With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic.
The implementation of the angular spectrum approach based on the two-dimensional fast Fourier transform is evaluated for near-field pressure simulations of square ultrasound transducers, where the three-dimensional pressure field is calculated from the normal velocity distribution on the transducer surface. The pressure field is propagated in the spatial frequency domain with the spatial propagator or the spectral propagator. The spatial propagator yields accurate results in the central portion of the computational grid while significant errors are produced near the edge due to the finite extent of the window applied to the spatial propagator. Likewise, the spectral propagator is inherently undersampled in the spatial frequency domain, and this causes high frequency errors in the computed pressure field. This aliasing problem is alleviated with angular restriction. The results show that, in nonattenuating media, the spatial propagator achieves smaller errors than the spectral propagator after the region of interest is truncated to exclude the windowing error. For pressure calculations in attenuating media or with apodized pistons as sources, the spatial and spectral propagator achieve similar accuracies. In all simulations, the angular spectrum calculations with the spatial propagator take more time than calculations with the spectral propagator. 相似文献
The mechanism is investigated for CptBuRh(OH)2-catalyzed annulation of 2-biphenylboronic acid with three activated alkenes using M06-2X functional. The reaction comprises transmetalation via two steps and following C-H activation producing reactive Rh-biphenyl complex with two Rh—C σ bonds. After the coordination/insertion of alkenes, respective fused or bridged cyclic products are yielded depending on different alkenes accompanied by the release of CptBuRh. The promotion of CptBuRh(OH)2 lies in the barrier decrease of transmetalation and C-H activation ready for coordination/insertion ensuring the smooth progress of common rate-limiting reductive elimination. The stereoselective transfer and ring rotation are specific for benzoquinone and cyclopropenone. The role of Rh(III) catalyst and release of Rh(I) is supported by Multiwfn analysis on frontier molecular orbital(FMO) of specific transiton states(TSs) and Mayer bond order(MBO) value of vital bonding, breaking. 相似文献
The maremycin biosynthetic gene cluster has been identified in Streptomyces sp. B9173. Comparative metabolic profiling with knockout mutant strains led to the identification of new products correlated to the maremycin biosynthesis, in particular the “demethyl”-maremycins with an unexpected D-tryptophan unit. A biosynthetic pathway for the maremycins is proposed and plausible reasoning for tryptophan epimerization in the demethylmaremycin biosynthesis is also provided. 相似文献