Caught! Crystal trapping of a side-on peroxo bound to Cr(IV)

A Cr(iv)η2–peroxo complex is a likely intermediate in catalytic disproportionation of H2O2 in solution – and solid state.</p

Acid-Triggered O−O Bond Heterolysis of a Nonheme FeIII (OOH) Species for the Stereospecific Hydroxylation of Strong C−H Bonds

A novel hydroperoxoiron(III) species [FeIII(OOH)(MeCN)(PyNMe3)]2+ (3) has been generated by reaction of its ferrous precursor [FeII(CF3SO3)2(PyNMe3)] (1) with hydrogen peroxide at low temperatures. This species has been characterized by several spectroscopic techniques and cryospray mass spectrometry. Similar to most of the previously described low‐spin hydroperoxoiron(III) compounds, 3 behaves as a sluggish oxidant and it is not kinetically competent for breaking weak C−H bonds. However, triflic acid addition to 3 causes its transformation into a much more reactive compound towards organic substrates that is capable of oxidizing unactivated C−H bonds with high stereospecificity. Stopped‐flow kinetic analyses and theoretical studies provide a rationale for the observed chemistry, a triflic‐acid‐assisted heterolytic cleavage of the O−O bond to form a putative strongly oxidizing oxoiron(V) species. This mechanism is reminiscent to that observed in heme systems, where protonation of the hydroperoxo intermediate leads to the formation of the high‐valent [(Porph.)FeIV(O)] (Compound I)

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

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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

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

Facile Conversion of syn-[Fe-IV(O)(TMC)](2+) into the anti Isomer via Meunier's Oxo-Hydroxo Tautomerism Mechanism

The syn and anti isomers of [Fe-IV(O)(TMC)](2+) (TMC=tetramethylcyclam) represent the first isolated pair of synthetic non-heme oxoiron(IV) complexes with identical ligand topology, differing only in the position of the oxo unit bound to the iron center. Both isomers have previously been characterized. Reported here is that the syn isomer [Fe-IV(O-syn)(TMC)(NCMe)](2+) (2) converts into its anti form [Fe-IV(O-anti)(TMC)(NCMe)](2+) (1) in MeCN, an isomerization facilitated by water and monitored most readily by (HNMR)-H-1 and Raman spectroscopy. Indeed, when (H2O)-O-18 is introduced to 2, the nascent 1 becomes O-18-labeled. These results provide compelling evidence for a mechanism involving direct binding of a water molecule trans to the oxo atom in 2 with subsequent oxo-hydroxo tautomerism for its incorporation as the oxo atom of 1. The nonplanar nature of the TMC supporting ligand makes this isomerization an irreversible transformation, unlike for their planar heme counterparts

High-spin and low-spin iron(II) complexes with facially-coordinated borohydride ligands

Rare examples of monometallic high-spin and low-spin L_3Fe(H_3BH) complexes have been characterized, where the two L_3 ligands are [Tp^(Ph2)] and [PhBP3] ([Tp^(Ph2)] = [HB(3,5-Ph_2pz)_3]− and [PhBP_3] = [PhB(CH_2PPh_2)_3]−). The structures are reported wherein the borohydride ligand is facially coordinated to the iron center in each complex. Density functional methods have been employed to explain the bonding in these unusual iron(II) centers. Despite the differences in spin states, short Fe–B distances are observed in both complexes and there is significant theoretical evidence to support a substantial bonding interaction between the iron and boron nuclei. In light of this interaction, we suggest that these complexes can be described as (L_3)Fe(η^4-H_3BH) complexes

Vibrational Spectroscopy and Analysis of Pseudo-tetrahedral Complexes with Metal Imido Bonds

A number of assignments have been previously posited for the metal−nitrogen stretch (ν(M-NR)), the N−R stretch (ν(MN−R)), and possible ligand deformation modes associated with terminally bound imides. Here we examine mononuclear iron(III) and cobalt(III) imido complexes of the monoanionic tridentate ligand [PhBP_(3)] ([PhBP_(3)] = [PhB(CH_(2)PPh_(2))_(3)]^(-)) to clarify the vibrational features for these trivalent metal imides. We report the structures of [PhBP_(3)]Fe≡N^(t)Bu and [PhBP_(3)]Co≡N^(t)Bu. Pseudo-tetrahedral metal imides of these types exhibit short bond lengths (ca. 1.65 Å) and nearly linear angles about the M−N−C linkages, indicative of multiple bond character. Furthermore, these compounds give rise to intense, low-energy visible absorptions. Both the position and the intensity of the optical bands in the [PhBP_(3)]M≡NR complexes depend on whether the substituent is an alkyl or aryl group. Excitation into the low-energy bands of [PhBP_(3)]Fe≡N^(t)Bu gives rise to two Raman features at 1104 and 1233 cm^(-1), both of which are sensitive to ^(15)N and ^(2)H labeling. The isotope labeling suggests the 1104 cm^(-1) mode has the greatest Fe−N stretching character, while the 1233 cm^(-1) mode is affected to a lesser extent by ^(15)N substitution. The spectra of the deuterium-labeled imides further support this assertion. The data demonstrate that the observed peaks are not simple diatomic stretching modes but are extensively coupled to the vibrations of the ancillary organic group. Therefore, describing these complexes as simple diatomic or even triatomic oscillators is an oversimplification. Analogous studies of the corresponding cobalt(III) complex lead to a similar set of isotopically sensitive resonances at 1103 and 1238 cm^(-1), corroborating the assignments made in the iron imides. Very minimal changes in the vibrational frequencies are observed upon replacement of cobalt(III) for iron(III), suggesting similar force constants for the two compounds. This is consistent with the previously proposed electronic structure model in which the added electron resides in a relatively nonbonding orbital. Replacement of the tBu group with a phenyl ring leads to a significantly more complicated resonance Raman spectrum, presumably due to coupling with the vibrations of the phenyl ring. Polarization studies demonstrate that the observed modes have A1 symmetry. In this case, a clearer resonance enhancement of the signals is observed, supporting a charge transfer designation for the electronic transitions. A series of isotope-labeling experiments has been carried out, and the modes with the greatest metal−nitrogen stretching character have been assigned to peaks at 960 and 1300 cm^(-1) in both the iron and cobalt [PhBP_(3)]M≡NPh complexes. These results are consistent with a multiple M−N bond for these metal imides