Local Luminous Infrared Galaxies. I. Spatially resolved observations with Spitzer/IRS

We present results from the Spitzer/IRS spectral mapping observations of 15 local luminous infrared galaxies (LIRGs). In this paper we investigate the spatial variations of the mid-IR emission which includes: fine structure lines, molecular hydrogen lines, polycyclic aromatic features (PAHs), continuum emission and the 9.7um silicate feature. We also compare the nuclear and integrated spectra. We find that the star formation takes place in extended regions (several kpc) as probed by the PAH emission as well as the [NeII] and [NeIII] emissions. The behavior of the integrated PAH emission and 9.7um silicate feature is similar to that of local starburst galaxies. We also find that the minima of the [NeIII]/[NeII] ratio tends to be located at the nuclei and its value is lower than that of HII regions in our LIRGs and nearby galaxies. It is likely that increased densities in the nuclei of LIRGs are responsible for the smaller nuclear [NeIII]/[NeII] ratios. This includes the possibility that some of the most massive stars in the nuclei are still embedded in ultracompact HII regions. In a large fraction of our sample the 11.3um PAH emission appears more extended than the dust 5.5um continuum emission. We find a dependency of the 11.3um PAH/7.7 um PAH and [NeII]/11.3um PAH ratios with the age of the stellar populations. Smaller and larger ratios respectively indicate recent star formation. The estimated warm (300 K < T < 1000 K) molecular hydrogen masses are of the order of 10^8 M_Sun, which are similar to those found in ULIRGs, local starbursts and Seyfert galaxies. Finally we find that the [NeII] velocity fields for most of the LIRGs in our sample are compatible with a rotating disk at ~kpc scales, and they are in a good agreement with H-alpha velocity fields.Comment: Comments: 52 pages, accepted for publicacion in ApJ

NuSTAR discovery of a luminosity dependent cyclotron line energy in Vela X-1

We present NuSTAR observations of Vela X-1, a persistent, yet highly variable, neutron star high-mass X-ray binary (HMXB). Two observations were taken at similar orbital phases but separated by nearly a year. They show very different 3–79 keV flux levels as well as strong variability during each observation, covering almost one order of magnitude in flux. These observations allow, for the first time ever, investigations on kilo-second time-scales of how the centroid energies of cyclotron resonant scattering features (CRSFs) depend on flux for a persistent HMXB. We find that the line energy of the harmonic CRSF is correlated with flux, as expected in the sub-critical accretion regime. We argue that Vela X-1 has a very narrow accretion column with a radius of around 0.4 km that sustains a Coulomb interaction dominated shock at the observed luminosities of L_x ~ 3 × 10^36 erg s^−1. Besides the prominent harmonic line at 55 keV the fundamental line around 25 keV is clearly detected. We find that the strengths of the two CRSFs are anti-correlated, which we explain by photon spawning. This anti-correlation is a possible explanation for the debate about the existence of the fundamental line. The ratio of the line energies is variable with time and deviates significantly from 2.0, also a possible consequence of photon spawning, which changes the shape of the line. During the second observation, Vela X-1 showed a short off-state in which the power-law softened and a cut-off was no longer measurable. It is likely that the source switched to a different accretion regime at these low mass accretion rates, explaining the drastic change in spectral shape

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Local Luminous Infrared Galaxies: Spatially resolved mid-infrared observations with Spitzer/IRS

Luminous Infrared (IR) Galaxies (LIRGs) are an important cosmological class of galaxies as they are the main contributors to the co-moving star formation rate density of the universe at z=1. In this paper we present a GTO Spitzer IRS program aimed to obtain spectral mapping of a sample of 14 local (d<76Mpc) LIRGs. The data cubes map, at least, the central 20arcsec x 20arcsec to 30arcsec x 30arcsec regions of the galaxies, and use all four IRS modules covering the full 5-38micron spectral range. The final goal of this project is to characterize fully the mid-IR properties of local LIRGs as a first step to understanding their more distant counterparts. In this paper we present the first results of this GTO program. The IRS spectral mapping data allow us to build spectral maps of the bright mid-IR emission lines (e.g., [NeII], [NeIII], [SIII], H_2), continuum, the 6.2 and 11.3micron PAH features, and the 9.7micron silicate feature, as well as to extract 1D spectra for regions of interest in each galaxy. The IRS data are used to obtain spatially resolved measurements of the extinction using the 9.7micron silicate feature, and to trace star forming regions using the neon lines and the PAH features. We also investigate a number of AGN indicators, including the presence of high excitation emission lines and a strong dust continuum emission at around 6micron. We finally use the integrated Spitzer/IRS spectra as templates of local LIRGs. We discuss several possible uses for these templates, including the calibration of the star formation rate of IR-bright galaxies at high redshift. We also predict the intensities of the brightest mid-IR emission lines for LIRGs as a function of redshift, and compare them with the expected sensitivities of future space IR missions.Comment: Accepted for publication in Advances in Space Researc

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies