Methylome and proteome integration in human skeletal muscle uncover group and individual responses to high-intensity interval training.

Exercise is a major beneficial contributor to muscle metabolism, and health benefits acquired by exercise are a result of molecular shifts occurring across multiple molecular layers (i.e., epigenome, transcriptome, and proteome). Identifying robust, across-molecular level targets associated with exercise response, at both group and individual levels, is paramount to develop health guidelines and targeted health interventions. Sixteen, apparently healthy, moderately trained (VO2 max = 51.0 ± 10.6 mL min-1 kg-1 ) males (age range = 18-45 years) from the Gene SMART (Skeletal Muscle Adaptive Responses to Training) study completed a longitudinal study composed of 12-week high-intensity interval training (HIIT) intervention. Vastus lateralis muscle biopsies were collected at baseline and after 4, 8, and 12 weeks of HIIT. DNA methylation (~850 CpG sites) and proteomic (~3000 proteins) analyses were conducted at all time points. Mixed models were applied to estimate group and individual changes, and methylome and proteome integration was conducted using a holistic multilevel approach with the mixOmics package. A total of 461 proteins significantly changed over time (at 4, 8, and 12 weeks), whilst methylome overall shifted with training only one differentially methylated position (DMP) was significant (adj.p-value < .05). K-means analysis revealed cumulative protein changes by clusters of proteins that presented similar changes over time. Individual responses to training were observed in 101 proteins. Seven proteins had large effect-sizes >0.5, among them are two novel exercise-related proteins, LYRM7 and EPN1. Integration analysis showed bidirectional relationships between the methylome and proteome. We showed a significant influence of HIIT on the epigenome and more so on the proteome in human muscle, and uncovered groups of proteins clustering according to similar patterns across the exercise intervention. Individual responses to exercise were observed in the proteome with novel mitochondrial and metabolic proteins consistently changed across individuals. Future work is required to elucidate the role of these proteins in response to exercise.

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which─similar to its sibling LFQ-Analyst─is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.

Nonarthroplasty options for massive, irreparable rotator cuff tears have improvement in range of motion and patient-reported outcomes at short-term follow-up: a systematic review.

PURPOSE: To compare various nonarthroplasty treatment options for massive, irreparable rotator cuff tears, including allograft bridging/augmentation, debridement, partial repair, superior capsule reconstruction (SCR), subacromial balloon spacer, and tendon transfer. METHODS: A comprehensive search was conducted through the PubMed, MEDLINE, and EMBASE databases for all articles pertaining to nonarthroplasty treatment options for irreparable rotator cuff tears. Inclusion criteria included manuscripts published between 2009 and 2020 with at least 1 year follow-up and Level I-IV evidence. Articles were separated into six groups: debridement, arthroscopic and open repair, allograft bridging/augmentation, SCR, subacromial balloon spacer, and tendon transfer. Data points included range of motion (external rotation, abduction, forward flexion, and internal rotation), visual analog scale (VAS) pain score, American Shoulder and Elbow Surgeons (ASES) score, Constant score, rate of revision surgery, and rate of conversion to arthroplasty. RESULTS: A total of 83 studies and 3363 patients were included. All treatment options had statistically significant improvements in postoperative range of motion and patient-reported outcomes. Debridement had statistically significantly greater postoperative abduction and forward flexion range of motion, as well as better VAS pain scores, compared to the other treatment options. The SCR subgroup had the greatest improvement in ASES scores postoperatively. The overall revision rate was 7.2% among all surgical options, with the allograft bridging/augmentation group having the lowest rate of revision at 0-8.3%. The overall rate of conversion to arthroplasty was 7.2%, with debridement having the greatest rate of conversion at 15.4%. CONCLUSION: All six nonarthroplasty treatment options for irreparable rotator cuff tears resulted in statistically significant improvements in range of motion and patient-reported outcomes at 1 year follow-up or more, with low rates of revision and conversion to arthroplasty. Debridement had statistically significantly greater postoperative abduction and forward flexion range of motion, as well as better VAS pain scores, compared to the other treatment options. However, these conclusions should be interpreted with caution due to the heterogeneous nature of the data, lack of prospective randomized control trials, and short-term follow-up. The findings of this study highlight the complexity of irreparable, massive rotator cuff tears, and the need for an individualized approach when treating these patients. LEVEL OF EVIDENCE: Level IV.

Temporal proteomics of human cerebrospinal fluid after severe traumatic brain injury.

The pathophysiology of traumatic brain injury (TBI) requires further characterization to fully elucidate changes in molecular pathways. Cerebrospinal fluid (CSF) provides a rich repository of brain-associated proteins. In this retrospective observational study, we implemented high-resolution mass spectrometry to evaluate changes to the CSF proteome after severe TBI. 91 CSF samples were analyzed with mass spectrometry, collected from 16 patients with severe TBI (mean 32 yrs; 81% male) on day 0, 1, 2, 4, 7 and/or 10 post-injury (8-16 samples/timepoint) and compared to CSF obtained from 11 non-injured controls. We quantified 1152 proteins with mass spectrometry, of which approximately 80% were associated with CSF. 1083 proteins were differentially regulated after TBI compared to control samples. The most highly-upregulated proteins at each timepoint included neutrophil elastase, myeloperoxidase, cathepsin G, matrix metalloproteinase-8, and S100 calcium-binding proteins A8, A9 and A12-all proteins involved in neutrophil activation, recruitment, and degranulation. Pathway enrichment analysis confirmed the robust upregulation of proteins associated with innate immune responses. Conversely, downregulated pathways included those involved in nervous system development, and several proteins not previously identified after TBI such as testican-1 and latrophilin-1. We also identified 7 proteins (GM2A, Calsyntenin 1, FAT2, GANAB, Lumican, NPTX1, SFRP2) positively associated with an unfavorable outcome at 6 months post-injury. Together, these findings highlight the robust innate immune response that occurs after severe TBI, supporting future studies to target neutrophil-related processes. In addition, the novel proteins we identified to be differentially regulated by severe TBI warrant further investigation as potential biomarkers of brain damage or therapeutic targets.

crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry.

SUMMARY: Unbiased detection of protein-protein and protein-RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein-protein and protein-RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures. AVAILABILITY AND IMPLEMENTATION: crisscrosslinkeR is a free and open-source package, available through GitHub: github.com/egmg726/crisscrosslinker. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Transcriptomic analysis of preovipositional embryonic arrest in a nonsquamate reptile (Chelonia mydas).

After gastrulation, oviductal hypoxia maintains turtle embryos in an arrested state prior to oviposition. Subsequent exposure to atmospheric oxygen upon oviposition initiates recommencement of embryonic development. Arrest can be artificially extended for several days after oviposition by incubation of the egg under hypoxic conditions, with development recommencing in an apparently normal fashion after subsequent exposure to normoxia. To examine the transcriptomic events associated with embryonic arrest in green sea turtles (Chelonia mydas), RNA-sequencing analysis was performed on embryos from freshly laid eggs and eggs incubated in either normoxia (oxygen tension ~159 mmHg) or hypoxia (<8 mmHg) for 36 h after oviposition (n = 5 per group). The patterns of gene expression differed markedly among the three experimental groups. Normal embryonic development in normoxia was associated with upregulation of genes involved in DNA replication, the cell cycle, and mitosis, but these genes were commonly downregulated after incubation in hypoxia. Many target genes of hypoxia inducible factors, including the gene encoding insulin-like growth factor binding protein 1 (igfbp1), were downregulated by normoxic incubation but upregulated by incubation in hypoxia. Notably, some of the transcriptomic effects of hypoxia in green turtle embryos resembled those reported to be associated with hypoxia-induced embryonic arrest in diverse taxa, including the nematode Caenorhabditis elegans and zebrafish (Danio rerio). Hypoxia-induced preovipositional embryonic arrest appears to be a unique adaptation of turtles. However, our findings accord with the proposition that the mechanisms underlying hypoxia-induced embryonic arrest per se are highly conserved across diverse taxa.

An Integrated Multi-Omic Network Analysis Identifies Seizure-Associated Dysregulated Pathways in the GAERS Model of Absence Epilepsy.

Absence epilepsy syndromes are part of the genetic generalized epilepsies, the pathogenesis of which remains poorly understood, although a polygenic architecture is presumed. Current focus on single molecule or gene identification to elucidate epileptogenic drivers is unable to fully capture the complex dysfunctional interactions occurring at a genetic/proteomic/metabolomic level. Here, we employ a multi-omic, network-based approach to characterize the molecular signature associated with absence epilepsy-like phenotype seen in a well validated rat model of genetic generalized epilepsy with absence seizures. Electroencephalographic and behavioral data was collected from Genetic Absence Epilepsy Rats from Strasbourg (GAERS, n = 6) and non-epileptic controls (NEC, n = 6), followed by proteomic and metabolomic profiling of the cortical and thalamic tissue of rats from both groups. The general framework of weighted correlation network analysis (WGCNA) was used to identify groups of highly correlated proteins and metabolites, which were then functionally annotated through joint pathway enrichment analysis. In both brain regions a large protein-metabolite module was found to be highly associated with the GAERS strain, absence seizures and associated anxiety and depressive-like phenotype. Quantitative pathway analysis indicated enrichment in oxidative pathways and a downregulation of the lysine degradation pathway in both brain regions. GSTM1 and ALDH2 were identified as central regulatory hubs of the seizure-associated module in the somatosensory cortex and thalamus, respectively. These enzymes are involved in lysine degradation and play important roles in maintaining oxidative balance. We conclude that the dysregulated pathways identified in the seizure-associated module may be involved in the aetiology and maintenance of absence seizure activity. This dysregulated activity could potentially be modulated by targeting one or both central regulatory hubs.

Phosphoproteomic characterization of the signaling network resulting from activation of the chemokine receptor CCR2.

Leukocyte recruitment is a universal feature of tissue inflammation and regulated by the interactions of chemokines with their G protein-coupled receptors. Activation of CC chemokine receptor 2 (CCR2) by its cognate chemokine ligands, including CC chemokine ligand 2 (CCL2), plays a central role in recruitment of monocytes in several inflammatory diseases. In this study, we used phosphoproteomics to conduct an unbiased characterization of the signaling network resulting from CCL2 activation of CCR2. Using data-independent acquisition MS analysis, we quantified both the proteome and phosphoproteome in FlpIn-HEK293T cells stably expressing CCR2 at six time points after activation with CCL2. Differential expression analysis identified 699 significantly regulated phosphorylation sites on 441 proteins. As expected, many of these proteins are known to participate in canonical signal transduction pathways and in the regulation of actin cytoskeleton dynamics, including numerous guanine nucleotide exchange factors and GTPase-activating proteins. Moreover, we identified regulated phosphorylation sites in numerous proteins that function in the nucleus, including several constituents of the nuclear pore complex. The results of this study provide an unprecedented level of detail of CCR2 signaling and identify potential targets for regulation of CCR2 function.

Behavioral, axonal, and proteomic alterations following repeated mild traumatic brain injury: Novel insights using a clinically relevant rat model.

A history of mild traumatic brain injury (mTBI) is linked to a number of chronic neurological conditions, however there is still much unknown about the underlying mechanisms. To provide new insights, this study used a clinically relevant model of repeated mTBI in rats to characterize the acute and chronic neuropathological and neurobehavioral consequences of these injuries. Rats were given four sham-injuries or four mTBIs and allocated to 7-day or 3.5-months post-injury recovery groups. Behavioral analysis assessed sensorimotor function, locomotion, anxiety, and spatial memory. Neuropathological analysis included serum quantification of neurofilament light (NfL), mass spectrometry of the hippocampal proteome, and ex vivo magnetic resonance imaging (MRI). Repeated mTBI rats had evidence of acute cognitive deficits and prolonged sensorimotor impairments. Serum NfL was elevated at 7 days post injury, with levels correlating with sensorimotor deficits; however, no NfL differences were observed at 3.5 months. Several hippocampal proteins were altered by repeated mTBI, including those associated with energy metabolism, neuroinflammation, and impaired neurogenic capacity. Diffusion MRI analysis at 3.5 months found widespread reductions in white matter integrity. Taken together, these findings provide novel insights into the nature and progression of repeated mTBI neuropathology that may underlie lingering or chronic neurobehavioral deficits.

Large reduction in opioid prescribing by a multipronged behavioral intervention after major urologic surgery.

BACKGROUND: Surgeons play a pivotal role in combating the opioid crisis that currently grips the United States. Changing surgeon behavior is difficult, and the degree to which behavioral science can steer surgeons toward decreased opioid prescribing is unclear. METHODS: This was a single-institution, single-arm, pre- and postintervention study examining the prescribing of opioids by urologists for adult patients undergoing prostatectomy or nephrectomy. The primary outcome was the quantity of opioids prescribed in oral morphine equivalents (OMEs) after hospital discharge. The primary exposure was a multipronged behavioral intervention designed to decrease opioid prescribing. The intervention had 3 components: 1) formal education, 2) individual audit feedback, and 3) peer comparison performance feedback. There were 3 phases to the study: a pre-intervention phase, an intervention phase, and a washout phase. RESULTS: Three hundred eighty-two patients underwent prostatectomy, and 306 patients underwent nephrectomy. The median OMEs decreased from 195 to 19 in the prostatectomy patients and from 200 to 0 in the nephrectomy patients (P < .05 for both). The median OMEs prescribed did not increase during the washout phase. Prostatectomy patients discharged with opioids had higher levels of anxiety than patients discharged without opioids (P < .05). Otherwise, prostatectomy and nephrectomy patients discharged with and without opioids did not differ in their perception of postoperative pain management, activity levels, psychiatric symptoms, or somatic symptoms (P > .05 for all). CONCLUSIONS: Implementing a multipronged behavioral intervention significantly reduced opioid prescribing for patients undergoing prostatectomy or nephrectomy without compromising patient-reported outcomes.

Prolactin-to-Testosterone Ratio Predicts Pituitary Abnormalities in Mildly Hyperprolactinemic Men with Symptoms of Hypogonadism.

PURPOSE: We aimed to identify predictor variables associated with pituitary abnormalities in hypogonadal men with mild hyperprolactinemia. We also sought to develop a decision-making aid to select patients for evaluation with pituitary magnetic resonance imaging. MATERIALS AND METHODS: We retrospectively examined men with mild hyperprolactinemia (15.1-50.0 ng/ml) who presented with symptoms of hypogonadism and underwent pituitary magnetic resonance imaging. Demographics, laboratory values and clinical data were obtained from the electronic medical record. Selected predictor variables were included in multivariable logistic regression and partitioning models. Cost avoidance analysis was performed on models achieving sensitivities ≥90%. RESULTS: A total of 141 men were included in the study, of whom 40 (28%) displayed abnormalities on pituitary magnetic resonance imaging. Patients with pituitary abnormalities exhibited higher prolactin (p=0.01), lower testosterone (p=0.0001) and lower luteinizing hormone (p=0.03) levels than those with normal anatomy, as well as higher prolactin-to-testosterone ratios (p <0.0001) and lower luteinizing hormone-to-follicle-stimulating hormone ratios (p=0.0001). These serological variables were identified as the best performing predictor variables. The partition incorporating a prolactin-to-testosterone ratio cutoff of 0.10 and prolactin cutoff of 25 ng/ml achieved 90% sensitivity and 48% specificity, and reduced diagnostic expenses by 28%. CONCLUSIONS: Hypogonadal men presenting with mild hyperprolactinemia and pituitary abnormalities declare themselves via endocrine studies routinely ordered to evaluate these conditions. The prolactin-to-testosterone ratio is the best independent predictor of finding a pituitary abnormality on magnetic resonance imaging, although sensitivity improves by referencing additional serological parameters. Significant cost avoidance may result from screening this population prior to ordering pituitary magnetic resonance imaging.

RaftProt V2: understanding membrane microdomain function through lipid raft proteomes.

Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contaminant proteins. To enable integrated analyses, we previously developed RaftProt (http://lipid-raft-database.di.uq.edu.au/), a searchable database of mammalian lipid raft-associated proteins. Despite being a highly used resource, further developments in annotation and utilities were required. Here, we present RaftProt V2 (http://raftprot.org), an improved update of RaftProt. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have implemented a stringent annotation based on experimental evidence level to assist in identification of possible contaminant proteins. RaftProt V2 allows for simultaneous search of multiple proteins/experiments at the cell/tissue type and UniRef/Gene level, where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed to enable interactive data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function through integrative analysis of datasets collected from diverse tissue and conditions. Database URL: http://raftprot.org.

Risk factors for hardware removal following operative treatment of middle- and distal-third clavicular fractures.

BACKGROUND: The incidence of hardware removal (HWR) after operative fixation of clavicular fractures varies widely. Risk factors related to HWR remain incompletely understood. The aim of this study was to evaluate the incidence of and risk factors for HWR after plate fixation of middle- and distal-third clavicular fractures. We hypothesized that (1) the total HWR incidence would be <20%, (2) the HWR incidence of operatively treated distal- and middle-third clavicular fractures would not be statistically different, and (3) symptomatic implants would be the most common HWR indication. METHODS: We performed a multi-hospital retrospective study of skeletally mature patients who underwent plate fixation of middle- and distal-third clavicular fractures from November 2008 to November 2018. Data included patient demographic characteristics, mechanism of injury, operative records, hardware-related symptoms, subsequent HWR, and complications. RESULTS: A total of 103 patients (aged 16-75 years, 76.7% male patients) were included. Of the patients, 87 (84.5%) underwent plate fixation for midshaft clavicular fractures and 16 (15.5%) underwent plate fixation for distal-third clavicular fractures. HWR was performed in 13 patients (12.6%). A significantly higher percentage of HWR procedures were performed for distal clavicular fractures (50%) than for middle-third clavicular fractures (4.9%, P < .0001). An initial high-energy mechanism of injury was associated with HWR (P = .0025). The most common indication for HWR was symptomatic hardware (69.2%). The overall complication rate was 14.5%. CONCLUSION: The overall incidence of clavicular HWR was 12.6%. A distal fracture location was associated with a significantly higher incidence of HWR. An initial high-energy mechanism of injury was a significant risk factor for HWR. The primary indication for HWR was symptomatic hardware.

Variation in technique and postoperative management of the Latarjet procedure among orthopedic surgeons.

BACKGROUND: The Latarjet procedure has become a treatment of choice for glenohumeral instability in the setting of large glenoid osseous defects (>20%) and for prior failed soft tissue repairs. However, surgical techniques and postoperative rehabilitation protocols vary among expert shoulder surgeons. The purpose of this survey study was to characterize the variation in current practice patterns among fellowship-trained orthopedic shoulder surgeons and identify factors related to variation. METHODS: A 9-question survey was created (SurveyMonkey, San Mateo, CA, USA) and distributed to orthopedic surgeons who are active members of the American Shoulder and Elbow Surgeons or American Orthopaedic Society for Sports Medicine. The survey asked questions regarding surgeon experience with the Latarjet procedure, fellowship training, open vs. arthroscopic approach, method of coracoid-to-glenoid fixation, period of sling use postoperatively, and time before clearance to return to sport. Subgroup analysis was performed to determine whether further variation was evident between surgeons who completed sports medicine vs. shoulder and elbow fellowship training. RESULTS: In total, 242 surgeons completed the survey. Of these, 55% indicated performing a sports medicine fellowship and 39% indicated completing a shoulder and elbow fellowship. Among all surgeons, the classic open Latarjet procedure was the strongly preferred technique (79%), followed by the open congruent-arc (17%) and all-arthroscopic (3%) techniques. With respect to fixation, 98% used screw fixation and only 1% indicated cortical button use. With respect to the postoperative course, >85% of surgeons preferred immobilization for 3-6 weeks after the procedure and 42% of respondents stated they waited ≥6 months prior to clearing their patients to return to sport. Subgroup analysis revealed that surgeons who completed a shoulder and elbow fellowship performed the classic open technique 89% of the time compared with 63% of those who completed a sports medicine fellowship (P < .001). CONCLUSION: The results of our survey study indicate an overall strong preference for the open classic Latarjet technique as well as an overall strong preference for screw fixation of the coracoid graft to the glenoid among all surgeons. Shoulder and elbow fellowship-trained surgeons are significantly more likely to perform open surgery with a classic technique compared with sports medicine fellowship-trained surgeons. Furthermore, the significant variation in postoperative sling use and return to sport suggests that further research is needed to develop an evidence-based postoperative Latarjet rehabilitation protocol.

LFQ-Analyst: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant.

Relative label-free quantification (LFQ) of shotgun proteomics data using precursor (MS1) signal intensities is one of the most commonly used applications to comprehensively and globally quantify proteins across biological samples and conditions. Due to the popularity of this technique, several software packages, such as the popular software suite MaxQuant, have been developed to extract, analyze, and compare spectral features and to report quantitative information of peptides, proteins, and even post-translationally modified sites. However, there is still a lack of accessible tools for the interpretation and downstream statistical analysis of these complex data sets, in particular for researchers and biologists with no or only limited experience in proteomics, bioinformatics, and statistics. We have therefore created LFQ-Analyst, which is an easy-to-use, interactive web application developed to perform differential expression analysis with "one click" and to visualize label-free quantitative proteomic data sets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result graphics to facilitate statistical and exploratory analysis of label-free quantitative data sets. LFQ-Analyst, including an in-depth user manual, is freely available at https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst .

Surgical Management of Adult Acquired Buried Penis.

PURPOSE OF REVIEW: Adult acquired buried penis is a morbid condition characterized by complete entrapment of the phallus as a result of morbid obesity, post-surgical cicatrix formation, or primary genital lymphedema. Hygienic voiding is not possible and urinary dribbling is frequent with accompanying inflammation, skin breakdown, and infection from the chronic moisture. The end result is penile skin fibrosis resulting in permanent functional loss. Herein, we describe the etiology of adult acquired buried penis, advances in its surgical management, and quality of life outcomes with treatment. RECENT FINDINGS: Adult acquired buried penis is increasing in incidence as morbid obesity becomes more prevalent. Frequently comorbid conditions affect treatment including those affecting wound healing such a diabetes mellitus. Functional and cosmetic surgical outcomes are being published in greater volume in recent years leading to more refined treatment algorithms. Patient quality of life is greatly improved by definitive surgical management. Adult acquired buried penis is a morbid condition that is increasing in incidence as obesity becomes more commonplace. Surgical management often necessitates surgical lipectomy of the suprapubic fat pad, scrotoplasty, and penile split thickness skin graft. Substantial quality of life improvements have been consistently reported after surgical treatment.

RaftProt: mammalian lipid raft proteome database.

RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community.

Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

Online quantitative proteomics p-value calculator for permutation-based statistical testing of peptide ratios.

The utility of high-throughput quantitative proteomics to identify differentially abundant proteins en-masse relies on suitable and accessible statistical methodology, which remains mostly an unmet need. We present a free web-based tool, called Quantitative Proteomics p-value Calculator (QPPC), designed for accessibility and usability by proteomics scientists and biologists. Being an online tool, there is no requirement for software installation. Furthermore, QPPC accepts generic peptide ratio data generated by any mass spectrometer and database search engine. Importantly, QPPC utilizes the permutation test that we recently found to be superior to other methods for analysis of peptide ratios because it does not assume normal distributions.1 QPPC assists the user in selecting significantly altered proteins based on numerical fold change, or standard deviation from the mean or median, together with the permutation p-value. Output is in the form of comma separated values files, along with graphical visualization using volcano plots and histograms. We evaluate the optimal parameters for use of QPPC, including the permutation level and the effect of outlier and contaminant peptides on p-value variability. The optimal parameters defined are deployed as default for the web-tool at http://qppc.di.uq.edu.au/ .