3D Hotspots Research Articles

Cys-functionalized AuNP substrates for improved sensing of the marine toxin STX by dynamic surface-enhanced Raman spectroscopy.

Saxitoxin (STX) as one of the most harmful and typical paralytic shellfish toxins, is posing a serious threat to environmental and human health, thus it is essential to develop a sensitive and reliable analytical method for STX detection. Herein, we proposed a strategy for rapid and sensitive detection of STX with surface-enhanced Raman spectroscopy (SERS), by employing cysteine modified gold nanoparticles (Cys-AuNPs) as SERS probe to capture STX molecules through electrostatic interactions and multiple hydrogen bonds between Cys and STX molecules. Moreover, the XPS and zeta potential results indicated that Cys could bond to AuNPs through Au-S bonds and the addition of STX could induce the efficient aggregation of Cys-AuNPs owing to the presence of electrostatic interactions and multiple hydrogen bonds between Cys and STX molecules. Furthermore, considering the high sensitivity and stability of the dynamic surface-enhanced Raman spectroscopy (D-SERS) strategy with the formation of a 3D hotspot matrix, the highly sensitive detection of STX was realized to a level of 1 × 10-7M by using the D-SERS strategy. Consequently, Cys-AuNPs as high affinity substrates can provide high sensitivity for the detection of STX through the D-SERS strategy. Graphical abstract.

3D Hot-Spot Localization by Lock-In Thermography

Abstract This article describes a form of lock-in thermography that achieves 3D localization of thermally active defects in stacked die packages. In this approach, phase shifts associated with thermal propagation delay are analyzed as a function of frequency. This allows for a precise localization of defects in all three spatial dimensions and can serve as a guide for subsequent high-resolution physical analyses.

3D hotspots of marine litter in the Mediterranean: A modeling study

The 3D dispersion of marine litter (ML) over the Mediterranean basin has been simulated using the velocity fields from a high resolution circulation model as base to run a 3D Lagrangian model. Three simulations have been performed to mimic the evolution of ML with density lower, similar, or higher than seawater. In all cases a realistic distribution of ML sources was used. Our results show that the accumulation/dispersion areas of the floating and buoyancy neutral particles are practically the same, although the latter are distributed in the water column, 80% of them found in the photic layer (average depth of 35m). Regarding to the densest particles, they rapidly sink and reach the seafloor close to their source. The regions of higher temporal variability mostly coincide with the ML accumulation regions. Weak seasonal variability occurs at a sub-basin scale as a result of the particles redistribution induced by the seasonal variability of the current field.

Gold Nanorod Array-Bridged Internal-Standard SERS Tags: From Ultrasensitivity to Multifunctionality.

Bimetallic gold core-silver shell (Au@Ag) surface-enhanced Raman scattering (SERS) tags draw broad interest in the fields of biological and environmental analysis. In reported tags, silver coating tended to smooth the surface and merge the original hotspot of Au cores, which was disadvantageous to signal enhancement from the aspect of surface topography. Herein, we developed gold nanorod (AuNR)-bridged Au@Ag SERS tags with uniform three-dimensional (3D) topography for the first time. This unique structure was achieved by selecting waxberry-like Au nanoparticles (NPs) as cores, which were capped by vertically oriented AuNR arrays. Upon selective surface blocking with thiol-ligands, Ag NPs were controlled to anisotropically grow on the tips of the AuNRs, producing high-density homo- (Ag-Ag) and hetero- (Au-Ag) hotspots in a single NP. The 3D hotspots rendered this NP extraordinary SERS enhancement ability (an analytical enhancement factor of 3.4 × 106) 30 times higher than the counterpart with a smooth surface, realizing signal detection from a single NP. More importantly, multiplexing signals ("blank" or multiplex "internal standard") can be achieved by simply changing thiol-ligands, as exemplified in the synthesis of NPs with 8 signatures. Furthermore, the multifunctionality has been demonstrated in living cell/in vivo imaging, photothermal therapy, and SERS substrates for ratiometric quantitative analysis, relying on the inherent internal standard signal. The prepared Au@Ag NPs have great potential as standard tools in many SERS-related fields.

Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies.

Rubella viruses (RV) have been found in an association with granulomas in children with primary immune deficiencies (PID). Here, we report the recovery and characterization of infectious immunodeficiency-related vaccine-derived rubella viruses (iVDRV) from diagnostic skin biopsies of four patients. Sequence evolution within PID hosts was studied by comparison of the complete genomic sequences of the iVDRVs with the genome of the vaccine virus RA27/3. The degree of divergence of each iVDRV correlated with the duration of persistence indicating continuous intrahost evolution. The evolution rates for synonymous and nonsynonymous substitutions were estimated to be 5.7 x 10−3 subs/site/year and 8.9 x 10−4 subs/site/year, respectively. Mutational spectra and signatures indicated a major role for APOBEC cytidine deaminases and a secondary role for ADAR adenosine deaminases in generating diversity of iVDRVs. The distributions of mutations across the genes and 3D hotspots for amino acid substitutions in the E1 glycoprotein identified regions that may be under positive selective pressure. Quasispecies diversity was higher in granulomas than in recovered infectious iVDRVs. Growth properties of iVDRVs were assessed in WI-38 fibroblast cultures. None of the iVDRV isolates showed complete reversion to wild type phenotype but the replicative and persistence characteristics of iVDRVs were different from those of the RA27/3 vaccine strain, making predictions of iVDRV transmissibility and teratogenicity difficult. However, detection of iVDRV RNA in nasopharyngeal specimen and poor neutralization of some iVDRV strains by sera from vaccinated persons suggests possible public health risks associated with iVDRV carriers. Detection of IgM antibody to RV in sera of two out of three patients may be a marker of virus persistence, potentially useful for identifying patients with iVDRV before development of lesions. Studies of the evolutionary dynamics of iVDRV during persistence will contribute to development of infection control strategies and antiviral therapies.

3D Hotspots Platform for Plasmon Enhanced Raman and Second Harmonic Generation Spectroscopies and Quantitative Analysis

AbstractConstructing plasmonic hotspots in metal nanostructures is essential for plasmon‐enhanced spectroscopies (PESs), but their application in quantitative analysis is a long‐standing challenge. Herein, highly uniform, reproducible, stable, and sensitive 3D hotspots platform substrates are assembled on hydrophobic silicon wafers using a drop of solution containing silica coated surface plasmon resonance (SPR) active nanoparticles (NPs). Plasmon‐enhanced second harmonic generation (PESHG) and surface‐enhanced Raman scattering (SERS) experimental signals increase sharply with the increase of droplet evaporation time, which is attributed to the rapid increase of 3D hotspots generated by gradual decrease of distance between adjacent NPs. Compared with 3D bare metal NP substrate, 3D metal shell‐isolated nanoparticles (SHINs) substrate demonstrates much more stable PESHG and SERS signals attributing to the protecting SiO2 shells. Besides that, uniform distribution of 3D “hotspots” on the hydrophobic substrate can facilitate the quantitative analysis of an analyte using SERS. Experimental and theoretical results demonstrate that the 3D hotspots platform has the potential to be developed as a plasmon‐enhanced substrate for linear and nonlinear spectroscopies with practical sensing applications.

Glycerol-Assisted Construction of Long-Life Three-Dimensional Surface-Enhanced Raman Scattering Hot Spot Matrix.

An evaporative self-assembly strategy for constructing a long-life 3D surface-enhanced Raman scattering (SERS) hot spot matrix is proposed with the assistance of glycerol to improve the spectral sensitivity and reproducibility. Different from the traditional wetting-state or drying-state methods, silver nanoparticles (AgNPs) in the glycerol-stabilized 3D SERS hot spot matrix can be maintained in the translation state for more than 7 days with the maximal uniformity of the interparticle distance. Brownian dynamics simulations reveal that more hot spots emerge in the glycerol-stabilized AgNPs matrix, and the distances between the AgNPs are not fixed but balanced in a small range by the interplay of the van der Waals attraction and the electrostatic repulsion. A 2 orders of magnitude extra SERS enhancement, more stable peak frequencies, and a narrower peak full width at half-maximum (fwhm) can therefore be obtained, which ensure extremely stable and reproducible SERS signals. Single-molecule detection sensitivity utilizing the glycerol-stabilized 3D SERS hot spot matrix has been demonstrated by collecting the SERS spectra of dye molecules at a concentration of as low as 0.5 aM (5 × 10-19 M) with a good signal-to-noise ratio. A long lifetime, ultrahigh SERS enhancement, and extremely stable peak shape make the 3D SERS hot spot matrix a sensitive, practical, and reliable tool for the detection and analysis of analytes at ultralow concentration or even at the single-molecule level in complex matrixes.

Three-Dimensional Surface-Enhanced Raman Scattering Platforms: Large-Scale Plasmonic Hotspots for New Applications in Sensing, Microreaction, and Data Storage.

Surface-enhanced Raman scattering (SERS) is a molecular-specific spectroscopic technique that provides up to 1010-fold enhancement of signature Raman fingerprints using nanometer-scale 0D to 2D platforms. Over the past decades, 3D SERS platforms with additional plasmonic materials in the z-axis have been fabricated at sub-micrometer to centimeter scale, achieving higher hotspot density in all x, y, and z spatial directions and higher tolerance to laser misalignment. Moreover, the flexibility to construct platforms in arbitrary sizes and 3D shapes creates attractive applications besides traditional SERS sensing. In this Account, we introduce our library of substrate-based and substrate-less 3D plasmonic platforms, with an emphasis on their non-sensing applications as microlaboratories and data storage labels. We aim to provide a scientific synopsis on these high-potential yet currently overlooked applications of SERS and ignite new scientific discoveries and technology development in 3D SERS platforms to tackle real-world issues. One highlight of our substrate-based SERS platforms is multilayered platforms built from micrometer-thick assemblies of plasmonic particles, which can achieve up to 1011 enhancement factor. As an alternative, constructing 3D hotspots on non-plasmonic supports significantly reduces waste of plasmonic materials while allowing high flexibility in structural design. We then introduce our emerging substrate-less plasmonic capsules including liquid marbles and colloidosomes, which we further incorporate the latter within an aerosol to form centimeter-scale SERS-active plasmonic cloud, the world's largest 3D SERS platform to date. We then discuss the various emerging applications arising only from these 3D platforms, in the fields of sensing, microreactions, and data storage. An important novel sensing application is the stand-off detection of airborne analytes that are several meters away, made feasible with aerosolized plasmonic clouds. We also describe plasmonic capsules as excellent miniature lab-in-droplets that can simultaneously provide in situ monitoring at the molecular level during reaction, owing to their ultrasensitive 3D plasmonic shells. We highlight the emergence of 3D SERS-based data storage platforms with 10-100-fold higher storage density than 2D platforms, featuring a new approach in the development of level 3 security (L3S) anti-counterfeiting labels. Ultimately, we recognize that 3D SERS research can only be developed further when its sensing capabilities are concurrently strengthened. With this vision, we foresee the creation of highly applicable 3D SERS platforms that excel in both sensing and non-sensing areas, providing modernsolutions in the ongoing Fourth Industrial Revolution.

Probing the Location of 3D Hot Spots in Gold Nanoparticle Films Using Surface-Enhanced Raman Spectroscopy.

Plasmonic "hot spots" play a key role in surface-enhanced Raman scattering (SERS) enabling its ultrahigh surface sensitivity. Thus, precise prediction and control of the location of hot spots in surface nanostructures is of great importance. However, it is difficult to predict the exact location of hot spots due to complex plasmon competition and synergistic effects in three-dimensional (3D) multiparticle surface configurations. In this work, three types of Au@probe@SiO2 core-shell nanoparticles were prepared and a 3D hot spots matrix was assembled via a consecutive layer on layer deposition method. Combined with SERS, distinct probe molecules were integrated into different layers of the 3D multiparticle nanostructure allowing for the hot spots to be precisely located. Importantly, the hot spots could be controlled and relocated by applying different excitation wavelengths, which was verified by simulations and experimental results. This work proposes a new insight and provides a platform for precisely probing and controlling chemical reactions, which has profound implications in both surface analysis and surface plasmonics.

A long-period and high-stability three-dimensional surface-enhanced Raman scattering hotspot matrix.

A novel long-period and high-stability 3D hotspot matrix was constructed with the assistance of glycerol based on our previous study on the dynamic-SERS approach in the water system: it could increase efficient hotspot duration from few seconds to twenty minutes and strongly improve sensitivity and reproducibility for SERS detection.

Plasmonic 3D Semiconductor-Metal Nanopore Arrays for Reliable Surface-Enhanced Raman Scattering Detection and In-Site Catalytic Reaction Monitoring.

It is urgent to develop a rapid, reliable, and in-site determination method to detect or monitor trace amounts of toxic substances in the field. Here, we report an alternative surface-enhanced Raman scattering (SERS) method coupled with a portable Raman device on a plasmonic three-dimension (3D) hot spot sensing surface. Plasmonic Ag nanoparticles (AgNPs) were uniformly deposited on 3D TiO2 nanopore arrays as a sensitive SERS substrate, and further coated with graphene oxide (GO). We demonstrate the plasmon-induced SERS enhancement (5.8-fold) and the improvement of catalytic activity by incorporation of plasmonic AgNPs into the 3D TiO2 nanopore arrays. The modification of GO on the TiO2-Ag nanopore array further increases by a 6.2-fold Raman enhancement compared to TiO2-Ag while maintaining good uniformity (RSD < 10%). The optimized TiO2-Ag-GO substrate shows powerful quantitative detection potential for drug residues in fish scales via a simple scrubbing method, and the limit of detection (LOD) for crystal violet (CV) was 10-8 M. The SERS substrate also showed detection practicability of pesticide residues in banana peel with an LOD of 10-7 M. In addition, our TiO2-Ag-GO substrate exhibits excellent SERS self-monitoring performance for catalytic reduction of multiple organics in NaBH4 solution, and the substrate shows good recyclability of 6 cycles. Such a 3D TiO2-Ag-GO substrate is a promising SERS substrate with good sensitivity, uniformity, and reusability, and may be utilized for further miniaturization for point of analytical applications.

New Outlier Top-Cut Method for Mineral Resource Estimation via 3D Hot Spot Analysis of Borehole Data

Three-dimensional (3D) analysis of borehole data is very important for effective mineral exploration. It can be used not only to understand the geological structure of the underground, but to estimate the amount of the resource. In the mining industry, the geostatistical interpolation, such as kriging, is widely used to predict the value of a whole section using this borehole data. In order to obtain reasonable prediction results, it is firstly necessary to verify assay and geological databases. In addition, if the assayed grade data deviates significantly from the average value, it is necessary to perform the prediction including the outlier top-cut because it may excessively affect the predicted value. However, the existing top-cut methods of determining a specific threshold value may cause an error by excluding significant data. In this study, to minimize the loss of such data, we developed a 3D hot spot analysis technique to analyze statistically significant outliers. In addition, it was applied to borehole data analysis of the Au deposit. As a result, we confirmed that the proposed method can mitigate the overestimation or underestimation that might occur when applying the existing methods.

Sensitive, reproducible, and stable 3D plasmonic hybrids with bilayer WS2 as nanospacer for SERS analysis.

The highly enhanced local electromagnetic field occurring through nanometer gap between the plamonic nanostructures provides the dominant contribution in surface enhancement Raman scattering (SERS) enhancement. Thence, we designed the remarkable SERS platform (AuNPs/WS2@AuNPs hybrids) by introducing bilayer WS2 film as the precise nanospacer. Bilayer WS2 film can realize the facile and tight combination with AuNPs via the thermal decomposition approach. Dense three-dimension (3D) hot spots provided by this hybrid plasmonic nanostructures are responsible for the extremely satisfying SERS performances. Using rhodamine 6G (R6G) as the probe molecules, the AuNPs/WS2@AuNPs hybrids perform the excellent sensitivity with the minimum detectable concentration as low as 10-11 M. Uniform and reproducible SERS signals illustrate that the synthesized SERS hybrids perform the splendid spot-to-spot reproducibility (RSD~5.4%) and substrate-to-substrate reproducibility (RSD~5.7%). The stability of AuNPs and the protection of WS2 film endow this hybrid plasmonic nanostructures with the brilliant anti-oxidation stability. Moreover, the enhanced electric field distribution simulated with the COMSOL software proves the remarkable SERS performance in theory. Therefore, AuNPs/WS2@AuNPs substrate not only widens the SERS research filed of WS2, but also shows vast potential as excellent SERS sensor for practical applicability.

3D hybrid MoS2/AgNPs/inverted pyramid PMMA resonant cavity system for the excellent flexible surface enhanced Raman scattering sensor

It is widely accepted that resonant cavity system represents the effective laser utilization due to the back and forth reflection and the electric field energy storage. Here, a three-dimensional (3D) hybrid MoS2/AgNPs/inverted pyramid polymethyl methacrylate (iPPMMA) resonant cavity system as a flexible surface enhanced Raman scattering (SERS) sensor was investigated in experiment and theory. The obtained resonant cavity between MoS2, iPPMMA and the plasmonic silver nanoparticles offers the tremendous local near-field enhancements, which is manifested using the finite-difference time-domain (FDTD) theoretical simulation. Additionally, by virtue of the lower light absorption, the iPPMMA gains the advantage over pyramid Si (PSi) in term of enhancing local electric field. The synergistic effects of MoS2, iPPMMA and AgNPs can generate the 3D dense hot spots and extremely contribute to the excellent ultrasensitivity, stablity, reproducibility and recyclability of the proposed flexible SERS sensor. Moreover, the fabricated MoS2/AgNPs/iPPMMA hybrid structure was housed at the end of the optical fiber to remotely detect the toxic mixtures solution, which demonstrates our flexible SERS sensor has enormous potential to be applied in food safety field.

Controlling the 3D Electromagnetic Coupling in Co-Sputtered Ag⁻SiO₂ Nanomace Arrays by Lateral Sizes.

Ag–SiO2 nanomace arrays were prepared on a two-dimensional ordered colloidal (2D) polystyrene sphere template by co-sputtering Ag and SiO2 in a magnetron sputtering system. The lateral size of the nanomaces and the distance between the neighbor nanomaces were controlled by adjusting the etching time of the 2D template. The nanomaces were composed of SiO2-isolated Ag nanoparticles, which produced surface-enhanced Raman scattering (SERS) enhancement, and 3D hot spots were created between the neighbor nanomaces. When the distance between the nanomaces was sufficiently large, triangle-shaped nanostructures on silicon substrate were observed, which also contributed to the enhancement of the SERS signals. The finite-difference time-domain (FDTD) method was used to calculate the electromagnetic field distributions in the Ag–SiO2 nanomace arrays, which generated physical reasons for the change of the SERS signals.

Phase confinement of self-migrated plasmonic silver in triphasic system: Offering 3D hot spots on hydrophobic paper for SERS detection

Hydrophobic paper decorated Ag nanoparticles (NPs) with a uniform distribution was fabricated in an oil-paper-aqueous triphasic system via a facile in situ interfacial reduction approach. Interestingly, the Ag NPs formed at the paper/aqueous interface could migrate to the oil/paper interface. Moreover, these Ag NPs would not continue to migrate away the paper surface into the oil phase but was completely confined in the solid paper matrix. This phase confinement of migrated Ag NPs in the paper matrix creates abundant 3D hot spots for plasmonic enhancement. The obtained Ag-loaded paper exhibits an excellent SERS activity, reliable reproducibility and autofluorescence suppression effect, which enabling it as a promising platform for qualitative and quantitative SERS study. Due to its condensation effect, the hydrophobic paper surface can be used as a concentrator to enrich water-soluble analytes over the SERS active domains for highly sensitive detection (10−9 mol/L−1). Furthermore, the Ag-loaded paper combined with the feature of chromatography and plamon-enhanced optical signals possesses ability to perform synchronous separation and surface-enhanced Raman scattering (SERS) detection of complex samples.

Experimental and theoretical investigation for a hierarchical SERS activated platform with 3D dense hot spots

Hot spots generated from the ultra-small nanogaps will tremendously contribute to the strong electromagnetic field. Therefore, the establishment and design of nanogaps are extremely significant. Here, a hierarchical structure, AgNPs/bilayer graphene/Au nanonet, was proposed to form the dense three-dimensional (3D) hot spots and demonstrated in experiment and theory. Numerous nanometer gaps in the complex Au nanonet structure (∼8.67 nm) and in AgNPs/Au nanonet isolated by bilayer graphene (0.64 nm) were achieved, which is much beneficial for the obtainment of the hot spots. Based on this surface enhanced Raman scattering (SERS) substrate, an excellent SERS activity (EF ∼ 9.1 × 109), high sensitivity (10−13 and 10−12 M respective for Rhodamine 6G (R6G) and crystal violet (CV)), and SERS signals homogeneity, outstanding reproducibility (maximum intensity deviation from substrate to substrate ∼10.43%) were obtained, which can be attributed to the abundant lateral and vertical hot spots introduced by the hierarchical structure. Moreover, the proposed SERS substrate was used to sensitively detect the harmful malachite green (MG), which exhibits a great prospect as a potential SERS sensor in food safety field and biochemical molecules.

3D Plasmon Coupling Assisted Sers on Nanoparticle-Nanocup Array Hybrids

Unique colorimetric optical properties of nanomaterials can effectively influence the light absorption or emission of molecules. Here, we design plasmonic substrate for surface-enhanced Raman scattering (SERS) by inducing three-dimensional (3D) hot spots on the sensing surface. The 3D hot spots are formed by the self-assembly of plasmonic nanoparticles (NPs) on a 3D plasmonic nanocup array structure. This 3D hot spot formation on the periodic nanocup arrays achieves much higher SERS enhancement factor than the 2D NP arrays, which have been conventionally sought SERS substrates. We also utilize the colorimetric properties of the nanocup arrays for an additional degree of SERS enhancement. Colorimetry, achieved by tunable plasmon resonance wavelength by controlling dielectric property on the nanocup array surface, eases the modulation of the plasmonic resonance condition without modifying the nanostructure design. By continuously monitoring the shifts of the plasmon resonance condition and its effect on the light absorption and emission of the nearby molecules, we verify that larger SERS enhancement is achieved when the plasmon resonance wavelength is matched with the Raman excitation wavelength. The ease of plasmon resonance tuning of this nanocup array-nanoparticle hybrid structure allows versatile SERS enhancement for a variety of different Raman measurement conditions.

Abstract 3606: Identification of oncogenic mutation hotspots via three-dimensional proximity

Abstract One of the greatest challenges in studying the genomic basis of human cancer is distinguishing the few mutations that directly contribute to tumorigenesis (“drivers”) from the many biologically neutral mutations (“passengers”). Existing methods can identify highly recurrent individual mutations or mutated genes, but capturing functional yet infrequent “long-tail” mutations remains challenging. While individually uncommon, these long-tail mutations are present in as many as one-third of cancer patients, and for many of them targeted therapies currently exist. Therefore, improved approaches to identify individual driver mutations in the long tail will facilitate our understanding of their potentially diverse biological and clinical significance. Some of these mutations can be identified as hotspots based on their recurrence on or around the same residue. Others may occur in different regions but are actually close in protein three-dimensional structures. We have developed a novel method that identifies mutations that significantly cluster together within three-dimensional proximity in protein structures, or 3D hotspots. We applied this method to a combined collection of mutation data of 21,000 sequenced tumor samples in 74 cancers. Our analysis confirmed many well-studied 3D hotspots of functional mutations in cancer genes such as KRAS, BRAF, IDH2, SMAD4, FBXW7, SPOP, RHOA, and PTPN11. Most of these genes have well known individual hotspots, but our analysis suggests that additional mutations in other residues of the protein are adjacent in the folded protein structure and may also be oncogenic. We also identified novel 3D hotspots in known cancer genes such as EP300, MAP2K1, and KDR, as well as several other genes of unknown significance that harbor 3D hotspots (e.g., DCC). Most of these hotspots are present in multiple cancers. To explore the functional consequences and potential translational significance of long-tail low-incidence mutations identified by our method, we assessed several MAP2K1 mutations in vitro. MAP2K1 (MEK1) is a critical effector of MAPK signaling, harbors conventional single-codon hotspots in several cancer types, and a number of selective MAPK pathway inhibitors are either FDA-approved or are being investigated in early-phase clinical trials. Our experiments confirmed that these mutations activate MAP2K1 and confer sensitivity to MAP2K1 inhibition. We have provided an implementation of the algorithm via an interactive web resource connecting to cBioPortal for Cancer Genomics (http://cbioportal.org/) for easy interpretation of cancer genomics data in the context of three-dimensional structures. By adding to cBioPortal's already powerful capacity of clinical decision support, our method and analysis provide a useful approach of interpretation, prioritization and extension of biologically significant and clinically actionable mutations in cancer. Citation Format: Jianjiong Gao, Matthew T. Chang, Brooke E. Sylvester, Hannah C. Johnsen, Sizhi P. Gao, S. Onur Sumer, David B. Solit, Barry S. Taylor, Nikolaus Schultz, Chris Sander. Identification of oncogenic mutation hotspots via three-dimensional proximity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3606.

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.

The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions.