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Body Deformation Correction for SPECT Imaging

Sun, 10/12/2014 - 2:20pm

Patient motion degrades the quality of SPECT studies. Body bend and twist are types of patient deformation, which may occur during SPECT imaging, and which has been generally ignored in SPECT motion correction strategies. To correct for these types of motion, we propose a deformation model and its inclusion within an iterative reconstruction algorithm. Two experiments were conducted to investigate the applicability of our model. In the first experiment, the return of the postmotion-compensation locations of markers on the body-surface of a volunteer to approximate their original coordinates is used to examine our method of estimating the parameters of our model and the parameters' use in undoing deformation. The second experiment employed simulated projections of the MCAT phantom formed using an analytical projector which includes attenuation and distance-dependent resolution to investigate applications of our model in reconstruction. We demonstrate in the simulation studies that twist and bend can significantly degrade SPECT image quality visually. Our correction strategy is shown to be able to greatly diminish the degradation seen in the slices, provided the parameters are estimated accurately. We view this work as a first step towards being able to estimate and correct patient deformation based on information obtained from marker tracking data.

Improved Dynamic Cardiac Phantom Based on 4D NURBS and Tagged MRI

Sun, 10/12/2014 - 2:20pm

We previously developed a realistic phantom for the cardiac motion for use in medical imaging research. The phantom was based upon a gated magnetic resonance imaging (MRI) cardiac study and using 4D non-uniform rational b-splines (NURBS). Using the gated MRI study as the basis for the cardiac model had its limitations. From the MRI images, the change in the size and geometry of the heart structures could be obtained, but without markers to track the movement of points on or within the myocardium, no explicit time correspondence could be established for the structures. Also, only the inner and outer surfaces of the myocardium could be modeled. We enhance this phantom of the beating heart using 4D tagged MRI data. We utilize NURBS surfaces to analyze the full 3D motion of the heart from the tagged data. From this analysis, time-dependent 3D NURBS surfaces were created for the right (RV) and left ventricles (LV). Models for the atria were developed separately since the tagged data only covered the ventricles. A 4D NURBS surface was fit to the 3D surfaces of the heart creating time-continuous 4D NURBS models. Multiple 4D surfaces were created for the left ventricle (LV) spanning its entire volume. The multiple surfaces for the LV were spline-interpolated about an additional dimension, thickness, creating a 4D NURBS solid model for the LV with the ability to represent the motion of any point within the volume of the LV myocardium at any time during the cardiac cycle. Our analysis of the tagged data was found to produce accurate models for the RV and LV at each time frame. In a comparison with segmented structures from the tagged dataset, LV and RV surface predictions were found to vary by a maximum of 1.5 mm's and 3.4 mm's respectively. The errors can be attributed to the tag spacing in the data (7.97 mm's). The new cardiac model was incorporated into the 4D NURBS-based Cardiac-Torso (NCAT) phantom widely used in imaging research. With its enhanced abilities, the model will provide a useful tool in the study of cardiac imaging and the effects of cardiac motion in medical images.

A quantitative evaluation study of four-dimensional gated cardiac SPECT reconstruction

Sun, 10/12/2014 - 2:20pm

In practice, gated cardiac SPECT images suffer from a number of degrading factors, including distance-dependent blur, attenuation, scatter and increased noise due to gating. Recently, we proposed a motion-compensated approach for four-dimensional (4D) reconstruction for gated cardiac SPECT and demonstrated that use of motion-compensated temporal smoothing could be effective for suppressing the increased noise due to lowered counts in individual gates. In this work, we further develop this motion-compensated 4D approach by also taking into account attenuation and scatter in the reconstruction process, which are two major degrading factors in SPECT data. In our experiments, we conducted a thorough quantitative evaluation of the proposed 4D method using Monte Carlo simulated SPECT imaging based on the 4D NURBS-based cardiac-torso (NCAT) phantom. In particular, we evaluated the accuracy of the reconstructed left ventricular myocardium using a number of quantitative measures including regional bias-variance analyses and wall intensity uniformity. The quantitative results demonstrate that use of motion-compensated 4D reconstruction can improve the accuracy of the reconstructed myocardium, which in turn can improve the detectability of perfusion defects. Moreover, our results reveal that while traditional spatial smoothing could be beneficial, its merit would become diminished with the use of motion-compensated temporal regularization. As a preliminary demonstration, we also tested our 4D approach on patient data. The reconstructed images from both simulated and patient data demonstrated that our 4D method can improve the definition of the LV wall.

Theoretical and Numerical Study of MLEM and OSEM Reconstruction Algorithms for Motion Correction in Emission Tomography

Sun, 10/12/2014 - 2:20pm

Patient body-motion and respiratory-motion impacts the image quality of cardiac SPECT and PET perfusion images. Several algorithms exist in the literature to correct for motion within the iterative maximum-likelihood reconstruction framework. In this work, three algorithms are derived starting with Poisson statistics to correct for patient motion. The first one is a motion compensated MLEM algorithm (MC-MLEM). The next two algorithms called MGEM-1 and MGEM-2 (short for Motion Gated OSEM, 1 and 2) use the motion states as subsets, in two different ways. Experiments were performed with NCAT phantoms (with exactly known motion) as the source and attenuation distributions. Experiments were also performed on an anthropomorphic phantom and a patient study. The SIMIND Monte Carlo simulation software was used to create SPECT projection images of the NCAT phantoms. The projection images were then modified to have Poisson noise levels equivalent to that of clinical acquisition. We investigated application of these algorithms to correction of (1) a large body-motion of 2 cm in Superior-Inferior (SI) and Anterior-Posterior (AP) directions each and (2) respiratory motion of 2 cm in SI and 0.6 cm in AP. We determined the bias with respect to the NCAT phantom activity for noiseless reconstructions as well as the bias-variance for noisy reconstructions. The MGEM-1 advanced along the bias-variance curve faster than the MC-MLEM with iterations. The MGEM-1 also lowered the noiseless bias (with respect to NCAT truth) faster with iterations, compared to the MC-MLEM algorithms, as expected with subset algorithms. For the body motion correction with two motion states, after the 9th iteration the bias was close to that of MC-MLEM at iteration 17, reducing the number of iterations by a factor of 1.89. For the respiratory motion correction with 9 motion states, based on the noiseless bias, the iteration reduction factor was approximately 7. For the MGEM-2, however, bias-plot or the bias-variance-plot saturated with iteration because of successive interpolation error. SPECT data was acquired simulating respiratory motion of 2 cm amplitude with an anthropomorphic phantom. A patient study acquired with body motion in a second rest was also acquired. The motion correction was applied to these acquisitions with the anthropomorphic phantom and the patient study, showing marked improvements of image quality with the estimated motion correction.

Estimation of Cardiac Respiratory-Motion by Semi-Automatic Segmentation and Registration of Non-Contrast-Enhanced 4D-CT Cardiac Datasets

Sun, 10/12/2014 - 2:20pm

The goal of this work is to investigate, for a large set of patients, the motion of the heart with respiration during free-breathing supine medical imaging. For this purpose we analyzed the motion of the heart in 32 non-contrast enhanced respiratory-gated 4D-CT datasets acquired during quiet unconstrained breathing. The respiratory-gated CT images covered the cardiac region and were acquired at each of 10 stages of the respiratory cycle, with the first stage being end-inspiration. We devised a 3-D semi-automated segmentation algorithm that segments the heart in the 4D-CT datasets acquired without contrast enhancement for use in estimating respiratory motion of the heart. Our semi-automated segmentation results were compared against interactive hand segmentations of the coronal slices by a cardiologist and a radiologist. The pairwise difference in segmentation among the algorithm and the physicians was on the average 11% and 10% of the total average segmented volume across the patient, with a couple of patients as outliers above the 95% agreement limit. The mean difference among the two physicians was 8% with an outlier above the 95% agreement limit. The 3-D segmentation was an order of magnitude faster than the Physicians' manual segmentation and represents significant reduction of Physicians' time. The segmented first stages of respiration were used in 12 degree-of-freedom (DOF) affine registration to estimate the motion at each subsequent stage of respiration. The registration results from the 32 patients indicate that the translation in the superior-inferior direction was the largest component motion, with a maximum of 10.7 mm, mean of 6.4 mm, and standard deviation of 2.2 mm. Translation in the anterior-posterior direction was the next largest component of motion, with a maximum of 4.0 mm, mean of 1.7 mm, and standard deviation of 1.0 mm. Rotation about the right-left axis was on average the largest component of rotation observed, with a maximum of 4.6 degrees, mean of 1.6 degrees, and standard deviation of 2.1 degrees. The other rotation and shear parameters were all close to zero on average indicting the motion could be reasonably well approximated by rigid-body motion. However, the product of the three scale factors averaged about 0.97 indicating the possibility of a small decrease in heart volume with expiration. The motion results were similar whether we used the Physician's segmentation or the 3-D algorithm.

Impact on reader performance for lesion-detection/ localization tasks of anatomical priors in SPECT reconstruction

Sun, 10/12/2014 - 2:20pm

With increasing availability of multimodality imaging systems, high-resolution anatomical images can be used to guide the reconstruction of emission tomography studies. By measuring reader performance on a lesion detection task, this study investigates the improvement in image-quality due to use of prior anatomical knowledge, for example organ or lesion boundaries, during SPECT reconstruction. Simulated (67)Ga -citrate source and attenuation distributions were created from the mathematical cardiac-torso (MCAT) anthropomorphic digital phantom. The SIMIND Monte Carlo software was then used to generate SPECT projection data. The data were reconstructed using the De Pierro maximum a posteriori (MAP) algorithm and the rescaled-block-iterative (RBI) algorithm for comparison. We compared several degrees of prior knowledge about the anatomy: no knowledge about the anatomy; knowledge of organ boundaries; knowledge of organ and lesion boundaries; and knowledge of organ, lesion, and pseudo-lesion (non-emission uptake altering) boundaries. The MAP reconstructions used quadratic smoothing within anatomical regions, but not across any provided region boundaries. The reconstructed images were read by human observers searching for lesions in a localization receiver operating characteristic (LROC) study of the relative detection/localization accuracies of the reconstruction algorithms. Area under the LROC curve was computed for each algorithm as the comparison metric. We also had humans read images reconstructed using different prior strengths to determine the optimal trade-off between data consistency and the anatomical prior. Finally by mixing together images reconstructed with and without the prior, we tested to see if having an anatomical prior only some of the time changes the observer's detection/localization accuracy on lesions where no boundary prior is available. We found that anatomical priors including organ and lesion boundaries improve observer performance on the lesion detection/localization task. Use of just organ boundaries did not provide a statistically significant improvement in performance however. We also found that optimal prior strength depends on the level of anatomical knowledge, with a broad plateau in which observer performance is near optimal. We found no evidence that having anatomical priors use lesion boundaries only when available changes the observer's performance when they are not available. We conclude that use of anatomical priors with organ and lesion boundaries improves reader performance on a lesion-detection/localization task, and that pseudo-lesion boundaries do not hurt reader performance. However, we did not find evidence that a prior using only organ boundaries helps observer performance. Therefore we suggest prior strength should be tuned to the organ-only case, since a prior will likely not be available for all lesions.

A flexible multicamera visual-tracking system for detecting and correcting motion-induced artifacts in cardiac SPECT slices

Sun, 10/12/2014 - 2:20pm

Patient motion is inevitable in SPECT and PET due to the lengthy period of time patients are imaged. The authors hypothesized that the use of external-tracking devices which provide additional information on patient motion independent of SPECT data could be employed to provide a more robust correction than obtainable from data-driven methods. Therefore, the authors investigated the Vicon MX visual-tracking system (VTS) which utilizes near-infrared (NIR) cameras to stereo-image small retroreflective markers on stretchy bands wrapped about the chest and abdomen of patients during cardiac SPECT. The chest markers are used to provide an estimate of the rigid-body (RB) motion of the heart. The abdomen markers are used to provide a signal used to bin list-mode acquisitions as part of correction of respiratory motion of the heart. The system is flexible in that the layout of the cameras can be designed to facilitate marker viewing. The system also automatically adapts marker tracking to employ all of the cameras visualizing a marker at any instant, with visualization by any two being sufficient for stereo-tracking. Herein the ability of this VTS to track motion with submillimeter and subdegree accuracy is established through studies comparing the motion of Tc-99m containing markers as assessed via stereo-tracking and from SPECT reconstructions. The temporal synchronization between motion-tracking data and timing marks embedded in list-mode SPECT acquisitions is shown to agree within 100 ms. In addition, motion artifacts were considerably reduced in reconstructed SPECT slices of an anthropomorphic phantom by employing within iterative reconstruction the motion-tracking information from markers attached to the phantom. The authors assessed the number and placement of NIR cameras required for robust motion tracking of markers during clinical imaging in 77 SPECT patients. They determined that they were able to track without loss during the entire period of SPECT and transmission imaging at least three of the four markers on the chest and one on the abdomen bands 94% and 92% of the time, respectively. The ability of the VTS to correct motion clinically is illustrated for ten patients who volunteered to undergo repeat-rest imaging with the original-rest SPECT study serving as the standard against which to compare the success of correction. Comparison of short-axis slices shows that VTS-based motion correction provides better agreement with the original-rest-imaging slices than either no correction or the vendor-supplied software for motion correction on, our SPECT system. Comparison of polar maps shows that VTS-based motion-correction results in less numerical difference on average in the segments of the polar maps between the original-rest study and the second-rest study than the other two strategies. The difference was statistically significant for the comparison between VTS-based and clinical vendor-supplied software correction. Taken together, these findings suggest that VTS-based motion correction is superior to either no-motion correction or the vendor-supplied software the authors investigated in clinical practice.

Estimation of Rigid-Body and Respiratory Motion of the Heart From Marker-Tracking Data for SPECT Motion Correction

Sun, 10/12/2014 - 2:20pm

Motion of patients undergoing cardiac SPECT perfusion imaging causes artifacts in the acquired images which may lead to difficulty in interpretation. Our work investigates a technique of obtaining patient motion estimates from retro-reflective markers on stretchy bands wrapped around the chest and abdomen of patients being imaged clinically. Motion signals obtained from the markers consist of at least two components, body motion (BM) and periodic motion (PM) due to respiration. We present a method for separating these components from the motion-tracking data of each marker, and then report a method for combining the BM estimated from chest markers to estimate the 6-degree-of-freedom (6-DOF) rigid-body motion (RBM) of the heart. Motion studies of volunteers and patients are used to evaluate the methods. Illustrative examples of the motion of the heart due to patient body movement and respiration (upward creep) are presented and compared to estimates of the motion of the heart obtained directly from SPECT data. Our motion-tracking method is seen to give reasonable agreement with the motion-estimates from the SPECT data while being considerably less noisy.

An evaluation of iterative reconstruction strategies based on mediastinal lesion detection using hybrid Ga-67 SPECT images

Sun, 10/12/2014 - 2:20pm

Using psychophysical studies, the authors have evaluated the effectiveness of various strategies for compensating for physical degradations in SPECT imaging. The particular application was Ga-67-citrate imaging of mediastinal tumors, which was chosen because Ga-67 is a particularly challenging radionuclide for imaging. The test strategies included compensations for nonuniform attenuation, distance-dependent spatial resolution, and scatter applied in various combinations as part of iterative reconstructions with the rescaled block iterative-expectation maximization (RBI-EM) algorithm. The authors also evaluated filtered backprojection reconstructions. Strategies were compared on the basis of human-observer studies of lesion localization and detection accuracy using the localization receiver operating characteristics (LROC) paradigm. These studies involved hybrid images which were obtained by adding the projections of Monte Carlo-simulated lesions to disease-free clinical projection data. The background variability in these images can provide a more realistic assessment of the relative utility of reconstruction strategies than images from anthropomorphic digital phantoms. The clinical datasets were obtained using a GE-VG dual-detector SPECT system with CT-estimated attenuation maps. After determining a target lesion contrast, they conducted pilot LROC studies to obtain a near-optimal set of reconstruction parameters for each strategy, and then conducted the strategy comparison study. The results indicate improved detection accuracy with RBI-EM as more compensations are applied within the reconstruction. The relative rankings of the test strategies agreed in most cases with those of previous studies that employed simulated projections of digital anthropomorphic phantoms, thus confirming the findings of those studies.

Convolution-Based Forced Detection Monte Carlo Simulation Incorporating Septal Penetration Modeling

Sun, 10/12/2014 - 2:20pm

In SPECT imaging, photon transport effects such as scatter, attenuation and septal penetration can negatively affect the quality of the reconstructed image and the accuracy of quantitation estimation. As such, it is useful to model these effects as carefully as possible during the image reconstruction process. Many of these effects can be included in Monte Carlo (MC) based image reconstruction using convolution-based forced detection (CFD). With CFD Monte Carlo (CFD-MC), often only the geometric response of the collimator is modeled, thereby making the assumption that the collimator materials are thick enough to completely absorb photons. However, in order to retain high collimator sensitivity and high spatial resolution, it is required that the septa be as thin as possible, thus resulting in a significant amount of septal penetration for high energy radionuclides. A method for modeling the effects of both collimator septal penetration and geometric response using ray tracing (RT) techniques has been performed and included into a CFD-MC program. Two look-up tables are pre-calculated based on the specific collimator parameters and radionuclides, and subsequently incorporated into the SIMIND MC program. One table consists of the cumulative septal thickness between any point on the collimator and the center location of the collimator. The other table presents the resultant collimator response for a point source at different distances from the collimator and for various energies. A series of RT simulations have been compared to experimental data for different radionuclides and collimators. Results of the RT technique matches experimental data of collimator response very well, producing correlation coefficients higher than 0.995. Reasonable values of the parameters in the lookup table and computation speed are discussed in order to achieve high accuracy while using minimal storage space for the look-up tables. In order to achieve noise-free projection images from MC, it is seen that the inclusion of the RT implementation for septal penetration increases the speed of the simulation by a factor of about 7,500 compared to the conventional SIMIND MC program.

Principles of Radiation Oncology

Tue, 10/07/2014 - 3:22pm

This chapter in Cancer Concepts: a Guidebook for the Non-Oncologist describes the principles of Radiation Oncology. Radiation Oncology utilizes ionizing radiation to treat cancer (and occasionally a few benign conditions). Radiotherapy or radiation therapy (RT) was initially developed in conjunction with diagnostic radiology, but has evolved into a separate specialty. Currently, more than fifty percent of cancer patients undergo RT at some point during the course of their cancer. Most receive treatment with curative intent (radical therapy); however, patients with incurable disease receive shorter, gentler courses of therapy to relieve cancer-induced symptoms.

The Agency for Healthcare Research and Quality Inpatient Quality Indicator #11 overall mortality rate does not accurately assess mortality risk after abdominal aortic aneurysm repair

Fri, 10/03/2014 - 11:29am

OBJECTIVE: The Agency for Healthcare Research and Quality (AHRQ) Inpatient Quality Indicator (IQI) #11, abdominal aortic aneurysm (AAA) repair mortality rate, is a measure of hospital quality that is publically reported but has not been externally validated. Because the IQI #11 overall mortality rate includes both intact and ruptured aneurysms and open and endovascular repair, we hypothesized that IQI #11 overall mortality rate does not provide accurate assessment of mortality risk after AAA repair and that AAA mortality cannot be accurately assessed by a single quality measure.

METHODS: Using AHRQ IQI software version 4.2, we calculated observed (O) and expected (E) mortality rates for IQI #11 for all hospitals performing more than 10 AAA repairs per year in the Nationwide Inpatient Sample for the years 2007 to 2011. We used Spearman correlation coefficient to compare expected rates as determined by IQI #11 overall mortality rate risk adjustment methodology and observed rates for all AAA repairs in four cohorts stratified by aneurysm stability (ruptured vs intact) and method of repair (open vs endovascular).

RESULTS: Among 187,773 AAA repairs performed at 1268 U.S. hospitals, hospitals' IQI #11 overall expected rates correlated poorly with their observed rates (E: 5.0% ± 4.4% vs O: 6.0% ± 9.8%; r = .49). For ruptured AAAs, IQI #11 overall mortality rate methodology underestimated the mortality risk of open repair (E: 34% ± 7.2% vs O: 40.1% ± 38.2%; r = 0.20) and endovascular repair (E: 24.8% ± 9% vs O: 27.3% ± 37.9%; r = 0.08). For intact AAA repair, IQI #11 overall mortality rate methodology underestimated the mortality risk of open repair (E: 4.3% ± 2.4% vs O: 6.3% ± 16.1%; r = .24) but overestimated the mortality risk of endovascular repair (E: 1.3% ± 0.8% vs O: 1.1% ± 3.7%; r = 0.25). Hospitals' observed mortality rates after intact AAA repair were not correlated with their mortality rates after ruptured AAA repair (r = 0.03).

CONCLUSIONS: IQI #11 overall mortality rate fails to provide accurate assessment of inpatient mortality risk after AAA repair. Thus, it is inappropriate to use IQI #11 overall mortality rate for quality reporting. The accuracy of separate quality measures that assess mortality risk after repair of ruptured and intact AAAs, stratified by the use of open or endovascular repair, should be examined.

High-grade atrioventricular block in acute coronary syndromes: insights from the Global Registry of Acute Coronary Events

Fri, 10/03/2014 - 11:14am

BACKGROUND: While prior work has suggested that a high-grade atrioventricular block (HAVB) in the setting of an acute coronary syndrome (ACS) is associated with in-hospital death, limited information is available on the incidence of, and death associated with, HAVB in ACS patients receiving contemporary management.

METHODS AND RESULTS: The incidence of HAVB was determined within The Global Registry of Acute Coronary Events (GRACE). The clinical characteristics, in-hospital therapies, and outcomes were compared between patients with and without HAVB. Factors associated with death in patients with HAVB were determined. A total of 59 229 patients with ACS between 1999 and 2007 were identified; 2.9% of patients had HAVB at any point during the index hospitalization; 22.7% of whom died in hospital [adjusted odds ratio (OR) = 4.2, 95% confidence interval (CI), 3.6-4.9, P < 0.001]. The association between HAVB and in-hospital death varied with type of ACS [OR: ST-segment elevation myocardial infarction (STEMI) = 3.0; non-STEMI = 6.4; unstable angina = 8.2, P for interaction < 0.001]. High-grade atrioventricular block present at the time of presentation to hospital (vs. occurring in-hospital) and early (12 h or no intervention) were associated with improved in-hospital survival, whereas temporary pacemaker insertion was not. Patients with HAVB surviving to discharge had similar adjusted survival at 6 months compared with those without HAVB. A reduction in the rate of, but not in-hospital mortality associated with, HAVB was noted over the study period.

CONCLUSION: Although the incidence of HAVB is low and decreasing, this complication continues to have a high risk of in-hospital death.

Inductive asymmetric cell division: The WRM leads the way

Wed, 10/01/2014 - 11:24am

C. elegans, with its invariant cell lineage, provides a powerful model system in which to study signaling-dependent asymmetric cell division. The C. elegans β-catenin-related protein, WRM-1, specifies endoderm at the 4-cell stage during the first cell signaling-induced asymmetric cell division of embryogenesis. During this interaction, Wnt signaling and the cell cycle regulator CDK-1 act together to induce the asymmetric cortical release of WRM-1 at prophase of the EMS cell cycle. Genetic studies suggest that release of WRM-1 unmasks a cortical site that drives EMS spindle rotation onto the polarized axis of the cell, simultaneously making WRM-1 available for nuclear translocation, and downstream signaling to specify endoderm. These studies suggest a general paradigm for how cortical factors like WRM-1 can function at the cell cortex to mask potentially confounding polarity cues, and when released with appropriate cell cycle timing, can also function downstream to define cell fate.

Food, pathogen, signal: The multifaceted nature of a bacterial diet

Wed, 10/01/2014 - 10:16am

C. elegans, both in the wild and in the lab, live on a diet of live bacteria. The bacterial diet provides nutrients for C. elegans, but can also play a number of other roles in C. elegans physiology. Recently, we compared the effects of different bacterial diets on life history traits and gene expression. Here, we discuss our recent findings in the context of other dietary studies and highlight challenges in understanding dietary effects. For instance, since bacteria can be pathogenic it can be difficult to disentangle pathogenic from dietary effects. Here we summarize different bacterial diets used for C. elegans and how they affect the animal.

Worms, bacteria, and micronutrients: an elegant model of our diet

Wed, 10/01/2014 - 10:16am

Micronutrients are required in small proportions in a diet to carry out key metabolic roles for biomass and energy production. Humans receive micronutrients either directly from their diet or from gut microbiota that metabolize other nutrients. The nematode Caenorhabditis elegans and its bacterial diet provide a relatively simple and genetically tractable model to study both direct and microbe-mediated effects of micronutrients. Recently, this model has been used to gain insight into the relationship between micronutrients, physiology, and metabolism. In particular, two B-type vitamins, vitamin B12 and folate, have been studied in detail. Here we review how C. elegans and its bacterial diet provide a powerful interspecies systems biology model that facilitates the precise delineation of micronutrient effects and the mechanisms involved.

Determination and inference of eukaryotic transcription factor sequence specificity

Wed, 10/01/2014 - 10:16am

Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only approximately 1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for approximately 34% of the approximately 170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.

Introduction to Cancer Concepts: A Guidebook for the Non-Oncologist

Fri, 09/26/2014 - 11:35am

This chapter in Cancer Concepts: A Guidebook for the Non-Oncologist presents an introduction to the Guidebook, which developed from the Cancer Concepts course at the University of Massachusetts Medical School.

Chronic alcohol-induced microRNA-155 contributes to neuroinflammation in a TLR4-dependent manner in mice

Thu, 09/25/2014 - 11:52am

INTRODUCTION: Alcohol-induced neuroinflammation is mediated by pro-inflammatory cytokines and chemokines including tumor necrosis factor-alpha (TNFalpha), monocyte chemotactic protein-1 (MCP1) and interleukin-1-beta (IL-1beta). Toll-like receptor-4 (TLR4) pathway induced nuclear factor-kappaB (NF-kappaB) activation is involved in the pathogenesis of alcohol-induced neuroinflammation. Inflammation is a highly regulated process. Recent studies suggest that microRNAs (miRNAs) play crucial role in fine tuning gene expression and miR-155 is a major regulator of inflammation in immune cells after TLR stimulation.

AIM: To evaluate the role of miR-155 in the pathogenesis of alcohol-induced neuroinflammation.

METHODS: Wild type (WT), miR-155- and TLR4-knockout (KO) mice received 5% ethanol-containing or isocaloric control diet for 5 weeks. Microglia markers were measured by q-RTPCR; inflammasome activation was measured by enzyme activity; TNFalpha, MCP1, IL-1beta mRNA and protein were measured by q-RTPCR and ELISA; phospho-p65 protein and NF-kappaB were measured by Western-blotting and EMSA; miRNAs were measured by q-PCR in the cerebellum. MiR-155 was measured in immortalized and primary mouse microglia after lipopolysaccharide and ethanol stimulation.

RESULTS: Chronic ethanol feeding up-regulated miR-155 and miR-132 expression in mouse cerebellum. Deficiency in miR-155 protected mice from alcohol-induced increase in inflammatory cytokines; TNFalpha, MCP1 protein and TNFalpha, MCP1, pro-IL-1beta and pro-caspase-1 mRNA levels were reduced in miR-155 KO alcohol-fed mice. NF-kappaB was activated in WT but not in miR-155 KO alcohol-fed mice. However increases in cerebellar caspase-1 activity and IL-1beta levels were similar in alcohol-fed miR-155-KO and WT mice. Alcohol-fed TLR4-KO mice were protected from the induction of miR-155. NF-kappaB activation measured by phosphorylation of p65 and neuroinflammation were reduced in alcohol-fed TLR4-KO compared to control mice. TLR4 stimulation with lipopolysaccharide in primary or immortalized mouse microglia resulted in increased miR-155.

CONCLUSION: Chronic alcohol induces miR-155 in the cerebellum in a TLR4-dependent manner. Alcohol-induced miR-155 regulates TNFalpha and MCP1 expression but not caspase-dependent IL-1beta increase in neuroinflammation.

Toll-like receptors in liver disease

Thu, 09/25/2014 - 11:52am

Activation of inflammatory signaling pathways is of central importance in the pathogenesis of alcoholic liver disease (ALD) and nonalcoholic steatohepatitis (NASH). Recent studies demonstrated that Toll-like receptors, the sensors of microbial and endogenous danger signals, are expressed and activated in innate immune cells as well as in parenchymal cells in the liver and thereby contribute to ALD and NASH. In this review, we emphasize the importance of gut-derived endotoxin and its recognition by TLR4 in the liver. The significance of TLR-induced intracellular signaling pathways and cytokine production as well as the contribution of individual cell types to the inflammation is evaluated. The contribution of TLR signaling to the induction of liver fibrosis and to the progression of liver pathology mediated by viral pathogens is reviewed in the context of ALD and NASH.