Biomedical subjects

Jason M Johnson

Publications and source records attributed to Jason M Johnson.

At least 19 recordsLinked to original sources

PubMed2006

Pulmonary embolism complicating bariatric surgery: detailed analysis of a single institution's 24-year experience.

BACKGROUND: Morbidly obese patients undergoing bariatric procedures are at risk for pulmonary embolism (PE). Because large series are required to analyze low-incidence complications, factors predictive of PE have not been clearly defined. Since 1992, short-course heparin prophylaxis, beginning immediately before operation, has been used in this center. STUDY DESIGN: Prospective data on 3,861 patients undergoing bariatric procedures between 1980 and 2004 were queried. Factors analyzed included age, gender, body mass index, interval between procedure and PE, inpatient versus outpatient status, mortality, access method (open versus laparoscopic), and comorbidities. RESULTS: PE within 60 days of operation occurred in 33 patients (23 women, 10 men), for an incidence of 0.85%. No difference in incidence was noted between open (0.84%) and laparoscopic (0.88%) groups, nor did routine prophylaxis with heparin since 1992 decrease the incidence. The interval between procedure and PE was 13.2+/-2.6 (mean +/- SEM) days (open=13.0+/-3.0 days, laparoscopic 14.1+/-6.49 days, p=0.9). One-third of PEs occurred after hospital discharge. Pulmonary embolism-related mortality was 27%. A statistically greater body mass index was noted in PE patients compared with non-PE patients (57.2+/-2.4 kg.m(2) versus 49.9+/-0.2 kg/m(2), p < 0.01, Wilcoxon rank test). Multivariate logistic regression confirmed a primary role for preoperative weight as a predictor of PE; univariate analysis suggested an increased PE risk with obesity hypoventilation syndrome, anastomotic leak, and chronic venous insufficiency. CONCLUSIONS: Data demonstrated persistence of PE risk in the anticoagulation, laparoscopic-access era at a rate similar to that in the preanticoagulation, open-access era. Because one-third of PEs occur after hospital discharge, consideration should be given to continuing anticoagulants longer and to adopting a more aggressive policy of inferior vena cava filter prophylaxis, particularly in patients with high body mass index, obese hyperventilation syndrome, and venous insufficiency.

Adolescent↗

PubMed2006

Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways.

BACKGROUND: Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention has been paid to methods for extracting biological meaning from these output lists. One powerful approach is to examine the expression of predefined biological pathways and gene sets, such as metabolic and signaling pathways and macromolecular complexes. Although many methods for measuring pathway expression have been proposed, a systematic analysis of the performance of multiple methods over multiple independent data sets has not previously been reported. RESULTS: Five different measures of pathway expression were compared in an analysis of nine publicly available mRNA expression data sets. The relative sensitivity of the metrics varied greatly across data sets, and the biological pathways identified for each data set are also dependent on the choice of pathway activation metric. In addition, we show that removing incoherent pathways prior to analysis improves specificity. Finally, we create and analyze a public map of pathway expression in human tissues by gene-set analysis of a large compendium of human expression data. CONCLUSION: We show that both the detection sensitivity and identity of pathways significantly perturbed in a microarray experiment are highly dependent on the analysis methods used and how incoherent pathways are treated. Analysts should thus consider using multiple approaches to test the robustness of their biological interpretations. We also provide a comprehensive picture of the tissue distribution of human gene pathways and a useful public archive of human pathway expression data.

Cell Line↗

PubMed2006

Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing.

Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended ("off-target") silencing can hinder the use of RNAi to define gene function. Here we describe position-specific, sequence-independent chemical modifications that reduced silencing of partially complementary transcripts by all siRNAs tested. Silencing of perfectly matched targets was unaffected by these modifications. The chemical modification also reduced off-target phenotypes in growth inhibition studies. Key to the modification was 2'-O-methyl ribosyl substitution at position 2 in the guide strand, which reduced silencing of most off-target transcripts with complementarity to the seed region of the siRNA guide strand. The sharp position dependence of 2'-O-methyl ribosyl modification contrasts with the broader position dependence of base-pair substitutions within the seed region, suggesting a role for position 2 of the guide strand distinct from its effects on pairing to target transcripts.

Base Sequence↗

PubMed2006

The long-term effects of gastric bypass on vitamin D metabolism.

OBJECTIVE: Alterations of the endocrine system in patients following Roux-en-Y gastric bypass (GBP) are poorly described and have prompted us to perform a longitudinal study of the effects of GBP on serum calcium, 25-hydroxy-vitamin-D (vitamin D), and parathyroid hormone (PTH). METHODS: Prospectively collected data were compiled to determine how GBP affects serum calcium, vitamin D, and PTH. Student t test, Fisher exact test, or linear regression was used to determine significance. RESULTS: Calcium, vitamin D, and PTH levels were drawn on 243 patients following GBP. Forty-one patients had long-limb bypass (LL-GBP), Roux >100 cm, and 202 had short-limb bypass (SL-GBP), Roux < or =100 cm. The mean (+/-SD) postoperative follow-up time was significantly longer in the LL-GBP group (5.7 +/- 2.5 years) than the SL-GBP group (3.1 +/- 3.6 years, P < 0.0001). When corrected for albumin levels, mean calcium was 9.3 mg/dL (range, 8.5-10.8 mg/dL), and no difference existed between LL-GBP and SL-GBP patients. For patients with low vitamin D levels (<8.9 ng/mL), 88.9% had elevated PTH (>65 pg/mL) and 58.0% of patients with normal vitamin D levels (> or =8.9 ng/mL) had elevated PTH (P < 0.0001). In individuals with vitamin D levels <30 ng/mL, 55.1% (n = 103) had elevated PTH, and of those with vitamin D levels > or =30 ng/mL 28.5% (n = 16) had elevated PTH (P = 0.0007). Mean vitamin D levels were lower in patients who had undergone LL-GBP as opposed to those with SL-GBP, 16.8 +/- 10.8 ng/mL versus 22.7 +/- 11.1 ng/mL (P = 0.0022), and PTH was significantly higher in patients who had a LL-GBP (113.5 +/- 88.0 pg/mL versus 74.5 +/- 52.7 pg/mL, P = 0.0002). There was a linear decrease in vitamin D (P = 0.005) coupled with a linear increase in PTH (P < 0.0001) the longer patients were followed after GBP. Alkaline phosphatase levels were elevated in 40.3% of patients and correlated with PTH levels. CONCLUSION: Vitamin D deficiency and elevated PTH are common following GBP and progress over time. There is a significant incidence of secondary hyperparathyroidism in short-limb GBP patients, even those with vitamin D levels > or =30 ng/mL, suggesting selective Ca malabsorption. Thus, calcium malabsorption is inherent to gastric bypass. Careful calcium and vitamin D supplementation and long-term screening are necessary to prevent deficiencies and the sequelae of secondary hyperparathyroidism.

Adult↗

PubMed2005

Impact of major co-morbidities on mortality and complications after gastric bypass.

BACKGROUND: We hypothesized that major co-morbidities affect survival and complications after gastric bypass. METHODS: A total of 1465 patients undergoing laparoscopic and open gastric bypass between 1995 and 2002 were studied. Patients with a body mass index >or= 35 kg/m(2) and major co-morbidities (group 1, n = 1045) were compared with patients with a body mass index >or= 40 kg/m(2) with minor/no co-morbidities (group 2, n = 420). RESULTS: Group 1 patients were older (43 versus 36 years, P < 0.001) and had a greater BMI (53 versus 50 kg/m(2), P < 0.001). Early postoperative complications were greater in group 1 than in group 2 and included leaks (4.1% versus 1.2%, P < 0.0032) and wound infections (3.9% versus 1.4%, P < 0.0133). Procedure-related mortality in the series was 1.7%. Mortality was 10-fold greater in group 1 (2.3% versus 0.2%, P < 0.0032). The incidence of small bowel obstruction, incisional hernia, and pulmonary embolism was similar in the two groups. Excess weight loss was significantly greater in group 2 (68% versus 62%, P < 0.001) at 1 year. Resolution of group 1 co-morbidities was great, including hypertension in 62%, diabetes in 75%, venous stasis disease in 96%, and pseudotumor cerebri in 98%. CONCLUSION: Outcomes analysis of obesity surgery requires risk stratification. The very low mortality rates in published studies are likely explained by surgical treatment of low-risk patients with minor co-morbidities, such as those seen in group 2. However, despite the increased perioperative risk, the group 1 patients (with major co-morbidities) demonstrated dramatic resolution of their co-morbid conditions, justifying the decision to go forward with surgery. The data support a radical change in treatment philosophy in which morbidly obese individuals should be offered bariatric surgery before major co-morbid conditions develop as a strategy to decrease the operative risk.

Adult↗

PubMed2005

Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2.

Rett syndrome (RTT) is a postnatal neurodevelopmental disorder characterized by the loss of acquired motor and language skills, autistic features, and unusual stereotyped movements. RTT is caused by mutations in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Mutations in MECP2 cause a variety of neurodevelopmental disorders including X-linked mental retardation, psychiatric disorders, and some cases of autism. Although MeCP2 was identified as a methylation-dependent transcriptional repressor, transcriptional profiling of RNAs from mice lacking MeCP2 did not reveal significant gene expression changes, suggesting that MeCP2 does not simply function as a global repressor. Changes in expression of a few genes have been observed, but these alterations do not explain the full spectrum of Rett-like phenotypes, raising the possibility that additional MeCP2 functions play a role in pathogenesis. In this study, we show that MeCP2 interacts with the RNA-binding protein Y box-binding protein 1 and regulates splicing of reporter minigenes. Importantly, we found aberrant alternative splicing patterns in a mouse model of RTT. Thus, we uncovered a previously uncharacterized function of MeCP2 that involves regulation of splicing, in addition to its role as a transcriptional repressor.

Animals↗

PubMed2005

Auriculo-condylar syndrome is associated with highly variable ear and mandibular defects in multiple kindreds.

We report on 20 individuals in 4 kindreds with auriculo-condylar syndrome (ACS), an autosomal dominant disorder characterized by congenital auricular clefts, mandibular condyle hypoplasia, temporomandibular joint (TMJ) abnormalities, micrognathia, microstomia, and a round facial appearance with prominent cheeks. Affected individuals have varying degrees of glossoptosis, respiratory distress, masticatory abnormalities, and malocclusion. Data from these families and those previously described suggest that this is a unique disorder with widely variable expression, including lack of obvious external anomalies in some individuals and severe ear malformations, condyle agenesis, and characteristic facial features in others. Early recognition of this condition should permit appropriate counseling and anticipatory guidance, including evaluation for reconstructive surgery and orthodontia and intervention for upper airway obstruction and sleep apnea.

Abnormalities, Multiple↗

PubMed2005

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10,818 pairs of human and mouse genes based on conservation at genome and transcript levels. Expression levels of conserved alternative splices in human and mouse expressed sequence tag databases show strong correlation, indicating that alternative splicing is similarly regulated in both species. A total of 43% (8921) of mouse alternative splices could be found in the human genome but not in human transcripts. Five of eleven tested mouse predictions were observed in human tissues, demonstrating that mouse transcripts provide a valuable resource for identifying alternative splicing events in human genes. Combining gene-specific measures of conserved and diverged alternative splicing with both gene classification based on Gene Ontology (GO) and microarray-determined gene expression in 52 diverse human tissues and cell lines, we found conserved alternative splicing most enriched in brain-expressed signaling pathways. Diverged alternative splicing is more prevalent in testis and cancerous cell line up-regulated processes, including protein biosynthesis, responses to stress and responses to endogenous stimuli. Using conservation as a surrogate for functional significance, these results suggest that alternative splicing plays an important role in enhancing the functional capacity of central nervous systems, while non-functional splicing more frequently occurs in testis and cell lines, possibly as a result of cellular stress and rapid proliferation.

Alternative Splicing↗

PubMed2005

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs.

MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression in plants and animals. To investigate the influence of miRNAs on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile. Here we show that delivering miR-124 causes the expression profile to shift towards that of brain, the organ in which miR-124 is preferentially expressed, whereas delivering miR-1 shifts the profile towards that of muscle, where miR-1 is preferentially expressed. In each case, about 100 messages were downregulated after 12 h. The 3' untranslated regions of these messages had a significant propensity to pair to the 5' region of the miRNA, as expected if many of these messages are the direct targets of the miRNAs. Our results suggest that metazoan miRNAs can reduce the levels of many of their target transcripts, not just the amount of protein deriving from these transcripts. Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans.

3' Untranslated Regions↗

PubMed2005

Effects of gastric bypass procedures on bone mineral density, calcium, parathyroid hormone, and vitamin D.

Weight loss after gastric bypass procedures has been well studied, but the long-term metabolic sequelae are not known. Data on bone mineral density (BMD), calcium, parathyroid hormone, and vitamin D were collected preoperatively and at yearly intervals after gastric bypass procedures. A total of 230 patients underwent preoperative BMD scans. Fifteen patients were osteopenic preoperatively, and three patients subsequently developed osteopenia postoperatively within the first year. No patient had or developed osteoporosis. At 1 year, total forearm BMD decreased by 0.55% (n = 91; P = .03) and radius BMD had increased overall by 1.85% (n = 23; P = .008); both total hip and lumbar spine BMD decreased by 9.27% (n = 22; P < .001) and 4.53% (n = 31; P < .001), respectively. By the second postoperative year, BMD in the total forearm had decreased an additional 3.62% (n = 14; P < .001), whereas radius BMD remained unchanged. Although total hip and lumbar spine BMD significantly decreased at 1 year, by year 2 both total hip and lumbar spine BMD only slightly decreased and were not significantly different from before the operation. Serum calcium decreased from 9.8 mg/dL to 9.2 during the first year (not significant [NS]) and then to 8.8 (NS) by the second year. Parathyroid hormone increased from 59.7 pg/mL (nl 10-65 pg/mL) preoperatively to 63.1 during year 1 (NS) and continued to increase to 64.7 by year 2 (NS). No difference was noted among levels of 25-hydroxy vitamin D preoperatively (25.2 ng/mL; nl 10-65 ng/mL), at 1 year (34.4), and at 2 years (35.4). Our data indicate that bone loss is highest in the first year after gastric bypass with stabilization, and that, in some cases, there is an increase in bone density after the first year.

Adult↗

PubMed2005

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.

Microarrays provide the opportunity to measure transcription from regions of the genome without bias towards the location of known genes. This technology thus offers an important source of genomic sequence annotation that is complementary to cDNA sequencing and computational gene-finding methods. Recent "tiling" microarray experiments that assay transcription at regular intervals throughout the genome have shown evidence of large amounts of transcription outside the boundaries of known genes. This transcription is observed in polyadenylated RNA samples and appears to be derived from intergenic regions, from introns of known genes and from sequences antisense to known transcripts. In this article, we discuss different explanations for this phenomenon.

Animals↗

PubMed2005

Onlay hiatal reinforcement utilizing human acellular dermal matrix: three case series.

Redo laparoscopic fundoplication and laparoscopic repair of large (>5cm) paraesophageal hernias have a high rate of recurrence after primary suture repair of the hiatal defect. As such, the use of mesh prosthesis as an interposition graft or onlay reinforcement is becoming more popular for the repair of larger, more complicated crural defects. We report three cases in which human acellular dermal matrix was used as an onlay reinforcement of the hiatus after primary suture closure. Two patients had large paraesophageal hernias (one type III and one type IV). The third patient became symptomatic after her second laparoscopic antireflux procedure and was found to have recurrent herniation of the fundus into the mediastinum. All three patients underwent successful laparoscopic repair. There were no intraoperative or postoperative complications. All three patients remain symptom free with follow-up ranging from 8 months to 10 months. Acellular dermal matrix appears to be a promising prosthetic for onlay reinforcement of the hiatus during redo laparoscopic fundoplication and repair of large paraesophageal hernias.

Aged↗

PubMed2005

Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.

There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and short-interfering RNAs. The method relies on primer extension conversion of RNA to cDNA by reverse transcription followed by quantitative, real-time PCR. Technical parameters critical to the success of the assay are presented. Measurements of microRNA levels are sensitive, with most assays allowing measurements in the femtomolar range, which corresponds to tens of copies per cell or less. The assay has a high dynamic range and provides linear readout over differences in microRNA concentrations that span 6-7 orders of magnitude. The assay is capable of discriminating between related microRNA family members that differ by subtle sequence differences. We used the method for quantitative analysis of six microRNAs across 12 tissue samples. The data confirm striking variation in the patterns of expression of these noncoding regulatory RNAs.

DNA Primers↗

PubMed2004

A comprehensive transcript index of the human genome generated using microarrays and computational approaches.

BACKGROUND: Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. RESULTS: The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. CONCLUSIONS: These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized.

Chromosomes, Human, Pair 20↗

PubMed2004

Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root ganglia.

Molecular medicine requires the precise definition of drug targets, and tools are now in place to provide genome-wide information on the expression and alternative splicing patterns of any known gene. DNA microarrays were used to monitor transcript levels of the nine well-characterized alpha-subunit sodium channel genes across a broad range of tissues from cynomolgus monkey, a non-human primate model. Alternative splicing of human transcripts for a subset of the genes that are expressed in dorsal root ganglia, SCN8A (Na(v)1.6), SCN9A (Na(v)1.7), and SCN11A (Na(v)1.9) was characterized in detail. Genomic sequence analysis among gene family paralogs and between cross-species orthologs suggested specific alternative splicing events within transcripts of these genes, all of which were experimentally confirmed in human tissues. Quantitative PCR revealed that certain alternative splice events are uniquely expressed in dorsal root ganglia. In addition to characterization of human transcripts, alternatively spliced sodium channel transcripts were monitored in a rat model for neuropathic pain. Consistent down-regulation of all transcripts was observed, as well as significant changes in the splicing patterns of SCN8A and SCN9A.

Alternative Splicing↗

PubMed2004

Protein interaction networks.

The study of protein interactions is playing an ever increasing role in our attempts to understand cells and diseases on a system-wide level. This article reviews several experimental approaches that are currently being used to measure protein-protein, protein-DNA and gene-gene interactions. These techniques have now been scaled up to produce extensive genome-wide data sets that are providing us with a first glimpse of global interaction networks. Complementing these experimental approaches, several computational methodologies to predict protein interactions are also reviewed. Existing databases that serve as repositories for protein interaction information and how such databases are used to analyze high-throughput data from a pathway perspective is also addressed. Finally, current efforts to combine multiple data types to obtain more accurate and comprehensive models of protein interactions are discussed. It is clear that the evolution of these experimental and computational approaches is rapidly changing our view of biology, and promises to provide us with an unprecedented ability to model cells and organisms at a system-wide level.

Animals↗

PubMed2003

Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.

Alternative pre-messenger RNA (pre-mRNA) splicing plays important roles in development, physiology, and disease, and more than half of human genes are alternatively spliced. To understand the biological roles and regulation of alternative splicing across different tissues and stages of development, systematic methods are needed. Here, we demonstrate the use of microarrays to monitor splicing at every exon-exon junction in more than 10,000 multi-exon human genes in 52 tissues and cell lines. These genome-wide data provide experimental evidence and tissue distributions for thousands of known and novel alternative splicing events. Adding to previous studies, the results indicate that at least 74% of human multi-exon genes are alternatively spliced.

Alternative Splicing↗

PubMed2003

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

Alternative Splicing↗