Highly Versatile Cloud-Based Automation Solution for the Remote Design and Execution of Experiment Protocols during the COVID-19 Pandemic

There is an urgent need to accelerate the development and validation of both diagnostics and vaccines for COVID-19. These priorities are challenging both public and private sector research groups around the world and have shone a spotlight on both existing bottlenecks in the research workflows involved as well as on the implications of having to do much of this work remotely because of enforced social distancing and lockdown measures. The ability to respond quickly to rapidly evolving events, coupled with an emerging understanding of the disease and its pathology, as well as different mutations of the virus, necessitates a highly flexible liquid-handling automation solution that is amenable to rapid switching between different assay workflows and processes to be exploited tactically as needed. In addition, the use of cloud-based software imparts a unique benefit in enabling multiple research groups and remote technical staff around the world to have ready access to the same protocols in real-time without delays, down to the required level of detail, sharing methods and data (for example, in faster clinical trials). Informed by a recent use case, this article explores these issues alongside the recent development and deployment of an automation solution, whose unique approach in terms of both its cloud-native software and its highly modular hardware aligns especially well with achieving the challenge set by this new frontier in the bioanalytical laboratory.

Vancomycin-intermediate Staphylococcus aureus isolates are attenuated for virulence when compared with susceptible progenitors

OBJECTIVES

Vancomycin-intermediate Staphylococcus aureus (VISA) is associated with genetic changes that may also impact upon pathogenicity. In the current study, we compared the virulence of clinical VISA strains with their isogenic vancomycin-susceptible progenitors (VSSA).

METHODS

Production of the critical virulence protein, α toxin, was assessed using Western blot analysis and was correlated to agr activity using a bioluminescent agr-reporter. Cytotoxicity and intracellular persistence were compared ex vivo for VSSA and VISA within non-professional phagocytes (NPP). Virulence and host immune responses were further explored in vivo using a murine model of bacteraemia.

RESULTS

VISA isolates produced up to 20-fold less α toxin compared with VSSA, and this was corroborated by either loss of agr activity due to agr mutation, or altered agr activity in the absence of mutation. VISA were less cytotoxic towards NPP and were associated with enhanced intracellular persistence, suggesting that NPP may act as a reservoir for VISA. Infection with VSSA strains produced higher mortality in a murine bacteraemia model (≥90% 7-day mortality) compared with infection with VISA isolates (20% to 50%, p <0.001). Mice infected with VISA produced a dampened immune response (4.6-fold reduction in interleukin-6, p <0.001) and persistent organ bacterial growth was observed for VISA strains out to 7 days.

CONCLUSIONS

These findings highlight the remarkable adaptability of S. aureus, whereby, in addition to having reduced antibiotic susceptibility, VISA alter the expression of pathogenic factors to circumvent the host immune response to favour persistent infection over acute virulence.

Abstract 3753: An integrated approach to identify functional signaling modules in retinoblastoma cancer progression

This study illustrates a multi-omics approach combining transcriptomics and metabolomics datasets to study molecular events leading to progression of retinoblastoma. Retinoblastoma is a pediatric ocular cancer affecting children usually less than five years of age. It is a complex disease predisposed primarily by biallelic inactivating mutations in the RB1 gene. This gene has essential roles in cell cycle, differentiation, chromosome stability and is implicated in other functions. From a cohort of 9 patients undergoing enucleation of the affected eyes, we obtained tumor, aqueous humor, vitreous humor and tear samples. We obtained retina, aqueous humor and vitreous humor from enucleated eyes of 2 deceased pediatric controls, whose cause of death is not due to any eye related disease. The patients comprise of both high and low clinical and pathological risks. In the first stage of the study, we performed mRNA and miRNA gene expression using microarrays followed by pathway analysis to identify gene enrichment that would enable functional characterization of tumors. Differential expression analysis was carried out using moderated t-test with Benjamini Hochberg multiple testing correction. 108 (p≤0.05, fold change≥10) genes were found to be unique to patients possessing high risk of metastasis. Pathway analysis revealed key pathways that are known to be involved in the progression of retinoblastoma including cell cycle and Rap1 signaling pathway. Many of these responders were verified by RT-PCR and corroborated by immuno histochemistry studies. The study also revealed 18 novel miRNAs which had not been previously implicated in the disease, with a significant overlap of the miRNA target list with our mRNA expression data set. Metabolomics studies were performed using monophasic solvent extraction of aqueous, vitreous and tear samples. The extracted metabolites were analyzed on Accurate Mass QTOF mass spectrometer in positive and negative mode on a reverse phase C18 and HILIC columns. Data dependent MS/MS analysis was performed to confirm the compounds. Pathway analysis of the differentially expressed metabolites revealed enrichment of several pathways, including nucleotide metabolism and amino acids among others. Combined pathway analysis of metabolomics and transcriptomics data was performed in order to gain an understanding of the interrelationship between changes in gene expression and metabolomic profile. The results show overlap of key cellular pathways which can be mechanistically linked to disease progression. The study provide new biological insights that are made accessible by combining data from different biological and biochemical domains with a comprehensive integrated method. The information is useful not only to correlate expression markers with disease mechanism but also to better predict appropriate chemotherapy regimens and identify new mechanisms to treat even advanced stages of retinoblastoma.

Citation Format: Nilanjan Guha, Deepak SA, Syed Lateef, Seetaraman Gundimeda, Arunkumar Padmanabhan, Carolina B Livi, Nigel Skinner, Arkasubhra Ghosh, Ashwin Mallipatna, Vishnu Suresh Babu, Arun Sreekumar. An integrated approach to identify functional signaling modules in retinoblastoma cancer progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3753. doi:10.1158/1538-7445.AM2015-3753

Functional genome-wide analysis: a technical review, its developments and its relevance to cancer research

A technique has emerged over the past decade combining chromatin immunoprecipitation with DNA microarray analysis. This is a powerful and sensitive strategy that has been used extensively to characterise protein interactions with chromatin and epigenetic changes such as acetylation and methylation throughout the genome of different organisms. This technique has revolutionised our understanding of molecular genomics, continues to be widely used and is currently being applied in novel areas of cancer research. In this publication we review the historical context of this technology and offer current and future perspectives on how this technique is currently being developed and modified to allow its use in novel areas of research. We discuss the potential for this technique and its ongoing important role in biological research particularly in relation to cancer research. We also offer insight into the potential clinical application of this technology in stratified medicine, particularly in the field of cancer therapy.

Metabolomics in toxicology and preclinical research

Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological status of a biological system, and about the changes caused by chemicals. Metabolomics analysis is used in many fields, ranging from the analysis of the physiological status of genetically modified organisms in safety science to the evaluation of human health conditions. In toxicology, metabolomics is the -omics discipline that is most closely related to classical knowledge of disturbed biochemical pathways. It allows rapid identification of the potential targets of a hazardous compound. It can give information on target organs and often can help to improve our understanding regarding the mode-of-action of a given compound. Such insights aid the discovery of biomarkers that either indicate pathophysiological conditions or help the monitoring of the efficacy of drug therapies. The first toxicological applications of metabolomics were for mechanistic research, but different ways to use the technology in a regulatory context are being explored. Ideally, further progress in that direction will position the metabolomics approach to address the challenges of toxicology of the 21st century. To address these issues, scientists from academia, industry, and regulatory bodies came together in a workshop to discuss the current status of applied metabolomics and its potential in the safety assessment of compounds. We report here on the conclusions of three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolomics in a regulatory context.

Toll-like receptor 3 and 7/8 function is impaired in hepatitis C rapid fibrosis progression post-liver transplantation

Recurrence of hepatitis C (HCV) postliver transplant is universal, with a subgroup developing rapid hepatic fibrosis. Toll-like receptors (TLRs) are critical to innate antiviral responses and HCV alters TLR function to evade immune clearance. Whether TLRs play a role in rapid HCV recurrence posttransplant is unknown. We stimulated peripheral blood mononuclear cells (PBMCs) from 70 patients with HCV postliver transplant with TLR subclass-specific ligands and measured cytokine production, TLR expression and NK cell function. Rate of fibrosis progression was calculated using posttransplant liver biopsies graded by Metavir scoring (F0-4; R=fibrosis stage/year posttransplant; rapid fibrosis defined as >0.4 units/year). Thirty of 70 (43%) patients had rapid fibrosis progression. PBMCs from HCV rapid-fibrosers produced less IFNα with TLR7/8 stimulation (p=0.039), less IL-6 at baseline (p=0.027) and with TLR3 stimulation (p=0.008) and had lower TLR3-mediated monocyte IL-6 production (p=0.028) compared with HCV slow fibrosers. TLR7/8-mediated NKCD56 dim cell secretion of IFNγ was impaired in HCV rapid fibrosis (p=0.006) independently of IFNα secretion and TLR7/8 expression, while cytotoxicity remained preserved. Impaired TLR3 and TLR7/8-mediated cytokine responses may contribute to aggressive HCV recurrence postliver transplantation through impaired immune control of HCV and subsequent activation of fibrogenesis.

Toll-like receptor 3 and 7/8 function is impaired in hepatitis C rapid fibrosis progression post-liver transplantation

Recurrence of hepatitis C (HCV) postliver transplant is universal, with a subgroup developing rapid hepatic fibrosis. Toll-like receptors (TLRs) are critical to innate antiviral responses and HCV alters TLR function to evade immune clearance. Whether TLRs play a role in rapid HCV recurrence posttransplant is unknown. We stimulated peripheral blood mononuclear cells (PBMCs) from 70 patients with HCV postliver transplant with TLR subclass-specific ligands and measured cytokine production, TLR expression and NK cell function. Rate of fibrosis progression was calculated using posttransplant liver biopsies graded by Metavir scoring (F0-4; R=fibrosis stage/year posttransplant; rapid fibrosis defined as >0.4 units/year). Thirty of 70 (43%) patients had rapid fibrosis progression. PBMCs from HCV rapid-fibrosers produced less IFNα with TLR7/8 stimulation (p=0.039), less IL-6 at baseline (p=0.027) and with TLR3 stimulation (p=0.008) and had lower TLR3-mediated monocyte IL-6 production (p=0.028) compared with HCV slow fibrosers. TLR7/8-mediated NKCD56 dim cell secretion of IFNγ was impaired in HCV rapid fibrosis (p=0.006) independently of IFNα secretion and TLR7/8 expression, while cytotoxicity remained preserved. Impaired TLR3 and TLR7/8-mediated cytokine responses may contribute to aggressive HCV recurrence postliver transplantation through impaired immune control of HCV and subsequent activation of fibrogenesis.

Systems toxicology

The need for a more mechanistic understanding of the ways in which chemicals modulate biological pathways is urgent if we are to identify and better assess safety issues relating to a wide range of substances developed by the pharmaceutical, chemical, agri-bio, and cosmetic industries. Omics technologies provide a valuable opportunity to refine existing methods and provide information for so-called integrated testing strategies via the creation of signatures of toxicity. By mapping these signatures to underlying pathways of toxicity, some of which have been identified by toxicologists over the last few decades, and bringing them together with pathway information determined from biochemistry and molecular biology, a "systems toxicology" approach will enable virtual experiments to be conducted that can improve the prediction of hazard and the assessment of compound toxicity.

A roadmap for the development of alternative (non-animal) methods for systemic toxicity testing

Systemic toxicity testing forms the cornerstone for the safety evaluation of substances. Pressures to move from traditional animal models to novel technologies arise from various concerns, including: the need to evaluate large numbers of previously untested chemicals and new products (such as nanoparticles or cell therapies), the limited predictivity of traditional tests for human health effects, duration and costs of current approaches, and animal welfare considerations. The latter holds especially true in the context of the scheduled 2013 marketing ban on cosmetic ingredients tested for systemic toxicity. Based on a major analysis of the status of alternative methods (Adler et al., 2011) and its independent review (Hartung et al., 2011), the present report proposes a roadmap for how to overcome the acknowledged scientific gaps for the full replacement of systemic toxicity testing using animals. Five whitepapers were commissioned addressing toxicokinetics, skin sensitization, repeated-dose toxicity, carcinogenicity, and reproductive toxicity testing. An expert workshop of 35 participants from Europe and the US discussed and refined these whitepapers, which were subsequently compiled to form the present report. By prioritizing the many options to move the field forward, the expert group hopes to advance regulatory science.

Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets

The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n=400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment.

Temporal characteristics of evaluation anxiety

The temporal characteristics of evaluation anxiety are not well-defined by previous research. We examined the effects of length of the pre-evaluation interval (3, 6, or 12 minutes) and stage of the pre-evaluation interval at which evaluation anxiety was measured (start, middle, or end) on evaluation anxiety while participants performed an activity that was the focus of the impending evaluation. Participants wrote their opinion on a controversial social issue while anticipating a subject matter expert's judgment of their social maturity, and evaluation anxiety was measured by a battery of state anxiety measures. Higher levels of evaluation anxiety were detected on the Worry-Emotionality Questionnaire (WEQ) Worry subscale at the end of the pre-evaluation interval than at earlier stages, regardless of interval length, although individual difference variables exerted an important influence. Individuals with high trait self-presentation concerns experienced particularly high state anxiety (State-Trait Anxiety Inventory) at the start of the longest pre-evaluation interval. Low self-efficacy individuals showed a U-shaped pattern across pre-evaluation stages on both the WEQ Worry and Emotionality subscales, while high self-efficacy participants showed either no change (worry) or an inverted-U pattern (emotionality). Implications for the experimental measurement of evaluation anxiety were discussed.

A low molecular weight endometrial secretory protein which is increased by ovine trophoblast protein-1 is a beta 2-microglobulin-like protein

Ovine trophoblast protein-1 (oTP-1), stimulates the secretion of several proteins in explant culture of day-12 cyclic ovine endometrium. We partially purified and identified one of these proteins, an 11,000 Mr, pI approx. 6 protein by N-terminal amino acid sequencing and immunoprecipitation using antibody to human beta 2-microglobulin. The protein was purified from cultures of endometrium collected from day-16 pregnant ewes. The N-terminal amino acid sequence was 40-55% homologous to beta 2-microglobulin from a variety of species. Antibody to human beta 2-microglobulin immunoprecipitated the protein and another protein of similar molecular weight but more acidic pI. Using immunoprecipitation of radiolabelled proteins from culture, we demonstrated that oTP-1 increased production of this protein by 40% (P less than 0.05). We conclude that oTP-1 increases the secretion of a beta 2-microglobulin-like protein from day-12 non-pregnant endometrium in culture.

Methylphenidate and stimulus control of avoidance behavior

The introduction of a warning signal that preceded a scheduled shock modified the temporal distribution of free-operant avoidance responses. With response-shock and shock-shock intervals held constant, response rates increased only slightly when the response-signal interval was reduced. The result is consistent with Sidman's (1955) findings under different conditions, but at variance with Ulrich, Holz, and Azrin's (1964) findings under similar conditions. Methylphenidate in graded doses increased response rates, modifying frequency distributions of interresponse times. Drug treatment may have disrupted a "temporal discrimination" formed within the signal-shock interval. More simply, methylphenidate influenced response rates by increasing short response latencies after signal onset; this effect was more prominent than the drug's tendency to increase the frequency of pre-signal responses. When signal-onset preceded shock by 2 sec, individual differences in performance were marked; methylphenidate suppressed responding in one rat as a function of increasing dose levels to a greater degree than in a second animal, but both subjects received more shocks than under control conditions.