Dr John Lock
Research Staff Level C

Dr John Lock

  • 2001-2006 PhD, Institute for Molecular Bioscience, University of Queensland.
  • 2000-2001 Honours (1st Class) Biochemistry, Institute for Molecular Bioscience, University of Queensland. 
  • 1997-2000 BSc (Biochemistry), University of Queensland.
Medicine & Health
School of Biomedical Sciences

Dr John Lock is Head of the Cancer Systems Microscopy lab within the School of Medical Sciences



Dr Lock completed his doctorate within the Institute for Molecular Bioscience at the University of Queensland. He then began postdoctoral research at the Karolinska Institute in Stockholm with 5 years of back to back fellowships from the Wenner-Gren Foundation and the Swedish Cancer Foundation. He received accelerated promotion to Assistant Professor in recognition of his role in pioneering Systems Microscopy and leading a 9-person multidisciplinary team in its application to fundamental cancer research.

Dr Lock returned to Australia with a senior position in the lab of Professor Katharina Gaus at UNSW, within the EMBL Node for Single Molecule Science. He helped conceive and fund formation of Australia’s first dedicated Systems Microscopy facility with $2.5M funding support from the Australian Research Council and the prestigious Ramaciotti Biomedical Research Award (co-CI, now academic lead of facility). This success enabled his initiation of the Cancer Systems Microscopy (CSM) lab in 2018.

The CSM lab has since formed collaborations with an array of fundamental and translational cancer researchers, cancer clinicians, commercial microscopy and automation technology developers, as well as data science, machine / deep learning and visual analytics experts. This forms a truly multidisciplinary ecosystem of interactions. Reflecting these, Dr Lock is an invited member of the UNSW Steering Committee for the >$10M Expanded Perception & Interaction Centre (EPICentre) for data visualisation and AI research, the UNSW Data Science Hub (uDASH) and the UNSW AI & Data Science Network.

Dr Lock co-founded (with Professor Sarah Russell, PeterMacCallum Cancer Centre, Melbourne) the Systems Microscopy Australia Network to build and extend multidisciplinary capacity and collaborations across Australia and beyond, and has become a co-organiser of the Functional High Throughput Technologies Australia meeting, which focuses on screening-related technologies and their applications to drug discovery, precision medicine and functional genomics.

Current Appointments & Positions Held

  • Senior Lecturer, Head of Cancer Systems Microscopy lab, Department of Pathology, School of Medical Sciences
  • Affiliate Researcher, Ingham Institute for Applied Medical Research
  • Academic Lead & Scientific Advisory Committee Chair, Ramaciotti Systems Microscopy Unit
  • Steering Committee Member for >$10M Expanded Perception and Interaction Centre (EPICentre) (UNSW Faculty of Art, Design & Architecture) (School of Medical Sciences Representative)
  • UNSW Data Science Hub member
  • UNSW AI & Data Science Network member
  • School of Medical Sciences Honours Committee Member
  • Co-founder, Systems Microscopy Australia Network
  • Co-organiser, Functional High Throughput Technologies Australia meeting

Membership in Societies

  • Australian and New Zealand Society for Cell and Developmental Biology
  • American Society for Cell Biology
  • Australian Microscopy & Microanalysis Society

Research keywords

Cell Biology, Cancer, Circulating Tumour Cells, Adhesion, Migration, Signalling, Imaging, Microscopy, Statistics, Data Visualisation, Machine Learning, Deep Learning


+61 2 9385 0016
School of Medical Sciences Wallace Wurth Building C27 Cnr High St & Botany St Sydney, NSW 2052 Australia
  • Book Chapters | 2021
    Wei W; Haidinger S; Lock J; Meijering E, 2021, 'Deep Representation Learning for Image-Based Cell Profiling', in Machine Learning in Medical Imaging, Springer International Publishing, pp. 487 - 497, http://dx.doi.org/10.1007/978-3-030-87589-3_50
    Book Chapters | 2018
    2018, 'Using systems microscopy to understand the emergence of cell migration from cell organization', in Cell Migration: Methods and Protocols, Springer, pp. 119 - 134, http://dx.doi.org/10.1007/978-1-4939-7701-7_10
  • Journal articles | 2022
    Burkhardt DB; San Juan BP; Lock JG; Krishnaswamy S; Chaffer CL, 2022, 'Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning', Cancer Discovery, 12, pp. 1847 - 1859, http://dx.doi.org/10.1158/2159-8290.CD-21-0282
    Journal articles | 2022
    Khan T; Lock JG; Ma Y; Harman DG; de Souza P; Chua W; Balakrishnar B; Scott KF; Becker TM, 2022, 'Choice of antibody is critical for specific and sensitive detection of androgen receptor splice variant-7 in circulating tumor cells', Scientific Reports, 12, pp. 16159, http://dx.doi.org/10.1038/s41598-022-20079-w
    Journal articles | 2020
    2020, 'The Prospect of Identifying Resistance Mechanisms for Castrate-Resistant Prostate Cancer Using Circulating Tumor Cells: Is Epithelial-to-Mesenchymal Transition a Key Player?', Prostate Cancer, 2020, pp. 7938280, http://dx.doi.org/10.1155/2020/7938280
    Journal articles | 2019
    Bryce NS; Failes TW; Stehn JR; Baker K; Zahler S; Arzhaeva Y; Bischof L; Lyons C; Dedova I; Arndt GM; Gaus K; Goult BT; Hardeman EC; Gunning PW; Lock JG, 2019, 'High-Content Imaging of Unbiased Chemical Perturbations Reveals that the Phenotypic Plasticity of the Actin Cytoskeleton Is Constrained', Cell Systems, 9, pp. 496 - 507.e5, http://dx.doi.org/10.1016/j.cels.2019.09.002
    Journal articles | 2019
    Bryce NS; Hardeman EC; Gunning PW; Lock JG, 2019, 'Chemical biology approaches targeting the actin cytoskeleton through phenotypic screening', Current Opinion in Chemical Biology, 51, pp. 40 - 47, http://dx.doi.org/10.1016/j.cbpa.2019.02.013
    Journal articles | 2019
    Lock JG; Baschieri F; Jones MC; Humphries JD; Montagnac G; Strömblad S; Humphries MJ, 2019, 'Clathrin-containing adhesion complexes', Journal of Cell Biology, 218, pp. 2086 - 2095, http://dx.doi.org/10.1083/jcb.201811160
    Journal articles | 2018
    Gong X; Didan Y; Lock JG; Strömblad S, 2018, 'KIF13A-regulated RhoB plasma membrane localization governs membrane blebbing and blebby amoeboid cell migration', EMBO Journal, 37, http://dx.doi.org/10.15252/embj.201898994
    Journal articles | 2018
    Lock JG; Jones MC; Askari JA; Gong X; Oddone A; Olofsson H; Göransson S; Lakadamyali M; Humphries MJ; Strömblad S, 2018, 'Reticular adhesions are a distinct class of cell-matrix adhesions that mediate attachment during mitosis', Nature Cell Biology, 20, pp. 1290 - 1302, http://dx.doi.org/10.1038/s41556-018-0220-2
    Journal articles | 2018
    Moshksayan K; Kashaninejad N; Warkiani ME; Lock JG; Moghadas H; Firoozabadi B; Saidi MS; Nguyen NT, 2018, 'Spheroids-on-a-chip: Recent advances and design considerations in microfluidic platforms for spheroid formation and culture', Sensors and Actuators, B: Chemical, 263, pp. 151 - 176, http://dx.doi.org/10.1016/j.snb.2018.01.223
    Journal articles | 2018
    Spiess M; Hernandez-Varas P; Oddone A; Olofsson H; Blom H; Waithe D; Lock JG; Lakadamyali M; Strömblad S, 2018, 'Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions', Journal of Cell Biology, 217, pp. 1929 - 1940, http://dx.doi.org/10.1083/jcb.201707075
    Journal articles | 2017
    2017, 'Reticular adhesions: A new class of adhesion complex that mediates cell-matrix attachment during mitosis', , http://dx.doi.org/10.1101/234237
    Journal articles | 2016
    Shafqat-Abbasi H; Kowalewski JM; Kiss A; Gong X; Hernandez-Varas P; Berge U; Jafari-Mamaghani M; Lock JG; Stromblad S, 2016, 'An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes', ELIFE, 5, http://dx.doi.org/10.7554/eLife.11384
    Journal articles | 2015
    Hernandez-Varas P; Berge U; Lock JG; Stromblad S, 2015, 'A plastic relationship between vinculin-mediated tension and adhesion complex area defines adhesion size and lifetime', NATURE COMMUNICATIONS, 6, http://dx.doi.org/10.1038/ncomms8524
    Journal articles | 2015
    Kowalewski JM; Shafqat-Abbasi H; Jafari-Mamaghani M; Ganebo BE; Gong X; Stromblad S; Lock JG, 2015, 'Disentangling Membrane Dynamics and Cell Migration; Differential Influences of F-actin and Cell-Matrix Adhesions', PLOS ONE, 10, http://dx.doi.org/10.1371/journal.pone.0135204
    Journal articles | 2015
    2015, 'Non-monotonic cellular responses to heterogeneity in talin protein expression-level', INTEGRATIVE BIOLOGY, 7, pp. 1171 - 1185, http://dx.doi.org/10.1039/c4ib00291a
    Journal articles | 2014
    Lock JG; Mamaghani MJ; Shafqat-Abbasi H; Gong X; Tyrcha J; Stromblad S, 2014, 'Plasticity in the Macromolecular-Scale Causal Networks of Cell Migration', PLOS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0090593
    Journal articles | 2014
    2014, 'Technical advance: live-imaging analysis of human dendritic cell migrating behavior under the influence of immune-stimulating reagents in an organotypic model of lung.', J Leukoc Biol, 96, pp. 481 - 489, http://dx.doi.org/10.1189/jlb.3TA0513-303R
    Journal articles | 2013
    Nystrom S; Antoine DJ; Lundback P; Lock JG; Nita AF; Hogstrand K; Grandien A; Erlandsson-Harris H; Andersson U; Applequist SE, 2013, 'TLR activation regulates damage-associated molecular pattern isoforms released during pyroptosis', EMBO JOURNAL, 32, pp. 86 - 99, http://dx.doi.org/10.1038/emboj.2012.328
    Journal articles | 2013
    2013, 'TLR activation regulates damage-associated molecular pattern isoforms released during pyroptosis', The EMBO journal, 32, pp. 172 - 172, http://dx.doi.org/10.1038/emboj.2012.344
    Journal articles | 2012
    Colo GP; Hernandez-Varas P; Lock J; Bartolome RA; Arellano-Sanchez N; Stromblad S; Teixido J, 2012, 'Focal adhesion disassembly is regulated by a RIAM to MEK-1 pathway', JOURNAL OF CELL SCIENCE, 125, pp. 5338 - 5352, http://dx.doi.org/10.1242/jcs.105270
    Journal articles | 2010
    An Z; Dobra K; Lock JG; Stromblad S; Hjerpe A; Zhang H, 2010, 'Kindlin-2 is expressed in malignant mesothelioma and is required for tumor cell adhesion and migration', INTERNATIONAL JOURNAL OF CANCER, 127, pp. 1999 - 2008, http://dx.doi.org/10.1002/ijc.25223
    Journal articles | 2010
    Li Z; Lock JG; Olofsson H; Kowalewski JM; Teller S; Liu Y; Zhang H; Stromblad S, 2010, 'Integrin-mediated Cell Attachment Induces a PAK4-dependent Feedback Loop Regulating Cell Adhesion through Modified Integrin alpha v beta 5 Clustering and Turnover', MOLECULAR BIOLOGY OF THE CELL, 21, pp. 3317 - 3329, http://dx.doi.org/10.1091/mbc.E10-03-0245
    Journal articles | 2010
    Lindberg K; Strom A; Lock JG; Gustafsson J-A; Haldosen L-A; Helguero LA, 2010, 'Expression of Estrogen Receptor beta Increases Integrin alpha 1 and Integrin beta 1 Levels and Enhances Adhesion of Breast Cancer Cells', JOURNAL OF CELLULAR PHYSIOLOGY, 222, pp. 156 - 167, http://dx.doi.org/10.1002/jcp.21932
    Journal articles | 2010
    Lock JG; Stromblad S, 2010, 'Systems microscopy: An emerging strategy for the life sciences', EXPERIMENTAL CELL RESEARCH, 316, pp. 1438 - 1444, http://dx.doi.org/10.1016/j.yexcr.2010.04.001
    Journal articles | 2010
    Plantard L; Arjonen A; Lock JG; Nurani G; Ivaska J; Stromblad S, 2010, 'PtdIns(3,4,5)P-3 is a regulator of myosin-X localization and filopodia formation', JOURNAL OF CELL SCIENCE, 123, pp. 3525 - 3534, http://dx.doi.org/10.1242/jcs.069609
    Journal articles | 2008
    Lieu ZZ; Lock JG; Hammond LA; La Gruta NL; Stow JL; Gleeson PA, 2008, 'A trans-Golgi network golgin is required for the 14 regulated secretion of TNF in activated macrophages in vivo', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105, pp. 3351 - 3356, http://dx.doi.org/10.1073/pnas.0800137105
    Journal articles | 2008
    Lock JG; Wehrle-Haller B; Stroemblad S, 2008, 'Cell-matrix adhesion complexes: Master control machinery of cell migration', SEMINARS IN CANCER BIOLOGY, 18, pp. 65 - 76, http://dx.doi.org/10.1016/j.semcancer.2007.10.001
    Journal articles | 2007
    Souslova EA; Belousov VV; Lock JG; Stromblad S; Kasparov S; Bolshakov AP; Pinelis VG; Labas YA; Lukyanov S; Mayr LM; Chudakov DM, 2007, 'Single fluorescent protein-based Ca2+ sensors with increased dynamic range', BMC BIOTECHNOLOGY, 7, http://dx.doi.org/10.1186/1472-6750-7-37
    Journal articles | 2005
    Lock JG; Stow JL, 2005, 'Rab11 in recycling endosomes regulates the sorting and basolateral transport of E-cadherin', MOLECULAR BIOLOGY OF THE CELL, 16, pp. 1744 - 1755, http://dx.doi.org/10.1091/mbc.E04-10-0867
    Journal articles | 2005
    2005, 'E-cadherin transport from the trans-Golgi network in tubulovesicular carriers is selectively regulated by Golgin-97', TRAFFIC, 6, pp. 1142 - 1156, http://dx.doi.org/10.1111/j.1600-0854.2005.00349.x
    Journal articles | 2004
    2004, 'Domains of the TGN: Coats, tethers and G proteins', TRAFFIC, 5, pp. 315 - 326, http://dx.doi.org/10.1111/j.1398-9219.2004.00182.x
    Journal articles | 2003
    2003, 'GAIP participates in budding of membrane carriers at the trans-Golgi network', TRAFFIC, 4, pp. 175 - 189, http://dx.doi.org/10.1034/j.1600-0854.2003.00106.x
    Journal articles | 2001
    2001, 'The GRIP domain is a specific targeting sequence for a population of trans-Golgi network derived tubulo-vesicular carriers', TRAFFIC, 2, pp. 336 - 344, http://dx.doi.org/10.1034/j.1600-0854.2001.002005336.x
    Journal articles |
    'The Limits of Phenotypic Plasticity in the Actin Cytoskeleton Revealed by Unbiased Chemical Perturbation', SSRN Electronic Journal, http://dx.doi.org/10.2139/ssrn.3299445
  • Preprints | 2023
    2023, Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport, , http://dx.doi.org/10.1101/2023.03.28.534644
    Conference Abstracts | 2022
    2022, 'Abstract 1029: The anti-androgen seviteronel sensitizes triple-negative breast cancer to chemotherapy', in Cancer Research, American Association for Cancer Research (AACR), Vol. 82, pp. 1029 - 1029, http://dx.doi.org/10.1158/1538-7445.am2022-1029
    Preprints | 2022
    2022, Choice of antibody is critical for specific and sensitive detection of androgen receptor splice variant-7 in circulating tumor cells, , http://dx.doi.org/10.21203/rs.3.rs-1602818/v1
    Preprints | 2022
    2022, Choice of antibody is critical for specific and sensitive detection of androgen receptor splice variant-7 in circulating tumor cells, , http://dx.doi.org/10.21203/rs.3.rs-1602818/v2
    Preprints | 2022
    2022, Copper chelation inhibits TGF-β pathways and suppresses epithelial-mesenchymal transition in cancer, , http://dx.doi.org/10.1101/2022.10.03.510707
    Preprints | 2022
    2022, Targeting phenotypic plasticity prevents metastasis and the development of chemotherapy-resistant disease, , http://dx.doi.org/10.1101/2022.03.21.22269988
    Conference Papers | 2018
    Lock J; Filonik D; Lawther R; Pather N; Gaus K; Kenderdine S; Bednarz T, 2018, 'Visual Analytics of Single Cell Microscopy Data Using a Collaborative Immersive Environment', in International Conference on Virtual Reality Continuum and its Applications in Industry (VRCAI '18), ACM, New York, Hachioji, Japan, presented at International Conference on Virtual Reality Continuum and its Applications in Industry (VRCAI '18), Hachioji, Japan, 02 December 2018 - 03 December 2018, http://dx.doi.org/10.1145/3284398.3284412

  • 2022: Tour de Cure Pioneering Grant - RSP547FY2023 Prototyping a Precision Diagnostic for Advanced Prostate Cancer
  • 2022: UNSW Commercialisation Seed Fund - CellaSense drug lead discovery platform development
  • 2021: ARC Discovery Project - DP220104036 Mapping networks governing cell state plasticity: how, where and when?
  • 2021: NHMRC Ideas – GNT2012848 for Revolutionising immunotherapy response prediction in non-small cell lung cancer
  • 2021: UNSW RIS – Spatial Light Interference Microscopy (SLIM) system
  • 2020 UNSW Research Fellowship
  • 2020 ARC LIEF LE210100011 for Multiplexed Imaging
  • 2019: NHMRC Ideas - GNT1184009 Revolutionising circulating tumour cell (CTC) analysis in castrate resistant prostate cancer
  • 2019: UNSW ResTech - BioDive integrated image and numerical data visualisation platform
  • 2018: UNSW RIS - Multi-Modal Collaborative High-End Visualisation System
  • 2018: UNSW RIS - Automated biological sample labelling system
  • 2017: Ramaciotti Biomedical Research Award for Systems Microscopy Facility – 1 awarded nationally every 2 years
  • 2017: ARC LIEF LE180100157 for Systems Microscopy
  • 2017: ARC DP170103599 - Statistical analyses for spatial organisation in T cell signalling
  • 2016: UNSW RIS - High-dimensional super-resolution live cell imaging

Research Interests

The Cancer Systems Microscopy Lab (CSM) aims to contribute to improved cancer treatment outcomes by advancing:

  •  Precision Diagnostics; using a unique suite of imaging-based methods for diagnosis of cancer-drivers in individual patients, enabling precision use of existing targeted therapies
  •  Targeted Therapies; via a novel high-content strategy for discovery and diversification of cancer therapy leads, supporting accelerated development of new targeted therapies
  •  Fundamental Insights; deploying multidisciplinary methods to analyse core mechanisms underpinning cancer progression, finding new vulnerabilities in human cancer
    • Including development of statistical, machine learning and data visualisation tools (together with UNSW EPICentre) to interrogate, interpret and communicate high-dimensional data derived from quantitative single cell imaging

The core research technologies of the CSM lab revolve around the concept of imaging-based systems biology, otherwise known as Systems Microscopy. As a result, the lab incorporates a multidisciplinary approach spanning novel aspects of experimental design, experimental automation, automated imaging, quantitative image analysis, statistical analysis, machine learning and data visualisation / visual analytics.

This builds on pioneering efforts in the initial conception of Systems Microscopy as a research strategy designed to replicate the scalability, reproducibility and quantitative rigour of existing single cell systems biology (‘Omics’) techniques, whilst also incorporating the critical dimensions of space and time into molecular analyses of cellular regulation and function. Not only a powerful approach for fundamental cell biology research, Systems Microscopy leverages the high signal-to-noise characteristics of (immuno)-fluorescence imaging to provide a powerful alternative / complement to current gold-standard strategies for precision medicine and also drug discovery. 

Below we outline a number of core projects developing within the lab.


Circulating tumour cell analysis for precision diagnostics

CTC project5.png

We aim to enable precision medicine in cancer by revolutionising analysis of signals driving disease progression and therapy-resistance. With longitudinally sampled circulating tumour cells (CTCs) analysed using Proteomic Microscopy, we image up to 50 markers per CTC to quantify activity across multiple resistance-linked signalling pathways. Using artificial intelligence (AI) to analyse this data, we classify resistant cancers by their signalling-drivers and train models predicting resistance mechanisms. This defines biomarker signatures with potential to guide patient stratification for targeted therapies. Beginning with a focus on prostate cancer, this precision diagnostic strategy is generalisable to a range of cancers.


Unbiased drug discovery for targeted therapy development

Together with UNSW Medicine collaborators Professors Peter Gunning and Edna Hardeman (CGMU), we have developed and tested a new strategy for drug lead-discovery that incorporates phenotypic screening of large-scale drug libraries (> 100, 000 compounds to-date) via high-throughput imaging, quantitative image analysis and multivariate statistical data analysis / machine learning to identify structurally and mechanistically diverse compounds with desirable biological effects. Already employed to explore the phenotypic plasticity of the actin cytoskeleton and at the same time identify new actin-regulating compounds, we are now working to generalise this approach in order to accelerate the discovery of lead compounds as part of the drug development pipeline.


Proteomic Microscopy analysis of subcellular signalling

Through sequential immunofluorescence multiplexing of subcellular signalling and regulatory protein markers, we aim to reconstruct signalling systems biology in situ within individual cells. Bridging the gap between the computational systems biology modelling approaches and the noisy complexity of signalling systems spatially distributed in heterogeneous cells, this approach has the potential to dramatically advance our understanding of competitive signal regulation in the four dimensions of space and time. Retaining our traditional focus on adhesion signalling biology in polarised and migrating cells, we aim to apply this approach to explore the fundamental processes and dynamics of cellular self-organisation.


Recent Selected Publications


Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning

Daniel B. Burkhardt, Beatriz P. San Juan, John G. Lock*, Smita Krishnaswamy*, Christine Chaffer*
Cancer Discovery
DOI: https://doi.org/10.1158/2159-8290.cd-21-0282

Phenotypic plasticity describes the ability of cancer cells to undergo dynamic, nongenetic cell state changes that amplify cancer heterogeneity to promote metastasis and therapy evasion. Thus, cancer cells occupy a continuous spectrum of phenotypic states connected by trajectories defining dynamic transitions upon a cancer cell state landscape. With technologies proliferating to systematically record molecular mechanisms at single-cell resolution, we illuminate manifold learning techniques as emerging computational tools to effectively model cell state dynamics in a way that mimics our understanding of the cell state landscape. We anticipate that “state-gating” therapies targeting phenotypic plasticity will limit cancer heterogeneity, metastasis, and therapy resistance. Significance: Nongenetic mechanisms underlying phenotypic plasticity have emerged as significant drivers of tumor heterogeneity, metastasis, and therapy resistance. Herein, we discuss new experimental and computational techniques to define phenotypic plasticity as a scaffold to guide accelerated progress in uncovering new vulnerabilities for therapeutic exploitation.


Deep Representation Learning for Image-Based Cell Profiling

Wenzhao Wei, Sacha Haidinger, John Lock*, Erik Meijering*

Machine Learning in Medical Imaging. MLMI 2021. Lecture Notes in Computer Science, vol 12966, pp. 487 - 497. Springer International Publishing

DOI: https://doi.org/10.1007/978-3-030-87589-3_50

High-content, microscopic image-based screening data are widely used in cell profiling to characterize cell phenotype diversity and extract explanatory biomarkers differentiating cell phenotypes induced by experimental perturbations or disease states. In recent years, high-throughput manifold embedding techniques such as t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), and generative networks have been increasingly applied to interpret cell profiling data. However, the resulting representations may not exploit the full image information, as these techniques are typically applied to quantitative image features defined by human experts. Here we propose a novel framework to analyze cell profiling data, based on two-stage deep representation learning using variational autoencoders (VAEs). We present quantitative and qualitative evaluations of the learned cell representations on two datasets. The results show that our framework can yield better representations than the currently popular methods. Also, our framework provides researchers with a more flexible tool to analyze underlying cell phenotypes and interpret the automatically defined cell features effectively.


The Prospect of Identifying Resistance Mechanisms for Castrate-Resistant Prostate Cancer Using Circulating Tumor Cells: Is Epithelial-to-Mesenchymal Transition a Key Player?

Tanzila Khan, Kieran F Scott, Therese M Becker, John Lock, Mohammed Nimir, Yafeng Ma, Paul de Souza

Prostate Cancer, volume 2020, Article ID 7938280

DOI: https://doi.org/10.1155/2020/7938280

Prostate cancer (PCa) is initially driven by excessive androgen receptor (AR) signaling with androgen deprivation therapy (ADT) being a major therapeutic approach to its treatment. However, the development of drug resistance is a significant limitation on the effectiveness of both first-line and more recently developed second-line ADTs. There is a need then to study AR signaling within the context of other oncogenic signaling pathways that likely mediate this resistance. This review focuses on interactions between AR signaling, the well-known phosphatidylinositol-3-kinase/AKT pathway, and an emerging mediator of these pathways, the Hippo/YAP1 axis in metastatic castrate-resistant PCa, and their involvement in the regulation of epithelial-mesenchymal transition (EMT), a feature of disease progression and ADT resistance. Analysis of these pathways in circulating tumor cells (CTCs) may provide an opportunity to evaluate their utility as biomarkers and address their importance in the development of resistance to current ADT with potential to guide future therapies.


High-Content Imaging of Unbiased Chemical Perturbations Reveals that the Phenotypic Plasticity of the Actin Cytoskeleton is Constrained.

Bryce NS, Failes TW, Stehn JR, Baker K, Zahler S, Arzhaeva Y, Bischof L, Lyons C, Dedova I, Arndt GM, Gaus K, Goult BT, Hardeman EC, Gunning PW, Lock JG.

Cell Systems. 2019-09

DOI: 10.1016/j.cels.2019.09.002

Although F-actin has a large number of binding partners and regulators, the number of phenotypic states available to the actin cytoskeleton is unknown. Here, we quantified 74 features defining filamentous actin (F-actin) and cellular morphology in >25 million cells after treatment with a library of 114,400 structurally diverse compounds. After reducing the dimensionality of these data, only 25 recurrent F-actin phenotypes emerged, each defined by distinct quantitative features that could be machine learned. We identified 2,003 unknown compounds as inducers of actin-related phenotypes, including two that directly bind the focal adhesion protein, talin. Moreover, we observed that compounds with distinct molecular mechanisms could induce equivalent phenotypes and that initially divergent cellular responses could converge over time. These findings suggest a conceptual parallel between the actin cytoskeleton and gene regulatory networks, where the theoretical plasticity of interactions is nearly infinite, yet phenotypes in vivo are constrained into a limited subset of practicable configurations.

Clathrin-containing adhesion complexes.

Lock JG, Baschieri F, Jones MC, Humphries JD, Montagnac G, Stromblad S, Humphries MJ.

J Cell Biol. 2019;218(7):2086-2095

DOI: 10.1083/jcb.201811160

An understanding of the mechanisms whereby cell adhesion complexes (ACs) relay signals bidirectionally across the plasma membrane is necessary to interpret the role of adhesion in regulating migration, differentiation, and growth. A range of AC types has been defined, but to date all have similar compositions and are dependent on a connection to the actin cytoskeleton. Recently, a new class of AC has been reported that normally lacks association with both the cytoskeleton and integrin-associated adhesome components, but is rich in components of the clathrin-mediated endocytosis machinery. The characterization of this new type of adhesion structure, which is emphasized by mitotic cells and cells in long-term culture, identifies a hitherto underappreciated link between the adhesion machinery and clathrin structures at the plasma membrane. While this discovery has implications for how ACs are assembled and disassembled, it raises many other issues. Consequently, to increase awareness within the field, and stimulate research, we explore a number of the most significant questions below.

Chemical biology approaches targeting the actin cytoskeleton through phenotypic screening.

Bryce NS, Hardeman EC, Gunning PW, Lock JG.

Curr Op Chem Biol. 2019;51:40-47

DOI: 10.1016/j.cbpa.2019.02.013

The actin cytoskeleton is dysregulated in cancer, yet this critical cellular machinery has not translated as a druggable clinical target due to cardio-toxic side-effects. Many actin regulators are also considered undruggable, being structural proteins lacking clear functional sites suitable for targeted drug design. In this review, we discuss opportunities and challenges associated with drugging the actin cytoskeleton through its structural regulators, taking tropomyosins as a target example. In particular, we highlight emerging data acquisition and analysis trends driving phenotypic, imaging-based compound screening. Finally, we consider how the confluence of these trends is now bringing functionally integral machineries such as the actin cytoskeleton, and associated structural regulatory proteins, into an expanded repertoire of druggable targets with previously unexploited clinical potential.

Reticular adhesions are a distinct class of cell-matrix adhesions that mediate attachment during mitosis.

Lock JG, Jones MC, Askari JA, Gong X, Oddone A, Olofsson H, Goransson S, Lakadamyali M, Humphries MJ, Stromblad S.

Nat Cell Biol. 2018;20(11):1290-1302.

DOI: 10.1038/s41556-018-0220-2

Adhesion to the extracellular matrix persists during mitosis in most cell types. However, while classical adhesion complexes, such as focal adhesions, do and must disassemble to enable mitotic rounding, the mechanisms of residual mitotic cell–extracellular matrix adhesion remain undefined. Here, we identify ‘reticular adhesions’, a class of adhesion complex that is mediated by integrin αvβ5, formed during interphase, and preserved at cell–extracellular matrix attachment sites throughout cell division. Consistent with this role, integrin β5 depletion perturbs mitosis and disrupts spatial memory transmission between cell generations. Reticular adhesions are morphologically and dynamically distinct from classical focal adhesions. Mass spectrometry defines their unique composition, enriched in phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2)-binding proteins but lacking virtually all consensus adhesome components. Indeed, reticular adhesions are promoted by PtdIns(4,5)P2, and form independently of talin and F-actin. The distinct characteristics of reticular adhesions provide a solution to the problem of maintaining cell–extracellular matrix attachment during mitotic rounding and division. Lock et al. identify reticular adhesion complexes that maintain cell–extracellular-matrix attachments during cell division. Reticular adhesions transmit spatial memory between cell generations, mediated by αvβ5 integrin and PtdIns(4,5)P2.

Visual Analytics of Single Cell Microscopy Data Using a Collaborative Immersive Environment.

Lock JG, Filonik D, Lawther R, Pather N, Gaus K, Kenderdine S, Bednarz T.

Proceedings of the 16th Acm Siggraph International Conference on Virtual-Reality Continuum and Its Applications in Industry (Vrcai 2018). 2018.

DOI: 10.1145/3284398.3284412

Understanding complex physiological processes demands the in- tegration of diverse insights derived from visual and quantitative analysis of bio-image data, such as microscopy images. This pro- cess is currently constrained by disconnects between methods for interpreting data, as well as by language barriers that hamper the necessary cross-disciplinary collaborations. Using immersive ana- lytics, we leveraged bespoke immersive visualizations to integrate bio-images and derived quantitative data, enabling deeper compre- hension and seamless interaction with multi-dimensional cellular information. We designed and developed a visualization platform that combines time-lapse confocal microscopy recordings of can- cer cell motility with image-derived quantitative data spanning 52 parameters. The integrated data representations enable rapid, in- tuitive interpretation, bridging the divide between bio-images and quantitative information. Moreover, the immersive visualization environment promotes collaborative data interrogation, supporting vital cross-disciplinary collaborations capable of deriving transfor- mative insights from rapidly emerging bio-image big data.

Active and inactive beta1 integrins segregate into distinct nanoclusters in focal adhesions.

Spiess M, Hernandez-Varas P, Oddone A, Olofsson H, Blom H, Waithe D, Lock JG, Lakadamyali M, Stromblad S.

J Cell Biol. 2018;217(6):1929-1940.

DOI: 10.1083/jcb.201707075

Integrins are the core constituents of cell–matrix adhesion complexes such as focal adhesions (FAs) and play key roles in physiology and disease. Integrins fluctuate between active and inactive conformations, yet whether the activity state influences the spatial organization of integrins within FAs has remained unclear. In this study, we address this question and also ask whether integrin activity may be regulated either independently for each integrin molecule or through locally coordinated mechanisms. We used two distinct superresolution microscopy techniques, stochastic optical reconstruction microscopy (STORM) and stimulated emission depletion microscopy (STED), to visualize active versus inactive β1 integrins. We first reveal a spatial hierarchy of integrin organization with integrin molecules arranged in nanoclusters, which align to form linear substructures that in turn build FAs. Remarkably, within FAs, active and inactive β1 integrins segregate into distinct nanoclusters, with active integrin nanoclusters being more organized. This unexpected segregation indicates synchronization of integrin activities within nanoclusters, implying the existence of a coordinate mechanism of integrin activity regulation.

Using Systems Microscopy to Understand the Emergence of Cell Migration from Cell Organization.

Stromblad S, Lock JG.

Methods Mol Biol. 2018;1749:119-134.

DOI: 10.1007/978-1-4939-7701-7_10

Cell migration is a dynamic process that emerges from fine-tuned networks coordinated in three-dimensional space, spanning molecular, subcellular, and cellular scales, and over multiple temporal scales, from milliseconds to days. Understanding how cell migration arises from this complexity requires data collection and analyses that quantitatively integrate these spatial and temporal scales. To meet this need, we have combined quantitative live and fixed cell fluorescence microscopy, customized image analysis tools, multivariate statistical methods, and mathematical modeling. Collectively, this constitutes the systems microscopy strategy that we have applied to dissect how cells organize themselves to migrate. In this overview, we highlight key principles, concepts, and components of our systems microscopy methodology, and exemplify what we have learnt so far and where this approach may lead.

KIF13A-regulated RhoB plasma membrane localization governs membrane blebbing and blebby amoeboid cell migration.

Gong X, Didan Y, Lock JG, Stromblad S.

EMBO J. 2018;37(17).

DOI: 10.15252/embj.201898994

Membrane blebbing‐dependent (blebby) amoeboid migration can be employed by lymphoid and cancer cells to invade 3D‐environments. Here, we reveal a mechanism by which the small GTPase RhoB controls membrane blebbing and blebby amoeboid migration. Interestingly, while all three Rho isoforms (RhoA, RhoB and RhoC) regulated amoeboid migration, each controlled motility in a distinct manner. In particular, RhoB depletion blocked membrane blebbing in ALL (acute lymphoblastic leukaemia), melanoma and lung cancer cells as well as ALL cell amoeboid migration in 3D‐collagen, while RhoB overexpression enhanced blebbing and 3D‐collagen migration in a manner dependent on its plasma membrane localization and down‐stream effectors ROCK and Myosin II. RhoB localization was controlled by endosomal trafficking, being internalized via Rab5 vesicles and then trafficked either to late endosomes/lysosomes or to Rab11‐positive recycling endosomes, as regulated by KIF13A. Importantly, KIF13A depletion not only inhibited RhoB plasma membrane localization, but also cell membrane blebbing and 3D‐migration of ALL cells. In conclusion, KIF13A‐mediated endosomal trafficking modulates RhoB plasma membrane localization to control membrane blebbing and blebby amoeboid migration. KIF13A kinesin regulates plasma membrane localization of the small GTPase RhoB, thereby controlling membrane blebbing and blebby amoeboid migration employed by lymphoid and cancer cells to invade 3D‐environments. Rho isoforms RhoA, RhoB and RhoC all regulate amoeboid migration but control motility in distinct manners. Membrane blebbing control by RhoB depends on its plasma membrane localization and down‐stream effectors ROCK and Myosin II. RhoB localization is controlled by internalization from the plasma membrane and different endosomal trafficking routes. KIF13A regulates cell membrane blebbing and 3D‐migration by controlling recycling of RhoB to the plasma membrane. Depletion of the kinesin KIF13A causes improper endosomal trafficking of RhoB to the plasma membrane, which in turn inhibits cancer cell 3D‐migration.

Spheroids-on-a-chip: Recent advances and design considerations in microfluidic platforms for spheroid formation and culture.

Moshksayan K, Kashaninejad N, Warkiani ME, Lock JG, Moghadas H, Firoozabadi B, Saidi MS, Nguyen NT.

Sensor Actuat B-Chem. 2018;263:151-176.

DOI: 10.1016/j.snb.2018.01.223

A cell spheroid is a three-dimensional (3D) aggregation of cells. Synthetic, in-vitro spheroids provide similar metabolism, proliferation, and species concentration gradients to those found in-vivo. For instance, cancer cell spheroids have been demonstrated to mimic in-vivo tumor microenvironments, and are thus suitable for in-vitro drug screening. The first part of this paper discusses the latest microfluidic designs for spheroid formation and culture, comparing their strategies and efficacy. The most recent microfluidic techniques for spheroid formation utilize emulsion, microwells, U-shaped microstructures, or digital microfluidics. The engineering aspects underpinning spheroid formation in these microfluidic devices are therefore considered. In the second part of this paper, design considerations for microfluidic spheroid formation chips and microfluidic spheroid culture chips (μSFCs and μSCCs) are evaluated with regard to key parameters affecting spheroid formation, including shear stress, spheroid diameter, culture medium delivery and flow rate. This review is intended to benefit the microfluidics community by contributing to improved design and engineering of microfluidic chips capable of forming and/or culturing three-dimensional cell spheroids.

The Limits of Phenotypic Plasticity in the Actin Cytoskeleton Revealed by Unbiased Chemical Perturbation.

Bryce NS, Failes TW, Stehn JR, Baker K, Zahler S, Arzhaeva Y, Bischof L, Lyons C, Dedova I, Arndt GM, Gaus K, Goult BT, Hardeman EC, Gunning PW, Lock JG.

SSRN Electronic Journal. 2018.

DOI: 10.2139/ssrn.3299445

Numerous proteins and pathways regulate F-actin organisation, meaning that, in combinatorial terms, an almost unlimited number of regulatory states are conceivable. Consequently, the potential for plasticity in F-actin phenotypes appears virtually unbounded. To estimate the actual limits of F-actin phenotype plasticity, we used a library of 114,400 structurally diverse compounds to induce unbiased chemical perturbations. Remarkably, just 25 distinct, recurrent F-actin phenotypes emerged. Correspondingly, select compounds with distinct molecular mechanisms inducede quivalent phenotypes, suggesting that these recurring phenotypes reflect a low number of equilibrium or attractorstates inactin organisation. This was supported by dynamic analyses comparing phenotype trajectories over time, showing how initially divergent phenotypes ultimately convergedinto equivalent end-states. We propose that infrequent attractor states in the actin phenotypic landscape reflect a channelling of high perturbative diversity into low phenotypic variety and consider how this may suppress chaotic outcomes during the evolution of this complex, functionally integral system.

Reticular adhesions: A new class of adhesion complex that mediates cell-matrix attachment during mitosis.

Lock JG, Jones MC, Askari JA, Gong X, Oddone A, Olofsson H, Goransson S, Lakadamyali M, Humphries MJ, Stromblad S.

BioRxiv. 2017.

DOI: 10.1101/234237

Adhesion to the extracellular matrix (ECM) persists during mitosis in most cell types. Yet, classical adhesion complexes (ACs), such as focal adhesions and focal complexes, do and must disassemble to enable cytoskeletal rearrangements associated with mitotic rounding. Given this paradox, mechanisms of mitotic cell-ECM adhesion remain undefined. Here, we identify ‘reticular adhesions’, a new class of AC that is mediated by integrin αvβ5, formed during interphase and preserved at cell-ECM attachment sites throughout cell division. Consistent with this role, integrin β5 depletion perturbs mitosis and disrupts spatial memory transmission between cell generations. Quantitative imaging reveals reticular adhesions to be both morphologically and dynamically distinct from classic focal adhesions, while mass spectrometry defines their unique composition; lacking virtually all consensus adhesome components. Indeed, remarkably, reticular adhesions are functionally independent of both talin and F-actin, yet are promoted by phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2). Overall, the distinct characteristics of reticular adhesions provide a unique solution to the problem of maintaining cell-ECM attachment during mitotic rounding and division.

An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes.

Shafqat-Abbasi H, Kowalewski JM, Kiss A, Gong X, Hernandez-Varas P, Berge U, Jafari-Mamaghani M, Lock JG#, Stromblad S#.

Elife. 2016;5:e11384.

DOI: 10.7554/elife.11384

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration.

Disentangling Membrane Dynamics and Cell Migration; Differential Influences of F-actin and Cell-Matrix Adhesions.

Kowalewski JM, Shafqat-Abbasi H, Jafari-Mamaghani M, Endrias Ganebo B, Gong X, Stromblad S, Lock JG.

PLoS One. 2015;10(8):e0135204.

DOI: 10.1371/journal.pone.0135204

Cell migration is heavily interconnected with plasma membrane protrusion and retraction (collectively termed "membrane dynamics"). This makes it difficult to distinguish regulatory mechanisms that differentially influence migration and membrane dynamics. Yet such distinctions may be valuable given evidence that cancer cell invasion in 3D may be better predicted by 2D membrane dynamics than by 2D cell migration, implying a degree of functional independence between these processes. Here, we applied multi-scale single cell imaging and a systematic statistical approach to disentangle regulatory associations underlying either migration or membrane dynamics. This revealed preferential correlations between membrane dynamics and F-actin features, contrasting with an enrichment of links between cell migration and adhesion complex properties. These correlative linkages were often non-linear and therefore context-dependent, strengthening or weakening with spontaneous heterogeneity in cell behavior. More broadly, we observed that slow moving cells tend to increase in area, while fast moving cells tend to shrink, and that the size of dynamic membrane domains is independent of cell area. Overall, we define macromolecular features preferentially associated with either cell migration or membrane dynamics, enabling more specific interrogation and targeting of these processes in future.

Non-monotonic cellular responses to heterogeneity in talin protein expression-level.

Kiss A, Gong X, Kowalewski JM, Shafqat-Abbasi H, Stromblad S, Lock JG.

Integr Biol (Camb). 2015;7(10):1171-1185.

DOI: 10.1039/c4ib00291a

Talin is a key cell-matrix adhesion component with a central role in regulating adhesion complex maturation, and thereby various cellular properties including adhesion and migration. However, knockdown studies have produced inconsistent findings regarding the functional influence of talin in these processes. Such discrepancies may reflect non-monotonic responses to talin expression-level variation that are not detectable via canonical "binary" comparisons of aggregated control versus knockdown cell populations. Here, we deployed an "analogue" approach to map talin influence across a continuous expression-level spectrum, which we extended with sub-maximal RNAi-mediated talin depletion. Applying correlative imaging to link live cell and fixed immunofluorescence data on a single cell basis, we related per cell talin levels to per cell measures quantitatively defining an array of cellular properties. This revealed both linear and non-linear correspondences between talin expression and cellular properties, including non-monotonic influences over cell shape, adhesion complex-F-actin association and adhesion localization. Furthermore, we demonstrate talin level-dependent changes in networks of correlations among adhesion/migration properties, particularly in relation to cell migration speed. Importantly, these correlation networks were strongly affected by talin expression heterogeneity within the natural range, implying that this endogenous variation has a broad, quantitatively detectable influence. Overall, we present an accessible analogue method that reveals complex dependencies on talin expression-level, thereby establishing a framework for considering non-linear and non-monotonic effects of protein expression-level heterogeneity in cellular systems.

A plastic relationship between vinculin-mediated tension and adhesion complex area defines adhesion size and lifetime.

Hernandez-Varas P, Berge U, Lock JG#, Stromblad S#.

Nat Commun. 2015;6:7524.

DOI: 10.1038/ncomms8524

Cell-matrix adhesions are central mediators of mechanotransduction, yet the interplay between force and adhesion regulation remains unclear. Here we use live cell imaging to map time-dependent cross-correlations between vinculin-mediated tension and adhesion complex area, revealing a plastic, context-dependent relationship. Interestingly, while an expected positive cross-correlation dominated in mid-sized adhesions, small and large adhesions display negative cross-correlation. Furthermore, although large changes in adhesion complex area follow vinculin-mediated tension alterations, small increases in area precede vinculin-mediated tension dynamics. Modelling based on this mapping of the vinculin-mediated tension-adhesion complex area relationship confirms its biological validity, and indicates that this relationship explains adhesion size and lifetime limits, keeping adhesions focal and transient. We also identify a subpopulation of steady-state adhesions whose size and vinculin-mediated tension become stabilized, and whose disassembly may be selectively microtubule-mediated. In conclusion, we define a plastic relationship between vinculin-mediated tension and adhesion complex area that controls fundamental cell-matrix adhesion properties.


Additional publications can be found here.

My Research Supervision

- Joint supervisor of 1 HDR student

- Co-supervisor of 1 Honours student (UNSW Medicine)