Systematic analysis of migration factors by MigExpress identifies essential cell migration control genes in non-small cell lung cancer

Cell migration is an essential process in health and in disease, including cancer metastasis. A comprehensive inventory of migration factors is nonetheless lacking-in part due to the difficulty in assessing migration using high-throughput technologies. Hence, there are currently very few screens that systematically reveal factors controlling cell migration. Here, we introduce MigExpress as a platform for the 'identification of Migration control genes by differential Expression'. MigExpress exploits the combination of in-depth molecular profiling and the robust quantitative analysis of migration capacity in a broad panel of samples and identifies migration-associated genes by their differential expression in slow- versus fast-migrating cells. We applied MigExpress to investigate non-small cell lung cancer (NSCLC), which is the most frequent cause of cancer mortality mainly due to metastasis. In 54 NSCLC cell lines, we comprehensively determined mRNA and protein expression. Correlating the transcriptome and proteome profiles with the quantified migration properties led to the discovery and validation of FLNC, DSE, CPA4, TUBB6, and BICC1 as migration control factors in NSCLC cells, which were also negatively correlated with patient survival. Notably, FLNC was the least expressed filamin in NSCLC, but the only one controlling cell migration and correlating with patient survival and metastatic disease stage. In our study, we present MigExpress as a new method for the systematic analysis of migration factors and provide a comprehensive resource of transcriptomic and proteomic data of NSCLC cell lines related to cell migration.

The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells

The class of circular RNA (circRNA) is characterized by head-to-tail bonds between exons formed by backsplicing. Here, we provide a resource of circRNA expression in a comprehensive panel of 60 lung cancer and non-transformed cell lines (FL3C dataset). RNA sequencing after depletion of ribosomal RNA quantified the expression of circRNA and linear RNA. We detected 148,811 circular RNAs quantified by 2.8 million backsplicing reads originating from 12,251 genes. The number of identified circRNAs was markedly higher using rRNA depletion compared to public polyA-enriched RNA-seq datasets. CircRNAs almost never started in the first exon nor ended in the last exon and started more frequently in earlier exons. Most circRNAs showed high cell line specificity and correlated positively with their linear RNA counterpart. Known cancer genes produced more circRNAs than non-cancer genes. Subsets of circRNAs correlated with cell proliferation, histological subtype or genotype. CircTNFRSF21 was translated crossing the backsplice site in two different reading frames. Overexpression of circPVT1, circERBB2, circHIPK3, circCCNB1, circSMAD2, circTNFRSF21 and circKIF5B significantly increased colony formation. In conclusion, our data provide a comprehensive map of circRNA expression in lung cancer cells and global patterns of circRNA production as a useful resource for future research into lung cancer circRNAs.

LINC00261 and the Adjacent Gene FOXA2 Are Epithelial Markers and Are Suppressed during Lung Cancer Tumorigenesis and Progression

Lung cancer continues to be the leading cause of cancer-related deaths worldwide, with little improvement in patient survival rates in the past decade. Long non-coding RNAs (lncRNAs) are gaining importance as possible biomarkers with prognostic potential. By large-scale data mining, we identified LINC00261 as a lncRNA which was significantly downregulated in lung cancer. Low expression of LINC00261 was associated with recurrence and poor patient survival in lung adenocarcinoma. Moreover, the gene pair of LINC00261 and its neighbor FOXA2 were significantly co-regulated. LINC00261 as well as FOXA2 negatively correlated with markers for epithelial-to-mesenchymal transition (EMT) and were suppressed by the EMT inducer TGFβ. Hierarchical clustering of gene expression data from lung cancer cell lines could further verify the association of high LINC00261/FOXA2 expression to an epithelial gene signature. Furthermore, higher expression of the LINC00261/FOXA2 locus was associated with lung cancer cell lines with lower migratory capacity. All these data establish LINC00261 and FOXA2 as an epithelial-specific marker pair, downregulated during EMT and lung cancer progression, and associated with lower cell migration potential in lung cancer cells.

Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins

Seasonal epidemics of influenza A virus are a major cause of severe illness and are of high socio-economic relevance. For the design of effective antiviral therapies, a detailed knowledge of pathways perturbed by virus infection is critical. We performed comprehensive expression and organellar proteomics experiments to study the cellular consequences of influenza A virus infection using three human epithelial cell lines derived from human lung carcinomas: A549, Calu-1 and NCI-H1299. As a common response, the type I interferon pathway was up-regulated upon infection. Interestingly, influenza A virus infection led to numerous cell line-specific responses affecting both protein abundance as well as subcellular localization. In A549 cells, the vesicular compartment appeared expanded after virus infection. The composition of autophagsomes was altered by targeting of ribosomes, viral mRNA and proteins to these double membrane vesicles. Thus, autophagy may support viral protein translation by promoting the clustering of the respective molecular machinery in autophagosomes in a cell line-dependent manner.

The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior

Despite being overexpressed in different tumor entities, RIO kinases are hardly characterized in mammalian cells. We investigated the role of these atypical kinases in different cancer cells. Using isogenic colon-, breast- and lung cancer cell lines, we demonstrate that knockdown of RIOK1, but not of RIOK2 or RIOK3, strongly impairs proliferation and invasiveness in conventional and 3D culture systems. Interestingly, these effects were mainly observed in RAS mutant cancer cells. In contrast, growth of RAS wildtype Caco-2 and Bcr-Abl-driven K562 cells is not affected by RIOK1 knockdown, suggesting a specific requirement for RIOK1 in the context of oncogenic RAS signaling. Furthermore, we show that RIOK1 activates NF-κB signaling and promotes cell cycle progression. Using proteomics, we identified the pro-invasive proteins Metadherin and Stathmin1 to be regulated by RIOK1. Additionally, we demonstrate that RIOK1 promotes lung colonization in vivo and that RIOK1 is overexpressed in different subtypes of human lung- and breast cancer. Altogether, our data suggest RIOK1 as a potential therapeutic target, especially in RAS-driven cancers.

Degradation of protein translation machinery by amino acid starvation-induced macroautophagy

Macroautophagy is regarded as a nonspecific bulk degradation process of cytoplasmic material within the lysosome. However, the process has mainly been studied by nonspecific bulk degradation assays using radiolabeling. In the present study we monitor protein turnover and degradation by global, unbiased approaches relying on quantitative mass spectrometry-based proteomics. Macroautophagy is induced by rapamycin treatment, and by amino acid and glucose starvation in differentially, metabolically labeled cells. Protein dynamics are linked to image-based models of autophagosome turnover. Depending on the inducing stimulus, protein as well as organelle turnover differ. Amino acid starvation-induced macroautophagy leads to selective degradation of proteins important for protein translation. Thus, protein dynamics reflect cellular conditions in the respective treatment indicating stimulus-specific pathways in stress-induced macroautophagy.

Macroautophagy Proteins Control MHC Class I Levels on Dendritic Cells and Shape Anti-viral CD8(+) T Cell Responses

The macroautophagy machinery has been implicated in MHC class II restricted antigen presentation. Here, we report that this machinery assists in the internalization of MHC class I molecules. In the absence of the autophagy factors Atg5 and Atg7, MHC class I surface levels are elevated due to decreased endocytosis and degradation. Internalization of MHC class I molecules occurs less efficiently if AAK1 cannot be recruited via Atg8/LC3B. In the absence of Atg-dependent MHC class I internalization, dendritic cells stimulate CD8(+) T cell responses more efficiently in vitro and in vivo. During viral infections, lack of Atg5 results in enhanced influenza- and LCMV-specific CD8(+) T cell responses in vivo. Elevated influenza-specific CD8(+) T cell responses are associated with better immune control of this infection. Thus, the macroautophagy machinery orchestrates T cell immunity by supporting MHC class II but compromises MHC class I restricted antigen presentation.

Autophagy proteins stabilize pathogen-containing phagosomes for prolonged MHC II antigen processing

A subset of phagosomes in human macrophages and dendritic cells that is marked by a coat of autophagy-related proteins maintains phagocytosed antigens for prolonged presentation on MHC class II molecules.

Antigen preservation for presentation is a hallmark of potent antigen-presenting cells. In this paper, we report that in human macrophages and dendritic cells, a subset of phagosomes gets coated with Atg8/LC3, a component of the molecular machinery of macroautophagy, and maintains phagocytosed antigens for prolonged presentation on major histocompatibility complex class II molecules. These Atg8/LC3-positive phagosomes are formed around the antigen with TLR2 agonists and require reactive oxygen species production by NOX2 for their generation. A deficiency in the NOX2-dependent formation of these antigen storage phagosomes could contribute to compromise antifungal immune control in chronic granulomatous disease patients.

Autophagosomal proteome analysis by protein correlation profiling-SILAC

Autophagy is one of the two major degradation pathways within eukaryotic cells. Nevertheless, little is known about the protein composition of autophagosomes, the vesicles shuttling proteins to lysosomes for degradation. Protein correlation profiling in combination with stable isotope labeling by amino acids in cell culture is a stringent method to investigate the dynamics of the autophagosomal proteome. It enables the discrimination between autophagosomal and co-purifying proteins identifying organellar candidate proteins for further investigation.

Characterization of early autophagy signaling by quantitative phosphoproteomics

Under conditions of nutrient shortage autophagy is the primary cellular mechanism ensuring availability of substrates for continuous biosynthesis. Subjecting cells to starvation or rapamycin efficiently induces autophagy by inhibiting the MTOR signaling pathway triggering increased autophagic flux. To elucidate the regulation of early signaling events upon autophagy induction, we applied quantitative phosphoproteomics characterizing the temporal phosphorylation dynamics after starvation and rapamycin treatment. We obtained a comprehensive atlas of phosphorylation kinetics within the first 30 min upon induction of autophagy with both treatments affecting widely different cellular processes. The identification of dynamic phosphorylation already after 2 min demonstrates that the earliest events in autophagy signaling occur rapidly after induction. The data was subjected to extensive bioinformatics analysis revealing regulated phosphorylation sites on proteins involved in a wide range of cellular processes and an impact of the treatments on the kinome. To approach the potential function of the identified phosphorylation sites we performed a screen for MAP1LC3-interacting proteins and identified a group of binding partners exhibiting dynamic phosphorylation patterns. The data presented here provide a valuable resource on phosphorylation events underlying early autophagy induction.

The degradative inventory of the cell: proteomic insights

SIGNIFICANCE

Protein degradation has been identified as being deregulated in numerous human diseases. Hence, proteins involved in proteasomal as well as lysosomal degradation are regarded as interesting potential drug targets and are thoroughly investigated in clinical studies.

RECENT ADVANCES

Technical advances in the field of quantitative mass spectrometry (MS)-based proteomics allow for detailed investigations of protein degradation dynamics and identifications of responsible protein-protein interaction networks enabling a systematic analysis of the degradative inventory of the cell and its underlying molecular mechanisms.

CRITICAL ISSUES

In the current review we outline recent technical advances and their limitations in MS-based proteomics and discuss their use for the analysis of protein dynamics involved in degradation processes.

FUTURE DIRECTIONS

In the next years the analysis of crosstalk between different posttranslational modifications (PTMs) will be a major focus of MS-based proteomics studies. Increasing evidence highlights the complexity of PTMs with positive and negative feedbacks being discovered. In this regard, the generation of absolute quantitative proteomic data will be essential for theoretical scientists to construct predictive network models that constitute a valuable tool for fast hypothesis testing and for explaining underlying molecular mechanisms.

Friend or food: different cues to the autophagosomal proteome

A hallmark of macroautophagy is the formation of autophagosomes, double-membrane vesicles that enwrap cellular components destined for lysosomal degradation. We examined autophagosomal protein dynamics under various inducing stimuli using a comprehensive mass spectrometry-based proteomics approach in combination with functional studies in yeast and human cell cultures. Time frame and stimuli type influenced the autophagosome proteome, underlining the dynamic constitution of the organelle. We identified both a core set of proteins always localizing to autophagosomes and stimulus-dependent components that will serve as a resource for further characterization of the autophagosomal machinery and cargo selection. Among the core proteins were newly discovered autophagy regulators found to be conserved from yeast to humans, as well as the proteasome.

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens

Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection.

The thrombotic profile of treatment-naive HIV-positive Black South Africans with acute coronary syndromes

BACKGROUND

Patients with human immunodeficiency virus (HIV) infection on protease inhibitors (PIs) have a heightened risk of arterial thrombosis but little is known about treatment-naive patients.

METHODS/RESULTS

Prospective study from South Africa comparing thrombotic profiles of HIV-positive and -negative patients with acute coronary syndrome (ACS). A total of 30 treatment-naive HIV-positive patients with ACS were compared to 30 HIV-negative patients with ACS. Patients with HIV were younger; and besides smoking (73% vs 33%) and low high-density lipoprotein (HDL; 0.8 ± 0.3 vs 1.1 ± 0.4), they had fewer risk factors. Thrombophilia was more common in HIV-positive patients with lower protein C (PC; 82 ± 22 vs 108 ± 20) and higher factor VIII levels (201 ± 87 vs 136 ± 45). Patients with HIV had higher frequencies of anticardiolipin (aCL; 47% vs 10%) and antiprothrombin antibodies (87% vs 21%).

CONCLUSION

Treatment-naive HIV-positive patients with ACS are younger, with fewer traditional risk factors but a greater degree of thrombophilia compared with HIV-negative patients.

Acute coronary syndromes in treatment-naïve black South africans with human immunodeficiency virus infection

BACKGROUND

HIV patients on protease inhibitors have greater risk of acute coronary syndromes (ACS) but little is known about treatment-naïve patients.

METHODS AND RESULTS

Authors conducted a prospective single-center study from Soweto, South Africa, comparing the clinical and angiographic features of treatment-naïve HIV positive and negative patients with ACS. Between March 2004 and February 2008, 30 consecutive treatment-naïve HIV patients with ACS were compared to the next HIV-negative patient as a 1:1 control. HIV patients were younger (43 +/- 7 vs. 54 +/- 13, P = 0.004) and, besides smoking (73% vs. 33%, P = 0.002), had fewer risk factors than the control group with less hypertension (23% vs. 77%, P = 0.0001), diabetes (3% vs. 23%, P = 0.05), LDL hyperlipidemia (2.2 +/- 0.9 vs. 3.0 +/- 1.2, P = 0.006), and other coronary risk factors (7% vs. 53%, P = 0.0001). HDL was lower in the HIV group (0.8 +/- 0.3 vs. 1.1 +/- 0.4, P = 0.001). Atherosclerotic burden was lower in the HIV group with more normal infarct-related arteries (47% vs. 13%, P = 0.005) but a higher degree of large thrombus burden (43% vs. 17%, P = 0.02). Stents were used to a similar degree in HIV and control patients (30% vs. 37%, P = 0.78) with more target lesion revascularization in the HIV group (56% vs. 0%, P = 0.008).

CONCLUSION

Treatment-naïve HIV patients with ACS are younger and have fewer traditional risk factors than HIV-negative patients. HIV patients have less atherosclerotic but higher thrombotic burden which may imply a prothrombotic state in the pathogenesis of ACS in these patients.

Early predictors of success of Kasai operation in children with biliary atresia

AIM

Aim of the study was the evaluation of early predictive parameters of event-free survival (not listed for liver transplantation, not transplanted, no death) in children suffering from biliary atresia after hepatoportoenterostomy (Kasai procedure) in order to optimize pretransplant management.

PATIENTS AND METHODS

Sixty-seven infants were treated with the Kasai operation at our institution over a 20-year period from 1978 until 1998. Median age at time of operation was 51 days after birth (range 19 - 180 days). Of these 67 infants, 24 children with complete datasets and an observation time of at least one year were evaluated retrospectively using a Cox regression model. The response variable was event-free survival after a median observation time of 4.9 years (1.11- 10.37 years). Six variables were entered as covariates: alanine aminotransferase (ALAT), cholinesterase activity, bilirubin, age at the time of Kasai operation and tracer excretion and uptake during hepatobiliary scintigraphy (HBSS). All variables were evaluated six weeks after operation. For subsequent cut-off determination, a receiver operating analysis (ROC analysis) was carried out.

RESULTS

Tracer excretion shown by HBSS showed the highest prognostic power to predict event-free survival after Kasai operation (log rank 18.68, p < 0.0001) followed by bilirubin and ALAT as further significant parameters in the first univariate step of the Cox regression model. In the subsequent multivariate step, the prognostic power of HBSS was improved only by bilirubin (log rank 24.6, p < 0.0001). The ROC analysis determined a cut-off for bilirubin concentrations of 57 micromol/l for event-free survival with a sensitivity of 80 % and a specificity of 78.6 %. The five-year event-free survival-rate was 100 % in the group with good tracer excretion and a bilirubin concentration of 57 micromol/l and 27 % for the other group (log rank test, p < 0. 0001).

CONCLUSION

Early predictors of success of the Kasai operation in children with biliary atresia are free tracer excretion as shown by HBSS and a serum bilirubin concentration < 57 micromol/l six weeks after the operation. Thus, children with bilirubin concentrations above this level should be carefully and frequently monitored with regard to a transplantation requirement in order to optimize pretransplant management.

Direct detection of a microlens in the Milky Way

The nature of dark matter remains mysterious, with luminous material accounting for at most approximately 25 per cent of the baryons in the Universe. We accordingly undertook a survey looking for the microlensing of stars in the Large Magellanic Cloud (LMC) to determine the fraction of Galactic dark matter contained in massive compact halo objects (MACHOs). The presence of the dark matter would be revealed by gravitational lensing of the light from an LMC star as the foreground dark matter moves across the line of sight. The duration of the lensing event is the key observable parameter, but gives non-unique solutions when attempting to estimate the mass, distance and transverse velocity of the lens. The survey results to date indicate that between 8 and 50 per cent of the baryonic mass of the Galactic halo is in the form of MACHOs (ref. 3), but removing the degeneracy by identifying a lensing object would tighten the constraints on the mass in MACHOs. Here we report a direct image of a microlens, revealing it to be a nearby low-mass star in the disk of the Milky Way. This is consistent with the expected frequency of nearby stars acting as lenses, and demonstrates a direct determination of a lens mass from a microlensing event. Complete solutions such as this for halo microlensing events will probe directly the nature of the MACHOs.

Effect of topical anesthesia of the laryngeal mucosa on upper airway mechanics in exercising horses

OBJECTIVE

To determine the effect of desensitization of the laryngeal mucosal mechanoreceptors on upper airway mechanics in exercising horses.

ANIMALS

6 Standardbreds.

PROCEDURE

In study 1, videoendoscopic examinations were performed while horses ran on a treadmill with and without topical anesthesia of the laryngeal mucosa. In study 2, peak tracheal and nasopharyngeal pressures and airflows were obtained from horses during incremental treadmill exercise tests, with and without topical anesthesia of the laryngeal mucosa. A nasal occlusion test was performed on each horse while standing during an endoscopic examination for both trials.

RESULTS

In study 1, horses had nasopharyngeal collapse while running on the treadmill when the laryngeal mucosa was anesthetized. In study 2, inspiratory upper airway and nasopharyngeal impedance were significantly higher, and peak tracheal inspiratory pressure, respiratory frequency, and minute ventilation were significantly lower in horses when the laryngeal mucosa was anesthetized, compared with values obtained when horses exercised without topical anesthesia. Peak inspiratory and expiratory airflows were lower in horses when the laryngeal mucosa was anesthetized, although differences did not quite reach significance (P = 0.06 and 0.09, respectively). During a nasal occlusion test, horses had episodes of nasopharyngeal collapse and dorsal displacement of the soft palate when the laryngeal mucosa was anesthetized. Upper airway function was normal in these horses without laryngeal mucosal anesthesia.

CONCLUSIONS AND CLINICAL RELEVANCE

Receptors within the laryngeal mucosa may be important in maintaining upper airway patency in exercising horses.