Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations

Oncology drug combinations can improve therapeutic responses and increase treatment options for patients. The number of possible combinations is vast and responses can be context-specific. Systematic screens can identify clinically relevant, actionable combinations in defined patient subtypes. We present data for 109 anticancer drug combinations from AstraZeneca's oncology small molecule portfolio screened in 755 pan-cancer cell lines. Combinations were screened in a 7 × 7 concentration matrix, with more than 4 million measurements of sensitivity, producing an exceptionally data-rich resource. We implement a new approach using combination Emax (viability effect) and highest single agent (HSA) to assess combination benefit. We designed a clinical translatability workflow to identify combinations with clearly defined patient populations, rationale for tolerability based on tumor type and combination-specific "emergent" biomarkers, and exposures relevant to clinical doses. We describe three actionable combinations in defined cancer types, confirmed in vitro and in vivo, with a focus on hematologic cancers and apoptotic targets.

SIGNIFICANCE

We present the largest cancer drug combination screen published to date with 7 × 7 concentration response matrices for 109 combinations in more than 750 cell lines, complemented by multi-omics predictors of response and identification of "emergent" combination biomarkers. We prioritize hits to optimize clinical translatability, and experimentally validate novel combination hypotheses. This article is featured in Selected Articles from This Issue, p. 695.

Defining the early stages of intestinal colonisation by whipworms

Whipworms are large metazoan parasites that inhabit multi-intracellular epithelial tunnels in the large intestine of their hosts, causing chronic disease in humans and other mammals. How first-stage larvae invade host epithelia and establish infection remains unclear. Here we investigate early infection events using both Trichuris muris infections of mice and murine caecaloids, the first in-vitro system for whipworm infection and organoid model for live helminths. We show that larvae degrade mucus layers to access epithelial cells. In early syncytial tunnels, larvae are completely intracellular, woven through multiple live dividing cells. Using single-cell RNA sequencing of infected mouse caecum, we reveal that progression of infection results in cell damage and an expansion of enterocytes expressing of Isg15, potentially instigating the host immune response to the whipworm and tissue repair. Our results unravel intestinal epithelium invasion by whipworms and reveal specific host-parasite interactions that allow the whipworm to establish its multi-intracellular niche.

Whipworms are large parasites causing chronic disease in humans and other mammals. Here, the authors show how larvae create tunnels inside the gut lining and reveal the early host response to infection via Isg15 in mice and murine caecaloids.

Effective drug combinations in breast, colon and pancreatic cancer cells

Combinations of anti-cancer drugs can overcome resistance and provide new treatments^1,2. The number of possible drug combinations vastly exceeds what could be tested clinically. Efforts to systematically identify active combinations and the tissues and molecular contexts in which they are most effective could accelerate the development of combination treatments. Here we evaluate the potency and efficacy of 2,025 clinically relevant two-drug combinations, generating a dataset encompassing 125 molecularly characterized breast, colorectal and pancreatic cancer cell lines. We show that synergy between drugs is rare and highly context-dependent, and that combinations of targeted agents are most likely to be synergistic. We incorporate multi-omic molecular features to identify combination biomarkers and specify synergistic drug combinations and their active contexts, including in basal-like breast cancer, and microsatellite-stable or KRAS-mutant colon cancer. Our results show that irinotecan and CHEK1 inhibition have synergistic effects in microsatellite-stable or KRAS–TP53 double-mutant colon cancer cells, leading to apoptosis and suppression of tumour xenograft growth. This study identifies clinically relevant effective drug combinations in distinct molecular subpopulations and is a resource to guide rational efforts to develop combinatorial drug treatments.

A survey of potency and efficacy of 2,025 clinically relevant two-drug combinations against 125 molecularly characterized breast, colorectal and pancreatic cancer cell lines identifies rare synergistic effects of anticancer drugs, informing rational combination treatments for specific cancer subtypes.

EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling

EROS (essential for reactive oxygen species) protein is indispensable for expression of gp91phox, the catalytic core of the phagocyte NADPH oxidase. EROS deficiency in humans is a novel cause of the severe immunodeficiency, chronic granulomatous disease, but its mechanism of action was unknown until now. We elucidate the role of EROS, showing it acts at the earliest stages of gp91phox maturation. It binds the immature 58 kDa gp91phox directly, preventing gp91phox degradation and allowing glycosylation via the oligosaccharyltransferase machinery and the incorporation of the heme prosthetic groups essential for catalysis. EROS also regulates the purine receptors P2X7 and P2X1 through direct interactions, and P2X7 is almost absent in EROS-deficient mouse and human primary cells. Accordingly, lack of murine EROS results in markedly abnormal P2X7 signalling, inflammasome activation, and T cell responses. The loss of both ROS and P2X7 signalling leads to resistance to influenza infection in mice. Our work identifies EROS as a highly selective chaperone for key proteins in innate and adaptive immunity and a rheostat for immunity to infection. It has profound implications for our understanding of immune physiology, ROS dysregulation, and possibly gene therapy.

An invariant Trypanosoma vivax vaccine antigen induces protective immunity

Trypanosomes are protozoan parasites that cause infectious diseases, including African trypanosomiasis (sleeping sickness) in humans and nagana in economically important livestock1,2. An effective vaccine against trypanosomes would be an important control tool, but the parasite has evolved sophisticated immunoprotective mechanisms-including antigenic variation3-that present an apparently insurmountable barrier to vaccination. Here we show, using a systematic genome-led vaccinology approach and a mouse model of Trypanosoma vivax infection4, that protective invariant subunit vaccine antigens can be identified. Vaccination with a single recombinant protein comprising the extracellular region of a conserved cell-surface protein that is localized to the flagellum membrane (which we term 'invariant flagellum antigen from T. vivax') induced long-lasting protection. Immunity was passively transferred with immune serum, and recombinant monoclonal antibodies to this protein could induce sterile protection and revealed several mechanisms of antibody-mediated immunity, including a major role for complement. Our discovery identifies a vaccine candidate for an important parasitic disease that has constrained socioeconomic development in countries in sub-Saharan Africa5, and provides evidence that highly protective vaccines against trypanosome infections can be achieved.

A systematic review to investigate the effect of digital antimicrobial stewardship tools on antimicrobial usage, length of stay, mortality and cost

Introduction

Antimicrobial drug resistance has been recognised by the World Health Organisation as ‘One of the biggest threats to global health today’.1 As the use of digital systems in the NHS increases, there is huge potential to use systems such as electronic prescribing and clinical decision support as part of Antimicrobial Stewardship Programmes (ASPs) i.e., initiatives to change prescribing practices to promote and monitor use of antimicrobials and preserve their future effectiveness. However, there is a lack of research that has investigated the impact of digital tools as part of ASPs.

Aim

We aimed to review the literature available on the use of digital antimicrobial stewardship tools on individual outcomes such as antimicrobial usage, length of stay, mortality and cost.

Methods

A systematic search was performed across three databases (Embase, MEDLINE and CINAHL) using MESH terms and key words relating to antimicrobial stewardship, hospitals, length of stay (LOS), clinical outcomes, cost and mortality. Duplicates were removed and articles screened at the title, abstract and full text stage by two authors (NT and RK) according to our inclusion and exclusion criteria. We included primary research articles that: had implemented an ASPs in an adult hospital setting for at least 6 months, reported antimicrobial usage as defined daily dose per 1000 patient days (DDD/1000) and at least one of the following outcomes: LOS, mortality or cost and discussed an ASP that included a digital component. Risk of bias assessment was performed using the Newcastle-Ottawa scale. We calculated the percentage change to determine the impact of digital ASPs across all outcomes using the formula (After - Before)/Before x 100 = % Change.

Before=pre-implementation results; after= results post-implementation

Results

We identified 3997 papers across all databases, and included 14 full texts that explored the impact of ASPs including a digital component (Figure 1). Of these, 14 papers reported the DDD/1000, 7 on mortality, 8 on LoS and 6 reported on cost. All studies evaluating DDD/1000 reported a decrease in antimicrobial usage ranging from -8.42% to -61.30%. Reductions in mortality (0 to -79%), LoS (25 to -27%) and costs (-8.42% to -69.19%) were also found. All ASPs utilised a digital component alongside a range of other interventions, such as the creation of formularies, guidelines and education emphasising the importance of using a combined approach in antimicrobial stewardship. Different interventions were found to have their own advantages, for example, education was key to sustainability and feedback was essential to improve prescribing practices. Users of the digital tools found that the tools were generally simple and user friendly, which facilitated their acceptance.

Conclusion

Our found that ASPs including a digital component were associated with reductions in antimicrobial usage, mortality, length of stay and cost. The positive effects were seen when such tools were combined with other approaches such as education and feedback approaches. We were unable to perform a meta-analysis due to the absence of confidence intervals and odds ratios in many of the included studies. Further research is needed to evaluate the cost-benefit associated with digital ASPs and whether sharing ASPs across multiple sites could reduce the maintenance burden for individual organisations.

References

1. World Health Organisation (2020), Antibiotic Resistance Factsheet, https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance [accessed on 18th October 2020]

Baseline Gut Microbiota Composition Is Associated With Schistosoma mansoni Infection Burden in Rodent Models

In spite of growing evidence supporting the occurrence of complex interactions between Schistosoma and gut bacteria in mice and humans, no data is yet available on whether worm-mediated changes in microbiota composition are dependent on the baseline gut microbial profile of the vertebrate host. In addition, the impact of such changes on the susceptibility to, and pathophysiology of, schistosomiasis remains largely unexplored. In this study, mice colonized with gut microbial populations from a human donor (HMA mice), as well as microbiota-wild type (WT) animals, were infected with Schistosoma mansoni, and alterations of their gut microbial profiles at 50 days post-infection were compared to those occurring in uninfected HMA and WT rodents, respectively. Significantly higher worm and egg burdens, together with increased specific antibody responses to parasite antigens, were observed in HMA compared to WT mice. These differences were associated to extensive dissimilarities between the gut microbial profiles of each HMA and WT groups of mice at baseline; in particular, the gut microbiota of HMA animals was characterized by low microbial alpha diversity and expanded Proteobacteria, as well as by the absence of putative immunomodulatory bacteria (e.g. Lactobacillus). Furthermore, differences in infection-associated changes in gut microbiota composition were observed between HMA and WT mice. Altogether, our findings support the hypothesis that susceptibility to S.mansoni infection in mice is partially dependent on the composition of the host baseline microbiota. Moreover, this study highlights the applicability of HMA mouse models to address key biological questions on host-parasite-microbiota relationships in human helminthiases.

Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

In order to control and eradicate epidemic cholera, we need to understand how epidemics begin, how they spread, and how they decline and eventually end. This requires extensive sampling of epidemic disease over time, alongside the background of endemic disease that may exist concurrently with the epidemic. The unique circumstances surrounding the Argentinian cholera epidemic of 1992-1998 presented an opportunity to do this. Here, we use 490 Argentinian V. cholerae genome sequences to characterise the variation within, and between, epidemic and endemic V. cholerae. We show that, during the 1992-1998 cholera epidemic, the invariant epidemic clone co-existed alongside highly diverse members of the Vibrio cholerae species in Argentina, and we contrast the clonality of epidemic V. cholerae with the background diversity of local endemic bacteria. Our findings refine and add nuance to our genomic definitions of epidemic and endemic cholera, and are of direct relevance to controlling current and future cholera epidemics.

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens

Low success rates during drug development are due, in part, to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs with genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate cellular drug mechanism-of-action. We observed an enrichment for positive associations between the profile of drug sensitivity and knockout of a drug's nominal target, and by leveraging protein-protein networks, we identified pathways underpinning drug sensitivity. This revealed an unappreciated positive association between mitochondrial E3 ubiquitin-protein ligase MARCH5 dependency and sensitivity to MCL1 inhibitors in breast cancer cell lines. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic data sets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.

AB1332-HPR ASSESSING THE PATIENT EXPERIENCE OF LUPUS NEPHRITIS: DEVELOPMENT OF A CONCEPTUAL MODEL AND REVIEW OF EXISTING PATIENT-REPORTED OUTCOME (PRO) MEASURES

Background:

Lupus nephritis (LN) is an autoimmune disease characterized by inflammation of the kidneys as a result of systemic lupus erythematosus (SLE). Approximately 50% of SLE patients will develop LN, which is considered to be one of the most severe manifestations of SLE and the leading cause of morbidity and mortality in SLE. While there is ample existing evidence on disease experience and PROs used in extra-renal SLE, little research has been done in LN. Qualitative interviews with patients can help identify concepts that are both important and relevant to the patient. In order to effectively evaluate treatment benefit, it is critical that PRO measures used to assess such concepts and define clinical trial endpoints are fit for purpose and have strong evidence of content validity in the specific context of use.

Objectives:

The objective of this study was to understand the patient experience of LN and to identify and characterize the signs and symptoms of LN and their impact on health-related quality of life (HRQoL) through the development of a disease-specific conceptual model. This model was then used to evaluate the content validity of existing PRO measures available for use in LN.

Methods:

A structured literature search was conducted in Medline, Embase and PsycINFO to identify qualitative research articles documenting the patient experience of LN. PRO measures developed or commonly used to assess patient experiences of LN were also identified. Semi-structured concept elicitation interviews were conducted with 15 adult patients in the US with a clinician-confirmed diagnosis of LN (defined in accordance with established clinical guidelines). Supplementary qualitative data were also collected from a review of publicly available online blogs/forums. Findings were used to inform the development of a conceptual model detailing the impact of LN signs, symptoms and HRQoL and evaluate the validity of existing measures used within LN.

Results:

Searches revealed a paucity of qualitative research conducted with LN patients, supporting the need for prospective research in LN. Consistent with existing literature in SLE, the core signs and symptoms identified from the qualitative literature review, interviews and blog/forum review included joint pain, fatigue, joint stiffness, swelling (particularly in the extremities) and skin rashes. LN patients also reported urinary frequency, urgency, foamy urine and blood in their urine. Disease impact on physical functioning, activities of daily living, emotions, social life, work/finances and sleep were reported. PRO measures commonly used to evaluate patient experiences in LN included the SF-36, LupusQOL, LupusPRO, SLE Symptom Checklist, KDQoL and KSQ. Conceptual mapping of instruments against the newly developed conceptual model (Figure 1) highlighted that no single measure provides a comprehensive assessment of all symptoms/impact important to LN patients. Furthermore, items are largely focused on impact of symptoms with few items on symptom severity.

Figure 1.

Conceptual model of lupus nephritis symptoms and associated impacts

Conclusion:

The presentation of signs and symptoms in LN patients appears similar to those reported in extra-renal SLE populations, with the addition of swelling and urinary symptoms. Qualitative research with LN patients guided the development of a comprehensive LN conceptual model outlining the disease experience from the patients’ perspective. These insights can be useful to inform PRO measurement strategies for clinical trials in LN.

Acknowledgments:

With thanks to Dr. Betty Diamond and Dr. David Wofsy for their collaboration and helpful insights

Disclosure of Interests:

Pamela Berry Employee of: Janssen, Kate Burrows Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract, Rebecca Hall Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract., Adam Gater Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract, Helena Bradley Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract, Amy Ward Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract, Chloe Tolley Consultant of: Adelphi Values a health outcomes research company commissioned by Janssen to conduct the research reported in this abstract, Patricia Delong Employee of: Janssen, Elizabeth C Hsia Shareholder of: Johnson & Johnson, Employee of: Janssen Research & Development, LLC

HaemoPREF: Further evaluation of patient perception and preference for treatment in a real world setting

INTRODUCTION

Adherence to haemophilia A (HA) treatment may be influenced by patients' beliefs about their condition and treatment. Furthermore, difficulties administering treatment may lead to poor adherence. New treatment strategies aim to reduce the burden associated with administration and to improve patient perception of treatment, which, in turn, increase adherence levels.

AIMS

This study aimed to examine patient perception of HA treatment and related factors using patient-reported outcome (PRO) questionnaires and to confirm the psychometric properties of a recently developed questionnaire, the HaemoPREF.

METHODS

A non-interventional, cross-sectional, questionnaire study was conducted with adult HA patients in Spain (n=31), Germany (n=10) and Italy (n=48), who were using ReFacto AF with the FuseNGo administration device. Patients completed the HaemoPREF and other questionnaires measuring related constructs: treatment adherence, satisfaction and well-being, online at two time points. Correlational, regression and psychometric analyses were conducted.

RESULTS

PRO scores indicated that patients are satisfied with and adherent to their treatment. Multivariate regression of the HaemoPREF global score identified a number of significant predictors (P≤.05). The HaemoPREF Global Score had a moderate relationship with subscales on the related questionnaires (mean correlation=0.43; range=0.39-0.48). The HaemoPREF demonstrated good test-retest reliability (intraclass correlation coefficient=0.82), internal consistency reliability (Cronbach's alpha range=0.69-0.82) and convergent validity with measures of treatment satisfaction (Spearman correlation coefficient, r=.48) and well-being (r=.41).

CONCLUSION

The findings suggest that patients using ReFacto AF with FuseNGo were satisfied with and adherent to their treatment. The HaemoPREF can identify important concepts relating to patient treatment experience in HA.