Turbo autoencoders for the DNA data storage channel with Autoturbo-DNA

DNA, with its high storage density and long-term stability, is a potential candidate for a next-generation storage device. The DNA data storage channel, composed of synthesis, amplification, storage, and sequencing, exhibits error probabilities and error profiles specific to the components of the channel. Here, we present Autoturbo-DNA, a PyTorch framework for training error-correcting, overcomplete autoencoders specifically tailored for the DNA data storage channel. It allows training different architecture combinations and using a wide variety of channel component models for noise generation during training. It further supports training the encoder to generate DNA sequences that adhere to user-defined constraints. Autoturbo-DNA exhibits error-correction capabilities close to non-neural-network state-of-the-art error correction and constrained codes for DNA data storage. Our results indicate that neural-network-based codes can be a viable alternative to traditionally designed codes for the DNA data storage channel.

RepairNatrix: a Snakemake workflow for processing DNA sequencing data for DNA storage

Motivation

There has been rapid progress in the development of error-correcting and constrained codes for DNA storage systems in recent years. However, improving the steps for processing raw sequencing data for DNA storage has a lot of untapped potential for further progress. In particular, constraints can be used as prior information to improve the processing of DNA sequencing data. Furthermore, a workflow tailored to DNA storage codes enables fair comparisons between different approaches while leading to reproducible results.

Results

We present RepairNatrix, a read-processing workflow for DNA storage. RepairNatrix supports preprocessing of raw sequencing data for DNA storage applications and can be used to flag and heuristically repair constraint-violating sequences to further increase the recoverability of encoded data in the presence of errors. Compared to a preprocessing strategy without repair functionality, RepairNatrix reduced the number of raw reads required for the successful, error-free decoding of the input files by a factor of 25-35 across different datasets.

Availability and implementation

RepairNatrix is available on Github: https://github.com/umr-ds/repairnatrix.

Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy

Next-generation sequencing has revolutionized the field of microbiology research and greatly expanded our knowledge of complex bacterial communities. Nanopore sequencing provides distinct advantages, combining cost-effectiveness, ease of use, high throughput, and high taxonomic resolution through its ability to process long amplicons, such as the entire 16s rRNA genome. We examine the performance of the conventional 27F primer (27F-I) included in the 16S Barcoding Kit distributed by Oxford Nanopore Technologies (ONT) and that of a more degenerate 27F primer (27F-II) in the context of highly complex bacterial communities in 73 human fecal samples. The results show striking differences in both taxonomic diversity and relative abundance of a substantial number of taxa between the two primer sets. Primer 27F-I reveals a significantly lower biodiversity and, for example, at the taxonomic level of the phyla, a dominance of Firmicutes and Proteobacteria as determined by relative abundances, as well as an unusually high ratio of Firmicutes/Bacteriodetes when compared to the more degenerate primer set (27F-II). Considering the findings in the context of the gut microbiomes common in Western industrial societies, as reported in the American Gut Project, the more degenerate primer set (27F-II) reflects the composition and diversity of the fecal microbiome significantly better than the 27F-I primer. This study provides a fundamentally relevant comparative analysis of the in situ performance of two primer sets designed for sequencing of the entire 16s rRNA genome and suggests that the more degenerate primer set (27F-II) should be preferred for nanopore sequencing-based analyses of the human fecal microbiome.

DNAsmart: Multiple attribute ranking tool for DNA data storage systems

In an ever-growing need for data storage capacity, the Deoxyribonucleic Acid (DNA) molecule gains traction as a new storage medium with a larger capacity, higher density, and a longer lifespan over conventional storage media. To effectively use DNA for data storage, it is important to understand the different methods of encoding information in DNA and compare their effectiveness. This requires evaluating which decoded DNA sequences carry the most encoded information based on various attributes. However, navigating the field of coding theory requires years of experience and domain expertise. For instance, domain experts rely on various mathematical functions and attributes to score and evaluate their encodings. To enable such analytical tasks, we provide an interactive and visual analytical framework for multi-attribute ranking in DNA storage systems. Our framework follows a three-step view with user-settable parameters. It enables users to find the optimal en-/de-coding approaches by setting different weights and combining multiple attributes. We assess the validity of our work through a task-specific user study on domain experts by relying on three tasks. Results indicate that all participants completed their tasks successfully under two minutes, then rated the framework for design choices, perceived usefulness, and intuitiveness. In addition, two real-world use cases are shared and analyzed as direct applications of the proposed tool. DNAsmart enables the ranking of decoded sequences based on multiple attributes. In sum, this work unveils the evaluation of en-/de-coding approaches accessible and tractable through visualization and interactivity to solve comparison and ranking tasks.

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage

The extensive information capacity of DNA, coupled with decreasing costs for DNA synthesis and sequencing, makes DNA an attractive alternative to traditional data storage. The processes of writing, storing, and reading DNA exhibit specific error profiles and constraints DNA sequences have to adhere to. We present DNA-Aeon, a concatenated coding scheme for DNA data storage. It supports the generation of variable-sized encoded sequences with a user-defined Guanine-Cytosine (GC) content, homopolymer length limitation, and the avoidance of undesired motifs. It further enables users to provide custom codebooks adhering to further constraints. DNA-Aeon can correct substitution errors, insertions, deletions, and the loss of whole DNA strands. Comparisons with other codes show better error-correction capabilities of DNA-Aeon at similar redundancy levels with decreased DNA synthesis costs. In-vitro tests indicate high reliability of DNA-Aeon even in the case of skewed sequencing read distributions and high read-dropout.

High-scale random access on DNA storage systems

Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.

Fractal construction of constrained code words for DNA storage systems

The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

Background

Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system.

Results

We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix).

Conclusion

Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.

MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors

Summary

The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes.

Availability and implementation

MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim.

Contact

dominik.heider@uni-marburg.de

Supplementary information

Supplementary data are available at Bioinformatics online.

CORDITE: The Curated CORona Drug InTERactions Database for SARS-CoV-2

Since the outbreak in 2019, researchers are trying to find effective drugs against the SARS-CoV-2 virus based on de novo drug design and drug repurposing. The former approach is very time consuming and needs extensive testing in humans, whereas drug repurposing is more promising, as the drugs have already been tested for side effects, etc. At present, there is no treatment for COVID-19 that is clinically effective, but there is a huge amount of data from studies that analyze potential drugs. We developed CORDITE to efficiently combine state-of-the-art knowledge on potential drugs and make it accessible to scientists and clinicians. The web interface also provides access to an easy-to-use API that allows a wide use for other software and applications, e.g., for meta-analysis, design of new clinical studies, or simple literature search. CORDITE is currently empowering many scientists across all continents and accelerates research in the knowledge domains of virology and drug design.

Propionate supplementation promotes the expansion of peripheral regulatory T-Cells in patients with end-stage renal disease

Patients with end-stage renal disease (ESRD) suffer from a progressively increasing low-grade systemic inflammation, which is associated with higher morbidity and mortality. Regulatory T cells (Tregs) play an important role in regulation of the inflammatory process. Previously, it has been demonstrated that short-chain fatty acids reduce inflammation in the central nervous system in a murine model of multiple sclerosis through an increase in tissue infiltrating Tregs. Here, we evaluated the effect of the short-chain fatty acid propionate on the chronic inflammatory state and T-cell composition in ESRD patients. Analyzing ESRD patients and healthy blood donors before, during, and 60 days after the propionate supplementation by multiparametric flow cytometry we observed a gradual and significant expansion in the frequencies of CD25^highCD127^- Tregs in both groups. Phenotypic characterization suggests that polarization of naïve T cells towards Tregs is responsible for the observed expansion. In line with this, we observed a significant reduction of inflammatory marker CRP under propionate supplementation. Of interest, the observed anti-inflammatory surroundings did not affect the protective pathogen-specific immunity as demonstrated by the stable frequencies of effector/memory T cells specific for tetanus/diphtheria recall antigens. Collectively, our data suggest that dietary supplements with propionate have a beneficial effect on the elevated systemic inflammation of ESRD patients. The effect can be achieved through an expansion of circulating Tregs without affecting the protective pathogen-reactive immunity.

Clinical results after different operative treatment methods of radial head and neck fractures: a systematic review and meta-analysis of clinical outcome

INTRODUCTION

There is no consensus on optimal treatment strategy for Mason type II-IV fractures. Most recommendations are based upon experts' opinion.

METHODS

An OVID-based literature search were performed to identify studies on surgical treatment of radial head and neck fracture. Specific focus was placed on extracting data describing clinical efficacy and outcome by using the Mason classification and including elbow function scores. A total of 841 clinical studies were identified describing in total the clinical follow-up of 1264 patients.

RESULTS

For type II radial head and neck fractures the significant best treatment option seems to be ORIF with an overall success rate of 98% by using screws or biodegradable (polylactide) pins. ORIF with a success rate of 92% shows the best results in the treatment of type III fractures and seem to be better than resection and implantation of a prosthesis. For this fracture type the ORIF with screws (96%), biodegradable (polylactide) pins (88%) and plates (83%) showed the best results. In the treatment of type IV fractures similar results could be found with a tendency of the best results after ORIF followed by resection and implantation of a prosthesis. If a prosthesis was implanted, the primary implantation seems to be associated with a better outcome after type III (87%) and IV (82%) fractures compared to the results after a secondary implantation.

DISCUSSION

Recommendations for surgical treatment of radial head and neck fractures according to the Mason classification can now be given with the best available evidence.

LEVEL OF EVIDENCE

IV.

Principles and clinical applications of liquid chromatography - tandem mass spectrometry for the determination of adrenal and gonadal steroid hormones

Liquid-chromatography - tandem mass spectrometry (LC-MS/MS) is becoming the method of choice for clinical steroid analysis. In most instances, it has the advantage of higher sensitivity, better reproducibility and greater specificity than commercial immunoassay techniques. The method requires only minimal sample preparation and a small sample volume. Furthermore, it has the potential to analyze multiple steroids simultaneously. Modern instruments guarantee high throughput, allowing an affordable price for the individual assay. All this makes LC-MS/MS an attractive method for use in a clinical setting. Reliable reference ranges for the detected analytes are the pre-requisite for their clinical use. If these are available, LC-MS/MS can find application in congenital disorders of steroid metabolism, such as congenital adrenal hyperplasia, disorders of sex development and disorders of salt homeostasis, as well as in acquired disorders of steroid metabolism, such as primary aldosteronism, Cushing's disease, Addison's disease, and hyperandrogenemia, as well as in psychiatric disease states such as depression or anxiety disorders. The principles of LC-MS/MS for steroid measurement, the pros and cons of LC-MS/MS compared with conventional immunoassays and the possible applications in clinical routine, with a special focus on pediatric endocrinology needs, are discussed here.

No correlation between androgen receptor CAG and GGN repeat length and the degree of genital virilization in females with 21-hydroxylase deficiency

CONTEXT

In 21-hydroxylase (CYP21A2) deficiency (21OHD), the level of in vitro enzymatic function allows for classification of mutation groups (null, A, B, C) and prediction of disease severity. However, genital virilization in affected females correlates only weakly with CYP21A2 mutation groups, suggesting the influence of genetic modifiers.

OBJECTIVE

The objective of the study was to investigate the influence of the polymorphic CAG and GGn repeats of the androgen receptor (AR) gene on the degree of genital virilization in 21OHD females.

DESIGN AND PATIENTS

Design of the study was the determination of CYP21A2 genotype, degree of genital virilization (Prader stage), and X-weighted biallelic mean of AR CAG and GGn repeat length in 205 females with 21OHD.

OUTCOME MEASUREMENTS

Correlation of AR CAG and GGn repeat lengths with Prader stages using nested stepwise logistic regression analysis was measured.

RESULTS

CYP21A2 mutation groups null and A showed significantly higher levels of genital virilization than groups B and C (P < 0.01). However, Prader stages varied considerably within mutation groups: null, Prader I-V (median IV); A, Prader I-V (median IV); B, Prader I-V (median III); C, 0-III (median I). Mean GGn repeat length of patients was not significantly associated with Prader stages, classified as low (0-I), intermediate (II-III), or severe (IV-V) (odds ratio per repeat: 0.98, 95% confidence interval 0.71-1.35). In contrast, patients with Prader 0-I showed a trend toward longer CAG repeats without reaching statistical significance (P = 0.07, odds ratio per repeat: 0.82, 95% confidence interval 0.65-1.02).

CONCLUSION

Neither CAG nor GGn repeat lengths are statistically significant modifiers of genital virilization in females with 21OHD.

The oral multitarget tumour growth inhibitor, ZK 304709, inhibits growth of pancreatic neuroendocrine tumours in an orthotopic mouse model

BACKGROUND AND AIMS

Current systemic therapies for neuroendocrine tumours (NETs) do not provide sufficient control of tumour growth. However, efficient evaluation of novel drugs is hindered by the lack of a suitable preclinical animal model. Here an orthotopic mouse model of pancreatic NET is established and used to study the action of ZK 304709, a first in class, oral multitarget tumour growth inhibitor. ZK 304709 is an inhibitor of cyclin-dependent kinases (Cdks) 1, 2, 4, 7 and 9, vascular endothelial growth factor receptor-type kinases (VEGF-RTKs) 1-3 and platelet-derived growth factor receptor-type kinase beta (PDGF-RTKss).

METHODS

BON and QGP-1 human NET cells were used to study proliferation, survival and cell cycle distribution in vitro. For induction of orthotopic NETs, BON cells were injected into the pancreas of NMRI(nu/nu) mice. Primary tumour growth and metastatic spread were recorded after 9 weeks, and apoptosis, microvessel density and lymphatic vessel density were determined.

RESULTS

ZK 304709 dose-dependently suppressed proliferation and colony formation of NET cells. Direct effects on NET cells were consistent with Cdk inhibition and involved G(2) cell cycle arrest and apoptosis induction, which was associated with reduced expression of MCL1 (myeloid cell leukaemia sequence 1), survivin and hypoxia-inducible factor 1alpha (HIF1alpha). Apoptosis similarly occurred in vivo in ZK 304709-treated orthotopic BON tumours, resulting in a 80% reduction of primary tumour growth. In contrast, treatment with lanreotide or 5-fluorouracil and streptozotocin failed to inhibit tumour gowth. ZK 304709 also reduced tumour microvessel density, implicating antiangiogenic mechanisms.

CONCLUSION

BON orthotopic tumours provide an informative model for preclinical drug evaluation in NETs. In this model, ZK 304709 achieved efficacious tumour growth control via induction of apoptosis and inhibition of tumour-induced angiogenesis.

In vivo effects of corticotropin-releasing hormone on femoral adipose tissue metabolism in women

OBJECTIVE

To investigate whether i.v. injected corticotropin-releasing hormone (CRH) (1 microg/kg) has a direct effect on adipose tissue metabolism in humans.

DESIGN

Double-blinded, placebo-controlled, crossover study.

SUBJECTS

Twelve healthy normal weight female volunteers (age 20-37 years, body mass index: 22.75+/-1.33 kg/m(2))

MEASUREMENTS

Assessment of local generation of glycerol, and glucose in adipose tissue by microdialysis. Measurement of adipose tissue and skin blood flow by laser Doppler flowmetry.

RESULTS

Injection of CRH acutely increases interstitial concentrations of glycerol (19.0+/-5.4%, P<0.05) and glucose (13.5+/-5.8%, P<0.05) reaching peak levels after 15 min. Plasma glycerol increases in parallel (Delta=16.7+/-5.9% after 15 min (P<0.05)), whereas plasma glucose remains unaffected. Changes in tissue blood flow do not explain interstitial metabolite alterations. Initial CRH effects on adipose tissue metabolism are short lasting and disappear after 15 min.

CONCLUSIONS

The importance of CRH on human energy metabolism is underlined by the present in vivo study demonstrating peptidergic effects on lipolysis and glucose homeostasis in human subcutaneous adipose tissue.

Interferon-gamma inhibits growth of human neuroendocrine carcinoma cells via induction of apoptosis

Although biotherapy of gastroenteropancreatic neuroendocrine tumors (NET) provides excellent control for the hypersecretion syndrome, tumor regression is rarely observed, implying the need for novel antiproliferative strategies. Here, we demonstrate that human pancreatic QGP-1 NET cells express functionally intact interferon-gamma (IFN-gamma) receptors and downstream effectors, including the putative tumor suppressor interferon regulatory factor-1 (IRF-1). IFN-gamma treatment profoundly inhibited anchorage-dependent and anchorage-independent growth of QGP-1 cells. Concomitant with the onset of growth inhibition, apoptotic cells were detected in cell cycle analyses of IFN-gamma treated cultures. Apoptosis was confirmed by evaluation of DNA fragmentation and PARP cleavage. Immunoblots of IFN-gamma treated QGP-1 cells revealed a substantial upregulation of caspase-1, followed by the appearance of active proteolytic fragments of caspase-3, suggesting that autocatalytic activation of caspase-1 might initiate the caspase cascade. Apoptosis induction by IFN-gamma was also observed in two of four primary cultures established from tumors of patients with for- and midgut NETs, respectively. Taken together our results characterize IFN-gamma as a potent proapoptotic stimulus in a subset of gastrointestinal NETs and suggest an IRF-1 mediated induction of caspase-1 as a relevant underlying mechanism. Based on these results, the potential of IFN-gamma in experimental biotherapeutic treatment of NETs can be further explored.

Interferon gamma inhibits growth of human pancreatic carcinoma cells via caspase-1 dependent induction of apoptosis

BACKGROUND AND AIMS

The poor prognosis of pancreatic cancer is partly due to resistance to a broad spectrum of apoptotic stimuli. To identify intact proapoptotic pathways of potential clinical relevance, we characterised the effects of interferon gamma (IFN-gamma) on growth and survival in human pancreatic cancer cells.

METHODS

IFN-gamma receptor expression and signal transduction were examined by reverse transcriptase-polymerase chain reaction (RT-PCR), immunoprecipitation, western blot analysis, and transactivation assays. Effects on cell growth and survival were evaluated in terms of cell numbers, colony formation, cell cycle analysis, DNA fragmentation, and poly(ADP ribose) polymerase (PARP) cleavage.

RESULTS

All four pancreatic cancer cell lines examined expressed functional IFN-gamma receptors and downstream effectors, including the putative tumour suppressor interferon regulatory factor 1 (IRF-1). IFN-gamma treatment profoundly inhibited anchorage dependent and independent growth of pancreatic cancer cells. Cell cycle analyses revealed subdiploid cells suggesting apoptosis, which was confirmed by demonstration of DNA fragmentation and PARP cleavage. Time and dose dependency of apoptosis induction and growth inhibition correlated closely, identifying apoptosis as the main, if not exclusive, mechanism responsible for growth inhibition. Apoptosis was preceded by upregulation of procaspase-1 and accompanied by proteolytic activation. Furthermore, the caspase inhibitor z-vad-fmk completely prevented IFN-gamma mediated apoptosis.

CONCLUSIONS

These results identify an intact proapoptotic pathway in pancreatic cancer cells and suggest that IRF-1 and/or procaspase-1 may represent potential therapeutic targets to be further explored.

Interferon-alpha delays S-phase progression in human hepatocellular carcinoma cells via inhibition of specific cyclin-dependent kinases

The potential antiproliferative effects of interferon-alpha (IFN-alpha) in the treatment of hepatocellular carcinoma (HCC) are controversial, and the growth inhibitory mechanisms remain poorly understood. Therefore, the current study was designed to delineate the molecular mechanisms responsible for direct antiproliferative actions of IFN-alpha in HCC cells. IFN-alpha receptor expression and signal transduction were examined by RT-PCR, immunoprecipitation, Western analysis, and transient transactivation assays. Effects of IFN-alpha on cell growth and cell-cycle distribution were evaluated based on cell numbers and flow cytometry. Composition and activity of cyclin-dependent kinase complexes were determined by immunoblotting and histone-H1-kinase assays. Expression of IFN-alpha receptors was found in all 3 HCC cell lines. IFN-alpha binding initiated phosphorylation of Jak1 and Tyk2 kinases leading to Stat1/Stat2 activation, nuclear translocation, and transactivation of an ISRE-luciferase reporter gene construct. IFN-alpha treatment resulted in a time- and dose-dependent reduction of proliferation. Cell cycle analysis of G1-synchronized, IFN-alpha-treated HCC cells revealed a substantial delay in S-phase progression but no alteration of G1/S-phase transition or evidence of apoptotic cell death. Reflecting the time course of S-phase accumulation, cell cycle-dependent induction of Cyclin A and Cyclin B was impaired, resulting in reduced activity of Cdk2 and Cdc2 kinases. Furthermore, Cdc25C was selectively down-regulated. IFN-alpha treatment inhibits growth of HCC cells by specifically delaying S-phase progression, most likely because of inhibition of Cyclin A induction, resulting in decreased activity of the associated Cdk2 and Cdc2 kinases.

A novel function for the tumor suppressor p16(INK4a): induction of anoikis via upregulation of the alpha(5)beta(1) fibronectin receptor

The tumor suppressor gene p16(INK4a) inhibits the kinase activity of the cyclin-dependent kinase 4-6/cyclin D complexes and subsequent phosphorylation of critical substrates necessary for transit through the G1 phase of the cell cycle. Recent studies suggested that control of the G1/S boundary might not be the sole biological function of p16(INK4a). We hypothesized that p16(INK4a) might influence hitherto unknown critical features of a malignant epithelial phenotype, such as anchorage dependence. Here we provide evidence that stable transfection of p16(INK4a) restitutes apoptosis induction upon loss of anchorage (anoikis) in a variety of human cancer cells. Anoikis in p16(INK4a)-transfected cells was evidenced by DNA fragmentation and poly(ADP-ribose) polymerase cleavage upon cultivation on polyhydroxyethylmethacrylate-coated dishes and was associated with suppression of anchorage-independent growth as well as complete loss of tumorigenicity. p16(INK4a)-mediated anoikis was due to selective transcriptional upregulation of the alpha(5) integrin chain of the alpha(5)beta(1) fibronectin receptor as detected by FACS((R)) analysis, immunoprecipitation, Northern blotting, and nuclear run-on assays. Addition of soluble fibronectin and inhibitory alpha(5) antibodies to nonadherent cells completely abolished p16(INK4a)-mediated anoikis, whereas laminin was ineffective. Furthermore, antisense-induced downregulation of the alpha(5) integrin chain in p16(INK4a)-transfected cells restored resistance to anoikis. These data suggest a novel functional interference between a cell cycle-regulating tumor suppressor gene and membrane-bound integrins, thus regulating a hallmark feature of an epithelial transformed phenotype: susceptibility to anoikis.

Activation of protein kinase Calpha inhibits growth of pancreatic cancer cells via p21(cip)-mediated G(1) arrest

We have analyzed human pancreatic cancer cells to explore the growth regulatory function of protein kinase C (PKC)alpha. PKCalpha subcellular redistribution, activation kinetics and downregulation were examined in detail and correlated to immediate and delayed effects on cell-cycle regulatory pathways. TPA treatment resulted in transient PKC(α) activation accompanied by translocation of the enzyme into membrane and nuclear compartments, and was followed by subsequent downregulation. TPA-induced inhibition of DNA synthesis was prevented by a PKC-antagonist and was reproduced by microinjection of recombinant PKCalpha, indicating that activation of this isoenzyme was required and sufficient for growth inhibitory effects. PKC(α) activation arrested cells in the G(1) phase of the cell cycle as a consequence of selective inhibition of cyclin dependent kinase (CDK)2 activity with concomitant hypophosphorylation of Rb. The inhibition of CDK2 activity resulted from induction of p21(cip1) cyclin-dependent kinase inhibitors. Levels of p21(cip1) remained elevated and CDK2 activity repressed in spite of PKCalpha downregulation, indicating that downstream effectors of PKCalpha are the primary determinants for the duration of PKC-mediated growth inhibition. The PKCalpha-induced block in cell proliferation persisted even though cells were kept in the presence of growth factors, suggesting that induction of PKCalpha results in a permanent withdrawal of pancreatic cancer cells from the cell cycle.

Molecular mechanism of interferon alfa-mediated growth inhibition in human neuroendocrine tumor cells

BACKGROUND & AIMS

Although human neuroendocrine tumors respond to interferon (IFN)-alpha treatment in vivo, the underlying mechanisms of growth inhibition are poorly understood. To characterize the antiproliferative effects at a molecular level, we explored the growth-regulatory action of IFN-alpha in the human neuroendocrine tumor cell lines BON and QGP1.

METHODS

IFN-alpha receptor expression and signal transduction were examined by reverse-transcription polymerase chain reaction, immunoblotting, subcellular fractionation, and transactivation assays. Growth regulation was evaluated by cell numbers, soft agar assays, and cell cycle analysis using flow cytometry. Expression and activity of cell cycle-regulatory molecules were determined by immunoblotting and histone H1-kinase assays.

RESULTS

Both cell lines expressed IFN-alpha receptor mRNA transcripts. Ligand binding initiated phosphorylation of Jak kinases and Stat transcription factors, resulting in Stat activation, nuclear translocation, and transcription from an ISRE-reporter construct. Prolonged IFN-alpha treatment dose-dependently inhibited both anchorage-dependent and -independent growth. Cell cycle analysis of IFN-alpha-treated, unsynchronized cultures revealed an increased S-phase population, which was further substantiated in G(1) synchronized QGP1 cells. IFN-alpha-treated cells entered S phase in parallel to control cultures, but their progress into G(2)/M phase was delayed. Both cellular cyclin B levels and CDC 2 activity were substantially reduced. The extent and time course of this reduction corresponded to the observed S-phase accumulation.

CONCLUSIONS

IFN-alpha directly inhibits growth of human neuroendocrine tumor cells by specifically delaying progression through S phase and into G(2)/M. These cell cycle changes are associated with inhibition of cyclin B expression, resulting in reduced CDC2 activity.

Rapid determination of gamma delta T-cell stimulation by microfluorimetry

Activated T-cell express CD25, the p55 chain of the IL-2 receptor. Here we report a reliable procedure for rapid determination of human gamma delta T cell activation by microfluorimetric measurement of CD25. Three days after initiation of culture, CD25 expression was determined. The sensitivity of this detection method was compared with [3H]thymidine incorporation at day 8. This proliferation assay allowed 3-5-fold higher dilution of the stimulatory ligand. However, monitoring of CD25 expression speeded up screening by 5 days. Therefore, for rapid screening of gamma delta T cell stimulation, e.g. for identification of activating ligands, monitoring of CD25 at day 3 is superior to [3H]thymidine measurement.

Superior efficacy of secreted over somatic antigen display in recombinant Salmonella vaccine induced protection against listeriosis

Vaccination provides the most potent measure against infectious disease, and recombinant (r) viable vaccines expressing defined pathogen-derived antigens represent powerful candidates for future vaccination strategies. In a new approach we constructed r-aroA- Salmonella typhimurium displaying p60 or listeriolysin (Hly) antigen of Listeria monocytogenes in secreted or somatic form in the host cell. Vaccination of mice with r-aroA- S. typhimurium induced protection against the intracellular pathogen L. monocytogenes only with secreted and not with somatic antigen. Secreted Hly was slightly more potent in inducing protective immunity than secreted p60. Both r-aroA- S. typhimurium secreting p60 in the endosome and r-aroA- S. typhimurium secreting Hly in the cytosol induced protective CD4+ and CD8+ T-cells suggesting CD8+ T-cell stimulation independent from intracellular residence of r-aroA- S. typhimurium carriers. Hence, not only the type of antigen but also its display by the r-carrier within the host cell critically influences vaccine efficacy.

Quantification of protein in dilute and complex samples: modification of the bicinchoninic acid assay

The colorimetric assay using bicinchoninic acid (BCA) as test reagent is useful for quantitative protein determinations due to its high sensitivity, ease, and tolerance to various contaminations present in biological samples or added during purification. For removal of interfering substances, protein precipitations have been described. Yet, obstructions became apparent with diluted and complex samples. Therefore we tested different solvents for removal of such interfering contaminants from the protein precipitate, and 1 M HCl was identified as the useful washing agent. The protocol described allows simple and accurate microdetermination in microtiter plates of proteins from complex samples.

Hydrophobic interaction chromatography for the purification of cytolytic bacterial toxins

The usefulness of hydrophobic interaction chromatography for the simple purification of cytolytic bacterial toxins was studied. Conditions are described for different hydrophobic interaction chromatographic media for purifying with high yields two different kinds of such haemolysins, the thiol-activated toxin listeriolysin O from Listeria monocytogenes and alpha-toxin from Staphylococcus aureus. For listeriolysin O, purification on butyl-Sepharose was followed by gel filtration chromatography. From butyl-Sepharose the recovery of 22%. Alpha-toxin was obtained by a single purification step from alkyl-Superose with 80% recovery and a specific activity of 29,000 U/mg. On sodium dodecyl sulphate polyacrylamide gel electrophoresis purified listeriolysin O and alpha-toxin showed a single band. Another thiol-activated toxin, streptolysin O from group A streptococci, showed a recovery of 38% from butyl-Sepharose. The results suggest the feasibility of using hydrophobic interaction chromatography, particularly with columns of weak hydrophobicity, for the purification of bacterial haemolysins in high yield.

Ontogenic development of murine fetal thymocytes is accelerated by 3,3',4,4'-tetrachlorobiphenyl

Polychlorinated hydrocarbons such as biphenyls or dioxins interfere with cellular processes by gene induction via ligand-activated binding of the cytosolic Ah-receptor to specific DNA elements. The thymus is a target organ for these processes and immunosuppression a hallmark of polychlorinated hydrocarbon toxicity. Using flow cytometry we analysed the development of thymocytes in fetal thymus organ cultures (FTOC) exposed to tetrachlorobiphenyl (TCB) for up to one week. We show that exposure to TCB changes the normal developmental pathways of fetal thymocytes within days. Overall fewer thymocytes are found in TCB-treated cultures from day 4 on, and significantly more CD8 positive thymocytes are detectable. These cells express the T-cell receptor, but not heat-stable antigen or IL2-receptor, giving them a mature phenotype. Moreover, relatively more CD4/CD8 double-negative thymocytes express CD44, a molecule involved in lymphocyte-epithelial interaction. We suggest that, at least for the CD8 single-positive thymocyte population, maturation is accelerated, and this may be due to TCB interference with physiological thymocyte-epithelial interactions.