Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples.

Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.

Investigations into the Potential of Using Open Source CFD to Analyze the Differences in Hemodynamic Parameters for Aortic Dissections (Healthy versus Stanford Type A and B).

BACKGROUND: The objective of this study was to develop a method to evaluate the effects of an aortic dissection on hemodynamic parameters by conducting a comparison with that of a healthy (nondissected) aorta. Open-source software will be implemented, no proprietary software/application will be used to ensure accessorily and repeatability, in all the data analysis and processing. Computed tomography (CT) images of aortic dissection are used for the model geometry segmentation. Boundary conditions from literature are implemented to computational fluid dynamics (CFD) to analyze the hemodynamic parameters. METHODS: A numerical simulation model was created by obtaining accurate 3-dimensional geometries of aortae from CT images. In this study, CT images of 8 cases of aortic dissection (Stanford type-A and type-B) and 3 cases of healthy aortae are used for the actual aorta model geometry segmentation. These models were exported into an open-source CFD software, OpenFOAM, where a simplified pulsating flow was simulated by controlling the flow pressure. Ten cycles of the pulsatile flow (0.50 sec/cycle) conditions, totaling 5 sec, were calculated. RESULTS: The pressure distribution, wall shear stress (WSS) and flow velocity streamlines within the aorta and the false lumen were calculated and visualized. It was found that the flow velocity and WSS had a high correlation in high WSS areas of the intermittent layer between the true and false lumen. Most of the Stanford type-A dissections in the study showed high WSS, over 38 Pa, at the systole phase. This indicates that the arterial walls in type-A dissections are more likely to be damaged with pulsatile flow. CONCLUSIONS: Using CFD to estimate localized high WSS areas may help in deciding to treat a type-A or B dissection with a stent graft to prevent a potential rupture.

Multiblock metabolomics: An approach to elucidate whole-body metabolism with multiblock principal component analysis.

Principal component analysis (PCA) is a useful tool for omics analysis to identify underlying factors and visualize relationships between biomarkers. However, this approach is limited in addressing life complexity and further improvement is required. This study aimed to develop a new approach that combines mass spectrometry-based metabolomics with multiblock PCA to elucidate the whole-body global metabolic network, thereby generating comparable metabolite maps to clarify the metabolic relationships among several organs. To evaluate the newly developed method, Zucker diabetic fatty (ZDF) rats (n = 6) were used as type 2 diabetic models and Sprague Dawley (SD) rats (n = 6) as controls. Metabolites in the heart, kidney, and liver were analyzed by capillary electrophoresis and liquid chromatography mass spectrometry, respectively, and the detected metabolites were analyzed by multiblock PCA. More than 300 metabolites were detected in the heart, kidney, and liver. When the metabolites obtained from the three organs were analyzed with multiblock PCA, the score and loading maps obtained were highly synchronized and their metabolism patterns were visually comparable. A significant finding in this study was the different expression patterns in lipid metabolism among the three organs; notably triacylglycerols with polyunsaturated fatty acids or less unsaturated fatty acids showed specific accumulation patterns depending on the organs.

Mitochondrial translation inhibition triggers ATF4 activation, leading to integrated stress response but not to mitochondrial unfolded protein response.

Mitochondrial-nuclear communication, known as retrograde signaling, is important for regulating nuclear gene expression in response to mitochondrial dysfunction. Previously, we have found that p32/C1qbp-deficient mice, which have a mitochondrial translation defect, show endoplasmic reticulum (ER) stress response and integrated stress response (ISR) gene expression in the heart and brain. However, the mechanism by which mitochondrial translation inhibition elicits these responses is not clear. Among the transcription factors that respond to mitochondrial stress, activating transcription factor 4 (ATF4) is a key transcription factor in the ISR. Herein, chloramphenicol (CAP), which inhibits mitochondrial DNA (mtDNA)-encoded protein expression, induced eukaryotic initiation factor 2 α subunit (eIF2α) phosphorylation and ATF4 induction, leading to ISR gene expression. However, the expression of the mitochondrial unfolded protein response (mtUPR) genes, which has been shown in Caenorhabditis elegans, was not induced. Short hairpin RNA-based knockdown of ATF4 markedly inhibited the CAP-induced ISR gene expression. We also observed by ChIP analysis that induced ATF4 bound to the promoter region of several ISR genes, suggesting that mitochondrial translation inhibition induces ISR gene expression through ATF4 activation. In the present study, we showed that mitochondrial translation inhibition induced the ISR through ATF4 activation rather than the mtUPR.

Vulnerability analysis on the interaction between Asymmetric stent and arterial layer.

The utilization of Asymmetric stent for recovering atherosclerotic diseases, particularly non-symmetric obstruction, is a quite challenging breakthrough treatment. In terms of eccentric plaque, the non-uniform stiffness of arterial layer causes the increasingly complex issues of vulnerability. This study investigated the vulnerability of the interaction between the Asymmetric stent and the surrounding arterial layer using structural transient dynamic analysis in ANSYS. Four combinations of stent deployment, i.e. the Sinusoidal stent expanded by the offset balloon, the Sinusoidal stent expanded by the ordinary cylindrical balloon, the Asymmetric stent expanded by the offset balloon, and the Asymmetric stent expanded by the ordinary cylindrical balloon, are generated for this comparative study. Multilayer material properties from recent in vitro experiments are adopted for the surrounding arterial layer, such as a fibrous cap, lipid core, diseased-healthy intima, and diseased-healthy media. In order to address plaque vulnerability, the Cauchy stresses and Hencky strains are used for stress measure because of convenience in comparison with the uniaxial/biaxial tension test data. The location-specific threshold value from the diseased human carotid artery is adopted for rupture criteria. The simulation indicated that as regards the eccentric plaque, the plaque vulnerability is caused by the plaque shape and components rather than caused by the geometrical structure of the stent or balloon expansion method. Nevertheless, the non-symmetric inflation of balloon, which leads against the plaque, contributed to an increase in the vulnerability of fibrous cap of fibroatheroma plaque.

Characterization of nucleolar localization and exclusion signals in terminal deoxynucleotidyltransferase interacting factor 2/estrogen receptor α-binding protein.

Terminal deoxynucleotidyltransferase interacting factor 2/estrogen receptor α-binding protein (TdIF2/ERBP) is a multifunctional nucleolar protein. The nucleolar localization of TdIF2/ERBP is important for its functions because it promotes ribosomal RNA transcription. However, signal sequences that direct TdIF2/ERBP to the nucleolus are not well characterized. We examined the TdIF2/ERBP sequence using truncation and mutation analyses to determine whether the nucleosome binding and C-terminal domains of TdIF2/ERBP possess nucleolar localization signals (NoLSs). In these domains, four NoLSs that could direct the mCherry protein to the nucleolus were detected. In addition, a short stretch of hydrophobic residues (VLLVL) in the center of TdIF2/ERBP acted as a nucleolar exclusion signal, which reduced the nucleolar accumulation of mCherry-NoLS fusion proteins. These results would contribute to improving the prediction of NoLSs from protein sequences. The short, transferrable localization signals would be valuable tools for understanding the association between localization and functions of nucleolar proteins. Abbreviations TdIF2: terminal deoxynucleotidyltransferase interacting factor 2; ERBP: estrogen receptor α-binding protein; EGFP: enhanced green fluorescent protein; NLS: nuclear localization signal; NoLS: nucleolar localization signal; NoES: nucleolar exclusion signal; DAPI: 4',6-diamidino-2-phenylindole.

Mitochondrial p32/C1qbp Is a Critical Regulator of Dendritic Cell Metabolism and Maturation.

Dendritic cell (DC) maturation induced by Toll-like receptor agonists requires activation of downstream signal transduction and metabolic changes. The endogenous metabolite citrate has recently emerged as a modulator of DC activation. However, the metabolic requirements that support citrate production remain poorly defined. Here, we demonstrate that p32/C1qbp, which functions as a multifunctional chaperone protein in mitochondria, supports mitochondrial metabolism and DC maturation. Metabolic analysis revealed that the citrate increase induced by lipopolysaccharide (LPS) is impaired in p32-deficient DCs. We also found that p32 interacts with dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase [PDH] complex) and positively regulates PDH activity in DCs. Therefore, we suggest that DC maturation is regulated by citrate production via p32-dependent PDH activity. p32-null mice administered a PDH inhibitor show decreased DC maturation and ovalbumin-specific IgG production in vivo, suggesting that p32 may serve as a therapeutic target for DC-related autoimmune diseases.

Development of asymmetric stent for treatment of eccentric plaque.

The selection of stent and balloon type is decisive in the stenting process. In the treatment of an eccentric plaque obstruction, a symmetric expansion from stent dilatation generates nonuniform stress distribution, which may aggravate fibrous cap prone to rupture. This paper developed a new stent design to treat eccentric plaque using structural transient dynamic analysis in ANSYS. A non-symmetric structural geometry of stent is generated to obtain reasonable stress distribution safe for the arterial layer surrounding the stent. To derive the novel structural geometry, a Sinusoidal stent type is modified by varying struts length and width, adding bridges, and varying curvature width of struts. An end ring of stent struts was also modified to eliminate dogboning phenomenon and to reduce the Ectropion angle. Two balloon types were used to deploy the stent, an ordinary cylindrical and offset balloon. Positive modification results were used to construct the final non-symmetric stent design, called an Asymmetric stent. Analyses of the deformation characteristics, changes in surface roughness and induced stresses within intact arterial layer were subsequently examined. Interaction between the stent and vessel wall was implemented by means of changes in surface roughness and stress distribution analyses. The Palmaz and the Sinusoidal stent were used for a comparative study. This study indicated that the Asymmetric stent types reduced the central radial recoiling and the dogboning phenomenon. In terms of changes in surface roughness and induced stresses, the Asymmetric stent has a comparable effect with that of the Sinusoidal stent. In addition, it could enhance the distribution of surface roughening as expanded by an offset balloon.

p32 is Required for Appropriate Interleukin-6 Production Upon LPS Stimulation and Protects Mice from Endotoxin Shock.

Sepsis is a major cause of morbidity and mortality in seriously ill patients and mitochondrial dysfunction is associated with poor outcomes in septic patients. Although interleukin-6 (IL-6) is a good prognostic marker for sepsis, the relationship between mitochondrial dysfunction and IL-6 remains poorly understood. We identified p32/C1QBP/HABP1 as a regulator of IL-6 production in response to lipopolysaccharide (LPS). LPS induced IL-6 overproduction in p32 deficient mouse embryonic fibroblasts (MEFs) through NF-κB independent but activating transcription factor (ATF) 4 dependent pathways. Short hairpin RNA-based knockdown of ATF4 in p32 deficient MEFs markedly inhibited LPS-induced IL-6 production. Furthermore, MEFs treated with chloramphenicol, an inhibitor of mitochondrial translation, produced excessive IL-6 via ATF4 pathways. Using a LPS-induced endotoxin shock model, mice with p32 ablation in myeloid cells showed increased lethality and overproduction of IL-6. Thus, this study provides a molecular link how mitochondrial dysfunction leads to IL-6 overproduction and poor prognosis of sepsis.

Effects of plaque lengths on stent surface roughness.

The physical properties of the stent surface influence the effectiveness of vascular disease treatment after stent deployment. During the expanding process, the stent acquires high-level deformation that could alter either its microstructure or the magnitude of surface roughness. This paper constructed a finite element simulation to observe the changes in surface roughness during the stenting process. Structural transient dynamic analysis was performed using ANSYS, to identify the deformation after the stent is placed in a blood vessel. Two types of bare metal stents are studied: a Palmaz type and a Sinusoidal type. The relationship between plaque length and the changes in surface roughness was investigated by utilizing three different length of plaque; plaque length longer than the stent, shorter than the stent and the same length as the stent. In order to reduce computational time, 3D cyclical and translational symmetry was implemented into the FE model. The material models used was defined as a multilinear isotropic for stent and hyperelastic for the balloon, plaque and vessel wall. The correlation between the plastic deformation and the changes in surface roughness was obtained by intermittent pure tensile test using specimen whose chemical composition was similar to that of actual stent material. As the plastic strain is achieved from FE simulation, the surface roughness can be assessed thoroughly. The study found that the plaque size relative to stent length significantly influenced the critical changes in surface roughness. It was found that the length of stent which is equal to the plaque length was preferable due to the fact that it generated only moderate change in surface roughness. This effect was less influential to the Sinusoidal stent.

On the finite element modelling of balloon-expandable stents.

Finite element method (FEM) has been extensively applied in the analyses of mechanical and biomechanical properties of stents. Geometrically, a closed-cell stent is an assembly of a number of repeated unit cells and exhibits periodicity in both longitudinal and circumferential directions. The objective of this paper is to study the FEM models for the analysis of stents. To this end, three models, termed respectively as the Panel, RUC (repeated unit cell) and RUC(+) (repeated unit cell with a free end) models, are proposed incorporating rotationally symmetrical, periodic and free edge conditions. The proposed models are applied to the analysis of stents of Palmaz-Schatz and sinusoidal types. The Panel model reduces the size of the numerical model from the full, half or quarter stent to a strip of it without losing the computational accuracy. The RUC model gives satisfactory results for the inner part of the stent except for the two ends. The RUC(+) model, described here for the first time, provides accurate results for both the inner part and the distal ends of the stent. In addition, it allows the prediction of the well-known phenomenon of "dog-boning", in which the balloon is excessively expanded at the two ends of the stent.