Comprehensive analysis of high-throughput screens with HiTSeekR.

High-throughput screening (HTS) is an indispensable tool for drug (target) discovery that currently lacks user-friendly software tools for the robust identification of putative hits from HTS experiments and for the interpretation of these findings in the context of systems biology. We developed HiTSeekR as a one-stop solution for chemical compound screens, siRNA knock-down and CRISPR/Cas9 knock-out screens, as well as microRNA inhibitor and -mimics screens. We chose three use cases that demonstrate the potential of HiTSeekR to fully exploit HTS screening data in quite heterogeneous contexts to generate novel hypotheses for follow-up experiments: (i) a genome-wide RNAi screen to uncover modulators of TNFα, (ii) a combined siRNA and miRNA mimics screen on vorinostat resistance and (iii) a small compound screen on KRAS synthetic lethality. HiTSeekR is publicly available at http://hitseekr.compbio.sdu.dk It is the first approach to close the gap between raw data processing, network enrichment and wet lab target generation for various HTS screen types.

Shift of microRNA profile upon glioma cell migration using patient-derived spheroids and serum-free conditions.

Glioblastoma multiforme (GBM) is the most frequent malignant primary brain tumor. A major reason for the overall median survival being only 14.6 months is migrating tumor cells left behind after surgery. Another major reason is tumor cells having a so-called cancer stem cell phenotype being therefore resistant towards traditional chemo- and radiotherapy. A group of novel molecular targets are microRNAs (miRNAs). MiRNAs are small non-coding RNAs exerting post-transcriptional regulation of gene expression. The aim of this study was to identify differentially expressed miRNAs in migrating GBM cells using serum-free stem cell conditions. We used patient-derived GBM spheroid cultures for a novel serum-free migration assay. MiRNA expression of migrating tumor cells isolated at maximum migration speed was compared with corresponding spheroids using an OpenArray Real-Time PCR System. The miRNA profiling revealed 30 miRNAs to be differentially expressed. In total 13 miRNAs were upregulated and 17 downregulated in migrating cells compared to corresponding spheroids. The three most deregulated miRNAs, miR-1227 (up-regulated), miR-32 (down-regulated) and miR-222 (down-regulated), were experimentally overexpressed. A non-significantly increased migration rate was observed after miR-1227 overexpression. A significantly reduced migration rate was observed after miR-32 and miR-222 overexpression. In conclusion a shift in microRNA profile upon glioma cell migration was identified using an assay avoiding serum-induced migration. Both the miRNA profiling and the functional validation suggested that miR-1227 may be associated with increased migration and miR-32 and miR-222 with decreased migration. These miRNAs may represent potential novel targets in migrating glioma cells.

Protein-based nanotoxicology assessment strategy.

The nanomaterial community calls for standardized in vitro assays to determine nanoparticle toxicity in the effort to reduce the number of in vivo validation experiments. We demonstrate that chip-based protein detection is suitable for assessing toxicity and may complement traditional assays to improve selection of primary hits for subsequent analysis. As nanodrug mimics, we analyzed the effect of transiently transfected siRNAs in MCF7 breast cancer cells and normal MCF12A breast cells, resembling a differential screen. As a measure of cytotoxicity, we determined cell viability as well as protein expression of glyceraldehyde-3-phosphate dehydrogenase, transferrin receptor, and the proliferation marker Ki67. The evaluation of cell lethality and protein expression unraveled cellular effects overseen by one method alone.

Shift of microRNA profile upon orthotopic xenografting of glioblastoma spheroid cultures.

Glioblastomas always recur despite surgery, radiotherapy and chemotherapy. A key player in the therapeutic resistance may be immature tumor cells with stem-like properties (TSCs) escaping conventional treatment. A group of promising molecular targets are microRNAs (miRs). miRs are small non-coding RNAs exerting post-transcriptional regulation of gene expression. In this study we aimed to identify over-expressed TSC-related miRs potentially amenable for therapeutic targeting. We used non-differentiated glioblastoma spheroid cultures (GSCs) containing TSCs and compared these to xenografts using a NanoString nCounter platform. This revealed 19 over-expressed miRs in the non-differentiated GSCs. Additionally, non-differentiated GSCs were compared to neural stem cells (NSCs) using a microarray platform. This revealed four significantly over-expressed miRs in the non-differentiated GSCs in comparison to the NSCs. The three most over-expressed miRs in the non-differentiated GSCs compared to xenografts were miR-126, -137 and -128. KEGG pathway analysis suggested the main biological function of these over-expressed miRs to be cell-cycle arrest and diminished proliferation. To functionally validate the profiling results suggesting association of these miRs with stem-like properties, experimental over-expression of miR-128 was performed. A consecutive limiting dilution assay confirmed a significantly elevated spheroid formation in the miR-128 over-expressing cells. This may provide potential therapeutic targets for anti-miRs to identify novel treatment options for GBM patients.

Microarray R-based analysis of complex lysate experiments with MIRACLE.

MOTIVATION: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. RESULTS: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. AVAILABILITY: Project URL: http://www.nanocan.org/miracle/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Long Term Cardiovascular Health Effects of Intelligent Physical Exercise Training Among Office Workers-A 2 Year Follow up of a Randomized Controlled Trial.

OBJECTIVE: The aim of the study is to assess long-term effects of intelligent physical exercise training (IPET) on cardiorespiratory fitness (VO 2max ) and cardiometabolic measures. METHODS: Office workers were randomized to a control group (CG, n = 194) or a training group (TG, n = 193). The TG received 1-hour weekly IPET during paid working hours for 2 years and recommendations to perform 30-minute leisure time physical activity 6 d/wk (LPA). RESULTS: Training group compared with CG demonstrated a significantly larger increase in VO 2max of 0.13 ± 0.06 L/min and improved cardiometabolic measures at 1-year follow-up that were maintained at 2-year follow-up, with larger increases in VO 2max among high-adherence participants. CONCLUSIONS: Intelligent physical exercise training and LPA showed the potential for long-term improved VO 2max and cardiometabolic measures. These findings emphasize the effectiveness of integrating IPET during paid working hours, and the significance of adherence to training was underlined.

Mandatory requirements for pediatric drug development in the EU and the US for novel drugs-A comparative study.

Mandatory pediatric legislation has been implemented in the European Union (EU) and the United States (US) to increase research and the availability of drugs for the pediatric population. Differences in the legislative framework can cause different pediatric requirements for similar indications granted for similar drugs across jurisdictions. This cross-sectional study compares the pediatric requirements for therapeutic indications granted at the time of initial approval for novel drugs approved in the two regions from 2010 to 2018. We collected the European Medicines Agency (EMA) and the US Food and Drug Administration (FDA) decisions to grant a waiver and/or to agree on a pediatric development plan and deferrals hereof at marketing authorization (MA) from publicly available documents. An agreed pediatric development plan was required for 66% (N = 188/285) and 63% (N = 134/212) of the indications granted in the EU and the US at the time of approval, respectively. Almost all (EU; 98%, US; 89%) were deferred until after MA. Based on the broad scope of the EU Pediatric Regulation, an additional 36 PIPs originated from the indications granted at MA. In the subset of indications granted for drugs approved in both the EU and the US (N = 232), significantly more indications resulted in an agreed pediatric development plan for one or more subsets of the pediatric population in the EU (N = 185) as compared to the US (N = 82). This was based on the exemption of orphan designated drugs in the US and the broader scope of the EU Pediatric Regulation. However, indications subject to the mandatory pediatric legislation in both regions (N = 131) most often had similar regulatory requirements for the inclusion of the pediatric population from the EMA and the US FDA (83%, N = 109). In conclusion, when comparing mandatory pediatric requirements, more pediatric development plans were agreed upon in the EU than in the US, in line with the broader mandates of the EU Pediatric Regulation. However, authorities most often had similar regulatory requirements when an indication was subject to pediatric legislation in both regions.

Status of Planned and Ongoing Paediatric Trials Investigating COVID-19 Vaccines: A Cross-Sectional Study of Paediatric Clinical Trials Planned in Agreed PIPs and/or Registered in Clinical Trial Databases.

BACKGROUND: The immune system matures throughout childhood; therefore, evidence about the safety and efficacy of vaccines for the prevention of COVID-19 in the paediatric population is important. Efficacy and safety have not been established for COVID-19 vaccines in a large part of the paediatric population at the time of the initial approval for use in adults. This study aims to provide an overview of planned and ongoing paediatric clinical trials investigating the safety and/or efficacy of COVID-19. METHODS: We identified all paediatric clinical trials investigating the safety and/or efficacy of COVID-19 vaccines in clinicaltrials.gov and clinicaltrialregister.eu, as well as all clinical trials planned in agreed PIPs (Paediatric Investigational Plans) as of 11 June 2021. Information about the study design, the paediatric age groups that they included, and the primary and secondary safety and efficacy outcomes were collected, together with expected timelines for the studies. RESULTS: 21 clinical trials were identified through the clinical trial registries and 19 clinical trials were specified in 6 agreed PIPs, 5 of these trials were also in the trial registers. All PIPs stipulated development of the COVID-19 vaccines for the full paediatric population, with a deferral. The earliest expected completion date of a PIPs is March 2024. The majority (14/21) of registered trials are randomised double-blinded studies. All investigated safety, 20 have a surrogate efficacy outcome (immunogenicity), of these 7 also measure clinical efficacy (COVID-19 infections). 18 studies were initiated, of these, all but one is still ongoing and one in adolescents has been finalised. CONCLUSION: Even though several trials have been planned in agreed PIPs, the registered paediatric clinical trials identified are most often not part of a PIP.

Guidance for pediatric use in prescription information for novel medicinal products in the EU and the US.

Pediatric legislations in the European Union (EU) and the United States (US) have increased medicines approved for use in the pediatric population. Despite many similarities between these frameworks, the EU Paediatric Regulation more often provides regulators with a mandate to require pediatric drug development for novel medicinal products compared to US regulators. If used, this could give rise to differences in the guidance for pediatric use provided for clinicians in the two regions. However, the level of discordance in the guidance for pediatric use between the two regions is unknown. This cross-sectional study compares guidance for pediatric use in the EU Summary of Product Characteristics (SmPC) and the US Prescription Information (USPI) on the level of indications granted for novel medicinal products approved after the pediatric legislations came in to force in both regions. For all indications granted as of March 2020 for novel medicinal products approved in both regions between 2010 and 2018, we compared the guidance for pediatric use in the EU SmPC and the USPI. The guidance for pediatric use differed for 18% (61/348) of the listed indications covering 21% (45/217) of the products, but without the guidance being contradictory. Where guidance differed, an equal share was observed for indications with a higher level of information for pediatric use in one region over the other (49% (30/61) in the US; 51% (31/61) in the EU). The discrepancies in pediatric information could be explained by differences in regulations for 21% (13/61) of the indications. Only a few conditions and diseases (EU n = 4; US n = 1) were observed to cover potential pediatric use outside the approved adult indication. Although the EU Paediatric Regulation more often provides regulators a mandate for requiring pediatric drug development as compared to the US PREA, this was not reflected in the prescription information approved by the two regulatory authorities.

New Information on Old Medicinal Products: A Cross-Sectional Analysis of Guidance for Paediatric Use for Substances on the European Priority List of Off-Patent Medicinal Products.

BACKGROUND: As part of the European Paediatric Regulation, the European Medicines Agency (former European Medicines Evaluation Agency) and the Paediatric Working Party (precursor for the Paediatric Committee) revised a priority list for studies on off-patent medicinal products in 2007 where a need for studies on paediatric medicinal products was emphasised. OBJECTIVES: We aimed to evaluate the status of guidance for paediatric use in the Summary of Product Characteristics for medicinal products on the priority list as well as the presence and status of Paediatric Investigation Plans for these medicinal products. METHODS: We included active pharmaceutical ingredients on the priority list authorised through the centralised procedure and/or marketed in Denmark. The status of guidance for paediatric use (indication, posology and/or contraindication) was reviewed from the most recent Summary of Product Characteristics uploaded on the European Medicines Agency or the Danish Medicines Agency website as of November 2020. Information on Paediatric Investigation Plans status (Paediatric Committee opinion, completion and waivers granted) was retrieved from the European Medicines Agency website. RESULTS: A total of 121 active pharmaceutical ingredients were included in this study. Seventy-one percent had guidance for paediatric use in the Summary of Product Characteristics for at least one paediatric subpopulation, more often concerning adolescents (70%) and children (70%) as compared with neonates (41%) and infants (49%). The guidance included a paediatric indication in 46% of the cases, but less often a contraindication (13%). Thirty-three active pharmaceutical ingredients had an agreed Paediatric Investigation Plan, six of these were completed. CONCLUSIONS: Most active pharmaceutical ingredients from the priority list had guidance for paediatric use in the Summary of Product Characteristics. However, there is still an unmet need in relation to guidance for use for the youngest paediatric subpopulation.

Screening of metabolic modulators identifies new strategies to target metabolic reprogramming in melanoma.

The prognosis of metastatic melanoma remains poor due to de novo or acquired resistance to immune and targeted therapies. Previous studies have shown that melanoma cells have perturbed metabolism and that cellular metabolic pathways represent potential therapeutic targets. To support the discovery of new drug candidates for melanoma, we examined 180 metabolic modulators, including phytochemicals and anti-diabetic compounds, for their growth-inhibitory activities against melanoma cells, alone and in combination with the BRAF inhibitor vemurafenib. Two positive hits from this screen, 4-methylumbelliferone (4-MU) and ursolic acid (UA), were subjected to validation and further characterization. Metabolic analysis showed that 4-MU affected cellular metabolism through inhibition of glycolysis and enhanced the effect of vemurafenib to reduce the growth of melanoma cells. In contrast, UA reduced mitochondrial respiration, accompanied by an increase in the glycolytic rate. This metabolic switch potentiated the growth-inhibitory effect of the pyruvate dehydrogenase kinase inhibitor dichloroacetate. Both drug combinations led to increased production of reactive oxygen species, suggesting the involvement of oxidative stress in the cellular response. These results support the potential use of metabolic modulators for combination therapies in cancer and may encourage preclinical validation and clinical testing of such treatment strategies in patients with metastatic melanoma.

CFP suppresses breast cancer cell growth by TES-mediated upregulation of the transcription factor DDIT3.

Breast cancer is a heterogeneous genetic disease driven by the accumulation of individual mutations per tumor. Whole-genome sequencing approaches have identified numerous genes with recurrent mutations in primary tumors. Although mutations in well characterized tumor suppressors and oncogenes are overrepresented in these sets, the majority of the genetically altered genes have so far unknown roles in breast cancer progression. To improve the basic understanding of the complex disease breast cancer and to potentially identify novel drug targets or regulators of known cancer-driving pathways, we analyzed 86 wild-type genes and 94 mutated variants for their effect on cell growth using a serially constructed panel of MCF7 cell lines. We demonstrate in subsequent experiments that the metal cation transporter CNNM4 regulates growth by induction of apoptosis and identified a tumor suppressive role of complement factor properdin (CFP) in vitro and in vivo. CFP appears to induce the intracellular upregulation of the pro-apoptotic transcription factor DDIT3 which is associated with endoplasmic reticulum-stress response.

Locked nucleic acid: modality, diversity, and drug discovery.

Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.

Efficient Management of High-Throughput Screening Libraries with SAVANAH.

High-throughput screening (HTS) has become an indispensable tool for the pharmaceutical industry and for biomedical research. A high degree of automation allows for experiments in the range of a few hundred up to several hundred thousand to be performed in close succession. The basis for such screens are molecular libraries, that is, microtiter plates with solubilized reagents such as siRNAs, shRNAs, miRNA inhibitors or mimics, and sgRNAs, or small compounds, that is, drugs. These reagents are typically condensed to provide enough material for covering several screens. Library plates thus need to be serially diluted before they can be used as assay plates. This process, however, leads to an explosion in the number of plates and samples to be tracked. Here, we present SAVANAH, the first tool to effectively manage molecular screening libraries across dilution series. It conveniently links (connects) sample information from the library to experimental results from the assay plates. All results can be exported to the R statistical environment or piped into HiTSeekR ( http://hitseekr.compbio.sdu.dk ) for comprehensive follow-up analyses. In summary, SAVANAH supports the HTS community in managing and analyzing HTS experiments with an emphasis on serially diluted molecular libraries.

Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma.

Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies.We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes. This was facilitated by a novel system for the construction of isogenic constitutive and inducible gain- and loss-of-function cell lines. Additionally, we demonstrate the construction of isogenic cell lines with combinations of the traits for advanced functional in vitro analyses. In a proof-of-concept experiment, a library of 108 isogenic melanoma cell lines was constructed and 8 genes were identified that significantly reduced viability in a discovery screen and in an independent validation screen. Here, we demonstrate the broad applicability of this recombination-based method and we proved its potential to identify new drug targets via the identification of the tumor suppressor DUSP6 as potential synthetic lethal target in melanoma cell lines with BRAF V600E mutations and high DUSP6 expression.

Exploring Valrubicin's Effect on Propionibacterium Acnes-Induced Skin Inflammation in Vitro and in Vivo.

Acne is a common skin disease involving colonization with Propionibacterium acnes (P. acnes), hyperproliferation of the follicular epithelium and inflammatory events. Valrubicin is a second-generation anthracycline, non-toxic upon contact, and available in a topical formulation. Valrubicin's predecessor doxorubicin possesses antibacterial effects and previously we demonstrated that valrubicin inhibits keratinocyte proliferation and skin inflammation suggesting beneficial topical treatment of acne with valrubicin. This study aims to investigate valrubicin's possible use in acne treatment by testing valrubicin's antibacterial effects against P. acnes and P. acnes-induced skin inflammation in vitro and in vivo. Valrubicin was demonstrated not to possess antibacterial effects against P. acnes. Additionally, valrubicin was demonstrated not to reduce mRNA and protein expression levels of the inflammatory markers interleukin (IL)-1ß, IL-8, and tumor necrosis factor (TNF)-α in vitro in human keratinocytes co-cultured with P. acnes. Moreover, in vivo, valrubicin, applied both topically and intra-dermally, was not able to reduce signs of inflammation in mouse ears intra-dermally injected with P. acnes. Taken together, this study does not support beneficial antibacterial and anti inflammatory effects of topical valrubicin treatment of acne.

[Breast milk as a cause of group B streptococcal sepsis]. / Modermaelk som årsag til gruppe B-streptokok-sepsis.

Group B beta-haemolytic streptococci (GBS) are the most common cause of serious bacterial infection in the neonate. Neonatal GBS sepsis is divided into early onset (1st- 6th day) and late onset (LO) (after 6th day of life). The incidence of both is increased in premature infants and infants with a low birth weight. The pathogenesis of LO GBS sepsis is poorly elucidated. Breast milk has been suggested as a source of infection. We describe three cases of sepsis in a premature girl nourished with mother's milk which illustrate the importance of investigating breast milk as a source of infection.

Decellularized matrix from tumorigenic human mesenchymal stem cells promotes neovascularization with galectin-1 dependent endothelial interaction.

BACKGROUND: Acquisition of a blood supply is fundamental for extensive tumor growth. We recently described vascular heterogeneity in tumours derived from cell clones of a human mesenchymal stem cell (hMSC) strain (hMSC-TERT20) immortalized by retroviral vector mediated human telomerase (hTERT) gene expression. Histological analysis showed that cells of the most vascularized tumorigenic clone, -BD11 had a pericyte-like alpha smooth muscle actin (ASMA+) and CD146+ positive phenotype. Upon serum withdrawal in culture, -BD11 cells formed cord-like structures mimicking capillary morphogenesis. In contrast, cells of the poorly tumorigenic clone, -BC8 did not stain for ASMA, tumours were less vascularized and serum withdrawal in culture led to cell death. By exploring the heterogeneity in hMSC-TERT20 clones we aimed to understand molecular mechanisms by which mesenchymal stem cells may promote neovascularization. METHODOLOGY/PRINCIPAL FINDINGS: Quantitative qRT-PCR analysis revealed similar mRNA levels for genes encoding the angiogenic cytokines VEGF and Angiopoietin-1 in both clones. However, clone-BD11 produced a denser extracellular matrix that supported stable ex vivo capillary morphogenesis of human endothelial cells and promoted in vivo neovascularization. Proteomic characterization of the -BD11 decellularized matrix identified 50 extracellular angiogenic proteins, including galectin-1. siRNA knock down of galectin-1 expression abrogated the ex vivo interaction between decellularized -BD11 matrix and endothelial cells. More stable shRNA knock down of galectin-1 expression did not prevent -BD11 tumorigenesis, but greatly reduced endothelial migration into -BD11 cell xenografts. CONCLUSIONS: Decellularized hMSC matrix had significant angiogenic potential with at least 50 angiogenic cell surface and extracellular proteins, implicated in attracting endothelial cells, their adhesion and activation to form tubular structures. hMSC -BD11 surface galectin-1 expression was required to bring about matrix-endothelial interactions and for xenografted hMSC -BD11 cells to optimally recruit host vasculature.

Construction of biosensor systems for determining the pathophysiological potential of carrageenan variants.

In vitro systems for monitoring safety of nutritional additives are desirable for high-throughput screenings and as a substitute for animal models. Carrageenan (CGN) is a sulfated polysaccharide widely used as a thickener and texturizer in human nutrition and is intensely discussed regarding its pathophysiological potential. Low molecular weight (lm) variants of CGN are considered to exert more profound pathophysiological effects in vivo than high molecular weight (hm) variants. We used a systematic approach to construct reporter systems allowing distinction between CGN-variants with different pathophysiological potential. Reporter systems utilizing segments of the CGN-responsive DMBT1 promoter did not display substantial activity in SW620 cells of intestinal epithelial origin. Genome-wide profiling revealed stronger qualitative and quantitative changes in global gene activities for hm-CGN than for lm-CGN (824 versus 91 genes; -6.64 to 22.33-fold for hm-CGN versus the range of -2.65 to 2.96-fold for lm-CGN). Reporter systems with segments of the IL-8 promoter showed a specific activation in response to hm-sulfated polysaccharides with lower pathophysiological potential in vivo and provided a better classification of CGN-variants than cytotoxicity assays in vitro. IL-8 reporter systems can be used for discerning between the effects of sulfated polysaccharides in vivo. Our data further provide initial insights into the molecular mechanisms that may play a role in the different effects of CGN-variants.