Model-free idealization: Adaptive integrated approach for idealization of ion-channel currents.

Single-channel electrophysiological recordings provide insights into transmembrane ion permeation and channel gating mechanisms. The first step in the analysis of the recorded currents involves an "idealization" process, in which noisy raw data are classified into two discrete levels corresponding to the open and closed states of channels. This provides valuable information on the gating kinetics of ion channels. However, the idealization step is often challenging in cases of currents with poor signal-to-noise ratios and baseline drifts, especially when the gating model of the target channel is not identified. We report herein on a highly robust model-free idealization method for achieving this goal. The algorithm, called adaptive integrated approach for idealization of ion-channel currents (AI2), is composed of Kalman filter and Gaussian mixture model clustering and functions without user input. AI2 automatically determines the noise reduction setting based on the degree of separation between the open and closed levels. We validated the method on pseudo-channel-current datasets that contain either computed or experimentally recorded noise. We also investigated the relationship between the noise reduction parameter of the Kalman filter and the cutoff frequency of the low-pass filter. The AI2 algorithm was then tested on actual experimental data for biological channels including gramicidin A, a voltage-gated sodium channel, and other unidentified channels. We compared the idealization results with those obtained by the conventional methods, including the 50%-threshold-crossing method.

Structural basis of transcription regulation by CNC family transcription factor, Nrf2.

Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf proteins to recognize CNC-sMaf binding DNA elements (CsMBEs) in competition with sMaf homodimers, but the functional role of the CNC motif remains elusive. In this study, we report the crystal structures of Nrf2/NFE2L2, a CNC family protein regulating anti-stress transcriptional responses, in a complex with MafG and CsMBE. The CNC motif restricts the conformations of crucial Arg residues in the basic region, which form extensive contact with the DNA backbone phosphates. Accordingly, the Nrf2-MafG heterodimer has approximately a 200-fold stronger affinity for CsMBE than canonical bZIP proteins, such as AP-1 proteins. The high DNA affinity of the CNC-sMaf heterodimer may allow it to compete with the sMaf homodimer on target genes without being perturbed by other low-affinity bZIP proteins with similar sequence specificity.

FLCN alteration drives metabolic reprogramming towards nucleotide synthesis and cyst formation in salivary gland.

FLCN is a tumor suppressor gene which controls energy homeostasis through regulation of a variety of metabolic pathways including mitochondrial oxidative metabolism and autophagy. Birt-Hogg-Dubé (BHD) syndrome which is driven by germline alteration of the FLCN gene, predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas, pulmonary cysts and less frequently, salivary gland tumors. Here, we report metabolic roles for FLCN in the salivary gland as well as their clinical relevance. Screening of salivary glands of BHD patients using ultrasonography demonstrated increased cyst formation in the salivary gland. Salivary gland tumors that developed in BHD patients exhibited an upregulated mTOR-S6R pathway as well as increased GPNMB expression, which are characteristics of FLCN-deficient cells. Salivary gland-targeted Flcn knockout mice developed cytoplasmic clear cell formation in ductal cells with increased mitochondrial biogenesis, upregulated mTOR-S6K pathway, upregulated TFE3-GPNMB axis and upregulated lipid metabolism. Proteomic and metabolite analysis using LC/MS and GC/MS revealed that Flcn inactivation in salivary gland triggers metabolic reprogramming towards the pentose phosphate pathway which consequently upregulates nucleotide synthesis and redox regulation, further supporting that Flcn controls metabolic homeostasis in salivary gland. These data uncover important roles for FLCN in salivary gland; metabolic reprogramming under FLCN deficiency might increase nucleotide production which may feed FLCN-deficient salivary gland cells to trigger tumor initiation and progression, providing mechanistic insight into salivary gland tumorigenesis as well as a foundation for development of novel therapeutics for salivary gland tumors.

BHD-associated kidney cancer exhibits unique molecular characteristics and a wide variety of variants in chromatin remodeling genes.

Birt-Hogg-Dubé (BHD) syndrome is a hereditary kidney cancer syndrome, which predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas and pulmonary cysts. The responsible gene FLCN is a tumor suppressor for kidney cancer, which plays an important role in energy homeostasis through the regulation of mitochondrial oxidative metabolism. However, the process by which FLCN-deficiency leads to renal tumorigenesis is unclear. In order to clarify molecular pathogenesis of BHD-associated kidney cancer, we conducted whole-exome sequencing analysis using next-generation sequencing technology as well as metabolite analysis using liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Whole-exome sequencing analysis of BHD-associated kidney cancer revealed that copy number variations of BHD-associated kidney cancer are considerably different from those already reported in sporadic cases. In somatic variant analysis, very few variants were commonly observed in BHD-associated kidney cancer; however, variants in chromatin remodeling genes were frequently observed in BHD-associated kidney cancer (17/29 tumors, 59%). Metabolite analysis of BHD-associated kidney cancer revealed metabolic reprogramming toward upregulated redox regulation which may neutralize reactive oxygen species potentially produced from mitochondria with increased respiratory capacity under FLCN-deficiency. BHD-associated kidney cancer displays unique molecular characteristics that are completely different from sporadic kidney cancer, providing mechanistic insight into tumorigenesis under FLCN-deficiency as well as a foundation for development of novel therapeutics for kidney cancer.

The significance of 123I-BMIPP delayed scintigraphic imaging in cardiac patients.

BACKGROUND: Earlier studies have not fully investigated the significance of radionuclide planar imaging in cardiac patients using the fatty acid analogue 123I-beta-methyl-iodophenylpentadecanoic acid (123I-BMIPP). OBJECTIVES: This study was to clarify the effectiveness of 123I-BMIPP in assessing the heart-to-mediastinum ratio (H/M) and myocardial washout rate (WR) in patients with heart disease. METHODS: Myocardial 123I-BMIPP imaging was performed in 33 patients (20 with chronic heart failure [CHF] and 13 with stable angina pectoris [AP]) and 11 control subjects. Myocardial 123I-BMIPP planner images were obtained 30 min (early image) and 4 h (delayed image) after tracer injection. The left ventricular ejection fraction (LVEF) was measured by quantitative gated single photon emission computed tomography. The concentration of plasma brain natriuretic peptide (BNP) was measured before the scintigraphic study. RESULTS: (1) Delayed H/M was much lower in CHF than in AP (1.93 +/- 0.37 vs. 2.21 +/- 0.38, p < 0.05) and controls (vs. 2.47 +/- 0.38, p < 0.001). (2) The WR in CHF and AP were higher than the WR in controls (39.8 +/- 12.7% and 38.7 +/- 11.1 vs. 27.9 +/- 10.2%, p < 0.01 and p < 0.05, respectively). (3) In all subjects, LVEF was correlated with delayed H/M (r = 0.39, p < 0.01). And, the BNP was correlated with both the WR (r = 0.36, p < 0.05) and delayed H/M (r = - 0.29, p = 0.05). CONCLUSION: These data strongly suggest that the delayed H/M and myocardial WR of 123I-BMIPP enhances the assessment of the myocardial fatty acid metabolism disorders in patients with heart disease in both masked and unmasked conditions.

Gender difference in the level of high-density lipoprotein cholesterol in elderly Japanese patients with coronary artery disease.

OBJECTIVE: High-density lipoprotein cholesterol (HDLC) levels are known to be reduced in the metabolic syndrome, but the HDLC profile of elderly patients with coronary artery disease (CAD) has not been well characterized. This study investigated the gender difference of HDLC levels in elderly Japanese patients with CAD. METHODS: Serum lipid data were analyzed retrospectively to assess sex-related differences of the lipid profile, and to evaluate the effects of pharmacotherapy or physical exercise on hyperlipidemia. PATIENTS: A total of 163 elderly (> or = 65 years) outpatients with CAD (128 men aged 70.6+/-5.2 years and 35 women aged 74.1+/-6.0 years [mean+/-SD]) were investigated. RESULTS: The mean total cholesterol (TC), low-density lipoprotein cholesterol (LDLC), and triglyceride (TG) levels were similar in men and women, while the mean HDLC level was significantly higher in women than men (58.3+/-18.1 vs. 50.3+/-13.5 mg/dL; p=0.0064). The HDLC level was not significantly influenced by oral lipid-lowering therapy or regular exercise in either sex. However, women without lipid-lowering therapy had significantly higher HDLC levels than men with (p=0.0312) or without (p=0.0338) lipid-lowering therapy, while women performing regular exercise had significantly higher HDLC levels than men with (p=0.0047) or without (p<0.001) regular exercise. CONCLUSION: Elderly women with CAD have higher HDLC levels relative to their postmenopausal state than those of men with CAD. Low HDLC levels, unlike in men, may not be a major risk factor for CAD in elderly women.