Ticagrelor was associated with lower fracture risk than clopidogrel in the dual anti-platelet regimen among patients with acute coronary syndrome treated with percutaneous coronary intervention

PURPOSE

Patients with coronary artery disease have increased fracture risks. P2Y12 inhibitors may impact fracture risks. We compared the fracture risks associated with ticagrelor and clopidogrel in dual anti-platelet therapy (DAPT).

METHODS

We identified all adults who underwent first-ever percutaneous coronary intervention (PCI) for acute coronary syndrome (ACS) between 2010 and 2017 from a territory-wide PCI registry in Hong Kong. Following 1:1 propensity-score matching for baseline characteristics, patients were followed up till event occurrence, death, or 30 June 2022. Outcomes of interest were major osteoporotic fractures (MOF) identified by validated ICD-9-CM codes. Cox proportional hazards regression was used to compute the hazard ratio (HR) for MOF associated with ticagrelor versus clopidogrel use.

RESULTS

3018 ticagrelor users and 3018 clopidogrel users were identified after propensity-score matching (mean age: 61.4 years; 84.1% men). Upon median follow-up of 6.5 years, 59 ticagrelor users and 119 clopidogrel users sustained MOF (annualized fracture risks: 0.34% and 0.56%, respectively). Ticagrelor use was associated with lower risks of MOF (HR 0.60, 95%CI 0.44-0.83; p = 0.002). Consistent HRs were observed for fractures over vertebrae, hip and upper limbs. Subgroup analyses showed no interaction according to age, sex, presence of diabetes, presence of chronic kidney disease and prior fracture history.

CONCLUSION

Among adults who underwent first-ever PCI for ACS, ticagrelor use in the DAPT was associated with a lower risk of MOF compared with clopidogrel. Our results support the use of ticagrelor in the DAPT from the perspective of bone health.

Preclinical evaluation of the VEGF/Ang2 bispecific nanobody BI 836880 in nasopharyngeal carcinoma models

Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) is endemic to parts of Asia and overexpression of vascular endothelial growth factor (VEGF) and hypoxia-inducible factor-1α are common in NPC. Anti-vascular agents have known clinical activity in patients with recurrent/ metastatic NPC and in this study, we investigated the anti-tumor effect of BI 836880, a humanized bispecific nanobody against VEGF and angiopoietin-2 (Ang2), in preclinical models of EBV-positive and EBV-negative NPC. The efficacy of BI 836880 was also compared with bevacizumab, a recombinant humanized monoclonal antibody against VEGF. We found that BI 836880 could exert growth-inhibitory effect on endothelial cells (HUVEC-C) and the EBV-negative NPC cell line (HK1), but to a lesser extent in the EBV-positive NPC cell lines, C17C and C666-1. In patients-derived xenograft (PDX) models of NPC - Xeno-2117 and Xeno-666, BI 836880 could suppress tumor growth and Ki67, as well as induce tumor necrosis and reduce microvessel density. Moreover, treatment with BI 836880 increased the level of macrophage infiltration in both PDX tumor models of NPC, suggesting that BI 836880 may exert immunomodulatory effect on the NPC immune microenvironment. When compared with bevacizumab, BI 836880 appeared to show at least comparable activity as bevacizumab in terms of its anti-proliferative and anti-angiogenic effects. This study showed that BI 836880 has anti-proliferative, anti-angiogenic and possibly immunomodulatory effect in clinical models of NPC, therefore the dual targeting of VEGF and Ang2 signaling in NPC should be further investigated.

Thermal Disorder in Finite-Length Carbon Nanowire

Enhancement in chemisorption is one of the active research areas in carbon materials. To remedy the thermally degraded chemisorption occurring at high temperatures, we report a comprehensive study of kink structures in free-standing monoatomic carbon nanowires upon heating. Our Monte Carlo simulation considers multi-monoatomic carbon chains laterally interacting by van der Waals forces. Our study reveals that carbon nanowires maintain their linearity regardless of chain length at low temperatures, but this is not the case at high temperatures. Disordered kink structure is observed in short carbon chains, especially above the Peierls transition temperature. A severe kink structure may increase the possibility of attaching negatively charged atoms, thereby contributing to the development of next-generation materials for chemisorption at high temperatures. We have also provided an important indication that any physical property of the finite-length carbon chain predicted by ab initio calculation should reconsider the atomic rearrangement due to thermal instability at high temperatures.

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.

Creation of Si quantum dots in a silica matrix due to conversion of radiation defects under pulsed ion-beam exposure

In this work we present an innovative method of creating Si quantum dots under pulsed ion-beam exposure. The evolution of defect structure ODC(II) → E'→ ODC(I) → Si QDs in glassy SiO₂ under ion-beam implantation was established by optical absorption and photoluminescence spectroscopies. Depending on the mode of ion exposure, it is possible to easily control the type and concentration of defects in the host and modify its optical properties for novel applications. Ab initio calculations confirm that bond softening in SiO₂ is attainable via the use of Gd ion implantation. According to our experimental and theoretical results, the three-stage interaction of primary oxygen-deficient centers leads to the formation of stable silicon quantum dots with a size of 3.6 nm and luminescence at 1.8 eV excited by incoherent light.

Impact of whole egg intake on blood pressure, lipids and lipoproteins in middle-aged and older population: A systematic review and meta-analysis of randomized controlled trials

BACKGROUND AND AIM

Effects of whole egg consumption on cardiovascular diseases (CVD) risk in the middle-aged and older population remain unclear due to inconsistent findings from observational and randomized controlled trials (RCTs). This meta-analysis aimed to assess the impacts of whole egg and egg category (whole eggs versus egg substitutes) intake quantity on CVD risk factors from systematically searched RCTs. Egg substitutes were hypothesized to have minimal effects of the blood lipid and lipoprotein profile as they are void of dietary cholesterol.

METHODS AND RESULTS

As many as 434 studies identified from PubMed, Cochrane Library, CINAHL and Medline (Ovid) databases were screened and data were extracted from 8 selected RCTs. Quality of the selected studies were assessed and the overall effect sizes of weighted mean differences (WMD) were calculated using a random effects model. Non-differential effects in blood pressures, lipids and lipoproteins were observed when >4 whole eggs/week compared to ≤4 whole eggs/week were consumed. Intake of >4 whole eggs/week compared to equivalent amounts of egg substitutes caused greater elevations in blood total cholesterol (WMD: 0.198 mmol/L; 95% CIs: 0.056, 0.339), HDL cholesterol (WMD: 0.068 mmol/L; 95% CIs: 0.006, 0.130) and LDL cholesterol (WMD: 0.171 mmol/L; 95% CIs: 0.028, 0.315) but did not differentially affect triglycerides concentration.

CONCLUSION

Overall, the results support the notion that quantity of whole egg intake does not affect CVD risk factors and consuming egg substitutes may also be beneficial compared to whole eggs on lowering CVD risk in the middle-aged and older population.

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Third generation single-molecule DNA sequencing technologies offer significantly longer read length that can facilitate the assembly of complex genomes and analysis of complex structural variants. Nanopore platforms perform single-molecule sequencing by directly measuring the current changes mediated by DNA passage through the pores and can generate hundreds of kilobase (kb) reads with minimal capital cost. This platform has been adopted by many researchers for a variety of applications. Achieving longer sequencing read lengths is the most critical factor to leverage the value of nanopore sequencing platforms. To generate ultra-long reads, special consideration is required to avoid DNA breakages and gain efficiency to generate productive sequencing templates. Here, we provide the detailed protocol of ultra-long DNA sequencing including high molecular weight (HMW) DNA extraction from fresh or frozen cells, library construction by mechanical shearing or transposase fragmentation, and sequencing on a nanopore device. From 20-25 µg of HMW DNA, the method can achieve N50 read length of 50-70 kb with mechanical shearing and N50 of 90-100 kb read length with transposase mediated fragmentation. The protocol can be applied to DNA extracted from mammalian cells to perform whole genome sequencing for the detection of structural variants and genome assembly. Additional improvements on the DNA extraction and enzymatic reactions will further increase the read length and expand its utility.

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing

Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.

Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions

Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d^-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d^-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.

Room temperature p-orbital magnetism in carbon chains and the role of group IV, V, VI, and VII dopants

The study of magnetism without the involvement of transition metals or rare earth ions is considered the key to the fabrication of next generation spintronic devices. Several recent reports claim that optimizing the occupation number of the mixed p-orbitals is the correct way to reinforce p-orbital magnetism in bulk crystals. We provide experimental evidence that the kinked monoatomic carbon chains, the so-called linear-chained carbon, generate intrinsic ferromagnetism even above room temperature. According to our ab initio calculations, unconventional magnetism has its origin in the p-shells. In contrast, the linear monoatomic carbon chains are non-magnetic. Although the optimized differential spin density of states at the Fermi level (SDOS) of the kinked carbon chains is higher than that of bulk Fe, the magnetic moment is as low as 0.3μB. In order to enhance the magnetic response, we decided to tune the p-orbital magnetism by adding dopants from groups IV to VII of the periodic table. We observed that the strength of the p-orbital magnetism and the sign of the exchange interaction depend not only on the kink angle, but also on the concentration of lone pair electrons, free radical electrons, lateral chain spacing, internal electric dipole, dative covalent bonds and the Bohr radius of the dopants. Surprisingly, the V and VII-doped carbon chains show a strong non-zero SDOS, which has its origin in the p-shells. The VII-doped carbon chains give the SDOS of the opposite sign. Our best system, the arsenic-doped carbon chain, exhibits a strong local magnetic moment of 1.5μB, which is comparable to that of the bulk Fe of 2.2μB, with the mean exchange-correlation energy reaching a 63% ratio relative to that of the bulk Fe.

Picky comprehensively detects high-resolution structural variants in nanopore long reads

Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.

A theoretical quest for high temperature superconductivity on the example of low-dimensional carbon structures

High temperature superconductivity does not necessarily require correlated electron systems with complex competing or coexisting orders. Instead, it may be achieved in a phonon-mediated classical superconductor having a high Debye temperature and large electronic density of states at the Fermi level in a material with light atoms and strong covalent bonds. Quasi-1D conductors seem promising due to the Van Hove singularities in their electronic density of states. In this sense, quasi-1D carbon structures are good candidates. In thin carbon nanotubes, superconductivity at ~15 K has been reported, and it is likely the strong curvature of the graphene sheet which enhances the electron-phonon coupling. We use an ab-initio approach to optimize superconducting quasi-1D carbon structures. We start by calculating a T_c of 13.9 K for (4.2) carbon nanotubes (CNT) that agrees well with experiments. Then we reduce the CNT to a ring, open the ring to form chains, optimize bond length and kink structure, and finally form a new type of carbon ring that reaches a T_c value of 115 K.

Views of faculty members in a medical school with regards to error disclosure and reporting to parents and/or higher authorities

BACKGROUND

Little is known about the views of faculty members who train medical students concerning open disclosure.

OBJECTIVES

The objectives of this study were to determine the views of faculty in a medical school on: 1 what constitutes a medical error and the severity of such an error in relation to medication use or diagnosis; 2 information giving following such an adverse event, based on severity; and 3 acknowledgement of responsibility, remedial action, compensation, disciplinary action, legal action, and reporting to a higher body in relation to such adverse event.

METHODS

We adapted and contextualized a questionnaire developed from a previous study. The questionnaire had 4 case vignettes that described 1 clear medication error with lifelong disability; 2 possible diagnostic error with lifelong disability; 3 possible diagnostic error without harm; and 4 clear medication error without harm. We invited all faculty members attached to the medical school at the International Medical University to participate in the study.

RESULTS

Seventy faculty members took part. Faculty members viewed a medical error as having taken place depending on how clearly an error had occurred (94% and 73% versus 53% and 27%). They viewed cases as more severe based on the severity of complications (85% and 46% versus 5% and 10%). With increasing severity, they tended to attribute responsibility for the event and the duty to disclose towards more senior clinicians. They were also more agreeable with remedial action, compensation, disciplinary action, and reporting to a higher agency. There was no strong evidence of association between these areas and the demographics of faculty members.

CONCLUSIONS

Faculty members are more likely to perceive an error had occurred depending on the clarity of the circumstances. They viewed severity based on the presence of complications. Severity determined how they attributed responsibility, duty to disclose, and other areas related to open disclosure.

Parental preferences with regards to disclosure following adverse events occurring in relation to medication use or diagnosis in the care of their children - perspectives from Malaysia

INTRODUCTION

Open disclosure is poorly understood in Malaysia but is an ethical and professional responsibility. The objectives of this study were to determine: (1) the perception of parents regarding the severity of medical error in relation to medication use or diagnosis; (2) the preference of parents for information following the medical error and its relation to severity; and (3) the preference of parents with regards to disciplinary action, reporting, and legal action.

METHODS

We translated and contextualised a questionnaire developed from a previous study. The questionnaire consisted of four case vignettes that described the following: medication error with a lifelong complication; diagnostic error with a lifelong complication; diagnostic error without lifelong effect; and medication error without lifelong effect. Each case vignette was followed by a series of questions examining the subject's perception on the above areas. We also determined the content validity of the questionnaire. We invited parents of Malaysian children admitted to the paediatric wards of Tuanku Jaafar Hospital to participate in the study.

RESULTS

One hundred and twenty-three parents participated in the study. The majority of parents wanted to be told regarding the event. As the severity of the case vignettes increased, the desire for information, remedial action, acknowledgement of responsibility, compensation, punishment, legal action, and reporting to a higher agency also increased. The findings did not have strong evidence of a relationship with subject's demographics.

CONCLUSION

This study gives insights into previously unexplored perspectives and preferences of parents in Malaysia regarding open disclosure. It also highlights the opportunity for more research in this area with potentially broad applications.

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells

Background

Germline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female germline stem cells remain poorly understood.

Results

We generate genome-wide profiles of the histone modifications H3K4me1, H3K27ac, H3K4me3, and H3K27me3, DNA methylation, and RNA polymerase II occupancy and perform transcriptome analysis in mouse female germline stem cells. Comparison of enhancer regions between embryonic stem cells and female germline stem cells identifies the lineage-specific enhancers involved in germline stem cell features. Additionally, our results indicate that DNA methylation primarily contributes to female germline stem cell unipotency by suppressing the somatic program and is potentially involved in maintenance of sexual identity when compared with male germline stem cells. Moreover, we demonstrate down-regulation of Prmt5 triggers differentiation and thus uncover a role for Prmt5 in maintaining the undifferentiated status of female germline stem cells.

Conclusions

The genome-wide epigenetic signatures and the transcription regulators identified here provide an invaluable resource for understanding the fundamental features of mouse female germline stem cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1023-z) contains supplementary material, which is available to authorized users.

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla

Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3’ UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.

A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data

In this article, we propose a new statistical method-MutRSeq-for detecting differentially expressed single nucleotide variants (SNVs) based on RNA-seq data. Specifically, we focus on nonsynonymous mutations and employ a hierarchical likelihood approach to jointly model observed mutation events as well as read count measurements from RNA-seq experiments. We then introduce a likelihood ratio-based test statistic, which detects changes not only in overall expression levels, but also in allele-specific expression patterns. In addition, this method can jointly test multiple mutations in one gene/pathway. The simulation studies suggest that the proposed method achieves better power than a few competitors under a range of different settings. In the end, we apply this method to a breast cancer data set and identify genes with nonsynonymous mutations differentially expressed between the triple negative breast cancer tumors and other subtypes of breast cancer tumors.

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Background

Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification.

Results

We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages.

Conclusions

Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2585-6) contains supplementary material, which is available to authorized users.

Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify transcriptional regulators of lipid accumulation, we performed an integrative chromatin signature and transcriptomic analysis to decipher the regulation of lipid biosynthesis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between the algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor, PSR1, as a pivotal switch that triggers cytosolic lipid accumulation. Dissection of the PSR1-induced lipid profiles corroborates its role in coordinating multiple lipid-inducing stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a transcriptional regulator of algal lipid metabolism will facilitate targeted engineering strategies to mediate high lipid production in microalgae.

Epilepsy in patients with primary brain tumors: The impact on mood, cognition, and HRQOL

BACKGROUND

A primary brain tumor (PBT) is often a fatal disease of the nervous system and has a serious impact on health-related quality of life (HRQOL). Presence of epilepsy and adverse reactions from tumor and epilepsy treatments may cause additional decline in HRQOL.

OBJECTIVES

We aimed to study the impact of epileptic seizures on cognition, mood, and HRQOL in patients with brain tumor-related epilepsy.

MATERIALS AND METHOD

Patients were grouped on an ordinal scale according to epilepsy burden from none to severe based on the presence of epileptic seizures and seizure frequency: L1, no epilepsy; L2, with epilepsy, seizure-free in the last 6 months with antiepileptic drugs; and L3, with epilepsy, at least one seizure in the last 6 months with AEDs. Health-related quality of life was measured by Functional Assessment of Cancer Therapy-Brain (FACT-Br) and Quality of Life in Epilepsy-31 (QOLIE-31) tools, cognition by the Montreal Cognitive Assessment (MoCA) tool and Frontal Assessment Battery (FAB), mood by the Hospital Anxiety and Depression Scale (HADS), activities of daily living (ADLs) by the Barthel Index (BI), and performance status by the Karnofsky Performance Status (KPS) scale in patients with primary brain tumors at least one month following neurosurgery with or without radiotherapy and chemotherapy.

RESULTS

Eighty-one patients with a diagnosis of primary brain tumors were recruited. Sixty-eight percent of patients were diagnosed with primary brain tumor-related epilepsy, 50.61% patients had cognitive impairment, 33% had abnormal scores in the anxiety scale, and 34% had abnormal scores in the depression scale. There were no statistically significant differences in these scores among L1, L2, and L3 groups. There were statistically significant differences in duration of disease and KPS and BI scores between L1 and L3 groups. The L3 group has significantly longer duration of disease and scored low in both the BI and KPS scale when compared to the L1 group. All patients with primary brain tumors scored significantly low in FACT-Br 'physical well-being' (PWB) and 'emotional well-being' (EWB) and high in 'social well-being' (SWB) when compared to healthy controls. When scores of each group were individually compared to healthy controls, the L3 group showed the lowest scores in PWB, EWB, and 'functional well-being'. In SWB, L1 and L2 groups showed statistically significantly high scores when compared to normative data. The QOLIE-31 applied to groups with epilepsy showed statistically significantly lower scores in the L3 group when compared to the L2 group in 'cognitive' and 'social functioning' domains. On multivariate analysis, both poor performance status and frequency of seizures were found to be independent risk factors for poor HRQOL when FACT-Br mean scores were compared. Level of seizures was found to be an independent risk factor for poor HRQOL when QOLIE-31 scores were compared between L2 and L3 groups.

DISCUSSION

Presence of brain tumors could be attributed to cognitive impairment irrespective of the presence of epilepsy in our cohort. High seizure burden is an independent risk factor for poor HRQOL in patients with primary brain tumors. The QOLIE-31 is a more sensitive tool than the FACT-Br because of the presence of a seizure-related questionnaire.

Molecular portraits of epithelial, mesenchymal, and hybrid States in lung adenocarcinoma and their relevance to survival

Epithelial-to-mesenchymal transition (EMT) is a key process associated with tumor progression and metastasis. To define molecular features associated with EMT states, we undertook an integrative approach combining mRNA, miRNA, DNA methylation, and proteomic profiles of 38 cell populations representative of the genomic heterogeneity in lung adenocarcinoma. The resulting data were integrated with functional profiles consisting of cell invasiveness, adhesion, and motility. A subset of cell lines that were readily defined as epithelial or mesenchymal based on their morphology and E-cadherin and vimentin expression elicited distinctive molecular signatures. Other cell populations displayed intermediate/hybrid states of EMT, with mixed epithelial and mesenchymal characteristics. A dominant proteomic feature of aggressive hybrid cell lines was upregulation of cytoskeletal and actin-binding proteins, a signature shared with mesenchymal cell lines. Cytoskeletal reorganization preceded loss of E-cadherin in epithelial cells in which EMT was induced by TGFβ. A set of transcripts corresponding to the mesenchymal protein signature enriched in cytoskeletal proteins was found to be predictive of survival in independent datasets of lung adenocarcinomas. Our findings point to an association between cytoskeletal and actin-binding proteins, a mesenchymal or hybrid EMT phenotype and invasive properties of lung adenocarcinomas.

Abstract 2485: Secretome signature associated with TITF1/NKX2-1-negative non-small cell lung cancer

Background: TITF1/NKX2-1 is a master transcription factor of peripheral airway cells and a known lineage-specific oncogene in lung cancer cells, whereas it also suppresses tumor progression and is associated with favorable prognosis of lung adenocarcinoma. In our previous study, a protein signature for TITF1 was found in plasmas of mouse models of lung adenocarcinoma, leading to the identification of concordant circulating protein signatures in human non-small cell lung cancer (NSCLC). Following study demonstrated one of TITF1 signature proteins, pro-SFTPB, as a predictive biomarker for NSCLC. To identify additional biomarkers which would complement the performance of pro-SFTPB, we studied secretome from forty NSCLC cell lines in terms of TITF1 expression.

Materials and Methods: Forty NSCLC cell lines were cultured according to the standard SILAC protocol. The same batch of cells was used for analysis of whole cell extract and conditioned media. Samples were fractionated and subjected to mass spectrometric analysis. Gene expression data for the same set of NSCLC cell lines were obtained using the Illumina Human WG-6 v3.0 Expression BeadChips.

Results: NSCLC cell lines were divided into two groups by median of TITF1 gene expression (TITF1-positive and negative). In secretome analysis, overall 10,399 proteins were identified and semi-quantified with using total number of spectral counts. Interestingly, top abundant secretome proteins in TITF1-negative NSCLC cell lines contain many cytokine/chemokines (IL6, CXCL1, CXCL2 and CXCL5) and growth factors (CTGF, PDGFA, PDGFC, and VEGFC). Among top abundant secretome proteins, gene expression of SRGN was most significantly and inversely correlated with TITF1 gene expression. SRGN is a proteoglycan and physiologically associated with some proteases and cytokine secretion in hematopoietic cells. In addition recent studies have indicated that SRGN is also associated with aggressive phenotype in some cancers, thus considered as a promising biomarker candidate for TITF1-negative NSCLC. Then we determined whether SRGN would be directly regulated by TITF1. Suppression of TITF1 by siRNA or TNF alpha treatment increased SRGN expression, suggesting potential transcriptional regulation of SRGN by TITF1. Finally we studied functional roles of SRGN in TITF1-negative cell lines. Knockdown of SRGN by siRNA did not affect cell proliferation. However two chemokines, CXCL1 and CXCL5, which are abundant in secretome of TITF1-negative cell lines, were decreased by SRGN knockdown. In addition, macrophage migration was also decreased in the conditioned media of SRGN knockdown cells compared with control cells.

Conclusion: Our findings suggest functional relevance of SRGN in tumor microenvironment and tumor aggressiveness in TITF1/NKX2-1-negative NSCLC. Validation study for plasma levels of CXCL1 and CXCL5 in NSCLC subjects is now on-going.

Citation Format: Ayumu Taguchi, Muge Celiktas, Dhillon Dilsher, Qing Zhang, Chee-Hong Wong, Alice Chin, Adi Gazdar, Samir Hanash. Secretome signature associated with TITF1/NKX2-1-negative non-small cell lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2485. doi:10.1158/1538-7445.AM2014-2485

A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets

Cancer/testis (CT) antigens are potential immunotherapeutic targets in cancer. However, the expression of particular antigens is limited to a subset of tumors of a given type. Thus, there is a need to identify antigens with complementary expression patterns for effective therapeutic intervention. In this study, we searched for genes that were distinctly expressed at a higher level in lung tumor tissue and the testes compared with other nontumor tissues and identified members of the VCX/Y gene family as novel CT antigens. VCX3A, a member of the VCX/Y gene family, was expressed at the protein level in approximately 20% of lung adenocarcinomas and 35% of squamous cell carcinomas, but not expressed in normal lung tissues. Among CT antigens with concordant mRNA and protein expression levels, four CT antigens, XAGE1, VCX, IL13RA2, and SYCE1, were expressed, alone or in combination, in about 80% of lung adenocarcinoma tumors. The CT antigen VCX/Y gene family broadens the spectrum of CT antigens expressed in lung adenocarcinomas for clinical applications.

Abstract B24: A systematic search for cancer/testis antigens in lung cancer identifies VCX/Y genes expanding the repertoire of potential immunotherapeutic targets

Background: A wide range of therapeutic cancer vaccines that target diverse tumor-associated antigens are currently been evaluated in early phase clinical trials. However the effectiveness of cancer vaccines is so far limited, potentially due in part to the limited availability of candidate targets with broad expression in a tumor type. Cancer/testis (CT) antigens are a major target of cancer vaccines, because CT antigens are specifically expressed in immune-privileged testis and placenta, and exhibit aberrant expression in various types of cancer, resulting in high immunogenicity with no self-tolerance and reduced adverse effects. However expression of particular antigens is limited to a subset of tumors of a given type. Thus there is a need to identify antigens with complementary expression patterns for more effective therapeutic intervention.

Methods: Gene expression data of BioGPS, and DNA methylation and RNA-seq data of TCGA lung cancer samples were downloaded. All lung cancer cell lines were cultured in RPMI1640 containing 10% FBS. A total of 83 pairs of treatment naive lung adenocarcinoma tissues and adjacent non-tumor lung tissues had been obtained earlier with informed consent. Gene expression data for cell lines and tissues were obtained using the Illumina Human WG-6 v3.0 Expression BeadChips. For mass spectrometric analysis, 38 non-small cell lung cancer (NSCLC) cell lines were cultured according to the standard SILAC protocol. The same batch of cells was used for analysis of whole cell extract, conditioned media and cell surface proteins. Tissue microarrays comprised 463 surgically resected NSCLC tumor specimens collected under an IRB protocol. Monoclonal anti-mouse VCX3A antibody was used for Western blot and immunohistochemistry analysis.

Results: With mining the public database BioGPS, we identified VCX/Y gene family as novel CT antigens in lung cancer. Our findings also suggested epigenetic regulation of VCX/Y gene expression, and potential oncogenic roles of VCX/Y genes. Expression of one of the VCX/Y family genes, VCX3A, was further confirmed at the protein level in ~20% of lung adenocarcinoma and ~35% of squamous cell carcinoma tumors. We further examined gene expression patterns of CT antigens to determine whether a panel could be assembled with broad representation in lung adenocarcinoma. Of 255 known CT antigens, 109 CT antigens were profiled at both mRNA and protein levels in 38 NSCLC cell lines. mRNA expression levels of 10 CT antigens were significantly and positively correlated with protein expression levels. We examined mRNA expression profiles of these 10 CT antigens, together with VCX and MAGEA3 which is a current target for vaccine immunotherapy, in 83 lung adenocarcinoma tumors. We selected XAGE1, VCX, IL13RA2, and SYCE1 to form a CT antigen panel and compared mRNA expression levels of these four genes between tumor and adjacent non-tumor tissue. One or more of the CT antigens in the panel were overexpressed in 66 (79.5%) of lung adenocarcinomas.

Conclusions: The present study identifies for the first time a novel CT antigen VCX/Y gene family in lung cancer. A CT antigen panel was found to provide a broad coverage of lung adenocarcinoma tumors tested, suggestive of a potential for more effective immunotherapy through targeting the combined antigen panel compared to a single antigen target.

Citation Format: Ayumu Taguchi, Allen D. Taylor, Jaime Rodriguez, Muge Celiktas, Hui Liu, Xiaotu Ma, Qing Zhang, Chee-Hong Wong, Alice Chin, Luc Girard, Carmen Behrens, Wan Lam, Stephen Lam, John D. Minna, Ignacio I. Wistuba, Adi F. Gazdar, Samir M. Hanash. A systematic search for cancer/testis antigens in lung cancer identifies VCX/Y genes expanding the repertoire of potential immunotherapeutic targets. [abstract]. In: Proceedings of the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; 2014 Jan 6-9; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2014;20(2Suppl):Abstract nr B24.

Early diagnosis of necrotizing fasciitis

BACKGROUND

Necrotizing fasciitis is a rapidly progressing skin infection characterized by necrosis of the fascia and subcutaneous tissue, accompanied by severe systemic toxicity. The objective of this systematic review was to identify clinical features and investigations that will aid early diagnosis.

METHODS

A systematic literature search of PubMed was undertaken using the keywords 'necrotising fasciitis', 'necrotising skin infection', 'diagnosis' and 'outcome'. Case series of 50 or more subjects with information on symptoms and signs at initial presentation, investigations and clinical outcome were included.

RESULTS

Nine case series were selected, with a total of 1463 patients. Diabetes mellitus was a co-morbidity in 44.5 per cent of patients. Contact with marine life or ingestion of seafood in patients with liver disease were risk factors in some parts of Asia. The top three early presenting clinical features were: swelling (80.8 per cent), pain (79.0 per cent) and erythema (70.7 per cent). These being non-specific features, initial misdiagnosis was common and occurred in almost three-quarters of patients. Clinical features that helped early diagnosis were: pain out of proportion to the physical findings; failure to improve despite broad-spectrum antibiotics; presence of bullae in the skin; and gas in the soft tissue on plain X-ray (although this occurred in only 24.8 per cent of patients).

CONCLUSION

A high index of suspicion of necrotizing fasciitis is needed in a patient presenting with cutaneous infection causing swelling, pain and erythema, with co-morbidity of diabetes or liver disease. The presence of bullae, or gas on plain X-ray can be diagnostic. Early surgical exploration is the best approach in the uncertain case.

ST2 as a marker for risk of therapy-resistant graft-versus-host disease and death

BACKGROUND

No plasma biomarkers are associated with the response of acute graft-versus-host disease (GVHD) to therapy after allogeneic hematopoietic stem-cell transplantation.

METHODS

We compared 12 biomarkers in plasma obtained a median of 16 days after therapy initiation from 10 patients with a complete response by day 28 after therapy initiation and in plasma obtained from 10 patients with progressive GVHD during therapy. The lead biomarker, suppression of tumorigenicity 2 (ST2), was measured at the beginning of treatment for GVHD in plasma from 381 patients and during the first month after transplantation in three independent sets totaling 673 patients to determine the association of this biomarker with treatment-resistant GVHD and 6-month mortality after treatment or transplantation.

RESULTS

Of the 12 markers, ST2 had the most significant association with resistance to GVHD therapy and subsequent death without relapse. As compared with patients with low ST2 values at therapy initiation, patients with high ST2 values were 2.3 times as likely to have treatment-resistant GVHD (95% confidence interval [CI], 1.5 to 3.6) and 3.7 times as likely to die within 6 months after therapy (95% CI, 2.3 to 5.9). Patients with low ST2 values had lower mortality without relapse than patients with high ST2 values, regardless of the GVHD grade (11% vs. 31% among patients with grade I or II GVHD and 14% vs. 67% among patients with grade III or IV GVHD, P<0.001 for both comparisons). Plasma ST2 values at day 14 after transplantation were associated with 6-month mortality without relapse, regardless of the intensity of the conditioning regimen.

CONCLUSIONS

ST2 levels measured at the initiation of therapy for GVHD and during the first month after transplantation improved risk stratification for treatment-resistant GVHD and death without relapse after transplantation. (Funded by the National Institutes of Health.)

Abstract 1492: Systems analysis of epithelial-mesenchymal transition and cell invasion identifies functional gene signatures predictive of survival in lung cancer

We have implemented a systems approach to identify molecular features associated with mesenchymal or epithelial phenotypes and cell behavior in 38 lung adenocarcinoma cell lines that encompassed common known genomic alterations that drive the development of lung adenocarcinoma. Cell line characterization based on morphology, invasiveness, motility and cell-cell adhesion was integrated with proteomic, gene expression, microRNA and methylation profiles. Signatures were established from differential expression of transcripts and proteins in subsets of cell lines with mesenchymal and epithelial characteristics as well as high or low invasion and motility. The mesenchymal, invasion and migration signatures had common upregulation of genes or proteins related to cytoskeletal and actin-binding proteins. Sets of 148 and 74 transcripts corresponding to proteins that were overexpressed in mesenchymal cell lines and high invasive cell lines, respectively, were highly predictive of survival in three independent lung adenocarcinoma datasets. Subsets of 39 and 21 transcripts corresponding to cytoskeletal and acting binding proteins in the mesenchymal and invasive signatures were found to also predict survival in the three independent lung adenocarcinoma datasets, pointing to an association between cytoskeletal and actin binding proteins, a mesenchymal phenotype and tumor progression in lung adenocarcinoma.

Citation Format: Mark J. Schliekelman, Ayumu Taguchi, Jun Zhu, Xudong Dai, Qing Zhang, Alice Chin, Chee-Hong Wong, Hong Wang, Adi Gazdar, Ite Laird-Offringa, Muneesh Tewari, Jean Paul Thiery, Samir Hanash. Systems analysis of epithelial-mesenchymal transition and cell invasion identifies functional gene signatures predictive of survival in lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1492. doi:10.1158/1538-7445.AM2013-1492

Topological transport in spin-orbit coupled bosonic Mott insulators

We investigate topological transport in spin-orbit coupled bosonic Mott insulators. We show that interactions can lead to anomalous quasiparticle dynamics even when the spin-orbit coupling is Abelian. To illustrate the latter, we consider the spin-orbit coupling realized in the experiment of Lin et al. [Nature (London) 471, 83 (2011)]. For this spin-orbit coupling, we compute the quasiparticle dispersions and spectral weights, the interaction-induced momentum-space Berry curvature, and the momentum-space distribution of spin density, and propose experimental signatures. Furthermore, we find that, for a generic spin orbit coupling, in our approximation for the single-particle propagator, the ground state can in principle support an integer Hall conductivity if the sum of the Chern numbers of the hole bands is nonzero.

Spin caloritronics in noncondensed Bose gases

We consider coupled spin and heat transport in a two-component atomic Bose gas in the noncondensed state. We find that the transport coefficients show a temperature dependence reflecting the bosonic enhancement of scattering and discuss experimental signatures of the spin-heat coupling in spin accumulation, spin separation, and total dissipation. Close to the critical temperature for Bose-Einstein condensation, we find that the spin-heat coupling is strongly reduced, which is also reflected in the spin caloritronics figure of merit that determines the thermodynamic efficiency of spin-heat conversion.

SUICIDAL MERCURY INJECTION INTO THE UPPER LIMB: A CASE STUDY

We report a rare case of self-injection of mercury into the subcutaneous tissue of the upper limb. A multi-disciplinary management approach was adopted including cooperation between toxicologists, orthopaedic surgeons, radiologists and environment safety personnel. Surgical removal of mercury under radiological screening and systemic intoxication treated by chelating agents, namely dimercaprol and succimer. Serial serum and urine mercury levels showed an initial rise despite surgical removal and returned to normal after a prolonged period of time. Safety precautions were taken during surgery to avoid inadvertent intoxication of staff. Contamination of the operation theatre was monitored by the amount of mercury vapour released into the air. All personnels involved in the management of the patient did not show any evidence of mercury intoxication.

ULTRASOUND FOR THE DETECTION OF VEGETATIVE FOREIGN BODY IN HAND — A CASE REPORT

Foreign bodies in soft tissues are commonly encountered in daily orthopaedic practice. While most of the metals and glass foreign bodies can be detected by plain radiograph, organic substances such as wood and vegetative materials are radiolucent. Unfortunately, these radiolucent foreign bodies are usually more prone to cause an inflammatory reaction and infection. The detection can be even more difficult in cases of multiple foreign bodies and in penetrating injuries with small innocuous skin wounds. Ultrasonography is a sensitive and reliable investigation for detection of foreign bodies in soft tissue. We present a case of penetration injury to thumb with residual radiolucent foreign bodies and demonstrate the proper role of ultrasonography in the management of foreign bodies in soft tissues.

Targets of the tumor suppressor miR-200 in regulation of the epithelial-mesenchymal transition in cancer

The microRNA-200 (miR-200) family restricts epithelial-mesenchymal transition (EMT) and metastasis in tumor cell lines derived from mice that develop metastatic lung adenocarcinoma. To determine the mechanisms responsible for EMT and metastasis regulated by this microRNA, we conducted a global liquid chromatography/tandem mass spectrometry analysis to compare metastatic and nonmetastatic murine lung adenocarcinoma cells which had undergone EMT because of loss of miR-200. An analysis of syngeneic tumors generated by these cells identified multiple novel proteins linked to metastasis. In particular, the analysis of conditioned media, cell surface proteins, and whole-cell lysates from metastatic and nonmetastatic cells revealed large-scale modifications in the tumor microenvironment. Specific increases were documented in extracellular matrix (ECM) proteins, peptidases, and changes in distribution of cell adhesion proteins in the metastatic cell lines. Integrating proteomic data from three subproteomes, we defined constituents of a multilayer protein network that both regulated and mediated the effects of TGFβ. Lastly, we identified ECM proteins and peptidases that were directly regulated by miR-200. Taken together, our results reveal how expression of miR-200 alters the tumor microenvironment to inhibit the processes of EMT and metastasis.

Lung cancer signatures in plasma based on proteome profiling of mouse tumor models

We investigated the potential of in-depth quantitative proteomics to reveal plasma protein signatures that reflect lung tumor biology. We compared plasma protein profiles of four mouse models of lung cancer with profiles of models of pancreatic, ovarian, colon, prostate, and breast cancer and two models of inflammation. A protein signature for Titf1/Nkx2-1, a known lineage-survival oncogene in lung cancer, was found in plasmas of mouse models of lung adenocarcinoma. An EGFR signature was found in plasma of an EGFR mutant model, and a distinct plasma signature related to neuroendocrine development was uncovered in the small-cell lung cancer model. We demonstrate relevance to human lung cancer of the protein signatures identified on the basis of mouse models.

Tumor microenvironment-derived proteins dominate the plasma proteome response during breast cancer induction and progression

Tumor development relies upon essential contributions from the tumor microenvironment and host immune alterations. These contributions may inform the plasma proteome in a manner that could be exploited for cancer diagnosis and prognosis. In this study, we employed a systems biology approach to characterize the plasma proteome response in the inducible HER2/neu mouse model of breast cancer during tumor induction, progression, and regression. Mass spectrometry data derived from approximately 1.6 million spectra identified protein networks involved in wound healing, microenvironment, and metabolism that coordinately changed during tumor development. The observed alterations developed prior to cancer detection, increased progressively with tumor growth and reverted toward baseline with tumor regression. Gene expression and immunohistochemical analyses suggested that the cancer-associated plasma proteome was derived from transcriptional responses in the noncancerous host tissues as well as the developing tumor. The proteomic signature was distinct from a nonspecific response to inflammation. Overall, the developing tumor simultaneously engaged a number of innate physiologic processes, including wound repair, immune response, coagulation and complement cascades, tissue remodeling, and metabolic homeostasis that were all detectable in plasma. Our findings offer an integrated view of tumor development relevant to plasma-based strategies to detect and diagnose cancer.

Plasma proteome profiles associated with inflammation, angiogenesis, and cancer

Tumor development is accompanied by a complex host systemic response, which includes inflammatory and angiogenic reactions. Both tumor-derived and systemic response proteins are detected in plasma from cancer patients. However, given their non-specific nature, systemic response proteins can confound the detection or diagnosis of neoplasia. Here, we have applied an in-depth quantitative proteomic approach to analyze plasma protein changes in mouse models of subacute irritant-driven inflammation, autoreactive inflammation, and matrix associated angiogenesis and compared results to previously described findings from mouse models of polyoma middle T-driven breast cancer and Pdx1-Cre Kras(G12D) Ink4a/Arf (lox/lox)-induced pancreatic cancer. Among the confounding models, approximately 1/3 of all quantified plasma proteins exhibited a significant change in abundance compared to control mice. Of the proteins that changed in abundance, the majority were unique to each model. Altered proteins included those involved in acute phase response, inflammation, extracellular matrix remodeling, angiogenesis, and TGFβ signaling. Comparison of changes in plasma proteins between the confounder models and the two cancer models revealed proteins that were restricted to the cancer-bearing mice, reflecting the known biology of these tumors. This approach provides a basis for distinguishing between protein changes in plasma that are cancer-related and those that are part of a non-specific host response.

Detection of elevated plasma levels of epidermal growth factor receptor before breast cancer diagnosis among hormone therapy users

Applying advanced proteomic technologies to prospectively collected specimens from large studies is one means of identifying preclinical changes in plasma proteins that are potentially relevant to the early detection of diseases such as breast cancer. We conducted 14 independent quantitative proteomics experiments comparing pooled plasma samples collected from 420 estrogen receptor-positive (ER(+)) breast cancer patients ≤17 months before their diagnosis and matched controls. Based on the more than 3.4 million tandem mass spectra collected in the discovery set, 503 proteins were quantified, of which 57 differentiated cases from controls with a P value of <0.1. Seven of these proteins, for which quantitative ELISA assays were available, were assessed in an independent validation set. Of these candidates, epidermal growth factor receptor (EGFR) was validated as a predictor of breast cancer risk in an independent set of preclinical plasma samples for women overall [odds ratio (OR), 1.44; P = 0.0008] and particularly for current users of estrogen plus progestin (E + P) menopausal hormone therapy (OR, 2.49; P = 0.0001). Among current E + P users, the EGFR sensitivity for breast cancer risk was 31% with 90% specificity. Whereas the sensitivity and specificity of EGFR are insufficient for a clinically useful early detection biomarker, this study suggests that proteins that are elevated preclinically in women who go on to develop breast cancer can be discovered and validated using current proteomic technologies. Further studies are warranted to examine the role of EGFR and to discover and validate other proteins that could potentially be used for early detection of breast cancer.

Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS

Stable isotope coding technique in combination with mass spectrometry has emerged as a powerful tool to accurately identify and differentially quantify proteins within complex protein mixtures. We present a novel methodology to increase the yield of quantified proteins while maintaining a high stable-isotopic labeling efficacy. With this approach, intact proteins in complex biological sample such as sera are labeled with the designated dual stable isotope coding (DSIC) systems. In brief, intact proteins are coded sequentially with acrylamide to label Cysteine residues (Cys) and with succinic anhydride to label Lysine residues (Lys). Protein samples coded with this dual stable isotope are subjected to an online 2D-HPLC fractionation. The resolved protein fractions are individually digested with trypsin and analyzed with nano LC-MS/MSMS. Our results show that the DSIC labeling efficiency is 100% for Cysteine (Cys) labeled with acrylamide and 98% for Lysine (Lys) labeled with succinic anhydride. A comparative analysis of DSIC labeling and single labeling of Cysteine residues was made. Analysis of an entire anion-exchange chromatography subfraction of sera yielded 165 identified proteins (criteria: error rate <5% and unique peptides >or=2), 104 of which were quantified using the single labeling method (i.e., Cysteine acrylamide labeling only). In contrast, using same criteria for identification, a total 185 proteins were identified and 174 proteins were quantified using the DSIC labeling technique.

Novel breast cancer metastasis-associated proteins

With the use of the breast cancer metastatic model, which comprises four isogenic cell lines, iTRAQ-based ESI-LC/MS/MS proteomics was employed to catalog protein expression changes as cancer cells acquire increasing metastatic potential. From more than 1000 proteins detected, 197 proteins, including drug-targetable kinases, phosphatases, proteases and transcription factors, displayed differential expression when cancer cells becomes more metastatic. Overall, the number of protein expression changes was evenly distributed across mildly ( approximately 30%), moderately ( approximately 40%) and aggressively ( approximately 30%) metastatic cancer cells. Some changes were found to be specific to one while others were required for two or more phenotypes. KEGG Orthology suggests major reprogramming in cell metabolism and to smaller extents in genetic and environmental information processing. Ten novel metastasis-associated proteins were identified and the iTRAQ-based expression profiles of 7 proteins were verified to be congruent with antibody-based methods. With the use of tissue microarrays comprising 50 matched cases of invasive and metastatic lesions, the expression profiles of SH3GLB1 and SUB1, SND1, TRIM28 were validated to be down- and up-regulated, respectively, during clinical progression of carcinoma in situ to invasive and metastatic carcinomas. Our study has unraveled proteome-wide molecular aberrations and potentially new players in breast cancer metastasis.

Phosphoproteomics, oncogenic signaling and cancer research

The past 5 years have seen an explosion of phosphoproteomics methods development. In this review, using epidermal growth-factor signaling as a model, we will discuss how phosphoproteomics, along with bioinformatics and computational modeling, have impacted key aspects of oncogenic signaling such as in the temporal fine mapping of phosphorylation events, and the identification of novel tyrosine kinase substrates and phosphorylation sites. We submit that the next decade will see considerable exploitation of phosphoproteomics in cancer research. Such a phenomenon is already happening as exemplified by its use in promoting the understanding of the molecular etiology of cancer and target-directed therapeutics.

Piriformis pyomyositis: a report of three cases

Pyomyositis is a subacute infection of skeletal muscles. It can be life-threatening if diagnosis and treatment are delayed. Only 5 cases of isolated piriformis pyomyositis have been reported. We report signs and symptoms of piriformis pyomyositis in 3 women who were treated mainly with antibiotics. Computed tomography is useful in making the diagnosis. Early diagnosis and treatment may avoid surgical treatment and reduce mortality.

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure.

Tumour seeding following percutaneous needle biopsy of hepatocellular carcinoma

We report a hepatocellular carcinoma seeding following needle biopsy in a 57-year-old man who first presented with a focal hepatic lesion at another hospital. The patient had been a hepatitis B carrier for 20 years. Initial surveillance ultrasonography showed a lesion in segment IV, in the background of non-cirrhotic liver and normal serum alpha-foetoprotein level (8 ng/ml). A percutaneous needle biopsy was done and histopathology confirmed well-differentiated hepatocellular carcinoma. The patient had refused surgery and preferred to try traditional medicine. He presented to us four months after the initial biopsy with epigastric swelling. This was found to be due to a tumour seeding along the previous biopsy tract. He was given radiofrequency ablation (RFA) of tumour along the needle tract, in addition to the primary tumour. We conclude that the need for percutaneous needle biopsy should be critically evaluated in patients presenting with focal hepatic lesions and the role of RFA in treating tumour seeding needs further evaluation.

Differential expression of novel tyrosine kinase substrates during breast cancer development

To identify novel tyrosine kinase substrates that have never been implicated in cancer, we studied the phosphoproteomic changes in the MCF10AT model of breast cancer progression using a combination of phosphotyrosyl affinity enrichment, iTRAQ technology, and LC-MS/MS. Using complementary MALDI- and ESI-based mass spectrometry, 57 unique proteins comprising tyrosine kinases, phosphatases, and other signaling proteins were detected to undergo differential phosphorylation during disease progression. Seven of these proteins (SPAG9, Toll-interacting protein (TOLLIP), WBP2, NSFL1C, SLC4A7, CYFIP1, and RPS2) were validated to be novel tyrosine kinase substrates. SPAG9, TOLLIP, WBP2, and NSFL1C were further proven to be authentic targets of epidermal growth factor signaling and Iressa (gefitinib). A closer examination revealed that the expression of SLC4A7, a bicarbonate transporter, was down-regulated in 64% of the 25 matched normal and tumor clinical samples. The expression of TOLLIP in clinical breast cancers was heterogeneous with 25% showing higher expression in tumor compared with normal tissues and 35% showing the reverse trend. Preliminary studies on SPAG9, on the other hand, did not show differential expression between normal and diseased states. This is the first time SLC4A7 and TOLLIP have been discovered as novel tyrosine kinase substrates that are also associated with human cancer development. Future molecular and functional studies will provide novel insights into the roles of TOLLIP and SLC4A7 in the molecular etiology of breast cancer.

Gastro-oesophageal reflux disease in chronic laryngitis: prevalence and response to acid-suppressive therapy

BACKGROUND

Gastro-oesophageal reflux is thought to cause chronic laryngitis through laryngopharyngeal reflux. Response of laryngitis to treatment with acid-suppressive therapy supports this causal link.

AIM

To determine the prevalence of gastro-oesophageal reflux disease in patients with chronic laryngitis and response to proton-pump inhibitor therapy.

METHODS

Patients with chronic laryngitis were recruited. The frequency and severity of reflux and laryngeal symptoms were scored and laryngitis graded by laryngoscopy. All patients underwent esophagogastroduodenoscopy and 24-h ambulatory pH monitoring before receiving lansoprazole 30 mg b.d. for 8 weeks.

RESULTS

The prevalence of gastro-oesophageal reflux disease was 65.6% (21 of 32). Based on positive pH test, the prevalence was 25% (eight of 32). The change in laryngeal symptom score and laryngitis grade was significantly higher in GERD compared with non-GERD patients (P = 0.010 for both). The proportion of patients with marked/moderate improvement in laryngeal symptoms were significantly higher in patients with reflux (14 of 21, 67%) compared to those without reflux (two of 11, 18%; P = 0.026).

CONCLUSIONS

The prevalence of gastro-oesophageal reflux disease amongst our patients with chronic laryngitis was high. The response to treatment with proton-pump inhibitors in patients with reflux disease compared to those without underlined the critical role of acid reflux in a subset of patients with chronic laryngitis.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data

BACKGROUND

We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable.

RESULTS

We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the Project Manager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping.

CONCLUSION

The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.