Dr Shamith Samarajiwa

Regulatory Dynamics, Genomics and Data Science

Systems Immunology

Cancer Immunotherapy

Systems Immunology: I develop integrative data science approaches to understand the biology of Innate Immunity, Inflammation and Cancer at a Systems level. Specifically, we study Interferons and other innate immune modulators that play important roles in both health and disease. The IFNs mediate their multiple functions by regulating a set of genes known as interferon-stimulated genes (ISGs). In order to understand the impact of IFNs in disease, we built INTERFEROME, a resource of IFN regulated genes and InterferonScape, an integrative web-based systems biology application developed to investigate ISG pathways, networks and regulation. We're particularly interested in the regulatory dynamics of immune epigenomes. Integrating and mining these using both statistical & AI (machine and deep learning) methods we are unravelling the complexities of innate immune responses in cancer and other diseases.

Key publications:

Samarajiwa, S.A., Mangan N.E., Hardy, M.P., Najdovska, M., Dubach, D., Noppert S-J, Owczarek C.M. and Hertzog, P.J "Soluble IFN receptor potentiates in vivo IFN beta signaling and exacerbates TLR4 mediated septic shock" J Immunol.. 2014 April; PMID 24696235

Bidwell BN, Slaney CY, Withana NP, Forster S, Cao Y, Loi S, Andrews D, Mikeska T, Mangan NE, Samarajiwa SA, de Weerd NA, Gould J, Argani P, Möller A, Smyth MJ, Anderson RL, Hertzog PJ, Parker BS. Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape. Nat Med. 2012 Jul 22. doi: 10.1038/nm.2830.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group; Co-chairs, Caldas C, Aparicio S; Writing committee, Curtis C, Shah SP, Caldas C, Aparicio S; Steering committee, Brenton JD, Ellis I, Huntsman D, Pinder S, Purushotham A, Murphy L, Caldas C, Aparicio S."The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups." Nature 2012 April PMID: 22522925

Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell. 2012 Jul 27;47(2):203-14.

Hertzog P, Forster S, Samarajiwa S. "Systems biology of interferon responses." J Interferon Cytokine Res. 2011 Jan; 31(1):5-11. PMID: 21226606

Narita M, Young AR, Arakawa S, Samarajiwa SA, Nakashima T, Yoshida S, Hong S, Berry LS, Reichelt S, Ferreira M, Tavaré S, Inoki K, Shimizu S, Narita M. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science. 2011 May 20;332(6032):966-70.

Harman AN, Lai J, Turville S, Samarajiwa S, Gray L, Marsden V, Mercier S, Jones K, Nasr N, Rustagi A, Cumming H, Donaghy H, Mak J, Gale M Jr, Churchill M, Hertzog P and Cunningham AL. "HIV infection of dendritic cells subverts the interferon induction pathway and inhibits Type 1 interferon production" Blood. 2011 May PMID: 21411754

Samarajiwa SA, Forster S, Auchettl K, Hertzog PJ. INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res. 2009 Jan;37(Database issue):D852-7.

de Weerd NA, Samarajiwa SA, Hertzog PJ. Type I interferon receptors: biochemistry and biological functions. J Biol Chem. 2007 Jul 13;282(28):20053-7.

Shamith Samarajiwa, William Wilson, Paul Hertzog 2006 “Type I Interferons: Genetics and Structure” in “The Interferons: characterization and application” Ed. Anthony Meager, Wiley-VCH.

Other publications: