A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results.

Owing to spatial segregation of tumor subclones, solid tumor sampling using formalin-fixed, paraffin-embedded blocks is often inadequate to represent the genomic heterogeneity of solid tumors. We present an approach, representative sampling, to dissect and homogenize leftover residual surgical tissue prior to sequencing. We also detail optional tumor cell enrichment and DNA preparation. This method, applicable only to surgically removed tumors with leftover tissue, facilitates robust sampling to avoid missing or over-representing actionable variants. For complete details on the use and execution of this protocol, please refer to Litchfield et al. (2020).

Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue.

Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB but low clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure.

BaTiO3-core Au-shell nanoparticles for photothermal therapy and bimodal imaging.

We report sub-100 nm metal-shell (Au) dielectric-core (BaTiO3) nanoparticles with bimodal imaging abilities and enhanced photothermal effects. The nanoparticles efficiently absorb light in the near infrared range of the spectrum and convert it to heat to ablate tumors. Their BaTiO3 core, a highly ordered non-centrosymmetric material, can be imaged by second harmonic generation, and their Au shell generates two-photon luminescence. The intrinsic dual imaging capability allows investigating the distribution of the nanoparticles in relation to the tumor vasculature morphology during photothermal ablation. Our design enabled in vivo real-time tracking of the BT-Au-NPs and observation of their thermally-induced effect on tumor vessels. STATEMENT OF SIGNIFICANCE: Photothermal therapy induced by plasmonic nanoparticles has emerged as a promising approach to treating cancer. However, the study of the role of intratumoral nanoparticle distribution in mediating tumoricidal activity has been hampered by the lack of suitable imaging techniques. This work describes metal-shell (Au) dielectric-core (BaTiO3) nanoparticles (abbreviated as BT-Au-NP) for photothermal therapy and bimodal imaging. We demonstrated that sub-100 nm BT-Au-NP can efficiently absorb near infrared light and convert it to heat to ablate tumors. The intrinsic dual imaging capability allowed us to investigate the distribution of the nanoparticles in relation to the tumor vasculature morphology during photothermal ablation, enabling in vivo real-time tracking of the BT-Au-NPs and observation of their thermally-induced effect on tumor vessels.

Extended Release of Native Drug Conjugated in Polyketal Microparticles.

Polyketals, which can be biodegradable, have good biocompatibility, and are pH-sensitive, could have broad applicability in drug delivery and other biomedical applications. However, facile synthesis of high molecular weight polyketals is challenging, and short durations of drug release from polyketal particulate formulations limit their application in drug delivery. Here we report the synthesis of a di-isopropenyl ether monomer and its use to synthesize high molecular weight estradiol-polyketal conjugates by addition polymerization. Microparticles were prepared from the estradiol-polyketal conjugate, where estradiol was incorporated into the polymer backbone. The particles had high drug loading and significantly prolonged drug release. Release of estradiol from the drug-polyketal conjugate microparticles was acid-responsive, as evidenced by faster drug release at low pH and with co-incorporation of PLGA. Tissue reaction to the microparticles was benign in vivo. Polyketal drug conjugates are promising candidates for long-acting drug delivery systems to treat chronic diseases.

A Supramolecular Shear-Thinning Anti-Inflammatory Steroid Hydrogel.

Shear-thinning and self-healing steroid-drug-based hydrogels are presented, which exhibit rapid and complete recovery of their mechanical properties within seconds following stress-induced flow. The hydrogels release steroid drug in vivo with no visible residue when release is complete.

Ultraviolet light-mediated drug delivery: Principles, applications, and challenges.

UV light has been extensively employed in drug delivery because of its versatility, ease of manipulation, and ability to induce chemical changes on the therapeutic carrier. Here we review the mechanisms by which UV light affects drug delivery systems. We will present the challenges facing UV-induced drug delivery and some of the proposed solutions.

Efficient Triplet-Triplet Annihilation-Based Upconversion for Nanoparticle Phototargeting.

High-efficiency upconverted light would be a desirable stimulus for triggered drug delivery. Here we present a general strategy to achieve photoreactions based on triplet-triplet annihilation upconversion (TTA-UC) and Förster resonance energy transfer (FRET). We designed PLA-PEG micellar nanoparticles containing in their cores hydrophobic photosensitizer and annihilator molecules which, when stimulated with green light, would undergo TTA-UC. The upconverted energy was then transferred by FRET to a hydrophobic photocleavable group (DEACM), also in the core. The DEACM was bonded to (and thus inactivated) the cell-binding peptide cyclo-(RGDfK), which was bound to the PLA-PEG chain. Cleavage of DEACM by FRET reactivated the PLA-PEG-bound peptide and allowed it to move from the particle core to the surface. TTA-UC followed by FRET allowed photocontrolled binding of cell adhesion with green light LED irradiation at low irradiance for short periods. These are attractive properties in phototriggered systems.

NIR-triggered drug delivery by collagen-mediated second harmonic generation.

Second harmonic generation is a process through which nonlinear materials such as collagen can absorb two photons and scatter one with twice the energy. Collagen upconverts 730 nm (near-IR) to 365 nm (UV) through second harmonic generation, which cleaves a molecule bound to collagen via a UV-sensitive linker.

Photothermally targeted thermosensitive polymer-masked nanoparticles.

The targeted delivery of therapeutic cargos using noninvasive stimuli has the potential to improve efficacy and reduce off-target effects (toxicity). Here, we demonstrate a targeting mechanism that uses a thermoresponsive copolymer to mask a peptide ligand that binds a widely distributed receptor (integrin ß1) on the surface of silica core-gold shell nanoparticles. The nanoparticles convert NIR light into heat, which causes the copolymer to collapse, exposing the ligand peptide, allowing cell binding. The use of NIR light could allow targeting of plasmonic nanoparticles deep within tissues. This approach could be extended to a variety of applications including photothermal therapy and drug delivery.

Enhanced photothermal effect of plasmonic nanoparticles coated with reduced graphene oxide.

We report plasmonic gold nanoshells and nanorods coated with reduced graphene oxide that produce an enhanced photothermal effect when stimulated by near-infrared (NIR) light. Electrostatic interactions between nanosized graphene oxide and gold nanoparticles followed by in situ chemical reduction generated reduced graphene oxide-coated nanoparticles; the coating was demonstrated using Raman and HR-TEM. Reduced graphene oxide-coated gold nanoparticles showed enhanced photothermal effect compared to noncoated or nonreduced graphene oxide-coated gold nanoparticles. Reduced graphene oxide-coated gold nanoparticles killed cells more rapidly than did noncoated or nonreduced graphene oxide-coated gold nanoparticles.

Gene silencing by gold nanoshell-mediated delivery and laser-triggered release of antisense oligonucleotide and siRNA.

RNA interference (RNAi)--using antisense DNA or RNA oligonucleotides to silence activity of a specific pathogenic gene transcript and reduce expression of the encoded protein--is very useful in dissecting genetic function and holds significant promise as a molecular therapeutic. A major obstacle in achieving gene silencing with RNAi technology is the systemic delivery of therapeutic oligonucleotides. Here we demonstrate an engineered gold nanoshell (NS)-based therapeutic oligonucleotide delivery vehicle, designed to release its cargo on demand upon illumination with a near-infrared (NIR) laser. A poly-L-lysine peptide (PLL) epilayer covalently attached to the NS surface (NS-PLL) is used to capture intact, single-stranded antisense DNA oligonucleotides, or alternatively, double-stranded short-interfering RNA (siRNA) molecules. Controlled release of the captured therapeutic oligonucleotides in each case is accomplished by continuous wave NIR laser irradiation at 800 nm, near the resonance wavelength of the nanoshell. Fluorescently tagged oligonucleotides were used to monitor the time-dependent release process and light-triggered endosomal release. A green fluorescent protein (GFP)-expressing human lung cancer H1299 cell line was used to determine cellular uptake and gene silencing mediated by the NS-PLL carrying GFP gene-specific single-stranded DNA antisense oligonucleotide (AON-GFP), or a double-stranded siRNA (siRNA-GFP), in vitro. Light-triggered delivery resulted in ~47% and ~49% downregulation of the targeted GFP expression by AON-GFP and siRNA-GFP, respectively. Cytotoxicity induced by both the NS-PLL delivery vector and by laser irradiation is minimal, as demonstrated by a XTT cell proliferation assay.

Orientation-preserving transfer and directional light scattering from individual light-bending nanoparticles.

A nanocup, or semishell, is an asymmetric plasmonic "Janus" nanoparticle with electric and magnetic plasmon modes; the latter scatters light in a direction controlled by nanoparticle orientation, making it the nanoscale analog of a parabolic antenna. Here we report a method for transferring nanocups from their growth substrate to oxide-terminated substrates that precisely preserves their three-dimensional orientation, enabling their use as nanophotonic components. This enables us to selectively excite and probe the electric and magnetic plasmon modes of individual nanocups, showing how the scattered light depends on the direction of incoming light and the orientation of this nanoparticle antenna.

Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

Visualizing light-triggered release of molecules inside living cells.

The light-triggered release of deoxyribonucleic acid (DNA) from gold nanoparticle-based, plasmon resonant vectors, such as nanoshells, shows great promise for gene delivery in living cells. Here we show that intracellular light-triggered release can be performed on molecules that associate with the DNA in a DNA host-guest complex bound to nanoshells. DAPI (4',6-diamidino-2-phenylindole), a bright blue fluorescent molecule that binds reversibly to double-stranded DNA, was chosen to visualize this intracellular light-induced release process. Illumination of nanoshell-dsDNA-DAPI complexes at their plasmon resonance wavelength dehybridizes the DNA, releasing the DAPI molecules within living cells, where they diffuse to the nucleus and associate with the cell's endogenous DNA. The low laser power and irradiation times required for molecular release do not compromise cell viability. This highly controlled co-release of nonbiological molecules accompanying the oligonucleotides could have broad applications in the study of cellular processes and in the development of intracellular targeted therapies.

Label-free detection of DNA hybridization using surface enhanced Raman spectroscopy.

The SERS spectrum of DNA is strongly dominated by the strong spectral feature of adenine at 736 cm(-1); the presence of adenine can serve as an endogenous marker for the label-free SERS-based detection of DNA hybridization when the probe DNA sequence is adenine-free. The substitution of 2-aminopurine for adenine on the probe DNA sequence enables the detection of a target sequence using SERS, upon hybridization of the target with the 2-AP-substituted probe DNA sequence.

Nanoshell-based substrates for surface enhanced spectroscopic detection of biomolecules.

Nanoshells are optically tunable core-shell nanostructures with demonstrated uses in surface enhanced spectroscopies. Based on their ability to support surface plasmons, which give rise to strongly enhanced electromagnetic fields at their surface, nanoshells provide simple, scalable, high-quality substrates. In this article, we outline the development and use of nanoshell-based substrates for direct, spectroscopic detection of biomolecules. Recent advances in the use of these nanostructures lead to improved spectroscopic quality, selectivity, and reproducibility.

Gold nanoparticles can induce the formation of protein-based aggregates at physiological pH.

Protein-nanoparticle interactions are of central importance in the biomedical applications of nanoparticles, as well as in the growing biosafety concerns of nanomaterials. We observe that gold nanoparticles initiate protein aggregation at physiological pH, resulting in the formation of extended, amorphous protein-nanoparticle assemblies, accompanied by large protein aggregates without embedded nanoparticles. Proteins at the Au nanoparticle surface are observed to be partially unfolded; these nanoparticle-induced misfolded proteins likely catalyze the observed aggregate formation and growth.

Correlation of molecular orientation and packing density in a dsDNA self-assembled monolayer observable with surface-enhanced Raman spectroscopy.

Observations of two spectrally distinct ring breathing modes of guanine and adenine in the surface-enhanced Raman spectrum (SERS) of a dsDNA self-assembled monolayer on an Au nanoshell SERS substrate provide information concerning the orientation of its constituent molecules. The two modes vary with DNA concentration in a highly systematic manner, consistent with studies suggesting DNA molecules tend toward a more horizontal orientation at low-surface concentrations and a more vertical conformation at high concentrations. The introduction of small molecular spacers coadsorbed onto the Au nanoshell surface to "raise" the DNA molecules yields a SERS spectrum consistent with a more upright molecular orientation.

Surface-enhanced Raman spectroscopy of DNA.

We report a method for obtaining highly reproducible surface-enhanced Raman spectroscopy (SERS) of single and double-stranded thiolated DNA oligomers. Following a protocol that relaxes the DNA into an extended conformation, SERS spectra of DNA oligonucleotides are found to be extremely similar, strongly dominated by the Stokes modes of adenine. A spectral correlation function analysis useful for assessing reproducibility and for quantifying the highly complex changes corresponding to modifications in molecular conformation of the adsorbate molecules is introduced. This approach is used to monitor the interaction of DNA with cisplatin, a chemotherapy agent in widespread use.