immunogenic mutations reveal higher predictive power than known resistance factors. Our results suggest that the clinical benefit of immunotherapy can be determined by neoantigens that induce immunity and functional mutations that facilitate immune evasion., Predicting response to cancer immunotherapy is still a challenge. Here, the authors show that their method of predicting MHC-binding peptides, combined with profiling anti-immunogenic mutations, can better predict the clinical benefit of immunotherapy.

Amine double-functionalized adsorbents were fabricated using silica gel as supports and their capabilities for CO2 capture were examined. Aminopropyltrimethoxysilane (1N-APS), and N1-(3-trimethoxysilylpropyl)diethylenetriamine (3N-APS) were used as grafted amine compounds, and tetraethylenepentamine and polyethyleneimine were used as impregnated species. The influence of double-functionalization method on the CO2 adsorption performance and textural properties of adsorbents was investigated. The adsorption capacity, the amine efficiency, and the thermal stability of double-functionalized sorbents depend strongly upon molecular variables associated with two different functional states (i.e., chemically grafted and physically impregnated amines). The temperature dependence of adsorption isotherms reveals that the CO2 adsorption behavior in the double-functionalized adsorbents follow the diffusion limitation model proposed by Xu et al. (Energy Fuels 16:1463–1469, 2002) where the CO2 adsorption is helped by the diffusion of impregnated amines. It is also found that the adsorption isotherm in the double-functionalized sorbent system with a proper choice for grafted and impregnated amines is nearly independent of temperature, which may offer a novel means to fabricate practically useful sorbents that can be used in a wide range of temperature without loss of CO2 adsorption capacity.

Purpose Natural orifice transluminal endoscopic surgery (NOTES) is a next generation surgical method with many promising benefits. Many snake-like NOTES platforms have been developed, but the lack of a proper control algorithm prevents those platforms from being used in practices. This study proposes an intuitive control algorithm for snake-like NOTES platforms, which is simple in structure and easily applicable to various NOTES systems.

A substantial fraction of disease-causing mutations are pathogenic through aberrant splicing. Although genome profiling studies have identified somatic single-nucleotide variants (SNVs) in cancer, the extent to which these variants trigger abnormal splicing has not been systematically examined. Here we analyzed RNA sequencing and exome data from 1,812 patients with cancer and identified ∼900 somatic exonic SNVs that disrupt splicing. At least 163 SNVs, including 31 synonymous ones, were shown to cause intron retention or exon skipping in an allele-specific manner, with ∼70% of the SNVs occurring on the last base of exons. Notably, SNVs causing intron retention were enriched in tumor suppressors, and 97% of these SNVs generated a premature termination codon, leading to loss of function through nonsense-mediated decay or truncated protein. We also characterized the genomic features predictive of such splicing defects. Overall, this work demonstrates that intron retention is a common mechanism of tumor-suppressor inactivation.

Organic-inorganic composite membranes were prepared with sulfonated poly(ether ether ketone) (SPEEK) and different amounts of silica to improve chemical stability and vanadium hindrance for a vanadium redox flow battery. The durability of the prepared composite membrane was verified using a self-made dummy cell system and fully charged vanadium cathode half-cell electrolyte, which contained oxidative vanadium ions (VO2+). The prepared composite membranes, with covalent crosslinking between the organic polymer and inorganic particles, resulted in reduced vanadium permeability and enhanced chemical stability. Ion exchange capacity, water uptake, proton conductivity, and vanadium permeability decreased with increasing silica content. Selectivity was defined to consider both permeability and proton conductivity and resulted in a membrane that exhibited both high proton conductivity and low ion permeability simultaneously. The prepared 1 wt% silica composite membrane showed 133-fold higher selectivity compared with that of a Nafion112 membrane. After the stability test, the composite membrane showed little change compared to the membrane before the stability test, which confirmed the commercial prospect of SPEEK/SiO2 composite membrane for a vanadium redox flow battery.

Purpose To assess the effects of probe load and speed on thyroid ultrasonography, an apparatus was designed to capture ultrasound images of a thyroid phantom under various ultrasound probe loads and speeds.

Purpose In this study, we measured the needle insertion force exerted on various breast tissues including those of a breast phantom, cattle tissue, and human tissue, according to needle insertion speed, and compared it using finite element analysis.

Rheological properties of the polystyrene (PS) and poly(methyl methacrylate) (PMMA) blends were studied by Advanced Rheometric Expansion System (ARES). Storage modulus and loss modulus of the PS and PMMA blends were measured, and the interfacial tension of the PS and PMMA blends were obtained with various emulsion models by using the storage modulus and loss modulus of the blends. The value of interfacial tension estimated from the Palierne emulsion model was found to be 2.0 mN/m. Also, the interfacial tension between PS and PMMA was calculated by a theoretical model. The values of interfacial tension of the PS and PMMA blends obtained by the experiment and theoretical model were found to be in good agreement.

Blends of a thermotropic liquid crystalline polymer (LCP) with poly(ether imide) (PEI), poly(ether ether ketone) (PEEK), polysulfone (PSF) and polyarylsulfone (PAS) prepared by screw extrusion have been investigated by differential scanning calorimeter and dynamic mechanical thermal analysis. From the measured glass transition temperature (Tg) and specific heat increment (ΔCp) at the Tg, it appears that the LCP dissolves more in the PEI- and PEEK-rich phases than does the PEI and PEEK in the LCP-rich phase. From the DSC study of PSF-LCP and PAS-LCP blends, the Tg(PSF) and Tg(PAS) of each blends are almost constant with blend composition. Therefore, it is concluded that PSF and PAS are immiscible with LCP. The polymer-polymer interaction parameter (χ12) and the degree of disorder (y/x1) of LCP have been investigated using the Flory lattice theory in which the anisotropy of LCP is considered. The χ12 values have been calculated from the Tg data and found to be 0.181 ± 0.004 at 593 K for the PEI-LCP blends and 0.069 ± 0.006 at 623 K for the PEEK-LCP blends. Using the previously presented method, the χ12 and y/x1 in partially miscible systems have been determined.