Patterns of somatic structural variation in human cancer genomes.

A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions-as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and-in liver cancer-frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

A potential physiological role for bi-directional motility and motor clustering of mitotic kinesin-5 Cin8 in yeast mitosis.

The bipolar kinesin-5 Cin8 switches from minus- to plus-end-directed motility under various conditions in vitro The mechanism and physiological significance of this switch remain unknown. Here, we show that under high ionic strength conditions, Cin8 moves towards and concentrates in clusters at the minus ends of stable and dynamic microtubules. Clustering of Cin8 induces a switch from fast minus- to slow plus-end-directed motility and forms sites that capture antiparallel microtubules (MTs) and induces their sliding apart through plus-end-directed motility. In early mitotic cells with monopolar spindles, Cin8 localizes near the spindle poles at microtubule minus ends. This localization is dependent on the minus-end-directed motility of Cin8. In cells with assembled bipolar spindles, Cin8 is distributed along the spindle microtubules. We propose that minus-end-directed motility is required for Cin8 clustering near the spindle poles before spindle assembly. Cin8 clusters promote the capture of microtubules emanating from the neighboring spindle poles and mediate their antiparallel sliding. This activity is essential to maximize microtubule crosslinking before bipolar spindle assembly and to induce the initial separation of the spindle poles.

Implications of Failure to Routinely Diagnose Resistance to Second-Line Drugs in Patients With Rifampicin-Resistant Tuberculosis on Xpert MTB/RIF: A Multisite Observational Study.

BACKGROUND.: Xpert MTB/RIF (Xpert) detects rifampicin-resistant tuberculosis (RR-tuberculosis), enabling physicians to rapidly initiate a World Health Organization-recommended 5-drug regimen while awaiting second-line drug-susceptibility test (DST) results. We quantified the second-line DST results time and proportion of patients potentially placed on suboptimal therapy. METHODS.: We included RR-tuberculosis patients detected using Xpert at the South African National Health Laboratory Services (NHLS) of the Western Cape between November 2011 and June 2013 and at Eastern Cape, Free State, and Gauteng NHLS between November 2012 and December 2013. We calculated time from specimen collection to phenotypic second-line DST results. We identified isoniazid and ethionamide resistance mutations on line probe assay and performed pyrazinamide sequencing. RESULTS.: Among 1332 RR-tuberculosis patients, only 44.7% (596) had second-line DST for both fluoroquinolones and second-line injectable: 55.8% (466 of 835) in the Western Cape and 26.2% (130 of 497) in the other provinces. Patients with smear negative disease and age ≤10 years were less likely to have a result (risk ratio [RR] = 0.72; 95% CI, 0.64-0.81 and RR = 0.49; 95% CI, 0.26-0.79). Median time to second-line DST was 53 days (range, 8-259). Of the 252 patients with complete second-line DST, 101 (40.1%) potentially initiated a suboptimal regimen: 46.8% in the Western Cape and 25.3% in the other provinces. CONCLUSIONS.: Many South Africans diagnosed with RR-tuberculosis by Xpert initiate a suboptimal regimen, with information to adjust therapy available in half of all patients after a median 7 weeks. Algorithm completion and time delays remain challenging.

Enabling enhanced emission and low-threshold lasing of organic molecules using special Fano resonances of macroscopic photonic crystals.

The nature of light interaction with matter can be dramatically altered in optical cavities, often inducing nonclassical behavior. In solid-state systems, excitons need to be spatially incorporated within nanostructured cavities to achieve such behavior. Although fascinating phenomena have been observed with inorganic nanostructures, the incorporation of organic molecules into the typically inorganic cavity is more challenging. Here, we present a unique optofluidic platform comprising organic molecules in solution suspended on a photonic crystal surface, which supports macroscopic Fano resonances and allows strong and tunable interactions with the molecules anywhere along the surface. We develop a theoretical framework of this system and present a rigorous comparison with experimental measurements, showing dramatic spectral and angular enhancement of emission. We then demonstrate that these enhancement mechanisms enable lasing of only a 100-nm thin layer of diluted solution of organic molecules with substantially reduced threshold intensity, which has important implications for organic light-emitting devices and molecular sensing.

Kinesin-5 Kip1 is a bi-directional motor that stabilizes microtubules and tracks their plus-ends in vivo.

In this study, we examined the anaphase functions of the S. cerevisiae kinesin-5 homolog Kip1. We show that Kip1 is attached to the mitotic spindle midzone during late anaphase. This attachment is essential to stabilize interpolar microtubule (iMTs) plus-ends. By detailed examination of iMT dynamics we show that at the end of anaphase, iMTs depolymerize in two stages: during the first stage, one pair of anti-parallel iMTs depolymerizes at a velocity of 7.7 µm/minute; during the second stage, ∼90 seconds later, the remaining pair of iMTs depolymerizes at a slower velocity of 5.4 µm/minute. We show that upon the second depolymerization stage, which coincides with spindle breakdown, Kip1 follows the plus-ends of depolymerizing iMTs and translocates toward the spindle poles. This movement is independent of mitotic microtubule motor proteins or the major plus-end binding or tracking proteins. In addition, we show that Kip1 processively tracks the plus-ends of growing and shrinking MTs, both inside and outside the nucleus. The plus-end tracking activity of Kip1 requires its catalytic motor function, because a rigor mutant of Kip1 does not exhibit this activity. Finally, we show that Kip1 is a bi-directional motor: in vitro, at high ionic strength conditions, single Kip1 molecules move processively in the minus-end direction of the MTs, whereas in a multi-motor gliding assay, Kip1 is plus-end directed. The bi-directionality and plus-end tracking activity of Kip1, properties revealed here for the first time, allow Kip1 to perform its multiple functions in mitotic spindle dynamics and to partition the 2-micron plasmid.

Fabricating centimeter-scale high quality factor two-dimensional periodic photonic crystal slabs.

We present a fabrication route for centimeter-scale two-dimensional defect-free photonic crystal slabs with quality factors bigger than 10,000 in the visible, together with a unique way to quantify their quality factors. We fabricate Si(3)N(4) photonic crystal slabs, and perform an angle-resolved reflection measurement. This measurement data is used to retrieve the quality factors of the slabs by fitting it to a model based on temporal coupled-mode theory. The macroscopic nature of the structure and the high quality factors of their resonances could open up new opportunities for realizing efficient macroscale optoelectronic devices such as sensors, lasers, and energy harvesting systems.

Direct atomic-level observation and chemical analysis of ZnSe synthesized by in situ high-throughput reactive fiber drawing.

We demonstrate a high-throughput method for synthesizing zinc selenide (ZnSe) in situ during fiber drawing. Central to this method is a thermally activated chemical reaction occurring across multiple interfaces between alternately layered elemental zinc- (Zn-) and selenium- (Se-) rich films embedded in a preform and drawn into meters of fiber at a temperature well below the melting temperature of either Zn or ZnSe. By depositing 50 nm thick layers of Zn interleaved between 1 µm thick Se layers, a controlled breakup of the Zn sheet is achieved, thereby enabling a complete and controlled chemical reaction. The thermodynamics and kinetics of this synthesis process are studied using thermogravimetric analysis and differential scanning calorimetry, and the in-fiber compound is analyzed by a multiplicity of materials characterization tools, including transmission electron microscopy, Raman microscopy, energy-dispersive X-ray spectroscopy, and X-ray diffraction, all resulting in unambiguous identification of ZnSe as the compound produced from the reactive fiber draw. Furthermore, we characterize the in-fiber ZnSe/Se97S3 heterojunction to demonstrate the prospect of ZnSe-based fiber optoelectronic devices. The ability to synthesize new compounds during fiber drawing at nanometer scale precision and to characterize them at the atomic-level extends the architecture and materials selection compatible with multimaterial fiber drawing, thus paving the way toward more complex and sophisticated functionality.

Asymmetric wave propagation in planar chiral fibers.

We demonstrate the realization of a two-dimensional chiral optical waveguide with an infinite translational symmetry that exhibits asymmetric wave propagation. The low-symmetry geometry of the cross-section that lacks any rotational and mirror symmetries shows in-principal directional asymmetric polarization rotation. We use general symmetry arguments to provide qualitative analysis of the waveguide's eigenstates and numerically corroborate this using finite element simulation. We show that despite the only perturbative break of time-reversal symmetry via small modal losses, the structure supports a non-degenerate pair of co-rotating elliptical modes. We fabricated meters long fiber with a spiral structure and studied its optical properties.

Preparation and transmission of low-loss azimuthally polarized pure single mode in multimode photonic band gap fibers.

We demonstrate the preparation and transmission of the lowest loss azimuthally polarized TE01₋ like mode in a photonic band gap (PBG) fiber. Using the nature of the mode and the properties of the band gap structure we construct a novel coupler that operates away from the band gap's center to enhance the differential losses and facilitate the radiative loss of hybrid fundamental fiber modes. Remarkably, even though the coupler is highly multimoded, a pure azimuthally polarized mode is generated after only 17 cm. Theoretical calculations verify the validity of this technique and accurately predict the coupling efficiency. The generation and single mode propagation of this unique azimuthally polarized, doughnut shaped mode in a large hollow-core fiber can find numerous applications including in optical microscopy, optical tweezers, and guiding particles along the fiber.

Enhanced chemiluminescent detection scheme for trace vapor sensing in pneumatically-tuned hollow core photonic bandgap fibers.

We demonstrate an in-fiber gas phase chemical detection architecture in which a chemiluminescent (CL) reaction is spatially and spectrally matched to the core modes of hollow photonic bandgap (PBG) fibers in order to enhance detection efficiency. A peroxide-sensitive CL material is annularly shaped and centered within the fiber's hollow core, thereby increasing the overlap between the emission intensity and the intensity distribution of the low-loss fiber modes. This configuration improves the sensitivity by 0.9 dB/cm compared to coating the material directly on the inner fiber surface, where coupling to both higher loss core modes and cladding modes is enhanced. By integrating the former configuration with a custom-built optofluidic system designed for concomitant controlled vapor delivery and emission measurement, we achieve a limit-of-detection of 100 parts per billion (ppb) for hydrogen peroxide vapor. The PBG fibers are produced by a new fabrication method whereby external gas pressure is used as a control knob to actively tune the transmission bandgaps through the entire visible range during the thermal drawing process.

Observation and differentiation of unique high-Q optical resonances near zero wave vector in macroscopic photonic crystal slabs.

We demonstrate and distinguish experimentally the existence of a special type of Fano resonances at k≈0 in a macroscopic two-dimensional photonic crystal slab. We fabricate a square lattice array of holes in a silicon nitride layer and perform an angular resolved spectral analysis of the various Fano resonances. We elucidate their radiation behavior using temporal coupled-mode theory and symmetry considerations. The unique simplicity of this system whereby an ultralong lifetime delocalized electromagnetic field can exist above the surface and consequently easily interact with added matter, provides exciting new opportunities for the study of light and matter interaction.

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma.

We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.

PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.

The role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of Diffuse Midline Gliomas (DMGs) and are enriched in primary pontine tumors. Through the development of DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D phosphatase activity is required for in vivo oncogenesis. Finally, we apply integrative phosphoproteomic and functional genomics assays and find that oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(-) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(-) cases are required to understand this important LUAD subset.

Polymer-composite fibers for transmitting high peak power pulses at 1.55 microns.

Hollow-core photonic bandgap fibers (PBG) offer the opportunity to suppress highly the optical absorption and nonlinearities of their constituent materials, which makes them viable candidates for transmitting high-peak power pulses. We report the fabrication and characterization of polymer-composite PBG fibers in a novel materials system, polycarbonate and arsenic sulfide glass. Propagation losses for the 60 microm-core fibers are less than 2dB/m, a 52x improvement over previous 1D-PBG fibers at this wavelength. Through preferential coupling the fiber is capable of operating with over 97% the fiber's power output in the fundamental (HE(11)) mode. The fiber transmitted pulses with peak powers of 11.4 MW before failure.

Enabling coherent superpositions of iso-frequency optical states in multimode fibers.

The ability to precisely and selectively excite superpositions of specific fiber eigenmodes allows one in principle to control the three dimensional field distribution along the length of a fiber. Here we demonstrate the dynamic synthesis and controlled transmission of vectorial eigenstates in a hollow core cylindrical photonic bandgap fiber, including a coherent superposition of two different angular momentum states. The results are verified using a modal decomposition algorithm that yields the unique complex superposition coefficients of the eigenstate space.

Exploiting collective effects of multiple optoelectronic devices integrated in a single fiber.

The opportunities and challenges of realizing sophisticated functionality by assembling many nanoscale devices, while covering large areas, remain for the most part unrealized and unresolved. In this work, we demonstrate the successful fabrication of an eight-device cascaded optoelectronic fiber structure in which components down to 100 nm are individually electrically addressed and can operate collectively to deliver novel functionality over large area coverage. We show that a tandem arrangement of subwavelength photodetecting devices integrated in a single fiber enables the extraction of information on the direction, wavelength, and potentially even color of incident radiation over a wide spectral range in the visible regime. Finally, we fabricated a 0.1 square meter single plane fiber assembly which uses polychromatic illumination to extract images without the use of a lens, representing an important step toward ambient light imaging fabrics.