bluuebunny/crossref_metadata_2025 huggingface dataset:
Toll-like receptor 3 upregulation by type I interferon in healthy and scleroderma dermal fibroblasts
Authors: Agarwal Sandeep K , Wu Minghua , Livingston Christopher K , Parks Donald H , Mayes Maureen D , Arnett Frank C , Tan Filemon K
Published: January 2011

Introduction

Increased levels of genes in the type I interferon (IFN) pathway have been observed in patients with systemic sclerosis (SSc), or scleroderma. How type I IFN regulates the dermal fibroblast and its participation in the development of dermal fibrosis is not known. We hypothesized that one mechanism by which type I IFN may contribute to dermal fibrosis is through upregulation of specific Toll-like receptors (TLRs) on dermal fibroblasts. Therefore, we investigated the regulation of TLR expression on dermal fibroblasts by IFN.

Methods

The expression of TLRs was assessed in cultured dermal fibroblasts from control and SSc patients stimulated with IFNα2. The ability of IFNα2 to regulate TLR-induced interleukin (IL)-6 and CC chemokine ligand 2 production was also assessed. Immunohistochemical analyses were performed to determine whether TLR3 was expressed in skin biopsies in the bleomycin-induced skin fibrosis model and in patients with SSc.

Results

IFNα2 increased TLR3 expression on human dermal fibroblasts, which resulted in enhanced TLR3-induced IL-6 production. SSc fibroblasts have an augmented TLR3 response to IFNα2 relative to control fibroblasts. Pretreatment of fibroblasts with transforming growth factor (TGF)-β increased TLR3 induction by IFNα2, but coincubation of TGF-β did not alter TLR3 induction by IFN. Furthermore, IFNα2 inhibits but does not completely block the induction of connective tissue growth factor and collagen expression by TGF-βin fibroblasts. TLR3 expression was observed in dermal fibroblasts and inflammatory cells from skin biopsies from patients with SSc as well as in the bleomycin-induced skin fibrosis model.

Conclusions

Type I IFNs can increase the inflammatory potential of dermal fibroblasts through the upregulation of TLR3.
A p53-independent role of Mdm2 in estrogen-mediated activation of breast cancer cell proliferation
Authors: Brekman Angelika , Singh Kathryn E , Polotskaia Alla , Kundu Nandini , Bargonetti Jill
Published: January 2011

Introduction

Estrogen receptor positive breast cancers often have high levels of Mdm2. We investigated if estrogen signaling in such breast cancers occurred through an Mdm2 mediated pathway with subsequent inactivation of p53.

Methods

We examined the effect of long-term 17β-estradiol (E2) treatment (five days) on the p53-Mdm2 pathway in estrogen receptor alpha (ERα) positive breast cancer cell lines that contain wild-type p53 (MCF-7 and ZR75-1). We assessed the influence of estrogen by examining cell proliferation changes, activation of transcription of p53 target genes, p53-chromatin interactions and cell cycle profile changes. To determine the effects of Mdm2 and p53 knockdown on the estrogen-mediated proliferation signals we generated MCF-7 cell lines with inducible shRNA for mdm2 or p53 and monitored their influence on estrogen-mediated outcomes. To further address the p53-independent effect of Mdm2 in ERα positive breast cancer we generated cell lines with inducible shRNA to mdm2 using the mutant p53 expressing cell line T-47D.

Results

Estrogen increased the Mdm2 protein level in MCF-7 cells without decreasing the p53 protein level. After estrogen treatment of MCF-7 cells, down-regulation of basal transcription of p53 target genes puma and p21 was observed. Estrogen treatment also down-regulated etoposide activated transcription of puma, but not p21. Mdm2 knockdown in MCF-7 cells increased p21 mRNA and protein, decreased cell growth in 3D matrigel and also decreased estrogen-induced cell proliferation in 2D culture. In contrast, knockdown of p53 had no effect on estrogen-induced cell proliferation. In T-47D cells with mutant p53, the knockdown of Mdm2 decreased estrogen-mediated cell proliferation but did not increase p21 protein.

Conclusions

Estrogen-induced breast cancer cell proliferation required a p53-independent role of Mdm2. The combined influence of genetic and environmental factors on the tumor promoting effects of estrogen implicated Mdm2 as a strong contributor to the bypass of cell cycle checkpoints. The novel finding that p53 was not the key target of Mdm2 in the estrogen activation of cell proliferation could have great benefit for future Mdm2-targeted breast cancer therapies.
Clinical accuracy of RIFLE and Acute Kidney Injury Network (AKIN) criteria for acute kidney injury in patients undergoing cardiac surgery
Authors: Englberger Lars , Suri Rakesh M , Li Zhuo , Casey Edward T , Daly Richard C , Dearani Joseph A , Schaff Hartzell V
Published: January 2011

Introduction

The RIFLE (risk, injury, failure, loss of kidney function, and end-stage renal failure) classification for acute kidney injury (AKI) was recently modified by the Acute Kidney Injury Network (AKIN). The two definition systems differ in several aspects, and it is not clearly determined which has the better clinical accuracy.

Methods

In a retrospective observational study we investigated 4,836 consecutive patients undergoing cardiac surgery with cardiopulmonary bypass from 2005 to 2007 at Mayo Clinic, Rochester, MN, USA. AKI was defined by RIFLE and AKIN criteria.

Results

Significantly more patients were diagnosed as AKI by AKIN (26.3%) than by RIFLE (18.9%) criteria (P < 0.0001). Both definitions showed excellent association to outcome variables with worse outcome by increased severity of AKI (P < 0.001, all variables). Mortality was increased with an odds ratio (OR) of 4.5 (95% CI 3.6 to 5.6) for one class increase by RIFLE and an OR of 5.3 (95% CI 4.3 to 6.6) for one stage increase by AKIN. The multivariate model showed lower predictive ability of RIFLE for mortality. Patients classified as AKI in one but not in the other definition set were predominantly staged in the lowest AKI severity class (9.6% of patients in AKIN stage 1, 2.3% of patients in RIFLE class R). Potential misclassification of AKI is higher in AKIN, which is related to moving the 48-hour diagnostic window applied in AKIN criteria only. The greatest disagreement between both definition sets could be detected in patients with initial postoperative decrease of serum creatinine.

Conclusions

Modification of RIFLE by staging of all patients with acute renal replacement therapy (RRT) in the failure class F may improve predictive value. AKIN applied in patients undergoing cardiac surgery without correction of serum creatinine for fluid balance may lead to over-diagnosis of AKI (poor positive predictive value). Balancing limitations of both definition sets of AKI, we suggest application of the RIFLE criteria in patients undergoing cardiac surgery.
Antibiotics or probiotics as preventive measures against ventilator-associated pneumonia: a literature review
Authors: Schultz Marcus J , Haas Lenneke E
Published: January 2011

Introduction

Mechanically ventilated critically ill patients frequently develop ventilator-associated pneumonia (VAP), a life-threatening complication. Proposed preventive measures against VAP include, but are not restricted to, selective decontamination of the digestive tract (SDD), selective oropharyngeal decontamination (SOD) and the use of probiotics. Probiotics are live bacteria that could have beneficial effects on the host by altering gastrointestinal flora. Similar to SDD and SOD, a prescription of probiotics aims at the prevention of secondary colonization of the upper and/or lower digestive tract.

Methods

We performed a literature review to describe the differences and similarities between SDD/SOD and probiotic preventive strategies, focusing on (a) efficacy, (b) risks, and (c) the routing of these strategies.

Results

Reductions in the incidence of VAP have been achieved with SDD and SOD. Two large randomized controlled trials even showed reduced mortality with these preventive strategies. Randomized controlled trials of probiotic strategies also showed a reduction of the incidence of VAP, but trials were too small to draw firm conclusions. Preventive strategies with antibiotics and probiotics may be limited due to the risk of emerging resistance to the locally applied antibiotics and the risk of probiotic-related infections, respectively. The majority of trials of SDD and SOD did not exhaustively address the issue of emerging resistance. Likewise, trials of probiotic strategies did not adequately address the risk of colonization with probiotics and probiotic-related infection. In studies of SDD and SOD the preventive strategy aimed at decontamination of the oral cavity, throat, stomach and intestines, and the oral cavity and throat, respectively. In the vast majority of studies of probiotic therapy the preventive strategy aimed at decontamination of the stomach and intestines.

Conclusions

Prophylactic use of antibiotics in critically ill patients is effective in reducing the incidence of VAP. Probiotic strategies deserve consideration in future well-powered trials. Future studies are needed to determine if preventive antibiotic and probiotic strategies are safe with regard to development of antibiotic resistance and probiotic infections. It should be determined whether the efficacy of probiotics improves when these agents are provided to the mouth and the intestines simultaneously.
Endogenous plasma activated protein C levels and the effect of enoxaparin and drotrecogin alfa (activated) on markers of coagulation activation and fibrinolysis in pulmonary embolism
Authors: Dempfle Carl-Erik H , Elmas Elif , Link Andreas , Suvajac Nenad , Liebe Volker , Janes Jonathan , Borggrefe Martin
Published: January 2011

Introduction

There are no published data on the status of endogenous activated protein C (APC) in pulmonary embolism (PE), and no data on the effect of drotrecogin alfa (activated) (DAA) given in addition to therapeutic dose enoxaparin.

Methods

In this double-blind clinical trial, 47 patients with computed tomography (CT)-confirmed acute submassive PE treated with 1 mg/kg body weight of enoxaparin twice daily were randomized to groups receiving a 12-hour intravenous infusion of 6, 12, 18, or 24 μg/kg/hour of DAA or a placebo. Blood samples were drawn before starting DAA infusion, after 4, 8 and 12 hours (at the end of the infusion period), and on treatment days 2, 3, 4, 5 and 6.

Results

Initial endogenous plasma activated protein C (APC) levels were 0.36 ± 0.48 ng/ml (<0.10 to 1.72 ng/ml) and remained in the same range in the placebo group. APC levels in patients treated with DAA were 13.67 ± 3.57 ng/ml, 32.71 ± 8.76 ng/ml, 36.13 ± 7.60 ng/ml, and 51.79 ± 15.84 ng/ml in patients treated with 6, 12, 18, and 24 μg/kg/hour DAA, respectively. In patients with a D-dimer level >4 mg/L indicating a high level of acute fibrin formation and dissolution, DAA infusion resulted in a more rapid drop in soluble fibrin, D-dimer, and fibrinogen/fibrin degradation products (FDP) levels, compared to enoxaparin alone. There was a parallel decline of soluble fibrin, D-dimer, FDP, and plasmin-plasmin inhibitor complex (PPIC) in response to treatment with enoxaparin ± DAA, with no evidence of a systemic profibrinolytic effect of the treatment.

Conclusions

In patients with acute submassive PE endogenous APC levels are low. DAA infusion enhances the inhibition of fibrin formation.

Trial registration

ClinicalTrials.gov: NCT00191724
Revisiting the value of pre-hospital tracheal intubation: an all time systematic literature review extracting the Utstein airway core variables
Authors: Lossius Hans Morten , Sollid Stephen JM , Rehn Marius , Lockey David J
Published: January 2011

Introduction

Although tracheal intubation (TI) in the pre-hospital setting is regularly carried out by emergency medical service (EMS) providers throughout the world, its value is widely debated. Heterogeneity in procedures, providers, patients, systems and stated outcomes, and inconsistency in data reporting make scientific reports difficult to interpret and compare, and the majority are of limited quality. To hunt down what is really known about the value of pre-hospital TI, we determined the rate of reported Utstein airway variables (28 core variables and 12 fixed-system variables) found in current scientific publications on pre-hospital TI.

Methods

We performed an all time systematic search according to the PRISMA guidelines of Medline and EMBASE to identify original research pertaining to pre-hospital TI in adult patients.

Results

From 1,076 identified records, 73 original papers were selected. Information was extracted according to an Utstein template for data reporting from in-the-field advanced airway management. Fifty-nine studies were from North American EMS systems. Of these, 46 (78%) described services in which non-physicians conducted TI. In 12 of the 13 non-North American EMS systems, physicians performed the pre-hospital TI. Overall, two were randomised controlled trials (RCTs), and 65 were observational studies. None of the studies presented the complete set of recommended Utstein airway variables. The median number of core variables reported was 10 (max 21, min 2, IQR 8-12), and the median number of fixed system variables was 5 (max 11, min 0, IQR 4-8). Among the most frequently reported variables were "patient category" and "service mission type", reported in 86% and 71% of the studies, respectively. Among the least-reported variables were "co-morbidity" and "type of available ventilator", both reported in 2% and 1% of the studies, respectively.

Conclusions

Core data required for proper interpretation of results were frequently not recorded and reported in studies investigating TI in adults. This makes it difficult to compare scientific reports, assess their validity, and extrapolate to other EMS systems. Pre-hospital TI is a complex intervention, and terminology and study design must be improved to substantiate future evidence based clinical practice.
Inhibition of caspase-1 activation in gram-negative sepsis and experimental endotoxemia
Authors: Giamarellos-Bourboulis Evangelos J , van de Veerdonk Frank L , Mouktaroudi Maria , Raftogiannis Maria , Antonopoulou Anastasia , Joosten Leo AB , Pickkers Peter , Savva Athina , Georgitsi Marianna , van der Meer Jos WM , Netea Mihai G
Published: January 2011

Introduction

Down-regulation of ex-vivo cytokine production is a specific feature in patients with sepsis. Cytokine downregulation was studied focusing on caspase-1 activation and conversion of pro-interleukin-1β into interleukin-1β (IL-1β).

Methods

Peripheral blood mononuclear cells were isolated from a) 92 patients with sepsis mainly of Gram-negative etiology; b) 34 healthy volunteers; and c) 5 healthy individuals enrolled in an experimental endotoxemia study. Cytokine stimulation was assessed in vitro after stimulation with a variety of microbial stimuli.

Results

Inhibition of IL-1β in sepsis was more profound than tumour necrosis factor (TNF). Down-regulation of IL-1β response could not be entirely explained by the moderate inhibition of transcription. We investigated inflammasome activation and found that in patients with sepsis, both pro-caspase-1 and activated caspase-1 were markedly decreased. Blocking caspase-1 inhibited the release of IL-1β in healthy volunteers, an effect that was lost in septic patients. Finally, urate crystals, which specifically induce the NLPR3 inflammasome activation, induced significant IL-1β production in healthy controls but not in patients with sepsis. These findings were complemented by inhibition of caspase-1 autocleavage as early as two hours after lipopolysaccharide exposure in volunteers.

Conclusions

These data demonstrate that the inhibition of caspase-1 and defective IL-1 β production is an important immunological feature in sepsis.
Impact of delayed admission to intensive care units on mortality of critically ill patients: a cohort study
Authors: Cardoso Lucienne TQ , Grion Cintia MC , Matsuo Tiemi , Anami Elza HT , Kauss Ivanil AM , Seko Ludmila , Bonametti Ana M
Published: January 2011

Introduction

When the number of patients who require intensive care is greater than the number of beds available, intensive care unit (ICU) entry flow is obstructed. This phenomenon has been associated with higher mortality rates in patients that are not admitted despite their need, and in patients that are admitted but are waiting for a bed. The purpose of this study is to evaluate if a delay in ICU admission affects mortality for critically ill patients.

Methods

A prospective cohort of adult patients admitted to the ICU of our institution between January and December 2005 were analyzed. Patients for whom a bed was available were immediately admitted; when no bed was available, patients waited for ICU admission. ICU admission was classified as either delayed or immediate. Confounding variables examined were: age, sex, originating hospital ward, ICU diagnosis, co-morbidity, Acute Physiology and Chronic Health Evaluation (APACHE) II score, therapeutic intervention, and Sequential Organ Failure Assessment (SOFA) score. All patients were followed until hospital discharge.

Results

A total of 401 patients were evaluated; 125 (31.2%) patients were immediately admitted and 276 (68.8%) patients had delayed admission. There was a significant increase in ICU mortality rates with a delay in ICU admission (P = 0.002). The fraction of mortality risk attributable to ICU delay was 30% (95% confidence interval (CI): 11.2% to 44.8%). Each hour of waiting was independently associated with a 1.5% increased risk of ICU death (hazard ratio (HR): 1.015; 95% CI 1.006 to 1.023; P = 0.001).

Conclusions

There is a significant association between time to admission and survival rates. Early admission to the ICU is more likely to produce positive outcomes.
Extracorporeal life support following out-of-hospital refractory cardiac arrest
Authors: Le Guen Morgan , Nicolas-Robin Armelle , Carreira Serge , Raux Mathieu , Leprince Pascal , Riou Bruno , Langeron Olivier
Published: January 2011

Introduction

Extracorporeal life support (ECLS) has recently shown encouraging results in the resuscitation of in-hospital (IH) refractory cardiac arrest. We assessed the use of ECLS following out-of-hospital (OH) refractory cardiac arrest.

Methods

We evaluated 51 consecutive patients who experienced witnessed OH refractory cardiac arrest and received automated chest compression and ECLS upon arrival in the hospital. Patients with preexisting severe hypothermia who experienced IH cardiac arrest were excluded. A femorofemoral ECLS was set up on admission to the hospital by a mobile cardiothoracic surgical team.

Results

Fifty-one patients were included (mean age, 42 ± 15 years). The median delays from cardiac arrest to cardiopulmonary resuscitation and ECLS were, respectively, 3 minutes (25th to 75th interquartile range, 1 to 7) and 120 minutes (25th to 75th interquartile range, 102-149). Initial rhythm was ventricular fibrillation in 32 patients (63%), asystole in 15 patients (29%) patients and pulseless rhythm in 4 patients (8%). ECLS failed in 9 patients (18%). Only two patients (4%) (95% confidence interval, 1% to 13%) were alive at day 28 with a favourable neurological outcome. There was a significant correlation (r = 0.36, P = 0.01) between blood lactate and delay between cardiac arrest and onset of ECLS, but not with arterial pH or blood potassium level. Deaths were the consequence of multiorgan failure (n = 43; 47%), brain death (n = 10; 20%) and refractory hemorrhagic shock (n = 7; 14%), and most patients (n = 46; 90%) died within 48 hours.

Conclusions

This poor outcome suggests that the use of ECLS should be more restricted following OH refractory cardiac arrest.
Red blood cell transfusion in patients with subarachnoid hemorrhage: a multidisciplinary North American survey
Authors: Kramer Andreas H , Diringer Michael N , Suarez Jose I , Naidech Andrew M , Macdonald Loch R , Le Roux Peter D
Published: January 2011

Introduction

Anemia is associated with poor outcomes in patients with aneurysmal subarachnoid hemorrhage (SAH). It remains unclear whether this association can be modified with more aggressive use of red blood cell (RBC) transfusions. The degree to which restrictive thresholds have been adopted in neurocritical care patients remains unknown.

Methods

We performed a survey of North American academic neurointensivists, vascular neurosurgeons and multidisciplinary intensivists who regularly care for patients with SAH to determine hemoglobin (Hb) concentrations which commonly trigger a decision to initiate transfusion. We also assessed minimum and maximum acceptable Hb goals in the context of a clinical trial and how decision-making is influenced by advanced neurological monitoring, clinician characteristics and patient-specific factors.

Results

The survey was sent to 531 clinicians, of whom 282 (53%) responded. In a hypothetical patient with high-grade SAH (WFNS 4), the mean Hb concentration at which clinicians administered RBCs was 8.19 g/dL (95% CI, 8.07 to 8.30 g/dL). Transfusion practices were comparatively more restrictive in patients with low-grade SAH (mean Hb 7.85 g/dL (95% CI, 7.73 to 7.97 g/dL)) (P < 0.0001) and more liberal in patients with delayed cerebral ischemia (DCI) (mean Hb 8.58 g/dL (95% CI, 8.45 to 8.72 g/dL)) (P < 0.0001). In each setting, there was a broad range of opinions. The majority of respondents expressed a willingness to study a restrictive threshold of ≤8 g/dL (92%) and a liberal goal of ≥10 g/dl (75%); in both cases, the preferred transfusion thresholds were significantly higher for patients with DCI (P < 0.0001). Neurosurgeons expressed higher minimum Hb goals than intensivists, especially for patients with high-grade SAH (β = 0.46, P = 0.003), and were more likely to administer two rather than one unit of RBCs (56% vs. 19%; P < 0.0001). Institutional use of transfusion protocols was associated with more restrictive practices. More senior clinicians preferred higher Hb goals in the context of a clinical trial. Respondents were more likely to transfuse patients with brain tissue oxygen tension values <15 mmHg and lactate-to-pyruvate ratios >40.

Conclusions

There is widespread variation in the use of RBC transfusions in SAH patients. Practices are heavily influenced by the specific dynamic clinical characteristics of patients and may be further modified by clinician specialty and seniority, the use of protocols and advanced neurological monitoring.
Application and comparison of scoring indices to predict outcomes in patients with healthcare-associated pneumonia
Authors: Fang Wen-Feng , Yang Kuang-Yao , Wu Chieh-Liang , Yu Chong-Jen , Chen Chang-Wen , Tu Chih-Yen , Lin Meng-Chih
Published: January 2011

Introduction

Healthcare-associated pneumonia (HCAP) is a relatively new category of pneumonia. It refers to infections that occur prior to hospital admission in patients with specific risk factors following contact or exposure to a healthcare environment. There is currently no scoring index to predict the outcomes of HCAP patients. We applied and compared different community acquired pneumonia (CAP) scoring indices to predict 30-day mortality and 3-day and 14-day intensive care unit (ICU) admission in patients with HCAP.

Methods

We conducted a retrospective cohort study based on an inpatient database from six medical centers, recruiting a total of 444 patients with HCAP between 1 January 2007 and 31 December 2007. Pneumonia severity scoring indices including PSI (pneumonia severity index), CURB 65 (confusion, urea, respiratory rate, blood pressure, age 65), IDSA/ATS (Infectious Diseases Society of America/American Thoracic Society), modified ATS rule, SCAP (severe community acquired pneumonia), SMART-COP (systolic blood pressure, multilobar involvement, albumin, respiratory rate, tachycardia, confusion, oxygenation, pH), SMRT-CO (systolic blood pressure, multilobar involvement, respiratory rate, tachycardia, confusion, oxygenation), and SOAR (systolic blood pressure, oxygenation, age, respiratory rate) were calculated for each patient. Patient characteristics, co-morbidities, pneumonia pathogen culture results, length of hospital stay (LOS), and length of ICU stay were also recorded.

Results

PSI (>90) has the highest sensitivity in predicting mortality, followed by CURB-65 (≥2) and SCAP (>9) (SCAP score (area under the curve (AUC): 0.71), PSI (AUC: 0.70) and CURB-65 (AUC: 0.66)). Compared to PSI, modified ATS, IDSA/ATS, SCAP, and SMART-COP were easy to calculate. For predicting ICU admission (Day 3 and Day 14), modified ATS (AUC: 0.84, 0.82), SMART-COP (AUC: 0.84, 0.82), SCAP (AUC: 0.82, 0.80) and IDSA/ATS (AUC: 0.80, 0.79) performed better (statistically significant difference) than PSI, CURB-65, SOAR and SMRT-CO.

Conclusions

The utility of the scoring indices for risk assessment in patients with healthcare-associated pneumonia shows that the scoring indices originally designed for CAP can be applied to HCAP.
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Authors: Mahony Shaun , Mazzoni Esteban O , McCuine Scott , Young Richard A , Wichterle Hynek , Gifford David K
Published: January 2011

Background

Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating retinoic acid receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the retinoid ligand. However, little is known about where RAR binds to the genome or how it selects target sites.

Results

We tested the constitutive RAR binding model using the retinoic acid-driven differentiation of mouse embryonic stem cells into differentiated motor neurons. We find that retinoic acid treatment results in widespread changes in RAR genomic binding, including novel binding to genes directly responsible for anterior-posterior specification, as well as the subsequent recruitment of the basal polymerase machinery. Finally, we discovered that the binding of transcription factors at the embryonic stem cell stage can accurately predict where in the genome RAR binds after initial differentiation.

Conclusions

We have characterized a ligand-dependent shift in RAR genomic occupancy at the initiation of neurogenesis. Our data also suggest that enhancers active in pluripotent embryonic stem cells may be preselecting regions that will be activated by RAR during neuronal differentiation.
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
Authors: Zmasek Christian M , Godzik Adam
Published: January 2011

Background

Genome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes.

Results

We reconstructed the domain repertoires of putative ancestral species at major divergence points, including the last eukaryotic common ancestor (LECA). We show that, surprisingly, during eukaryotic evolution domain losses in general outnumber domain gains. Only at the base of the animal and the vertebrate sub-trees do domain gains outnumber domain losses. The observed gain/loss balance has a distinct functional bias, most strikingly seen during animal evolution, where most of the gains represent domains involved in regulation and most of the losses represent domains with metabolic functions. This trend is so consistent that clustering of genomes according to their functional profiles results in an organization similar to the tree of life. Furthermore, our results indicate that metabolic functions lost during animal evolution are likely being replaced by the metabolic capabilities of symbiotic organisms such as gut microbes.

Conclusions

While protein domain gains and losses are common throughout eukaryote evolution, losses oftentimes outweigh gains and lead to significant differences in functional profiles. Results presented here provide additional arguments for a complex last eukaryotic common ancestor, but also show a general trend of losses in metabolic capabilities and gain in regulatory complexity during the rise of animals.
Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility
Authors: Quigley David A , To Minh D , Kim Il Jin , Lin Kevin K , Albertson Donna G , Sjolund Jonas , Pérez-Losada Jesús , Balmain Allan
Published: January 2011

Background

Germline polymorphisms can influence gene expression networks in normal mammalian tissues and can affect disease susceptibility. We and others have shown that analysis of this genetic architecture can identify single genes and whole pathways that influence complex traits, including inflammation and cancer susceptibility. Whether germline variants affect gene expression in tumors that have undergone somatic alterations, and the extent to which these variants influence tumor progression, is unknown.

Results

Using an integrated linkage and genomic analysis of a mouse model of skin cancer that produces both benign tumors and malignant carcinomas, we document major changes in germline control of gene expression during skin tumor development resulting from cell selection, somatic genetic events, and changes in the tumor microenvironment. The number of significant expression quantitative trait loci (eQTL) is progressively reduced in benign and malignant skin tumors when compared to normal skin. However, novel tumor-specific eQTL are detected for several genes associated with tumor susceptibility, including IL18 (Il18), Granzyme E (Gzme), Sprouty homolog 2 (Spry2), and Mitogen-activated protein kinase kinase 4 (Map2k4).

Conclusions

We conclude that the genetic architecture is substantially altered in tumors, and that eQTL analysis of tumors can identify host factors that influence the tumor microenvironment, mitogen-activated protein (MAP) kinase signaling, and cancer susceptibility.
Identification of fusion genes in breast cancer by paired-end RNA-sequencing
Authors: Edgren Henrik , Murumagi Astrid , Kangaspeska Sara , Nicorici Daniel , Hongisto Vesa , Kleivi Kristine , Rye Inga H , Nyberg Sandra , Wolf Maija , Borresen-Dale Anne-Lise , Kallioniemi Olli
Published: January 2011

Background

Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements.

Results

We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival.

Conclusions

In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.
A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language
Authors: Herzog Ronny , Schwudke Dominik , Schuhmann Kai , Sampaio Julio L , Bornstein Stefan R , Schroeder Michael , Shevchenko Andrej
Published: January 2011

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
Pralatrexate in Patients With Relapsed or Refractory Peripheral T-Cell Lymphoma: Results From the Pivotal PROPEL Study
Authors: O'Connor Owen A. , Pro Barbara , Pinter-Brown Lauren , Bartlett Nancy , Popplewell Leslie , Coiffier Bertrand , Jo Lechowicz Mary , Savage Kerry J. , Shustov Andrei R. , Gisselbrecht Christian , Jacobsen Eric , Zinzani Pier Luigi , Furman Richard , Goy Andre , Haioun Corinne , Crump Michael , Zain Jasmine M. , Hsi Eric , Boyd Adam , Horwitz Steven
Published: January 2011

Purpose

Peripheral T-cell lymphoma (PTCL) is a poor prognosis subtype of non-Hodgkin's lymphoma with no accepted standard of care. This study evaluated the efficacy and tolerability of pralatrexate, a novel antifolate with promising activity.

Patients and Methods

Patients with independently confirmed PTCL who progressed following ≥ 1 line of prior therapy received pralatrexate intravenously at 30 mg/m2/wk for 6 weeks in 7-week cycles. Primary assessment of response was made by independent central review using the International Workshop Criteria. The primary end point was overall response rate. Secondary end points included duration of response, progression-free survival (PFS), and overall survival (OS).

Results

Of 115 patients enrolled, 111 were treated with pralatrexate. The median number of prior systemic therapies was three (range, 1 to 12). The response rate in 109 evaluable patients was 29% (32 of 109), including 12 complete responses (11%) and 20 partial responses (18%), with a median DoR of 10.1 months. Median PFS and OS were 3.5 and 14.5 months, respectively. The most common grade 3/4 adverse events were thrombocytopenia (32%), mucositis (22%), neutropenia (22%), and anemia (18%).

Conclusion

To our knowledge, PROPEL (Pralatrexate in Patients with Relapsed or Refractory Peripheral T-Cell Lymphoma) is the largest prospective study conducted in patients with relapsed or refractory PTCL. Pralatrexate induced durable responses in relapsed or refractory PTCL irrespective of age, histologic subtypes, amount of prior therapy, prior methotrexate, and prior autologous stem-cell transplant. These data formed the basis for the US Food and Drug Administration approval of pralatrexate, the first drug approved for this disease.
Histopathologic-Based Prognostic Factors of Colorectal Cancers Are Associated With the State of the Local Immune Reaction
Authors: Mlecnik Bernhard , Tosolini Marie , Kirilovsky Amos , Berger Anne , Bindea Gabriela , Meatchi Tchao , Bruneval Patrick , Trajanoski Zlatko , Fridman Wolf-Herman , Pagès Franck , Galon Jérôme
Published: January 2011

Purpose

The prognosis of patients with colorectal cancer has sometimes proved uncertain; thus, the prognostic significance of immune criteria was compared with that of the tumor extension criteria using the American Joint Committee on Cancer/International Union Against Cancer–TNM (AJCC/UICC-TNM) staging system.

Patients and Methods

We studied the intratumoral immune infiltrates in the center of the tumor and in the invasive margin of 599 specimens of stage I to IV colorectal cancers from two independent cohorts. We analyzed these findings in relation to the degree of tumor extension and to the frequency of recurrence.

Results

Growth of the primary tumor and metastatic spread were associated with decreased intratumoral immune T-cell densities. Sixty percent of patients with high densities of CD8+cytotoxic T-lymphocyte infiltrate presented with stage Tis/T1 tumor, whereas no patients with low densities presented with such early-stage tumor. In patients who did not relapse, the density of CD8 infiltrates was inversely correlated with T stage. In contrast, in patients whose tumor recurred, the number of CD8 cells was low regardless of the T stage of the tumor. Univariate analysis showed that the immune score was significantly associated with differences in disease-free, disease-specific, and overall survival (hazard ratio [HR], 0.64, 0.60, and 0.70, respectively; P < .005). Time-dependent receiver operating characteristic curve analysis illustrated the predictive accuracy of the immune parameters (c-index = 65.3%, time-dependent c-index [Cτ] = 66.5%). A final stepwise model for Cox multivariate analysis supports the advantage of the immune score (HR, 0.64; P < .001; Cτ = 67.9%) compared with histopathologic features in predicting recurrence as well as survival.

Conclusion

Assessment of CD8+cytotoxic T lymphocytes in combined tumor regions provides an indicator of tumor recurrence beyond that predicted by AJCC/UICC-TNM staging.
Parent Reports of Quality of Life for Pediatric Patients With Cancer With No Realistic Chance of Cure
Authors: Tomlinson Deborah , Hinds Pamela S. , Bartels Ute , Hendershot Eleanor , Sung Lillian
Published: January 2011

Purpose

To compare quality of life of children with cancer with no reasonable chance of cure reported by parents 6 months or fewer versus more than 6 months before death.

Patients and Methods

This cross-sectional study included children between the ages of 2 and 18 years with cancer and no reasonable chance of cure at The Hospital for Sick Children, Toronto, Ontario, Canada. Parents reported quality of life on behalf of their children. Outcomes were the PedsQL 4.0 Generic Core Scales, Acute Cancer Module, and Multidimensional Fatigue Scale.

Results

Seventy-three parents of children participated. Compared with children who survived more than 6 months (n = 43), those who died at 6 months or fewer (n = 30) had significantly worse physical health (mean difference, 15.9; 95% CI, 1.8 to 30.0; P = .028), more pain and hurt (mean difference, 15.5; 95% CI, 0.9 to 30.0; P = .037), and worse general fatigue (mean difference, 15.8; 95% CI, 2.4 to 29.1; P = .021) and sleep/rest fatigue (mean difference, 16.0; 95% CI, 3.5 to 28.5; P = .013). Among the entire cohort, those with leukemia/lymphoma had worse physical and psychosocial quality of life compared with those with solid or brain tumors. Recent stem-cell transplantation was associated with worse psychosocial health.

Conclusion

Parents of children with cancer reported worse physical health, pain, and fatigue proximal to death. Those with leukemia/lymphoma were at higher risk for impaired quality of life. This knowledge can help in the design of targeted interventions to improve quality of life for children dying as a result of cancer.
Human cardiomyopathy mutations induce myocyte hyperplasia and activate hypertrophic pathways during cardiogenesis in zebrafish
Authors: Becker Jason R. , Deo Rahul C. , Werdich Andreas A. , Panàkovà Daniela , Coy Shannon , MacRae Calum A.
Published: January 2011

To assess the effects during cardiac development of mutations that cause human cardiomyopathy, we modeled a sarcomeric gene mutation in the embryonic zebrafish. We designed morpholino antisense oligonucleotides targeting the exon 13 splice donor site in the zebrafish cardiac troponin T (tnnt2) gene, in order to precisely recapitulate a human TNNT2 mutation that causes hypertrophic cardiomyopathy (HCM). HCM is a disease characterized by myocardial hypertrophy, myocyte and myofibrillar disarray, as well as an increased risk of sudden death. Similar to humans with HCM, the morphant zebrafish embryos displayed sarcomere disarray and there was a robust induction of myocardial hypertrophic pathways. Microarray analysis uncovered a number of shared transcriptional responses between this zebrafish model and a well-characterized mouse model of HCM. However, in contrast to adult hearts, these embryonic hearts developed cardiomyocyte hyperplasia in response to this genetic perturbation. The re-creation of a human disease-causing TNNT2 splice variant demonstrates that sarcomeric mutations can alter cardiomyocyte biology at the earliest stages of heart development with distinct effects from those observed in adult hearts despite shared transcriptional responses.
LSR defines cell corners for tricellular tight junction formation in epithelial cells
Authors: Masuda Sayuri , Oda Yukako , Sasaki Hiroyuki , Ikenouchi Junichi , Higashi Tomohito , Akashi Masaya , Nishi Eiichiro , Furuse Mikio
Published: January 2011

Epithelial cell contacts consist of not only bicellular contacts but also tricellular contacts, where the corners of three cells meet. At tricellular contacts, tight junctions (TJs) generate specialized structures termed tricellular TJs (tTJs) to seal the intercellular space. Tricellulin is the only known molecular component of tTJs and is involved in the formation of tTJs, as well as in the normal epithelial barrier function. However, the detailed molecular mechanism of how tTJs are formed and maintained remains elusive. Using a localization-based expression cloning method, we identified a novel tTJ-associated protein known as lipolysis-stimulated lipoprotein receptor (LSR). Upon LSR knockdown in epithelial cells, tTJ formation was affected and the epithelial barrier function was diminished. Tricellulin accumulation at the tricellular contacts was also diminished in these cells. By contrast, LSR still accumulated at the tricellular contacts upon tricellulin knockdown. Analyses of deletion mutants revealed that the cytoplasmic domain of LSR was responsible for the recruitment of tricellulin. On the basis of these observations, we propose that LSR defines tricellular contacts in epithelial cellular sheets by acting as a landmark to recruit tricellulin for tTJ formation.
Wnt signaling in estrogen-induced lactotroph proliferation
Authors: Giles Adam , Madec Frederic , Friedrichsen Sönke , Featherstone Karen , Chambers Tom , Harper Claire V. , Resch Julia , Brabant Georg , Davis Julian R. E.
Published: January 2011

Prolactinomas are the most common type of functioning pituitary adenoma in humans, but the control of lactotroph proliferation remains unclear. Here, using microarray analysis, we show that estrogen treatment increased expression of Wnt4 mRNA in adult Fischer rat pituitary tissue. Dual immunofluorescence analysis revealed that Wnt4 expression was not confined to lactotrophs, but that it was expressed in all anterior pituitary cell types. Estradiol induced proliferation in the somatolactotroph GH3 cell line, in parallel with Wnt4 mRNA and protein induction. A reporter gene assay for TCF- and LEF-dependent transcription revealed that there was no activation of the canonical Wnt pathway in GH3 cells upon stimulation with Wnt-conditioned culture medium or coexpression of constitutively active mutant β-catenin. Expression of β-catenin in both GH3 cells and normal rat anterior pituitary cells was restricted to the cell membrane and was unaltered by treatment with estradiol, with no nuclear β-catenin being detected under any of the conditions tested. We show for the first time that Wnt4 affects non-canonical signaling in the pituitary by inhibiting Ca2+ oscillations in GH3 cells, although the downstream effects are as yet unknown. In summary, Wnt4 is expressed in the adult pituitary gland, and its expression is increased by estrogen exposure, suggesting that its involvement in adult tissue plasticity is likely to involve β-catenin-independent signaling pathways.
Information Goods vs. Industrial Goods: Cost Structure and Competition
Authors: Jones Roy , Mendelson Haim
Published: January 2011

We study markets for information goods and find that they differ significantly from markets for traditional industrial goods. Markets for information goods in which products are vertically differentiated lack the segmentation inherent in markets for industrial goods. As a result, a monopoly will offer only a single product. Competition leads to highly concentrated information-good markets, with the leading firm behaving almost like a monopoly even with free entry and without network effects. We study how the structure of the firms' cost functions drives our results.

This paper was accepted by Barrie R. Nault, information systems.
Hearing While Blinking: Multisensory Attentional Blink Revisited
Authors: Haroush Keren , Deouell Leon Y. , Hochstein Shaul
Published: January 2011

It is well established that cognitive system overload is reflected in the attentional blink (AB), the failure to report a second target when it closely follows detection of a first target within a rapid series of stimuli. However, there is intense controversy concerning the effect of first-target detection in one modality on subsequent dynamics of attentional resources in other modalities. Mixed results were found using an audiovisual AB paradigm: depletion of resources in one modality either impaired performance in the other modality or had no effect. Here, we circumvent the need for task switching by measuring an event-related potential, the mismatch negativity, which reflects implicit auditory change detection without requiring task engagement and is present even for background sounds that participants ignore. Surprisingly, we find that during the visual AB, auditory processing is enhanced rather than inhibited, as would be expected by system overload. We suggest that multimodal attentional resources may be freed rather than engaged during the visual AB. Suppression of irrelevant input may require active control by a central executive, which is preoccupied during the visual AB, and/or there may be no reason to suppress other-modal input since the visual system will miss its second target anyway.
PSD-95 Alters Microtubule Dynamics via an Association With EB3
Authors: Sweet Eric S. , Previtera Michelle L. , Fernández Jose R. , Charych Erik I. , Tseng Chia-Yi , Kwon Munjin , Starovoytov Valentin , Zheng James Q. , Firestein Bonnie L.
Published: January 2011

Little is known about how the neuronal cytoskeleton is regulated when a dendrite decides whether to branch or not. Previously, we reported that postsynaptic density protein 95 (PSD-95) acts as a stop signal for dendrite branching. It is yet to be elucidated how PSD-95 affects the cytoskeleton and how this regulation relates to the dendritic arbor. Here, we show that the SH3 (src homology 3) domain of PSD-95 interacts with a proline-rich region within the microtubule end-binding protein EB3. Overexpression of PSD-95 or mutant EB3 results in a decreased lifetime of EB3 comets in dendrites. In line with these data, transfected rat neurons show that overexpression of PSD-95 results in less organized microtubules at dendritic branch points and decreased dendritogensis. The interaction between PSD-95 and EB3 elucidates a function for a novel region of EB3 and provides a new and important mechanism for the regulation of microtubules in determining dendritic morphology.