Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors.

The detection of recurrent gene fusions can help confirm diagnoses in solid tumors, particularly when the morphology and staining are unusual or nonspecific, and can guide therapeutic decisions. Although fluorescence in situ hybridization and PCR are often used to identify fusions, the rearrangement must be suspected, with only a few prioritized probes run. It was hypothesized that the Illumina TruSight RNA Fusion Panel, which detects fusions of 507 genes and their partners, would uncover fusions with greater sensitivity than other approaches, leading to changes in diagnosis, prognosis, or therapy. Targeted RNA sequencing was performed on formalin-fixed, paraffin-embedded sarcoma and carcinoma cases in which fluorescence in situ hybridization, RT-PCR, or DNA-based sequencing was conducted during the diagnostic workup. Of the 153 cases, 138 (90%) were sequenced with adequate quality control metrics. A total of 101 of 138 (73%) cases were concordant by RNA sequencing and the prior test method. RNA sequencing identified an additional 30 cases (22%) with fusions that were not detected by conventional methods. In seven cases (5%), the additional fusion information provided by RNA sequencing would have altered diagnosis and management. A total of 19 novel fusion pairs (not previously described in the literature) were discovered (14%). Overall, the findings show that a targeted RNA-sequencing method can detect gene fusions in formalin-fixed, paraffin-embedded specimens with high sensitivity.

Impact of Reducing DNA Input on Next-Generation Sequencing Library Complexity and Variant Detection.

PCR amplification, a key step in next-generation sequencing (NGS) library construction, can generate an unlimited amount of product from limited input; however, it cannot create more information than was present in the original template. Thus, NGS libraries can be made from very little DNA, but reducing the input may compromise assay sensitivity in ways that are difficult to ascertain unless library complexity (ie, the number of unique DNA molecules represented in the library) and depth of coverage with unique sequence reads (those derived from input DNA molecules) versus duplicate sequence reads (those resulting from overamplification of particular molecules) are discretely measured. A series of experiments was performed to explore the impact of low DNA input on an amplicon-based NGS assay using unique molecular identifiers to track unique versus duplicate reads. At high sequencing depths, unique and total (unique plus duplicate) read coverage are not well correlated, so increasing the number of sequenced reads does not necessarily improve sensitivity. Unique coverage depth tends to improve with more input, but improvements are not consistent. Fluctuations in library complexity complicated variant detection using both standardized and clinical specimens, often resulting in technical replicates with vastly different estimates of variant allelic fraction. In conclusion, depth of coverage with unique reads must be tracked in clinical NGS to ensure that sensitivity and accuracy are maintained.

An atom efficient, single-source precursor route to plasmonic CuS nanocrystals.

The synthesis of colloidal semiconductor nanocrystals (NCs) from single-source precursors offers simplified manufacturing processes at the cost of reduced atom efficiency. Self-capping routes have the potential to maximise this efficiency although investigation has so far been limited to organic solvents. Here we present the synthesis of copper sulfide NCs via the decomposition of a copper dithiocarbamate complex in water. Nanocrystalline covellite particles were prepared without the need for additional capping ligand and exhibited a hollow nanosphere morphology. Mass spectrometry of the water-stable NCs indicated the presence of a number of surface ligands, including a small amine fragment of the single-source precursor (SSP) complex. A broad plasmon resonance in the near-infrared (NIR) at 990 nm was also observed and the photothermal effect of this demonstrated. Cytotoxicity experiments indicated cell viability remained above 95% for NC concentrations up to 1 mg mL-1, indicating high biocompatibility.

Requirement for MUC5AC in KRAS-dependent lung carcinogenesis.

With more than 150,000 deaths per year in the US alone, lung cancer has the highest number of deaths for any cancer. These poor outcomes reflect a lack of treatment for the most common form of lung cancer, non-small cell lung carcinoma (NSCLC). Lung adenocarcinoma (ADC) is the most prevalent subtype of NSCLC, with the main oncogenic drivers being KRAS and epidermal growth factor receptor (EGFR). Whereas EGFR blockade has led to some success in lung ADC, effective KRAS inhibition is lacking. KRAS-mutant ADCs are characterized by high levels of gel-forming mucin expression, with the highest mucin levels corresponding to worse prognoses. Despite these well-recognized associations, little is known about roles for individual gel-forming mucins in ADC development causatively. We hypothesized that MUC5AC/Muc5ac, a mucin gene known to be commonly expressed in NSCLC, is crucial in KRAS/Kras-driven lung ADC. We found that MUC5AC was a significant determinant of poor prognosis, especially in patients with KRAS-mutant tumors. In addition, by using mice with lung ADC induced chemically with urethane or transgenically by mutant-Kras expression, we observed significantly reduced tumor development in animals lacking Muc5ac compared with controls. Collectively, these results provide strong support for MUC5AC as a potential therapeutic target for lung ADC, a disease with few effective treatments.

CNS Masson Tumors: Frequent Association With Therapeutic Radiation.

Masson tumor (MT, papillary endothelial hyperplasia) is an exaggerated form of thrombus reorganization rarely occurring in the central nervous system (CNS), where it presents as a mass or hemorrhage in parenchyma, meninges, or venous sinuses. MT is subclassified as type 1 arising within a histologically normal vessel, type 2 associated with a ruptured vascular malformation, and extravascular. Limited reports of CNS MT after radiosurgery, or especially external radiation therapy, have emerged. We searched our databases for cases reported from 2008 to present. Nine cases were identified, 6 of which were associated with receipt of therapeutic radiation for known lesions, with intervals of 1 to 25+ years to MT development (4 neoplasms=external beam radiation; 1 neoplasm=external beam radiation+radiosurgery, 1 arteriovenous malformation=radiosurgery). MTs were coassociated with radiation-induced vascular malformations (1 cavernoma-like, 1 massive) only in 2 of 6 irradiated patients, whereas the other 4 had MTs only. The 3 MTs in nonirradiated patients were extravascular, with 1 spontaneously developing in a hemangioblastoma. Seven of 9 MTs were intracerebral, 1 was within the spinal cord, and 1 was subdural. Papillary MT architecture was best appreciated by CD31 or CD34 immunohistochemistry, although ERG verified the endothelial monolayer population. Most CNS MTs at our institution have arisen in patients who have received therapeutic cranial radiation, many of whom received only external beam radiation. Although MTs could conceivably represent early, severe phases in radiation-induced cavernoma development, most were not found coassociated with the latter. This study further extends our knowledge of types of radiation-induced CNS vascular abnormalities.

Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity.

MICA is a major histocompatibility complex-like protein that undergoes a structural transition from disorder to order upon binding its immunoreceptor, NKG2D. We redesigned the disordered region of MICA with RosettaDesign to increase NKG2D binding. Mutations that stabilize this region were expected to increase association kinetics without changing dissociation kinetics, increase affinity of interaction, and reduce entropy loss upon binding. MICA mutants were stable in solution, and they were amenable to surface plasmon resonance evaluation of NKG2D binding kinetics and thermodynamics. Several MICA mutants bound NKG2D with enhanced affinity, kinetic changes were primarily observed during association, and thermodynamic changes in entropy were as expected. However, none of the 15 combinations of mutations predicted to stabilize the receptor-bound MICA conformation enhanced NKG2D affinity, whereas all 10 mutants predicted to be destabilized bound NKG2D with increased on-rates. Five of these had affinities enhanced by 0.9-1.8 kcal/mol over wild type by one to three non-contacting substitutions. Therefore, in this case, mutations designed to mildly destabilize a protein enhanced association and affinity.