Comparison of Protein-like Model Particles Fabricated by Micro 3D Printing to Established Standard Particles

Innovative analytical instruments and development of new methods has provided a better understanding of protein particle formation in biopharmaceuticals but have also challenged the ability to obtain reproducible and reliable measurements. The need for protein-like particle standards mimicking the irregular shape, translucent nature and near-to-neutral buoyancy of protein particles remained one of the hot topics in the field of particle detection and characterization in biopharmaceutical formulations. An innovative protein-like particle model has been developed using two photo polymerization (2PP) printing allowing to fabricate irregularly shaped particles with similar properties as protein particles at precise size of 50 µm and 150 µm, representative of subvisible particles and visible particles, respectively. A study was conducted to compare the morphological, physical, and optical properties of artificially generated protein particles, polystyrene spheres, ETFE, and SU-8 particle standards, along with newly developed protein-like model particles manufactured using 2PP printing. Our results suggest that 2PP printing can be used to produce protein-like particle standards that might facilitate harmonization and standardization of subvisible and visible protein particle characterization across laboratories and organizations.

Visualizing Synaptic Multi-Protein Patterns of Neuronal Tissue With DNA-Assisted Single-Molecule Localization Microscopy

The development of super-resolution microscopy (SRM) has widened our understanding of biomolecular structure and function in biological materials. Imaging multiple targets within a single area would elucidate their spatial localization relative to the cell matrix and neighboring biomolecules, revealing multi-protein macromolecular structures and their functional co-dependencies. SRM methods are, however, limited to the number of suitable fluorophores that can be imaged during a single acquisition as well as the loss of antigens during antibody washing and restaining for organic dye multiplexing. We report the visualization of multiple protein targets within the pre- and postsynapse in 350–400 nm thick neuronal tissue sections using DNA-assisted single-molecule localization microscopy (SMLM). In a single labeling step, antibodies conjugated with short DNA oligonucleotides visualized multiple targets by sequential exchange of fluorophore-labeled complementary oligonucleotides present in the imaging buffer. This approach avoids potential effects on structural integrity when using multiple rounds of immunolabeling and eliminates chromatic aberration, because all targets are imaged using a single excitation laser wavelength. This method proved robust for multi-target imaging in semi-thin tissue sections with a lateral resolution better than 25 nm, paving the way toward structural cell biology with single-molecule SRM.

Automated highly multiplexed super-resolution imaging of protein nano-architecture in cells and tissues

Understanding the nano-architecture of protein machines in diverse subcellular compartments remains a challenge despite rapid progress in super-resolution microscopy. While single-molecule localization microscopy techniques allow the visualization and identification of cellular structures with near-molecular resolution, multiplex-labeling of tens of target proteins within the same sample has not yet been achieved routinely. However, single sample multiplexing is essential to detect patterns that threaten to get lost in multi-sample averaging. Here, we report maS³TORM (multiplexed automated serial staining stochastic optical reconstruction microscopy), a microscopy approach capable of fully automated 3D direct STORM (dSTORM) imaging and solution exchange employing a re-staining protocol to achieve highly multiplexed protein localization within individual biological samples. We demonstrate 3D super-resolution images of 15 targets in single cultured cells and 16 targets in individual neuronal tissue samples with <10 nm localization precision, allowing us to define distinct nano-architectural features of protein distribution within the presynaptic nerve terminal.

Super-resolution imaging of multiple target proteins in the same sample can provide important information of cellular nanostructure, but has not been routinely achieved. Here, the authors present a fully automated 3D STORM approach using a re-staining protocol to image 15 targets in single cells and 16 targets in neuronal tissue.

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis

We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico. By applying the matrices in a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq), we analyze developmental states of thousands of single human pluripotent stem cells, either in different maintenance media or upon Wnt/β-catenin pathway activation, which identifies the mechanisms of differentiation induction. Moreover, we apply BART-Seq to the genetic screening of breast cancer patients and identify BRCA mutations with very high precision. The processing of thousands of samples and dynamic range measurements that outperform global transcriptomics techniques makes BART-Seq first targeted sequencing technique suitable for numerous research applications.

Altered relaxation times in MRI indicate bronchopulmonary dysplasia

We developed a MRI protocol using transverse (T2) and longitudinal (T1) mapping sequences to characterise lung structural changes in preterm infants with bronchopulmonary dysplasia (BPD). We prospectively enrolled 61 infants to perform 3-Tesla MRI of the lung in quiet sleep. Statistical analysis was performed using logistic Group Lasso regression and logistic regression. Increased lung T2 relaxation time and decreased lung T1 relaxation time indicated BPD yielding an area under the curve (AUC) of 0.80. Results were confirmed in an independent study cohort (AUC 0.75) and mirrored by lung function testing, indicating the high potential for MRI in future BPD diagnostics. TRIAL REGISTRATION: DRKS00004600.

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

Copy number aberrations (CNAs) are known to strongly affect oncogenes and tumour suppressor genes. Given the critical role CNAs play in cancer research, it is essential to accurately identify CNAs from tumour genomes. One particular challenge in finding CNAs is the effect of confounding variables. To address this issue, we assessed how commonly used CNA identification algorithms perform on SNP 6.0 genotyping data in the presence of confounding variables. We simulated realistic synthetic data with varying levels of three confounding variables-the tumour purity, the length of a copy number region and the CNA burden (the percentage of CNAs present in a profiled genome)-and evaluated the performance of OncoSNP, ASCAT, GenoCNA, GISTIC and CGHcall. Furthermore, we implemented and assessed CGHcall*, an adjusted version of CGHcall accounting for high CNA burden. Our analysis on synthetic data indicates that tumour purity and the CNA burden strongly influence the performance of all the algorithms. No algorithm can correctly find lost and gained genomic regions across all tumour purities. The length of CNA regions influenced the performance of ASCAT, CGHcall and GISTIC. OncoSNP, GenoCNA and CGHcall* showed little sensitivity. Overall, CGHcall* and OncoSNP showed reasonable performance, particularly in samples with high tumour purity. Our analysis on the HapMap data revealed a good overlap between CGHcall, CGHcall* and GenoCNA results and experimentally validated data. Our exploratory analysis on the TCGA HNSCC data revealed plausible results of CGHcall, CGHcall* and GISTIC in consensus HNSCC CNA regions. Code is available at https://github.com/adspit/PASCAL.

Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify miRNAs involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas lung adenocarcinoma patient cohort (sequencing data; n = 449) and subsequently validated by qRT-PCR in an independent clinical cohort (n = 108). Overexpression of miRNAs located on chromosome 14q32 was associated with metastasis in lung adenocarcinoma patients. Importantly, Kaplan-Meier analysis and log-rank test revealed that higher expression levels of individual 14q32 miRNAs (mir-539, mir-323b, and mir-487a) associated with worse disease-free survival of never-smoker patients. Epigenetic analysis including DNA methylation microarray data and bisulfite sequencing validation demonstrated that the induction of 14q32 cluster correlated with genomic hypomethylation of the 14q32 locus. CRISPR activation technology, applied for the first time to functionally study the increase of clustered miRNA levels in a coordinated manner, showed that simultaneous overexpression of 14q32 miRNAs promoted tumor cell migratory and invasive properties. Analysis of individual miRNAs by mimic transfection further illustrated that miR-323b-3p, miR-487a-3p, and miR-539-5p significantly contributed to the invasive phenotype through the indirect regulation of different target genes. In conclusion, overexpression of 14q32 miRNAs, associated with the respective genomic hypomethylation, promotes metastasis and correlates with poor patient prognosis in lung adenocarcinoma.Implications: This study points to chromosome 14q32 miRNAs as promising targets to inhibit tumor cell dissemination and to predict patient prognosis in lung adenocarcinoma. Mol Cancer Res; 16(3); 390-402. ©2018 AACR.

MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM

Glioblastoma is the most aggressive brain tumor in adults with a median survival below 12 months in population-based studies. The main reason for tumor recurrence and progression is constitutive or acquired resistance to the standard of care of surgical resection followed by radiotherapy with concomitant and adjuvant temozolomide (TMZ/RT→TMZ). Here, we investigated the role of microRNA (miRNA) alterations as mediators of alkylator resistance in glioblastoma cells. Using microarray-based miRNA expression profiling of parental and TMZ-resistant cultures of three human glioma cell lines, we identified a set of differentially expressed miRNA candidates. From these, we selected miR-138 for further functional analyses as this miRNA was not only upregulated in TMZ-resistant versus parental cells, but also showed increased expression in vivo in recurrent glioblastoma tissue samples after TMZ/RT→TMZ treatment. Transient transfection of miR-138 mimics in glioma cells with low basal miR-138 expression increased glioma cell proliferation. Moreover, miR-138 overexpression increased TMZ resistance in long-term glioblastoma cell lines and glioma initiating cell cultures. The apoptosis regulator BIM was identified as a direct target of miR-138, and its silencing mediated the induced TMZ resistance phenotype. Altered sensitivity to apoptosis played only a minor role in this resistance mechanism. Instead, we identified the induction of autophagy to be regulated downstream of the miR-138/BIM axis and to promote cell survival following TMZ exposure. Our data thus define miR-138 as a glioblastoma cell survival-promoting miRNA associated with resistance to TMZ therapy in vitro and with tumor progression in vivo.

Abstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination

Background:

Non-small cell lung cancer (NSCLC) is one of the most aggressive tumor entities and first data indicate that microRNAs (miRNAs) are central regulators of NSCLC dissemination. Since each miRNA is able to modulate the expression of several transcripts, they are promising targets for the development of drugs that cause efficient antitumor effects and low resistance. However, the relevant network of miRNA/mRNA driving NSCLC metastasis has not been identified yet.

Methods:

The differential expression of miRNAs was compared between NSCLC samples from patients with and without lymph node metastasis (N1, N2 and N3 vs. N0) in a cohort of The Cancer Genomic Atlas (TCGA) database (n = 449). The dysregulation of the miRNAs in tumors versus normal lung samples (n = 39) was also analyzed. For validation, fresh-frozen samples from an independent patient cohort (n = 108) were analyzed by qRT-PCR. The role of selected miRNAs in tumor dissemination was assessed by migration and invasion experiments after transfection of respective antagomirs and agomirs in NSCLC cells (time-lapse microscopy). The novel algorithm “miRlastic” was used to identify potential miRNA targets through the integration of miRNA-mRNA expression data by negative multiple linear regression analysis. Moreover, differential methylation of the miRNA genomic locations was studied as a possible mechanism of miRNA dysregulation by analyzing Illumina Infinium 450 k DNA methylation TCGA data (n = 29).

Results:

By using a stringent selection process, we identified 135 miRNAs differentially induced or reduced in NSCLCs with lymph node metastasis (p≤0.05). Interestingly, 22/135 (16.3%) of the selected miRNAs were located in the chromosomal cluster 14q32.31. Elevated expression of miR-323b, miR-487a and miR-539, which are located in 14q32.31, significantly correlated with poor patient survival. Time-resolved and quantitative analysis of lateral migration illustrated that these miRNAs increased tumor migration without affecting cell viability. Moreover, miRlastic identified several metastasis-related genes as potential downstream targets of these miRNAs. The connection between miRNAs encoded in 14q32.31 and candidate targets was confirmed in NSCLC cell lines (e.g. Pumilio RNA-Binding Family Member-2; PUM2). Lastly, hypomethylation of the 14q32.31 cluster in tumor tissues might explain increased expression of these miRNAs.

Conclusions: Our results demonstrate that miRNAs located in the chromosomal cluster 14q32.31 are driving NSCLC dissemination. Therefore, we hypothesize that the coordinated overexpression of these miRNAs is part of a genetic network supporting cancer progression and that they represent promising cancer biomarkers and therapeutic targets.

Citation Format: Margarita González-Vallinas, Marco Albrecht, Adriana Pitea, Manuel Rodríguez-Paredes, Damian Stichel, Steffen Sass, Julian Gutekunst, Jennifer Schmitt, Thomas Muley, Michael Meister, Arne Warth, Peter Schirmacher, Fabian J. Theis, Nikola S. Müller, Franziska Matthäus, Kai Breuhahn. Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1945.

Epigenetic germline inheritance of diet-induced obesity and insulin resistance

There is considerable controversy regarding epigenetic inheritance in mammalian gametes. Using in vitro fertilization to ensure exclusive inheritance via the gametes, we show that a parental high-fat diet renders offspring more susceptible to developing obesity and diabetes in a sex- and parent of origin-specific mode. The epigenetic inheritance of acquired metabolic disorders may contribute to the current obesity and diabetes pandemic.

Abstract P1-06-02: A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells

We have developed an organoid regeneration assay to quantify the ability of freshly isolated, single human mammary epithelial cells to generate complex branched ductal structures with basal and luminal features.

For this purpose, cells are cultured in adherent or floating collagen gels, corresponding to a rigid or compliant matrix. In both conditions, single luminal progenitors form spheres, whereas basal cells generate branched ductal structures. In compliant but not rigid collagen gels, branching ducts in multicellular structures generated by basal cells develop a lumen and alveoli at their tips. Importantly, branched structures generated by single basal cells express basal and luminal markers at correct positions, thereby demonstrating bi-potential. Functionally, basal cells in branched structures display cellular contractility, which we reveal to be required for alveologenesis. In conclusion, branched structures generated by single basal cells in compliant collagen gels resemble terminal ductal-lobular units (TDLU), the functional units of the mammary gland.

To prospectively isolate basal cells with regenerative potential, we added the membrane metallo-endopeptidase CD10 as a cell surface marker to existing sorting protocols, thereby enriching for TDLU-formation and enabling rigorous quantification of regenerative potential by extreme limiting dilution assay (ELDA). Moreover, the use of CD10 as a cell surface marker reveals the presence of stromal cells with endothelial qualities within the CD49fhi/EpCAM– population, previously labeled basal. In summary, we describe a defined in vitro assay system to quantify primary human mammary epithelial cells with regenerative potential and systematically investigate their interaction with the physical environment at distinct steps of morphogenesis.

Citation Format: Scheel CH, Linnemann JR, Miura H, Meixner LK, Irmler M, Kloos UJ, Hirschi B, Bartsch HS, Sass S, Beckers J, Theis FJ, Gabka C, Sotlar K. A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-06-02.

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1

Introduction

Skeletal muscle cell differentiation is impaired by elevated levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α) with pathological significance in chronic diseases or inherited muscle disorders. Insulin like growth factor-1 (IGF1) positively regulates muscle cell differentiation. Both, TNF-α and IGF1 affect gene and microRNA (miRNA) expression in this process. However, computational prediction of miRNA-mRNA relations is challenged by false positives and targets which might be irrelevant in the respective cellular transcriptome context. Thus, this study is focused on functional information about miRNA affected target transcripts by integrating miRNA and mRNA expression profiling data.

Methodology/Principal Findings

Murine skeletal myocytes PMI28 were differentiated for 24 hours with concomitant TNF-α or IGF1 treatment. Both, mRNA and miRNA expression profiling was performed. The data-driven integration of target prediction and paired mRNA/miRNA expression profiling data revealed that i) the quantity of predicted miRNA-mRNA relations was reduced, ii) miRNA targets with a function in cell cycle and axon guidance were enriched, iii) differential regulation of anti-differentiation miR-155-5p and miR-29b-3p as well as pro-differentiation miR-335-3p, miR-335-5p, miR-322-3p, and miR-322-5p seemed to be of primary importance during skeletal myoblast differentiation compared to the other miRNAs, iv) the abundance of targets and affected biological processes was miRNA specific, and v) subsets of miRNAs may collectively regulate gene expression.

Conclusions

Joint analysis of mRNA and miRNA profiling data increased the process-specificity and quality of predicted relations by statistically selecting miRNA-target interactions. Moreover, this study revealed miRNA-specific predominant biological implications in skeletal muscle cell differentiation and in response to TNF-α or IGF1 treatment. Furthermore, myoblast differentiation-associated miRNAs are suggested to collectively regulate gene clusters and targets associated with enriched specific gene ontology terms or pathways. Predicted miRNA functions of this study provide novel insights into defective regulation at the transcriptomic level during myocyte proliferation and differentiation due to inflammatory stimuli.

Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts

We analyzed an ex vivo model of in situ aged human dermal fibroblasts, obtained from 15 adult healthy donors from three different age groups using an unbiased quantitative proteome-wide approach applying label-free mass spectrometry. Thereby, we identified 2409 proteins, including 43 proteins with an age-associated abundance change. Most of the differentially abundant proteins have not been described in the context of fibroblasts’ aging before, but the deduced biological processes confirmed known hallmarks of aging and led to a consistent picture of eight biological categories involved in fibroblast aging, namely proteostasis, cell cycle and proliferation, development and differentiation, cell death, cell organization and cytoskeleton, response to stress, cell communication and signal transduction, as well as RNA metabolism and translation. The exhaustive analysis of protein and mRNA data revealed that 77% of the age-associated proteins were not linked to expression changes of the corresponding transcripts. This is in line with an associated miRNA study and led us to the conclusion that most of the age-associated alterations detected at the proteome level are likely caused post-transcriptionally rather than by differential gene expression. In summary, our findings led to the characterization of novel proteins potentially associated with fibroblast aging and revealed that primary cultures of in situ aged fibroblasts are characterized by moderate age-related proteomic changes comprising the multifactorial process of aging.

Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes

Direct lineage reprogramming induces dramatic shifts in cellular identity, employing poorly understood mechanisms. Recently, we demonstrated that expression of Neurog2 or Ascl1 in postnatal mouse astrocytes generates glutamatergic or GABAergic neurons. Here, we take advantage of this model to study dynamics of neuronal cell fate acquisition at the transcriptional level. We found that Neurog2 and Ascl1 rapidly elicited distinct neurogenic programs with only a small subset of shared target genes. Within this subset, only NeuroD4 could by itself induce neuronal reprogramming in both mouse and human astrocytes, while co-expression with Insm1 was required for glutamatergic maturation. Cultured astrocytes gradually became refractory to reprogramming, in part by the repressor REST preventing Neurog2 from binding to the NeuroD4 promoter. Notably, in astrocytes refractory to Neurog2 activation, the underlying neurogenic program remained amenable to reprogramming by exogenous NeuroD4. Our findings support a model of temporal hierarchy for cell fate change during neuronal reprogramming.

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Neurog2 and Ascl1 regulate largely non-overlapping neurogenic targets

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A subset of genes is required and sufficient to convert astrocytes and fibroblasts

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Neurog2 and REST compete for binding to the NeuroD4 promoter

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REST deletion enhances Neurog2-mediated reprogramming in vitro

Quantification of regenerative potential in primary human mammary epithelial cells

We present an organoid regeneration assay in which freshly isolated human mammary epithelial cells are cultured in adherent or floating collagen gels, corresponding to a rigid or compliant matrix environment. In both conditions, luminal progenitors form spheres, whereas basal cells generate branched ductal structures. In compliant but not rigid collagen gels, branching ducts form alveoli at their tips, express basal and luminal markers at correct positions, and display contractility, which is required for alveologenesis. Thereby, branched structures generated in compliant collagen gels resemble terminal ductal-lobular units (TDLUs), the functional units of the mammary gland. Using the membrane metallo-endopeptidase CD10 as a surface marker enriches for TDLU formation and reveals the presence of stromal cells within the CD49f(hi)/EpCAM(-) population. In summary, we describe a defined in vitro assay system to quantify cells with regenerative potential and systematically investigate their interaction with the physical environment at distinct steps of morphogenesis.

Stem-cell-like properties and epithelial plasticity arise as stable traits after transient Twist1 activation

Master regulators of the epithelial-mesenchymal transition such as Twist1 and Snail1 have been implicated in invasiveness and the generation of cancer stem cells, but their persistent activity inhibits stem-cell-like properties and the outgrowth of disseminated cancer cells into macroscopic metastases. Here, we show that Twist1 activation primes a subset of mammary epithelial cells for stem-cell-like properties, which only emerge and stably persist following Twist1 deactivation. Consequently, when cells undergo a mesenchymal-epithelial transition (MET), they do not return to their original epithelial cell state, evidenced by acquisition of invasive growth behavior and a distinct gene expression profile. These data provide an explanation for how transient Twist1 activation may promote all steps of the metastatic cascade; i.e., invasion, dissemination, and metastatic outgrowth at distant sites.

Posttranscriptional regulatory networks: from expression profiling to integrative analysis of mRNA and microRNA data

Protein coding RNAs are posttranscriptionally regulated by microRNAs, a class of small noncoding RNAs. Insights in messenger RNA (mRNA) and microRNA (miRNA) regulatory interactions facilitate the understanding of fine-tuning of gene expression and might allow better estimation of protein synthesis. However, in silico predictions of mRNA-microRNA interactions do not take into account the specific transcriptomic status of the biological system and are biased by false positives. One possible solution to predict rather reliable mRNA-miRNA relations in the specific biological context is to integrate real mRNA and miRNA transcriptomic data as well as in silico target predictions. This chapter addresses the workflow and methods one can apply for expression profiling and the integrative analysis of mRNA and miRNA data, as well as how to analyze and interpret results, and how to build up models of posttranscriptional regulatory networks.

A modular framework for gene set analysis integrating multilevel omics data

Modern high-throughput methods allow the investigation of biological functions across multiple ‘omics’ levels. Levels include mRNA and protein expression profiling as well as additional knowledge on, for example, DNA methylation and microRNA regulation. The reason for this interest in multi-omics is that actual cellular responses to different conditions are best explained mechanistically when taking all omics levels into account. To map gene products to their biological functions, public ontologies like Gene Ontology are commonly used. Many methods have been developed to identify terms in an ontology, overrepresented within a set of genes. However, these methods are not able to appropriately deal with any combination of several data types. Here, we propose a new method to analyse integrated data across multiple omics-levels to simultaneously assess their biological meaning. We developed a model-based Bayesian method for inferring interpretable term probabilities in a modular framework. Our Multi-level ONtology Analysis (MONA) algorithm performed significantly better than conventional analyses of individual levels and yields best results even for sophisticated models including mRNA fine-tuning by microRNAs. The MONA framework is flexible enough to allow for different underlying regulatory motifs or ontologies. It is ready-to-use for applied researchers and is available as a standalone application from http://icb.helmholtz-muenchen.de/mona.

A molecular characterization of the choroid plexus and stress-induced gene regulation

The role of the choroid plexus (CP) in brain homeostasis is being increasingly recognized and recent studies suggest that the CP has a more important role in physiological and pathological brain functions than currently appreciated. To obtain additional insight on the CP function, we performed a proteomics and transcriptomics characterization employing a combination of high resolution tandem mass spectrometry and gene expression analyses in normal rodent brain. Using multiple protein fractionation approaches, we identified 1400 CP proteins in adult CP. Microarray-based comparison of CP gene expression with the kidney, cortex and hippocampus showed significant overlap between the CP and the kidney. CP gene profiles were validated by in situ hybridization analysis of several target genes including klotho, CLIC 6, OATP 14 and Ezrin. Immunohistochemical analyses were performed for CP and enpendyma detection of several target proteins including cytokeratin, Rab7, klotho, tissue inhibitor of metalloprotease 1 (TIMP1), MMP9 and glial fibrillary acidic protein (GFAP). The molecular functions associated with various proteins of the CP proteome indicate that it is a blood-cerebrospinal fluid (CSF) barrier that exhibits high levels of metabolic activity. We also analyzed the gene expression changes induced by stress, an exacerbating factor for many illnesses, particularly mood disorders. Chronic stress altered the expression of several genes, downregulating 5HT2C, glucocorticoid receptor and the cilia genes IFT88 and smoothened while upregulating 5HT2A, BDNF, TNFα and IL-1b. The data presented here attach additional significance to the emerging importance of CP function in brain health and CNS disease states.

MicroRNAs coordinately regulate protein complexes

Background

In animals, microRNAs (miRNAs) regulate the protein synthesis of their target messenger RNAs (mRNAs) by either translational repression or deadenylation. miRNAs are frequently found to be co-expressed in different tissues and cell types, while some form polycistronic clusters on genomes. Interactions between targets of co-expressed miRNAs (including miRNA clusters) have not yet been systematically investigated.

Results

Here we integrated information from predicted and experimentally verified miRNA targets to characterize protein complex networks regulated by human miRNAs. We found striking evidence that individual miRNAs or co-expressed miRNAs frequently target several components of protein complexes. We experimentally verified that the miR-141-200c cluster targets different components of the CtBP/ZEB complex, suggesting a potential orchestrated regulation in epithelial to mesenchymal transition.

Conclusions

Our findings indicate a coordinate posttranscriptional regulation of protein complexes by miRNAs. These provide a sound basis for designing experiments to study miRNA function at a systems level.

Factors contributing to seasonal increases in inoculative freezing resistance in overwintering fire-colored beetle larvae dendroides canadensis

The insects and microarthropods that vary seasonally in susceptibility to cross-cuticular inoculation by external ice (inoculative freezing) represent a phylogenetically diverse group; however, few studies have explored possible mechanisms experimentally. This study documents seasonally variable inoculative freezing resistance in Dendroides canadensis beetle larvae and combines immunofluorescence, in vivo removal of epicuticular lipids and in vitro chamber studies to explore the roles of seasonal modification in the cuticle and in epidermal and hemolymph antifreeze proteins (AFPs). Seasonal cuticular modifications contribute to the inhibition of inoculative freezing since more cold-hardy larvae froze inoculatively when epicuticular waxes were removed with hexane and, in in vitro chamber experiments, cuticle patches (with the underlying epidermis removed) from winter larvae provided greater protection from inoculative freezing than did cuticle patches from summer larvae. The results indicate that seasonal modifications in epidermal and hemolymph AFPs contribute most strongly to the inhibition of inoculative freezing. Subcuticular epidermal AFPs were present in immunocytochemically labeled transverse sections of winter larvae but were absent in summer ones. Winter integument patches (cuticle with epidermis) were more resistant to inoculative freezing than were summer integument patches. Integument patches resisted inoculative freezing as well as live winter-collected larvae only when hemolymph AFP was added. The results also suggest that some integumentary ice nucleators are removed in cold-hardy larvae and that AFP promotes supercooling by inhibiting the activity of these nucleators.

Breast-feeding policies and routines among Arizona hospitals and nursery staff: results and implications of a descriptive study

In 1988, Arizona's 61 hospitals providing obstetrical services were canvased with regard to hospital routines that favor either breast-feeding or bottle-feeding. Forty-five hospitals provided responses that were used in the survey. Practices favoring breast-feeding, which were reported by a majority of the hospitals (more than 50%), were demand feeding, staff assessment for "latch-on" (the action of nipple presentation and sucking initiation) and positioning, "rooming-in" (the practice of minimal mother-infant separation), and information about follow-up support services. Hospital practices suggested to promote bottle-feeding were the provision of pacifiers and supplemental water or glucose, issuance of formula packs at discharge, and a first feed of sterile water. A positive significant relationship was identified for policies advocating breast-feeding and the prevalence of breast-feeding encouragement from professional staff. Of 44 respondents, 41 indicated that their hospital's policies endorse breast-feeding as the ideal method of feeding healthy newborns. Hospital staff perceived that they encourage mothers to breast-feed and offer support to those who initiate breast-feeding. On the basis of this information, we conclude that dietetics practitioners should evaluate current breast-feeding practices and integrate policies supportive of breast-feeding into the health care system.

Influence of collateral blood flow and of variations in MVO2 on tissue-ATP content in ischemic and infarcted myocardium

The left anterior descending coronary artery was occluded for 22.5, 45, 90, 180, and 360 mins in anesthesized open-chest dogs and pigs and thereafter reperfused for 30 min. Myocardial oxygen consumption was varied in dogs by cholinergic stimulation (bradycardia) and by cutting of the right and left vagus nerve (tachycardia). Regional myocardial blood flow was measured with radioactive tracer microspheres at the end of the occlusion period and 5 and 30 min after reflow. Tissue content of adenine nucleotides and of phosphocreatine were determined in the subendo- and subepicardium of transmural biopsies at the end of reflow. Infarct size was determined with nitrobluetetrazolium and compared with risk region size. Porcine hearts developed infarcts sooner. Those canines with a high MVO2 due to tachycardia had larger infarcts than those with bradycardia and resembled infarct development in the pig. The evolution of infarcts with time depended strongly on collateral flow which was significantly higher in canine hearts. Higher collateral flow and lower MVO2 in one group of canine hearts also resulted in better preserved tissue ATP. The fall in tissue ATP with time after coronary occlusion was compared with the O2-supply via collateral flow during occlusion. Assuming that the oxygen entering ischemic myocardium was used for ADP phosphorylation, we could estimate the degree of ATP-"overspending". Overspending was highest in low-flow ischemia and it correlated well with the speed of infarction. The ATP-data are best explained by the phosphocreatine energy shuttle model and by assuming slow access of cytosolic ATP to the ATP-splitting sites at the myofibrils. In conclusion, we postulate that both collateral flow as well as myocardial oxygen consumption before and during occlusion determine infarct size.

Effect of myocardial oxygen consumption on infarct size in experimental coronary artery occlusion

The influence of myocardial oxygen consumption (MVO2) at the moment of coronary occlusion on the size of the ensuing necrosis was investigated in 12 anaesthetised dogs. A two-infarction model was used with a sequential occlusion of two distant coronary branches in the same heart, however under different levels of MVO2. One group of occlusions was produced at a high MVO2 of 21.6 +/- 3.0 ml O2 . min-1 . 100 g-1. This group was compared with a second in which necrosis proceeded at a low MVO2 estimated to be 5.9 +/- 1.5 ml O2 . min-1 . 100 g-1 averaged over a 90-min occlusion period. Infarct size expressed as percentage of perfusion area was 43 +/- 28% in group 1 and 11 +/- 11% in group 2 (p less than 0.005). The mass of the perfusion area was equal in both groups (17 +/- 4 g, 19 +/- 6 g). The amount of myocardial necrosis, which after a 90-min occlusion depends on the acute collateral blood flow, was in every case greater under high MVO2. Thus a low MVO2 at the moment of occlusion can postpone myocardial necrosis.

The regulation of nucleotide metabolism of immune cells: papaverine induced nucleotide breakdown

During a period of prelabeling of mouse thymus cells with any nucleoside at 4 degrees C, nucleoside phosphates accumulated, but no nucleic acid synthesis occurred. Elevating the temperature to 37 degrees C then led to incorporation into the respective nucleic acid reaching a maximum in 5--15 min. Papaverine inhibited this incorporation (IC50:50 muM) and caused an efflux of label into the medium as a nonphosphorylated product. The responses of the different nucleotide phosphate pools showed more dependency on the base then the sugar moeity. The effect of papaverine could not be altered or mimicked by deprivation of oxygen, glucose, or calcium. Mouse spleen cells responded like thymocytes to papaverine, but rat GH3 pituitary cell DNA syntesis was only transiently inhibited with no concomitant efflux of 3H into the medium. As expected, thymus cellular adenosine triphosphate (ATP), determined by the luciferin-luciferase reaction, decreased in the presence of papaverine; suprisingly, extracellular ATP fell as well. The results suggest that decreases in cellular ATP of mouse thymus cells leads to reductions of all nucleoside phosphates and the efflux of the resultant nucleosides. Papaverine may effect a decrease in the ATP levels by activating a phosphohydrolase rather than, or in addition to, the previously suggested inhibition of mitochondrial electron transport.

Enzyme alterable alkylating agents. 8. Clinical trials with intra-arterial infusion of an alkylating agent with a half-life of 0.2 second

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