Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

The mechanism underlying the development of tumors, particularly at early stages, still remains mostly elusive. Here, we report whole-genome long and short read sequencing analysis of 76 lung cancers, focusing on very early-stage lung adenocarcinomas such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma. The obtained data is further integrated with bulk and spatial transcriptomic data and epigenomic data. These analyses reveal key events in lung carcinogenesis. Minimal somatic mutations in pivotal driver mutations and essential proliferative factors are the only detectable somatic mutations in the very early-stage of AIS. These initial events are followed by copy number changes and global DNA hypomethylation. Particularly, drastic changes are initiated at the later AIS stage, i.e., in Noguchi type B tumors, wherein cancer cells are exposed to the surrounding microenvironment. This study sheds light on the pathogenesis of lung adenocarcinoma from integrated pathological and molecular viewpoints.

Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins

Atrial fibrillation (AF) is the most frequent persistent arrhythmia. Many genes have been reported as a genetic background for AF. However, most transcriptome analyses of AF are limited to the atrial samples and have not been evaluated by multiple cardiac regions. In this study, we analyzed the expression levels of protein-coding and long noncoding RNAs (lncRNAs) in six cardiac regions by RNA-seq. Samples were donated from six subjects with or without persistent AF for left atria, left atrial appendages, right atria, sinoatrial nodes, left ventricles, right ventricles, and pulmonary veins (PVs), and additional four right atrial appendages samples were collected from patients undergoing mitral valve replacement. In total, 23 AF samples were compared to 23 non-AF samples. Surprisingly, the most influenced heart region in gene expression by AF was the PV, not the atria. The ion channel-related gene set was significantly enriched upon analysis of these significant genes. In addition, some significant genes are cancer-related lncRNAs in PV in AF. A co-expression network analysis could detect the functional gene clusters. In particular, the cancer-related lncRNA, such as SAMMSON and FOXCUT, belong to the gene network with the cancer-related transcription factor FOXC1. Thus, they may also play an aggravating role in the pathogenesis of AF, similar to carcinogenesis. In the least, this study suggests that (1) RNA alteration is most intense in PVs and (2) post-transcriptional gene regulation by lncRNA may contribute to the progression of AF. Through the screening analysis across the six cardiac regions, the possibility that the PV region can play a role other than paroxysmal triggering in the pathogenesis of AF was demonstrated for the first time. Future research with an increase in the number of PV samples will lead to a novel understanding of the pathophysiology of AF.

Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.

Phasing analysis of lung cancer genomes using a long read sequencer

Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with >99% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.

Cribriform carcinoma in the lymph nodes is associated with distant metastasis, recurrence, and survival among patients with node-positive colorectal cancer

Cribriform lymph node pattern is an independent risk factor for metachronous or synchronous distant metastasis in patients with stage III and IV node-positive colorectal cancer. Multivariable analysis in patients with stage III disease indicated that the cribriform pattern of carcinoma in the lymph nodes was an independent risk factor for recurrence and survival. Kaplan–Meier analysis demonstrated that the group with stage III cribriform-type lymph node carcinoma had shorter recurrence-free and overall survival times than the stage III group with the tubular type (P < 0.001).

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

BACKGROUND

Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified.

RESULTS

Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection.

CONCLUSIONS

Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.

Observational Evidence for Stochastic Shock Drift Acceleration of Electrons at the Earth's Bow Shock

The first-order Fermi acceleration of electrons requires an injection of electrons into a mildly relativistic energy range. However, the mechanism of injection has remained a puzzle both in theory and observation. We present direct evidence for a novel stochastic shock drift acceleration theory for the injection obtained with Magnetospheric Multiscale observations at the Earth's bow shock. The theoretical model can explain electron acceleration to mildly relativistic energies at high-speed astrophysical shocks, which may provide a solution to the long-standing issue of electron injection.

Disturbance of the Front Region of Magnetic Reconnection Outflow Jets due to the Lower-Hybrid Drift Instability

A 3D fully kinetic simulation shows that the lower-hybrid drift instability disturbs the front of magnetic reconnection outflow jets and additionally causes energy dissipation. The result is very consistent with a disturbance observed at the dipolarization front (DF) in Earth's magnetotail by the Magnetospheric Multiscale (MMS) mission. A fully kinetic dispersion relation solver, validated by the MMS observations, further predicts that the disturbance of the reconnection jet front could occur over different parameter regimes in space plasmas including Earth's DF and solar flares.

P2725Transthyretin cardiac amyloidosis in heart failure with preserved ejection fraction: Imaging by Tc-99m bone scan

Background

Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous clinical syndrome with multiple underlying causes. Transthyretin amyloidosis (ATTR) is an underdiagnosed cause of HFpEF. Extraosseous uptake, in particular, myocardial uptake, was observed in a number of ATTR patients examined with the bone scan tracers.

Objectives

We sought to determine the prevalence of ATTR as detected by the bone scan among the patients admitted due to HFpEF.

Methods

We screened all consecutive patients ≥60 years old admitted due to HFpEF (left ventricular ejection fraction ≥50%). All eligible patients were offered an echocardiogram and a bone scan (a 99mTc-DPD/MDP/HMDP scintigraphy). Echocardiographic and clinical variables were gathered in all the subjects. The intensity of the myocardial uptake was graded according to a visual scale ranging from 0 to 3 points, in which the absence of uptake was assigned a score of 0 points; uptake less than that of bone (referred to as the adjacent rib), 1 point; uptake similar to that of bone, 2 points; and uptake greater than that of bone, 3 points. The distribution of the uptake in myocardium was defined as focal uptake, diffuse uptake, uptake in a ventricular wall segment, diffuse ventricular uptake, or diffuse biventricular uptake.

Results

The study included 62 HFpEF patients (52% women, 73±9 years). The bone scintigraphic analysis revealed relatively intense myocardial uptake in 7 of 62 patients (11.2%). 7 patients had intense Tc-99m uptake (score of 2–3) in the cardiac region, showing deposition in both right and left ventricles in every case. Patients with amyloid deposition were older (78±6 vs. 70±12 years, p<0.05), had a lower systolic blood pressure (118±23 vs. 148±28 mmHg, p<0.05), and left ventricular ejection fraction (52±11 vs. 58±6%, p<0.05). Both groups had at least moderate left ventricular hypertrophy and abnormal global longitudinal strain with no significant difference between groups. In 6 all the cases, the final diagnosis of amyloidosis was based on the results of abdominal fat aspiration biopsy.

Conclusion

ATTR is an underdiagnosed disease that accounts for a significant number (11.2%) of HFpEF cases. These findings create an opportunity for further investigation in the targeted therapy of patients with HFpEF.

Beam Energy and Centrality Dependence of Direct-Photon Emission from Ultrarelativistic Heavy-Ion Collisions

The PHENIX collaboration presents first measurements of low-momentum (0.4<p_{T}<3  GeV/c) direct-photon yields from Au+Au collisions at sqrt[s_{NN}]=39 and 62.4 GeV. For both beam energies the direct-photon yields are substantially enhanced with respect to expectations from prompt processes, similar to the yields observed in Au+Au collisions at sqrt[s_{NN}]=200. Analyzing the photon yield as a function of the experimental observable dN_{ch}/dη reveals that the low-momentum (>1  GeV/c) direct-photon yield dN_{γ}^{dir}/dη is a smooth function of dN_{ch}/dη and can be well described as proportional to (dN_{ch}/dη)^{α} with α≈1.25. This scaling behavior holds for a wide range of beam energies at the Relativistic Heavy Ion Collider and the Large Hadron Collider, for centrality selected samples, as well as for different A+A collision systems. At a given beam energy, the scaling also holds for high p_{T} (>5  GeV/c), but when results from different collision energies are compared, an additional sqrt[s_{NN}]-dependent multiplicative factor is needed to describe the integrated-direct-photon yield.

Publisher Correction: Electron magnetic reconnection without ion coupling in Earth's turbulent magnetosheath

Change history: In this Letter, the y-axis values in Fig. 3f should go from 4 to -8 (rather than from 4 to -4), the y-axis values in Fig. 3h should appear next to the major tick marks (rather than the minor ticks), and in Fig. 1b, the arrows at the top and bottom of the electron-scale current sheet were going in the wrong direction; these errors have been corrected online.

Loss of the small GTPase Arl8b results in abnormal development of the roof plate in mouse embryos

Lysosomes are acidic organelles responsible for degrading both exogenous and endogenous materials. The small GTPase Arl8 localizes primarily to lysosomes and is involved in lysosomal function. In the present study, using Arl8b gene-trapped mutant (Arl8b^-/- ) mice, we show that Arl8b is required for the development of dorsal structures of the neural tube, including the thalamus and hippocampus. In embryonic day (E) 10.5 Arl8b^-/- embryos, Sox1 (a neuroepithelium marker) was ectopically expressed in the roof plate, whereas the expression of Gdf7 and Msx1 (roof plate markers) was reduced in the dorsal midline of the midbrain. Ectopic expression of Sox1 in Arl8b^-/- embryos was detected also at E9.0 in the neural fold, which gives rise to the roof plate. In addition, the levels of Bmp receptor IA and phosphorylated Smad 1/5/8 (downstream of BMP signaling) were increased in the neural fold of E9.0 Arl8b^-/- embryos. These results suggest that Arl8b is involved in the development of the neural fold and the subsequently formed roof plate, possibly via control of BMP signaling.

The Space Physics Environment Data Analysis System (SPEDAS)

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.

Electron-scale dynamics of the diffusion region during symmetric magnetic reconnection in space

Magnetic reconnection is an energy conversion process that occurs in many astrophysical contexts including Earth's magnetosphere, where the process can be investigated in situ by spacecraft. On 11 July 2017, the four Magnetospheric Multiscale spacecraft encountered a reconnection site in Earth's magnetotail, where reconnection involves symmetric inflow conditions. The electron-scale plasma measurements revealed (i) super-Alfvénic electron jets reaching 15,000 kilometers per second; (ii) electron meandering motion and acceleration by the electric field, producing multiple crescent-shaped structures in the velocity distributions; and (iii) the spatial dimensions of the electron diffusion region with an aspect ratio of 0.1 to 0.2, consistent with fast reconnection. The well-structured multiple layers of electron populations indicate that the dominant electron dynamics are mostly laminar, despite the presence of turbulence near the reconnection site.

Abstract 1883: A novel Axl and Mertk dual inhibitor ONO-7475: A new therapeutic agent for the treatment of FLT3-ITD and -wild-type acute myeloid leukemia (AML) overexpressing

Introduction: The TAM (Tyro3, Axl, and Mertk) receptor tyrosine kinases (RTKs) together with their ligands Gas6 and Pros1 play diverse roles in survival signaling in cancers. Currently, the consensus indicates that therapeutic targeting of TAM RTKs will prove direct antitumor activity and may complement existing immunotherapy regimens to unleash the full power of the anticancer immune response. A number of small-molecule kinase inhibitors targeting TAM RTKs are being developed and tested in preclinical models. ONO-7475 is a highly potent and oral dual inhibitor of Axl and Mertk, currently in a phase 1 clinical study as a therapeutic agent for AML (NCT03176277). Our previous studies demonstrated that ONO-7475 induced complete tumor remission in the FLT3-internal tandem duplication (ITD)-positive AML cell line MV-4-11 mouse xenograft model (Yasuhiro et al., Blood 2014). However, the antitumor activity against FLT3-ITD AML cells was due to Axl inhibition (Ruvolo et al., Haematologica 2017) and the mechanism of Mertk regulation in AML has not been determined. To evaluate this question, we screened 28 AML-derived cell lines for FLT3-wild type (WT) and analyzed the influence of Mertk in proliferation.

Methods: Twenty-eight FLT3-WT AML cell lines were treated with ONO-7475 for 72 hours, and the cell viabilities (IC50 values) were determined. Phospho-Axl (P-Axl), Axl and Mertk were determined by Western blot analysis. P-Mertk was determined by immunoprecipitation. Gene knockdown was achieved in FLT3-WT AML by transfecting with Axl, Mertk, Gas6, Pros1, or scrambled control siRNA.

Results: Six out of 28 FLT3-WT cell lines responded to ONO-7475, and two cell lines, MOLM16 and MKPL1, were highly sensitive (IC50: 4.7nM and 83.5nM). Western blot analysis demonstrated that Axl, Mertk and P-Mertk were overexpressed in these ONO-7475-sensitive cells, and both are classified as megakaryoblastic leukemia (FAB-M7). SiRNA knockdown studies showed that the cell growth in MOLM16 was partially dependent on Mertk (63.5%) but totally dependent on double genes, Axl and Mertk. Furthermore, knockdown of the ligands Gas6 and Pros1 also partially inhibited the cell growth in MOLM16, respectively (46.0%, 49.2%).

Conclusion: Our data suggest that Mertk may play an important role in survival signaling in FLT3-WT AML. Therefore, targeting both Axl and Mertk by ONO-7475 could be a new strategy for the treatment of FLT3-WT patients with AML in addition to FLT3-ITD. Additional work to investigate and clarify for target populations in both FLT3-ITD and -WT AML is currently under way.

Citation Format: Kohei Tanaka, Cuifang Li, Tomomi Hirosaki, Hikaru Kato, Yoshinori Ishikawa, Miho Oka, Hiroshi Egawa, Ryohei Kozaki, Toshio Yoshizawa. A novel Axl and Mertk dual inhibitor ONO-7475: A new therapeutic agent for the treatment of FLT3-ITD and -wild-type acute myeloid leukemia (AML) overexpressing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1883.

Differential Cross Section and Photon-Beam Asymmetry for the γ[over →]p → π^{-}Δ^{++}(1232) Reaction at Forward π^{-} Angles for E_{γ}=1.5-2.95 GeV

Differential cross sections and photon-beam asymmetries for the γ[over →]p→π^{-}Δ^{++}(1232) reaction have been measured for 0.7<cosθ_{π}^{c.m.}<1 and E_{γ}=1.5-2.95  GeV at SPring-8/LEPS. The first-ever high statistics cross-section data are obtained in this kinematical region, and the asymmetry data for 1.5<E_{γ}(GeV)<2.8 are obtained for the first time. This reaction has a unique feature for studying the production mechanisms of a pure uu[over ¯] quark pair in the final state from the proton. Although there is no distinct peak structure in the cross sections, a non-negligible excess over the theoretical predictions is observed at E_{γ}=1.5-1.8  GeV. The asymmetries are found to be negative in most of the present kinematical regions, suggesting the dominance of π exchange in the t channel. The negative asymmetries at forward meson production angles are different from the asymmetries previously measured for the photoproduction reactions producing a dd[over ¯] or an ss[over ¯] quark pair in the final state. Advanced theoretical models introducing nucleon resonances and additional unnatural-parity exchanges are needed to reproduce the present data.