Flow Cytometry Core Facility

Staff Profile

Dr Andrew Filby

Flow Cytometry Core Facility Director (SESO)

Background

I am currently director of the Flow CytometryCore Facility (FCCF) at Newcastle University (NU), also part of the Newcastle University Single Cell Unit (NUSCU).  This is a world-renowned facility supporting cutting-edge research through the provision of a comprehensive cytomics resource to both internal and external research groups, operating at the forefront of cytometric applications and method-focused research.  As part of this role, my group have been developing, validating and applying both imaging and non-imaging cytometry-based methods to study several important aspects of cell biology and support various key research themes here at NU.  Having completed my PhD and subsequent post-doctoral work at the NIMR I have a strong grounding in basic and translational research and consistently contribute to high profile publications.  I won the award for best paper in Cytometry part A in 2011 and also made key contributions to work published in Science (2012 and 2017) and Cell (2013).  Furthermore, I present my method development work at key conferences both nationally and internationally as well as contributing to the presentations and abstracts of others.  I am a peer reviewer for several journals including Cytometry Part A, specialising in imaging cytometry data and recently published some guidelines for data standards in the field.  I was selected by ISAC as one of only three individuals worldwide to be part of the Shared Resource Laboratory (SRL) emerging leaders’ programme.  This is a scholarship that recognises exceptional contribution to the worldwide cytometry community from those working in core facilities.


Key points:

1.  Recognised at an international level as an expert in the field of Cytometry and Core Facility operations.

2.  Strong publication record in high impact journals such as Science, Cell and Nature Communications.

3.  Invited to speak at several national and international Cytometry meetings.

4.  Part of the Cytometry Part A Associate Editor Scholar Programme

Research

My labs current research focus spans all aspects of Cytometry/Single Cell analysis. 

Specifically however we are interested in:

1.  Multi-dimensional cytometry technologies including classical Fluorescence-based Flow Cytometry, Mass Cytometry and Imaging Cytometry. 

2.  Developing new cytometry-based methodologies and techniques to better understand cellular functions at a population level with true single cell resolution.

3.  To employ new analytical strategies such as machine/deep learning to better interpret complex cytometry-derived data sets toward a better understanding of human health and disease.


Key local and international collaborators:


Professor Muzlifah Haniffa, Newcastle University. 

Exploring human dendritic cell biology at the single cell level through advanced cytometry methodologies


Dr Jaume Bacardit, Newcastle University.

Machine learning for Cytometry data.


Professor Paul Rees, Swansea University, UK and the Broad Institute, USA

Advanced machine/deep learning approaches to extract meaningful biological data from complex cytomerty-derived data sets.


Professor Ann Carpenter, Broad Institute, USA

Image Cytometry data analysis pipelines


Professor Fabian Theis, Helmholtz Zentrum, Germany

Advanced machine/deep learning approaches to extract meaningful biological data from complex cytomerty-derived data sets.







 

Teaching

I currently teach on the following courses:

MMB8022 Stem cells and Regenerative Medicine

CSC8309 High Throughput Technologies


I also teach externally on:


The EMBL practical Flow Cytometry Course

The EMBL Fundamentals of Cell sorting Course

The RMS Flow Cytometry Course

ExCyte Flow Cytometry training course as a consultant



Publications

  • Villani A-C, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017, 356(6335).
  • Thaunat O, Granja AG, Barral P, Filby A, Montaner B, Collinson L, Martinez-Martin N, Harwoo NE, Bruckbauer A, Batista FD. Asymmetric segregation of polarized antigen on B cell division shapes presentation capacity. Science 2012.
  • Schraml BU, vanBlijswijk J, Zelenay S, Whitney PG, Filby A, Acton SE, Rogers NC, Moncaut N, Carvaja JJ, ReiseSousa C. Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 2013.
  • Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications 2016, 7, 10256.
  • Merkenschlager J, Ploquin MJ, Eksmond U, Andargachew R, Thorborn G, Filby A, Pepper M, Evavold B, Kassiotis G. Stepwise B-cell-dependent expansion of T helper clonotypes diversifies the T-cell response. Nature Communications 2016, 7, 10281.
  • Pal D, Blair HJ, Elder A, Dormon K, Rennie KJ, Coleman DJL, Weiland J, Rankin KS, Filby A, Heidenreich O, Vormoor J. Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia. Leukemia 2016, 30, 1691-1700.
  • Cerveira J, Begum J, Barros RD, van der Veen AG, Filby A. An imaging flow cytometry-based approach to measuring the spatiotemporal calcium mobilisation in activated T cells. Journal of Immunological Methods 2015, 423, 120-130.
  • Filby A, Begum J, Jalal M, Day W. Appraising the suitability of succinimidyl and lipophilic fluorescent dyes to track proliferation in non-quiescent cells by dye dilution. Methods 2015, 82, 29-37.
  • Patterson JO, Swaffer M, Filby A. An Imaging Flow Cytometry-based approach to analyse the fission yeast cell cycle in fixed cells. Methods 2015, 82, 74-84.
  • Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods 2017, 112, 201-210.
  • Borger JG, Morrison VL, Filby A, Garcia C, Uotila LM, Simbari F, Fagerholm SC, Zamoyska R. Caveolin-1 Influences LFA-1 Redistribution upon TCR Stimulation in CD8 T Cells. Journal of Immunology 2017, 199(3), 874-884.
  • Filby A, Day W, Purewal S, Martinez-Martin N. The Analysis of Cell Cycle, Proliferation, and Asymmetric Cell Division by Imaging Flow Cytometry. In: Methods in Molecular Biology. New York: Springer, 2017, pp.71-95.
  • Griessinger E, Anjos-Afonso F, Vargaftig J, Taussig DC, Lassailly F, Prebet T, Imbert V, Nebout M, Vey N, Chabannon C, Filby A, Bollet-Quivogne F, Gribben JG, Peyron JF, Bonnet D. Frequency and Dynamics of Leukemia-Initiating Cells during Short-term Ex Vivo Culture Informs Outcomes in Acute Myeloid Leukemia Patients. Cancer Research 2016, 76(8), 2082-2086.
  • Filby A. Sample preparation for flow cytometry benefits from some lateral thinking. Cytometry Part A 2016, 89(12), 1054-1056.
  • Filby A. New, clear fusion from the cellular perspective: Measuring cellular fusion in Saccharomyces cerevisiae by flow cytometry. Cytometry Part A 2015, 87(9), 797-799.
  • Filby A. "Mega" cytometry for a "mega" challenging cell type. Cytometry Part A 2014, 85(4), 289-291.
  • Begum J, Day W, Henderson C, Purewal S, Cerveira J, Summers H, Rees P, Davies D, Filby A. A method for evaluating the use of fluorescent dyes to track proliferation in cell lines by dye dilution. Cytometry Part A 2013, 83(12), 1085-1095.
  • Borger JG, Filby A, Zamoyska R. Differential polarization of C-terminal Src kinase between naive and antigen-experienced CD8+ T cells. Journal of Immunology 2013.
  • Hawkins ED, Oliaro J, Kallies A, Belz GT, Filby A, Hogan T, Haynes N, Ramsbottom KM, VanHam V, Kinwell T, Seddon B, Davies D, Tarlinton D, Lew AM, Humbert PO, Russell SM. Regulation of asymmetric cell division and polarity by Scribble is not required for humoral immunity. Nature Communications 2013.
  • Filby A, Davies D. Reporting imaging flow cytometry data for publication: why mask the detail?. Cytometry Part A 2012.
  • Filby A, Perucha E, Summers H, Rees P, Chana P, Heck S, Lord GM, Davies D. An imaging flow cytometric method for measuring cell division history and molecular symmetry during mitosis. Cytometry Part A 2011.
  • Gandillet A, Park S, Lassailly F, Griessinger E, Vargaftig J, Filby A, Lister TA, Bonnet D. Heterogeneous sensitivity of human acute myeloid leukemia to β-catenin down-modulation. Leukemia 2011.
  • Salmond RJ, Filby A, Pirinen N, Magee AI, Zamoyska R. Mislocalization of Lck impairs thymocyte differentiation and can promote development of thymomas. Blood 2010.
  • Pike R, Filby A, Ploquin MJ, Eksmond U, Marques R, Antunes I, Hasenkrug K, Kassiotis G. Race between retroviral spread and CD4+ T-cell response determines the outcome of acute Friend virus infection. Journal of Virology 2009.
  • Salmon RJ, Filby A, Qureshi I, Caserta S, Zamoyska R. T-cell receptor proximal signaling via the Src-family kinases, Lck and Fyn, influences T-cell activation, differentiation, and tolerance. Immunological Reviews 2009.
  • Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, Schraven B, Zamoyska R. Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, Schraven B, Zamoyska R. Journal of Immunology 2007.
  • Lovatt M, Filby A, Parravicini V, Werlen G, Palmer E, Zamoyska R. Lck regulates the threshold of activation in primary T cells, while both Lck and Fyn contribute to the magnitude of the extracellular signal-related kinase response. Molecular and Cellular Biology 2006.
  • Zamoysk R, Basson A, Filby A, Legname G, Lovatt M, Seddon B. The influence of the src-family kinases, Lck and Fyn, on T cell differentiation, survival and activation. Immunological Reviews 2003.
  • Dearman RJ, Filby A, Humphreys IR, Kimber I. Interleukins 5 and 13 characterize immune responses to respiratory sensitizing acid anhydrides. Journal of Applied Toxicology 2002, 22(5), 317-325.
  • Srivastava S, Ramsbottom SA, Molinari E, Alkanderi S, Filby A, White K, Henry C, Saunier S, Miles CG, Sayer JA. A human patient-derived cellular model of Joubert syndrome reveals ciliary defects which can be rescued with targeted therapies. Human Molecular Genetics 2017, 26(23), 4657-4667.
  • Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA. Reconstructing cell cycle and disease progression using deep learning. Nature Communications 2017, (8), 463.
  • Reis M, McDonald D, Nicholson L, Godthardt K, Knobel S, Dickinson AM, Filby A, Wang X-N. Global phenotypic characterisation of human platelet lysate expanded MSCs by high-throughput flow cytometry. Scientific Reports 2018, 8(1), 3907.
  • Cossarizza A, Chang H-D, Radbruch A, Andra I, Annunziato F, Bacher P, Barnaba V, Battistini L, Bauer WM, Baumgart S, Becher B, Beisker W, Berek C, Blanco A, Borsellino G, Boulais PE, Brinkman RR, Buscher M, Busch DH, Bushnell TP, Cao X, Cavani A, Chattopadhyay PK, Cheng Q, Chow S, Clerici M, Cooke A, Cosma A, Cosmi L, Cumano A, Dang VD, Davies D, De Biasi S, Del Zotto G, Della Bella S, Dellabona P, Deniz G, Dessing M, Diefenbach A, Di Santo J, Dieli F, Dolf A, Donnenberg VS, Dorner T, Ehrhardt GRA, Endl E, Engel P, Engelhardt B, Esser C, Everts B, Falk CS, Fehniger TA, Filby A, Fillatreau S, Follo M, Forster I, Foster J, Foulds GA, Frenette PS, Galbraith D, Garbi N, Garcia-Godoy MD, Ghoreschi K, Gibellini L, Goettlinger C, Goodyear CS, Gori A, Grogan J, Gross M, Grutzkau A, Grummitt D, Hahn J, Hammer Q, Hauser AE, Haviland DL, Hedley D, Herrera G, Herrmann M, Hiepe F, Holland T, Hombrink P, Houston JP, Hoyer BF, Huang B, Hunter CA, Iannone A, Jack H-M, Javega B, Jonjic S, Juelke K, Jung S, Kaiser T, Kalina T, Keller B, Khan S, Kienhofer D, Kroneis T, Kunkel D, Kurts C, Kvistborg P, Lannigan J, Lantz O, Larbi A, LeibundGut-Landmann S, Leipold MD, Levings MK, Litwin V, Liu Y, Lohoff M, Lombardi G, Lopez L, Lovett-Racke A, Lubberts E, Ludewig B, Lugli E, Maecker HT, Martrus G, Matarese G, Maueroder C, McGrath M, McInnes I, Mei HE, Melchers F, Melzer S, Mielenz D, Mills K, Mjosberg J, Moore J, Moran B, Moretta A, Moretta L, Mosmann TR, Muller S, Muller W, Munz C, Multhoff G, Munoz LE, Murphy KM, Nakayama T, Nasi M, Neudorfl C, Nolan J, Nourshargh S, O'Connor J-E, Ouyang W, Oxenius A, Palankar R, Panse I, Peterson P, Peth C, Petriz J, Philips D, Pickl W, Piconese S, Pinti M, Pockley AG, Podolska MJ, Pucillo C, Quataert SA, Radstake TRDJ, Rajwa B, Rebhahn JA, Recktenwald D, Remmerswaal EBM, Rezvani K, Rico LG, Robinson JP, Romagnani C, Rubartelli A, Ruland J, Sakaguchi S, Sala-de-Oyanguren F, Samstag Y, Sanderson S, Sawitzki B, Scheffold A, Schiemann M, Schildberg F, Schimisky E, Schmid SA, Schmitt S, Schober K, Schuler T, Schulz AR, Schumacher T, Scotta C, Shankey TV, Shemer A, Simon A-K, Spidlen J, Stall AM, Stark R, Stehle C, Stein M, Steinmetz T, Stockinger H, Takahama Y, Tarnok A, Tian Z, Toldi G, Tornack J, Traggiai E, Trotter J, Ulrich H, van der Braber M, van Lier RAW, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk H-D, von Volkmann K, Waisman A, Walker R, Ward MD, Warnatz K, Warth S, Watson JV, Watzl C, Wegener L, Wiedemann A, Wienands J, Willimsky G, Wing J, Wurst P, Yu L, Yue A, Zhang Q, Zhao Y, Ziegler S, Zimmermann J. Guidelines for the use of flow cytometry and cell sorting in immunological studies. European Journal of Immunology 2017, 47(10), 1584-1797.