Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer.

BACKGROUND: Neurogenic differentiation 1 (NeuroD1) is a representative small cell lung cancer (SCLC) transcription regulator involved in the carcinogenesis and behavior of SCLC. Histone modifications play an important role in transcription, and H3 lysine 4 trimethylation (H3K4me3) is primarily associated with promoter regions. METHODS: We investigated the association between single nucleotide polymorphisms (SNPs) in NeuroD1 and H3K4me3 coincident regions, selected using ChIP sequencing (ChIP-seq), and the clinical outcomes of 261 patients with SCLC. RESULTS: Among 230 SNPs, two were significantly associated with both the chemotherapy response and overall survival (OS) of patients with SCLC. RNF145 rs2043268A>G was associated with worse chemotherapy response and OS (under a recessive model, adjusted odds ratio [aOR], 0.50, 95% confidence interval [CI], 0.26-0.94, P = 0.031, and adjusted hazard ratio [aHR], 1.88, 95% CI, 1.38-2.57, P < 0.001). CINP rs762105A>G was also associated with worse chemotherapy response and OS (under a dominant model, aOR, 0.47, 95% CI, 0.23-0.99, P = 0.046, and aHR, 2.03, 95% CI, 1.47-2.82, P < 0.001). ChIP-quantitative polymerase chain reaction and luciferase assay confirmed that the two SNPs were located in the active promoter regions and influenced the promoter activity of each gene. CONCLUSION: To summarize, among SNPs selected using ChIP-seq in promoter regions with high peaks in both NeuroD1 and H3K4me3, RNF145 rs2043268A>G and CINP rs762105A>G were associated with clinical outcomes in patients with SCLC and also affected the promoter activity of each gene.

Genetic variants in key necroptosis regulators predict prognosis of non-small cell lung cancer after surgical resection.

BACKGROUND: Necroptosis is a regulated inflammatory cell death which plays a significant role in cancer development and progression. In this study, we evaluated whether genetic variants in key regulators of necroptosis may affect survival outcome of non-small cell lung cancer (NSCLC) patients after surgical resection. METHODS: A total of 674 patients who underwent curative surgery were included. Fifteen genetic variants in key regulators of necroptosis (RIPK1, RIPK3, and MLKL) were selected. The association of these variants with survival outcomes was evaluated. RESULTS: Two variants, RIPK1 rs17548629C > T and MLKL rs877375G > C, were associated with better overall survival and disease-free survival in multivariate analyses. When the patients were divided according to histology, the associations were significant only in adenocarcinoma, but not in squamous cell carcinoma. RIPK1 rs17548629 C-to-T change was associated with significantly increased luciferase activity by modulating the binding of miR-642a. Promoter assays showed a significantly increased promoter activity in MLKL rs877375C allele compared to G allele. Consistently, the mRNA expression level of RIPK1 and MLKL showed significant positive correlation with RIPK1 rs17548629C-to-T and MLKL rs877375G-to-C changes. CONCLUSION: Two genetic variants in key regulators in necroptosis, RIPK1 rs17548629C > T and MLKL rs877375G > C, may be used as biomarkers to predict survival outcomes in surgically resected NSCLC patients.

Genetic variants of NEUROD1 target genes are associated with clinical outcomes of small-cell lung cancer patients.

BACKGROUND: Neurogenic differentiation factor 1 (NEUROD1) is frequently overexpressed in small-cell lung cancer (SCLC). NEUROD1 plays an important role in promoting malignant behavior and survival. METHODS: In this study, we evaluated the association between putative functional polymorphisms in 45 NEUROD1 target genes and chemotherapy response and survival outcomes in 261 patients with SCLC. Among the 100 single nucleotide polymorphisms (SNPs) studied, two were significantly associated with both chemotherapy response and overall survival (OS) of patients with SCLC. RESULTS: The SNP rs3806915C>A in semaphorin 6A (SEMA6A) gene was significantly associated with better chemotherapy response and OS (p = 0.04 and p = 0.04, respectively). The SNP rs11265375C>T in nescient helix-loop helix 1 (NHLH1) gene was also associated with better chemotherapy response and OS (p = 0.04 and p = 0.02, respectively). Luciferase assay showed a significantly higher promoter activity of SEMA6A with the rs3806915 A allele than C allele in H446 lung cancer cells (p = 4 × 10-6 ). The promoter activity of NHLH1 showed a significantly higher with the rs11265375 T allele than C allele (p = 0.001). CONCLUSION: These results suggest that SEMA6A rs3806915C>A and NHLH1 rs11265375C>T polymorphisms affect the promoter activity and expression of the genes, which may affect the survival outcome of patients with SCLC.

Genetic Variants in Histone Modification Regions Predict Clinical Outcomes of Pemetrexed Chemotherapy in Lung Adenocarcinoma.

OBJECTIVE: This study was conducted to investigate the association between genetic variants in histone modification regions and clinical outcomes of PEM chemotherapy in patients with lung adenocarcinoma. METHODS: Potentially functional SNPs were selected using integrated analysis of ChIP-seq and RNA-seq. The associations of 279 SNPs with chemotherapy response and overall survival (OS) were analyzed in 314 lung adenocarcinoma patients who underwent PEM chemotherapy. RESULTS: Among the SNPs investigated, 18 were significantly associated with response to chemotherapy, while 28 with OS. Of these SNPs, rs549794A>G in an enhancer which is expected to regulate the expression of ribosomal protein S3 (RPS3) gene was significantly associated with both worse response to chemotherapy and worse OS (adjusted odds ratio = 0.59, 95% CI = 0.36-0.97, p = 0.04; adjusted hazard ratio = 1.44, 95% CI = 1.09-1.91, p = 0.01, respectively). Previous studies suggested that RPS3, a multi-functional protein with various extraribosomal activities, may play a role in chemotherapy resistance. Therefore, it is postulated that rs549794-induced change in the expression level of RPS3 may affect the response to PEM chemotherapy and consequently the survival outcomes in lung adenocarcinoma patients. CONCLUSION: This study suggests that genetic variants in the histone modification regions may be useful for the prediction of clinical outcomes of PEM chemotherapy in advanced lung adenocarcinoma.

Neutrophil-derived trail is a proinflammatory subtype of neutrophil-derived extracellular vesicles.

Aims: Extracellular vesicles (EVs) are membrane-derived vesicles that mediate intercellular communications. Neutrophils produce different subtypes of EVs during inflammatory responses. Neutrophil-derived trails (NDTRs) are generated by neutrophils migrating toward inflammatory foci, whereas neutrophil-derived microvesicles (NDMVs) are thought to be generated by neutrophils that have arrived at the inflammatory foci. However, the physical and functional characteristics of neutrophil-derived EVs are incompletely understood. In this study, we aimed to investigate the differences between NDTRs and NDMVs. Methods: The generation of neutrophil-derived EVs were visualized by live-cell fluorescence images and the physical characteristics were further analyzed using nanotracking analysis assay, scanning electron microscopic analysis, and marker expressions. Functional characteristics of neutrophil-derived EVs were analyzed using assays for bactericidal activity, monocyte chemotaxis, phenotype polarization of macrophages, and miRNA sequencing. Finally, the effects of neutrophil-derived EVs on the acute and chronic inflammation were examined in vivo. Results: Both EVs share similar characteristics including stimulators, surface marker expression, bactericidal activity, and chemoattractive effect on monocytes via MCP-1. However, the integrin-mediated physical interaction was required for generation of NDTRs whereas NDMV generation was dependent on PI3K pathway. Interestingly, NDTRs contained proinflammatory miRNAs such as miR-1260, miR-1285, miR-4454, and miR-7975, while NDMVs contained anti-inflammatory miRNAs such as miR-126, miR-150, and miR-451a. Although both EVs were easily uptaken by monocytes, NDTRs enhanced proinflammatory macrophage polarization whereas NDMVs induced anti-inflammatory macrophage polarization. Moreover, NDTRs showed protective effects against lethality in a murine sepsis model and pathological changes in a murine chronic colitis model. Conclusion: These results suggest that NDTR is a proinflammatory subtype of neutrophil-derived EVs distinguished from NDMV.

Gold Nanoparticle-Enhanced and Roll-to-Roll Nanoimprinted LSPR Platform for Detecting Interleukin-10.

Localized surface plasmon resonance (LSPR) is a powerful platform for detecting biomolecules including proteins, nucleotides, and vesicles. Here, we report a colloidal gold (Au) nanoparticle-based assay that enhances the LSPR signal of nanoimprinted Au strips. The binding of the colloidal Au nanoparticle on the Au strip causes a red-shift of the LSPR extinction peak, enabling the detection of interleukin-10 (IL-10) cytokine. For LSPR sensor fabrication, we employed a roll-to-roll nanoimprinting process to create nanograting structures on polyethylene terephthalate (PET) film. By the angled deposition of Au on the PET film, we demonstrated a double-bent Au structure with a strong LSPR extinction peak at ~760 nm. Using the Au LSPR sensor, we developed an enzyme-linked immunosorbent assay (ELISA) protocol by forming a sandwich structure of IL-10 capture antibody/IL-10/IL-10 detection antibody. To enhance the LSPR signal, we introduced colloidal Au nanocube (AuNC) to be cross-linked with IL-10 detection antibody for immunogold assay. Using IL-10 as a model protein, we successfully achieved nanomolar sensitivity. We confirmed that the shift of the extinction peak was improved by 450% due to plasmon coupling between AuNC and Au strip. We expect that the AuNC-assisted LSPR sensor platform can be utilized as a diagnostic tool by providing convenient and fast detection of the LSPR signal.

Range-dependent waveguide scattering model calibrated for bottom reverberation in a continental shelf environment.

An analytic model is developed for scattering from random inhomogeneities in range-dependent ocean waveguides using the Rayleigh-Born approximation to Green's theorem. The expected scattered intensity depends on statistical moments of fractional changes in compressibility and density, which scatter as monopoles and dipoles, respectively, and the coherence volume of the inhomogeneities. The model is calibrated for ocean bottom scattering using data acquired by instantaneous wide-area ocean acoustic waveguide remote sensing (OAWRS) and geophysical surveys of the ONR Geoclutter Program. The scattering strength of the seafloor on the New Jersey shelf, a typical continental shelf environment, is found to depend on wave number k, medium coherence volume V(c), and seabed depth penetration factor F(p) following a 10 log(10)(F(p)V(c)k(4)) dependence. A computationally efficient numerical approach is developed to rapidly compute bottom reverberation over wide areas using the parabolic equation by exploiting correlation between monopole and dipole scattering terms and introducing seafloor depth penetration factors. An approach is also developed for distinguishing moving clutter from statistically stationary background reverberation by tracking temporal and spatial fluctuations in OAWRS intensity images.

A case of amyotrophic lateral sclerosis in electronic parts manufacturing worker exposed to lead.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting the motor neurons of the spinal cord and brain. Although the definite etiology of ALS remains unclear, occupational or environmental exposures have been considered as one of the potential causes of ALS. Here, we report the case of a patient with ALS who used to work in a factory manufacturing electronic parts and has evidence of acute exposure to lead in excess. A 39-year-old man visited a neurology clinic with symptoms of progressive limb weakness and spasticity, which began 2 years ago. Upon neurological examination, symptoms of atrophy, spasticity and fasciculation of the lower extremities were evident. There were no signs of impairment of the cranial nerves, and cognitive and sensory functions were normal. Complete blood counts, blood chemistries and urinalysis were normal. Serial electromyography showed progressive denervative changes, which were consistent with motor neuron diseases. ALS was diagnosed according to the standard of the "Diagnostic criteria of the World Federation of Neurology". The patient was handling lead oxide (PbO) for development of positive temperature coefficient (PTC) thermist, without being provided with proper respiratory protective equipment. Blood lead level of the patient was measured at 30.86 microg/dL 6 months after he quit his job. Bone lead levels from X-ray fluorescence (XRF) were below the normal range (3 ppm). Blood lead level of his co-workers at the same workplace were above the ACGIH recommended biological exposure index (BEI: 30 microg/dL). We speculated that the ALS in this case was related to excessive exposure to lead.

Fish population and behavior revealed by instantaneous continental shelf-scale imaging.

Until now, continental shelf environments have been monitored with highly localized line-transect methods from slow-moving research vessels. These methods significantly undersample fish populations in time and space, leaving an incomplete and ambiguous record of abundance and behavior. We show that fish populations in continental shelf environments can be instantaneously imaged over thousands of square kilometers and continuously monitored by a remote sensing technique in which the ocean acts as an acoustic waveguide. The technique has revealed the instantaneous horizontal structural characteristics and volatile short-term behavior of very large fish shoals, containing tens of millions of fish and stretching for many kilometers.

The array invariant.

A method is derived for instantaneous source-range estimation in a horizontally stratified ocean waveguide from passive beam-time intensity data obtained after conventional plane-wave beamforming of acoustic array measurements. The method has advantages over existing source localization methods, such as matched field processing or the waveguide invariant. First, no knowledge of the environment is required except that the received field should not be dominated by purely waterborne propagation. Second, range can be estimated in real time with little computational effort beyond plane-wave beamforming. Third, array gain is fully exploited. The method is applied to data from the Main Acoustic Clutter Experiment of 2003 for source ranges between 1 to 8 km, where it is shown that simple, accurate, and computationally efficient source range estimates can be made.