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Background Breast cancer (BC) has the highest cancer incidence and mortality in women worldwide. Observational epidemiological studies suggest a positive association between testosterone, estradiol, dehydroepiandrosterone sulphate (DHEAS) and other sex steroid hormones with postmenopausal BC. We used a two-sample Mendelian randomization analysis to investigate this association. Methods Genetic instruments for nine sex steroid hormones and sex hormone-binding globulin (SHBG) were obtained from genome-wide association studies (GWAS) of UK Biobank (total testosterone (TT) N: 230,454, bioavailable testosterone (BT) N: 188,507 and SHBG N: 189,473), The United Kingdom Household Longitudinal Study (DHEAS N: 9722), the LIFE-Adult and LIFE-Heart cohorts (estradiol N: 2607, androstenedione N: 711, aldosterone N: 685, progesterone N: 1259 and 17-hydroxyprogesterone N: 711) and the CORtisol NETwork (CORNET) consortium (cortisol N: 25,314). Outcome GWAS summary statistics were obtained from the Breast Cancer Association Consortium (BCAC) for overall BC risk (N: 122,977 cases and 105,974 controls) and subtype-specific analyses. Results We found that a standard deviation (SD) increase in TT, BT and estradiol increased the risk of overall BC (OR 1.14, 95% CI 1.09–1.21, OR 1.19, 95% CI 1.07–1.33 and OR 1.03, 95% CI 1.01–1.06, respectively) and ER + BC (OR 1.19, 95% CI 1.12–1.27, OR 1.25, 95% CI 1.11–1.40 and OR 1.06, 95% CI 1.03–1.09, respectively). An SD increase in DHEAS also increased ER + BC risk (OR 1.09, 95% CI 1.03–1.16). Subtype-specific analyses showed similar associations with ER+ expressing subtypes: luminal A-like BC, luminal B-like BC and luminal B/HER2-negative-like BC. Conclusions TT, BT, DHEAS and estradiol increase the risk of ER+ type BCs similar to observational studies. Understanding the role of sex steroid hormones in BC risk, particularly subtype-specific risks, highlights the potential importance of attempts to modify and/or monitor hormone levels in order to prevent BC.

BackgroundBreast cancer (BC) is the cancer with the highest incidence and mortality in women worldwide. Observational epidemiological studies suggest a positive association between testosterone, estradiol, dehydroepiandrosterone sulphate (DHEAS) and both pre- and post-menopausal BC. Since previous studies may be prone to bias and confounding, we used a two-sample Mendelian randomization (MR) analysis to investigate this association.MethodsGenetic instruments for nine sex steroid hormones and sex hormone binding globulin (SHBG) were obtained from genome-wide association studies (GWAS) conducted in the UK Biobank (total testosterone (TT) N:230,454, bioavailable testosterone (BT) N: 188,507 and SHBG N: 189,473), The United Kingdom Household Longitudinal Study (DHEAS N: 9,722), the LIFE-Adult and LIFE-Heart cohorts (estradiol N: 2,607), the LIFE-Heart cohort only (androstenedione N: 711, aldosterone N: 685, progesterone N: 1,259 and 17-hydroxyprogesterone N: 711) and the CORtisol NETwork (CORNET) consortium (cortisol N: 25,314). GWAS summary statistics were also obtained from the Breast Cancer Association Consortium (BCAC) for overall BC risk (N: 122,977 cases and 105,974 controls) and BC mortality (96,661 BC cases and 7,697 BC-specific deaths). Subtype specific analysis were carried out for incidence of estrogen receptor (ER)+ BC, ER- BC, luminal A-like BC, luminal B-like BC, luminal B/HER2-negative-like BC, HER2-enriched-like BC, triple negative BC (TNBC) and BRCA1 mutated TNBC.ResultsUsing an inverse-variance weighted (IVW) approach, we found that a standard deviation (SD) increase in TT, BT and estradiol increased the risk of overall BC (OR: 1.14, 95% CI: 1.09-1.21, OR: 1.19, 95% CI: 1.07-1.33 and OR: 1.03, 95% CI: 1.01-1.06, respectively) and ER+ BC (OR: 1.19, 95% CI: 1.12-1.27, OR: 1.25, 95% CI: 1.11-1.40 and OR: 1.06, 95% CI: 1.03-1.09, respectively). A SD increase in DHEAS also increased ER+ BC risk (OR: 1.09, 95% CI: 1.03-1.09). Subtype specific analyses showed similar associations with ER+ expressing subtypes: luminal A-like BC, luminal B-like BC and luminal B/HER2-negative-like BC. A SD increase in cortisol was associated with poor survival after a diagnosis of ER-BC (HR: 2.35, 95% CI: 1.00-5.49).Discussion/ConclusionTT, BT, DHEAS and estradiol increase the risk of ER+ type BCs similar to observational studies, but none of these hormone measures are associated with BC survival. We found some evidence that cortisol reduced ER- BC survival. Stronger genetic instruments are required before definitive conclusions can be made about the role of other sex-steroid hormones in breast cancer. Understanding the role of sex steroid hormones in BC risk, particularly subtype-specific risks, highlights the potential importance of attempts to modify and/or monitor hormone levels in order to prevent BC.

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Motivation Computational approaches for predicting drug–target interactions (DTIs) can provide valuable insights into the drug mechanism of action. DTI predictions can help to quickly identify new promising (on-target) or unintended (off-target) effects of drugs. However, existing models face several challenges. Many can only process a limited number of drugs and/or have poor proteome coverage. The current approaches also often suffer from high false positive prediction rates. Results We propose a novel computational approach for predicting drug target proteins. The approach is based on formulating the problem as a link prediction in knowledge graphs (robust, machine-readable representations of networked knowledge). We use biomedical knowledge bases to create a knowledge graph of entities connected to both drugs and their potential targets. We propose a specific knowledge graph embedding model, TriModel, to learn vector representations (i.e. embeddings) for all drugs and targets in the created knowledge graph. These representations are consequently used to infer candidate drug target interactions based on their scores computed by the trained TriModel model. We have experimentally evaluated our method using computer simulations and compared it to five existing models. This has shown that our approach outperforms all previous ones in terms of both area under ROC and precision–recall curves in standard benchmark tests. Availability and implementation The data, predictions and models are available at: drugtargets.insight-centre.org. Supplementary information Supplementary data are available at Bioinformatics online.

Background: Evidence for aspirin's chemopreventative properties on colorectal cancer (CRC) is substantial, but its mechanism of action is not well-understood. We combined a proteomic approach with Mendelian randomization (MR) to identify possible new aspirin targets that decrease CRC risk. Methods: Human colorectal adenoma cells (RG/C2) were treated with aspirin (24 hours) and a stable isotope labeling with amino acids in cell culture (SILAC) based proteomics approach identified altered protein expression. Protein quantitative trait loci (pQTLs) from INTERVAL (N = 3,301) and expression QTLs (eQTLs) from the eQTLGen Consortium (N = 31,684) were used as genetic proxies for protein and mRNA expression levels. Two-sample MR of mRNA/protein expression on CRC risk was performed using eQTL/pQTL data combined with CRC genetic summary data from the Colon Cancer Family Registry (CCFR), Colorectal Transdisciplinary (CORECT), Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia and UK Biobank (55,168 cases and 65,160 controls). Results: Altered expression was detected for 125/5886 proteins. Of these, aspirin decreased MCM6, RRM2, and ARFIP2 expression, and MR analysis showed that a standard deviation increase in mRNA/protein expression was associated with increased CRC risk (OR: 1.08, 95% CI, 1.03–1.13; OR: 3.33, 95% CI, 2.46–4.50; and OR: 1.15, 95% CI, 1.02–1.29, respectively). Conclusions: MCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation, indicating a possible role in aspirin's reduction of metastasis. Impact: Our approach has shown how laboratory experiments and population-based approaches can combine to identify aspirin-targeted proteins possibly affecting CRC risk.

Understanding the different effects of chemical substances on human proteins is fundamental for designing new drugs. It is also important for elucidating the different mechanisms of action of drugs that can cause side-effects. In this context, computational methods for predicting chemical-protein interactions can provide valuable insights on the relation between therapeutic chemical substances and proteins. Their predictions therefore can help in multiple tasks such as drug repurposing, identifying new drug side-effects, etc. Despite their useful predictions, these methods are unable to predict the different implications — such as change in protein expression, abundance, etc, — of chemical — protein interactions. Therefore, In this work, we study the modelling of chemical-protein interactions’ effects on proteins activity using computational approaches. We hereby propose using 3D tensors to model chemicals, their target proteins and the effects associated to their interactions. We then use multi-part embedding tensor factorisation to predict the different effects of chemicals on human proteins. We assess the predictive accuracy of our proposed method using a benchmark dataset that we built. We then show by computational experimental evaluation that our approach outperforms other tensor factorisation methods in the task of predicting effects of chemicals on human proteins.

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Complex biological systems are traditionally modelled as graphs of interconnected biological entities. These graphs, i.e. biological knowledge graphs, are then processed using graph exploratory approaches to perform different types of analytical and predictive tasks. Despite the high predictive accuracy of these approaches, they have limited scalability due to their dependency on time-consuming path exploratory procedures. In recent years, owing to the rapid advances of computational technologies, new approaches for modelling graphs and mining them with high accuracy and scalability have emerged. These approaches, i.e. knowledge graph embedding (KGE) models, operate by learning low-rank vector representations of graph nodes and edges that preserve the graph s inherent structure. These approaches were used to analyse knowledge graphs from different domains where they showed superior performance and accuracy compared to previous graph exploratory approaches. In this work, we study this class of models in the context of biological knowledge graphs and their different applications. We then show how KGE models can be a natural fit for representing complex biological knowledge modelled as graphs. We also discuss their predictive and analytical capabilities in different biology applications. In this regard, we present two example case studies that demonstrate the capabilities of KGE models: prediction of drug target interactions and polypharmacy side effects. Finally, we analyse different practical considerations for KGEs, and we discuss possible opportunities and challenges related to adopting them for modelling biological systems. The work presented in this paper was supported by the CLARIFY project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 875160, and by Insight research centre supported by the Science Foundation Ireland (SFI) grant (12/RC/2289_2) peer-reviewed 2021-02-17

The field of drug discovery has entered a plateau stage lately. It is increasingly more expensive and time-demanding to introduce new drugs into the market. One of the main reasons is the slow progress in finding novel targets for drug candidates and the lack of insight in terms of the associated mechanisms of action. Current works in this area mainly utilise different chemical, genetic and proteomic methods, which are limited in terms of the scalability of experimentation and the scope of studied drugs and targets per experiment. This is mainly due to their dependency on laboratory experiments and available physical resource. This has led to an increasing importance of computational methods for the identification of candidate drug targets. In this work, we introduce a novel computational approach for predicting drug target proteins. We approach the problem as a link prediction task on knowledge graphs. We process drug and target information as a knowledge graph of interconnected drugs, proteins, disease, pathways and other relevant entities. We then apply knowledge graph embedding (KGE) models over this data to enable scoring drug-target associations, where we employ a customised version of state-of-the-art KGE model ComplEx. We generate a benchmarking dataset based on KEGG database to train and evaluate our method. Our experiments show that our method achieves best results in comparison to other traditional KGE models. Specifically, the method predicts drug target links with mean reciprocal rank (MRR) of 0.78 and Hits@10 of 0.88. This provides a promising basis for further experimentation and comparisons with domain-specific predictive models. This work has been supported by Insight Centre for Data Analytics at National University of Ireland Galway, Ireland (supported by the Science Foundation Ireland grant 12/RC/2289). The GPU card used in our experiments is granted to us by the Nvidia GPU Grant Program. peer-reviewed 2019-04-08