Baillie lab, Roslin Institute,
University of Edinburgh


Translational genomics in critical illness


We are trying to understand the mechanisms that make people desperately sick in sepsis, influenza and emerging infections, so that we can find ways to help them survive and recover. Since there is biological variation in the host response to injury, and some of this variation is genetic, we can use this genetic variation to find new treatments.

Combining signals by meta-analysis

We develop and use computational methods to combine data from different sources. The ultimate aim is to use these signals to lead us to biological processes that might be amenable to treatment. We influenza as a model for the broader host response to critical injury.

We develop and apply computational tools, and use in vitro and in vivo genome editing with CRISPR to generate and test hypotheses.

Read a summary of our approach in this perspective article:
Baillie JK. Translational genomics: targeting the host immune response to fight infection. Science (New York, N.Y.): 2014;344: 807-8. doi:10.1126/science.1255074

MAIC results for host genes implicated in influenza virus replication. This graph is a representation of the shared information content between each data source after MAIC. Size of data source blocks is proportional to information content – i.e. the total MAIC scores contributed by each data source. Lines showing shared information content are colored according to the dominant data source.

Combining CRISPR screen with diverse experimental sources: meta-analysis by information content (MAIC)


Using genome-wide CRISPR knockdown in human cells, we found 121 host genes that the flu virus needs to replicate itself. About half of them are new discoveries, and might make good therapeutic targets (https://www.nature.com/articles/s41467-019-13965-x). This is important because we've argued for a while that if we design drugs to target these host genes/proteins, it will be harder for the virus to evolve resistance to our treatments (http://dx.doi.org/10.1126/science.1255074).

We found a lot of new genes, but we also validated many findings from previous groups. So we've taken the concept of meta-analysis - well established in clinical research - into basic science.

We developed an algorithm called meta-analysis by information content (MAIC) to integrate our new findings with many previous studies of host genes required by flu.

Click here to run a MAIC analysis or view the published results for influenza virus host factors.

Code to run the MAIC algorithm can be downloaded from github.com/baillielab/maic.

Li B et al. Nature Communications 11:164(2020)

Combining genetic signals with cellular transcriptomics: coexpression of GWAS hits


Our post-GWAS analysis method (network density analysis; NDA) reveals new biological features of numerous disease states and traits. It works by examining a coexpression network of transcription start sites (discovered in FANTOM5). We find that transcripts containing GWAS hits for a given trait tend to fall into more dense groupings in the coexpression network than randomly-selected transcripts.

NDA demonstrates that GWAS hits for a given disease tend to be near promoter/enhancer elements with similar expression profiles, which enables us to find more hits, fine map probable causative SNPs, and implicate cell types in pathogenesis. Surprisingly, for some diseases, the underlying variants fall into distinct functional groups, suggesting either dual mechanisms of disease, or distinct disease endotypes.

Click here to run an analysis or view the published results.

Baillie JK et al. Shared Activity Patterns Arising at Genetic Susceptibility Loci Reveal Underlying Genomic and Cellular Architecture of Human Disease.PLOS Computational Biology 14, no. 3 (March 1, 2018): e1005934. PMC5849332.

Pairwise coexpression networks derived from GWAS results. Each coloured ball indicates a transcription start region containing a GWAS-associated variant. Red - significantly coexpressed by network density analysis. Light blue - all other transcription region containing GWAS-associated variants for this phenotype.

(3d visualisation by vasturiano)
Gene set hypothesis testing.

Combining biological hypotheses with genetic signals: gene set hypothesis testing


The lack of specific hypotheses in traditional genome-wide association studies has a disadvantage - it greatly limits the statistical power, ensuring that only the strongest signals can be detected, even with very large numbers of subjects.

Gene set hypothesis testing (GSHT) enables investigators to take a biological hypothesis and test it using GWAS data. For example, in our paper, we tested the hypothesis that failure to downregulate inflammatory signals during macrophage maturation is a key mechanism in the pathogenesis of Crohn's disease. We defined search criteria to find inflammatory genes that are downregulated during macrophage differentiation, and then empirically tested the hypothesis that these genes are likely to be associated with Crohn's disease.

Baillie, J. K. et al. PLOS Genetics 13, e1006641 (Mar. 6, 2017).

Testing guilt-by-association: FANTOM5


In the FANTOM5 consortium we showed that, with a sufficiently rich expression dataset, it is possible to infer functional relationships between genes (and other transcribed elements in the genome, such as enhancers and lncRNAs) by grouping them according to similarities in expression. We proved this using known pathways, but the real value of this finding is that it enables us to discover relationships between genomic regions about which almost nothing is already known.

Forrest*, Kawaji*, Rehli*, Baillie*, et al. A promoter-level mammalian expression atlas. Nature: 2014;507: 462-70. PMC4529748
FANTOM5 coexpression network

Stratified medicine


Throughout the history of medicine, progress has been made by recognizing patterns of disease, or syndromes. When new technologies are invented, they can reveal observable characteristics that have close relationships to disease trajectories, outcomes, and most importantly of all, response to therapy. Genomics and transcriptomics have these properties, but raise an additional challenge: the scale of the data is such that detecting relevant signals is a substantial computational and mathematical challenge.

Scicluna BP , Baillie JK. The Search for Efficacious New Therapies in Sepsis Needs to Embrace Heterogeneity. American Journal of Respiratory and Critical Care Medicine: 2018;doi:10.1164/rccm.201811-2148ED
Russell, C. D. & Baillie, J. K. Treatable traits and therapeutic targets: Goals for systems biology in infectious disease. Current Opinion in Systems Biology 2, 139–145 (Apr. 2017).
Applications of computational biology in critical care medicine.

Key papers

Russell CD , Millar JE, Baillie JK. Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet (London, England): 2020; doi:10.1016/S0140-6736(20)30317-2

Li B , Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, ..., Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nature Communications: 2020; 11: 164. doi:10.1038/s41467-019-13965-x

Clohisey S , Baillie JK. Host susceptibility to severe influenza A virus infection. Critical Care (London, England): 2019; 23: 303. doi:10.1186/s13054-019-2566-7

Bretherick AD , Canela-Xandri O, Joshi PK, Clark DW, Rawlik K, Boutin TS, Zeng Y, Amador C, Navarro P, Rudan I, ..., Ponting*, Chris P., Baillie*, J Kenneth, Haley*, Chris. Proteome-by-Phenome Mendelian Randomisation Detects 38 Proteins with Causal Roles in Human Diseases and Traits bioRxiv: 2019; 631747. doi:10/gf2zwm

Clohisey S , Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, Consortium F, Summers KM, Carninci P, Forrest AA, ..., Baillie JK. Comprehensive Characterisation of Molecular Host-Pathogen Interactions in Influenza A Virus-Infected Human Macrophages bioRxiv: 2019; 670919. doi:10/gf5dvf

Neyton L , Zheng X, Skouras C, Wilson AB, Gutmann MU, Yau C, Uings IJ, Rao FV, Nicolas A, Marshall C, ..., Baillie*, J Kenneth, Mole*, Damian James. Multiomic Definition of Generalizable Endotypes in Human Acute Pancreatitis. bioRxiv: 2019; 539569. doi:10/gf2zwn

Baillie JK , Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, ..., Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Computational Biology: 2018; 14: e1005934. PMC5849332

Roach RC , Hackett PH, Oelz O, Bärtsch P, Luks AM, MacInnis MJ, Baillie JK. The 2018 Lake Louise Acute Mountain Sickness Score. High Altitude Medicine and Biology: 2018; 19: 4-6. PMC6191821

Baillie JK , Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest ARR, Hayashizaki Y, Faulkner GJ, ..., Hume DA. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genetics: 2017; 13: e1006641. PMC5358891

Arabi YM , Balkhy HH, Hayden FG, Bouchama A, Luke T, Baillie JK, Al-Omari A, Hajeer AH, Senga M, Denison MR, Nguyen-Van-Tam JS, ..., Fowler RA. Middle East Respiratory Syndrome. The New England Journal of Medicine: 2017; 376: 584-594. PMC5362064

Grabert K , Michoel T, Karavolos MH, Clohisey S, Baillie JK, Stevens MP, Freeman TC, Summers KM, McColl BW. Microglial brain region-dependent diversity and selective regional sensitivities to aging. Nature Neuroscience: 2016; 19: 504-16. PMC4768346

Arner E , Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AMN, Arner P, Axton R, Baillie JK, ..., Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (New York, N.Y.): 2015; 347: 1010-4. PMC4681433

Hall DP , MacCormick IJC, Phythian-Adams AT, Rzechorzek NM, Hope-Jones D, Cosens S, Jackson S, Bates MGD, Collier DJ, Hume DA, ..., Baillie JK. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness. PloS One: 2014; 9: e81229. PMC3898916

Forrest ARR*, Kawaji H*, Rehli M*, Baillie JK* , de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ..., Hayashizaki Y. A promoter-level mammalian expression atlas. Nature: 2014; 507: 462-70. PMC4529748

Dunning JW , Merson L, Rohde GGU, Gao Z, Semple MG, Tran D, Gordon A, Olliaro PL, Khoo SH, Bruzzone R, ..., Baillie JK. Open source clinical science for emerging infections. The Lancet. Infectious Diseases: 2014; 14: 8-9. doi:10.1016/S1473-3099(13)70327-X

Baillie JK . Translational genomics. Targeting the host immune response to fight infection. Science (New York, N.Y.): 2014; 344: 807-8. doi:10.1126/science.1255074

Andersson R , Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, ..., Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature: 2014; 507: 455-461. PMC5215096

Shukla R , Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, ..., Faulkner GJ. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell: 2013; 153: 101-11. PMC3898742

Baillie JK , Digard P. Influenza–time to target the host? The New England Journal of Medicine: 2013; 369: 191-3. doi:10.1056/NEJMcibr1304414

Everitt AR , Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ, ..., Baillie JK, Walsh TS, Hume DA, Palotie A, Xue Y, Colonna V, Tyler-Smith C, Dunning J, Gordon SB, Smyth RL, Openshaw PJ, Dougan G, Brass AL, Kellam P. IFITM3 restricts the morbidity and mortality associated with influenza. Nature: 2012; 484: 519-23. PMC3648786

Baillie JK , Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, ..., Faulkner GJ. Somatic retrotransposition alters the genetic landscape of the human brain. Nature: 2011; 479: 534-7. PMC3224101


Funding

We are very grateful to recieve funding from the following sources: Wellcome Trust, BBSRC, Sepsis Research (FEAT), Intensive Care Society, MRC.

Contact

Email: web_enquiries@baillielab.net