Our laboratory takes a single cell systems biology approach to studying how haematopoietic stem cells ultimately generate all of the red and white blood cells of the immune system.

We are a very technology-driven lab with the philosophy that studying single cells at different functional and molecular levels, and integrating this information, will reveal the mechanisms behind their fate specification in health and disease. To this purpose, we perform single cell analysis in vivo using:

  • cellular barcoding
  • cell division tracking in vitro using long-term imaging for family tree construction
  • single cell RNA-sequencing for lineage priming program identification.

Combined, we anticipate this suite of tools will allow us to gain a high-resolution understanding into the principles and molecular mechanism governing development and the establishment of lineage fate in normal and cancerous tissues, with view to therapeutic interventions.


Selected publications from Prof Shalin Naik

Schlitzer A, Sivakamasundari V, Chen J, Sumatoh HR, Schreuder J, Lum J, Malleret B, Zhang S, Larbi A, Zolezzi F, Renia L, Poidinger M, Naik S, Newell EW, Robson P, Ginhoux F. Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat Immunol. 2015 Jul;16(7):718-28 PMID: 26054720

Sathe P, Metcalf D, Vremec D, Naik SH, Langdon WY, Huntington ND, Wu L, Shortman K. Lymphoid tissue and plasmacytoid dendritic cells and macrophages do not share a common macrophage-dendritic cell-restricted progenitor. Immunity. 2014 Jul 17;41(1):104-15. PMID: 25035955.

Naik SH, Schumacher TN, Perie L. Cellular barcoding: a technical appraisal. Exp Hematol. 2014 Aug;42(8):598-608. PMID: 24996012.

Guilliams M, Ginhoux F, Jakubzick C, Naik SH, Onai N, Schraml BU, Segura E, Tussiwand R, Yona S. Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny. Nat Rev Immunol. 2014 Aug;14(8):571-8. PMID: 25033907.

Naik SH, Perie L, Swart E, Gerlach C, van Rooij N, de Boer RJ, Schumacher TN. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature. 2013 Apr 11;496(7444):229-32. PMID: 23552896.

Gerlach C, Rohr JC, Perie L, van Rooij N, van Heijst JW, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TN. Heterogeneous differentiation patterns of individual CD8+ T cells. Science. 2013 May 3;340(6132):635-9. PMID: 23493421.

Naik SH. Demystifying the development of dendritic cell subtypes, a little. Immunol Cell Biol. 2008 Jul;86(5):439-52. PMID: 18414430.

Shortman K, Naik SH. Steady-state and inflammatory dendritic-cell development. Nat Rev Immunol. 2007 Jan;7(1):19-30. PMID: 17170756.

Naik SH, Sathe P, Park HY, Metcalf D, Proietto AI, Dakic A, Carotta S, O’Keeffe M, Bahlo M, Papenfuss A, Kwak JY, Wu L, Shortman K. Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo. Nat Immunol. 2007 Nov;8(11):1217-26. PMID: 17922015.

Naik SH, Metcalf D, van Nieuwenhuijze A, Wicks I, Wu L, O’Keeffe M, Shortman K. Intrasplenic steady-state dendritic cell precursors that are distinct from monocytes. Nat Immunol. 2006 Jun;7(6):663-71. PMID: 16680143.

Lab research projects

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