Swarbrick Lab

Selected Publications

Top 4 Publications (As of July 2022. Bold=corresponding authorships)

1) Wu, S.Z., Al-Eryani, G., Roden, D.L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J.R., Bartonicek, N., Wang, T., Larsson, L., Kaczorowski, D., Weisenfeld, N.I., Uytingco, C.R., Chew, J.G., Bent, Z.W., Chan, C.L., Gnanasambandapillai, V., Dutertre, C.A., Gluch, L., Hui, M.N., Beith, J., Parker, A., Robbins, E., Segara, D., Cooper, C., Mak, C., Chan, B., Warrier, S., Ginhoux, F., Millar, E., Powell, J.E., Williams, S.R., Liu, X.S., O'Toole, S., Lim, E., Lundeberg, J., Perou, C.M., Swarbrick, A. 2021 A single-cell and spatially resolved atlas of human breast cancers. Nat Genet. 53 (9): 1334-1347

Impact Factor (IF) - 38.33 / Citations– 70 / Field-weighted Citation Index (FWCI) = 7.82 / Altmetric of  277 / Manuscript downloads > 39,000

Data downloads > 3,700 from Broad Institute single cell data portal

This study maps the cellular landscape of primary breast cancers, focussing primarily on cellular states. We define a detailed cellular taxonomy of up to 52 states across epithelial, stromal & immune cells & develop a new single-cell classifier of intrinsic subtype, ‘scSubtyper’ (provisional patent application filed). Using spatial transcriptomics we map these cells into cellular communities, revealing the important spatial relationships between certain subsets of stromal cells & lymphocytes, which we are now pursuing as therapeutic targets. Finally, we reveal that breast cancers can be stratified into clinically-meaningful groups based on their cellular composition, a concept we coin ‘ecotypes’ (provisional patent application filed). This is a landmark paper in breast cancer biology.


2) Wu, S.Z., Roden, D.L., Wang, C., Holliday, H., Harvey, K., Cazet, A.S., Murphy, K.J., Pereira, B., Al-Eryani, G., Bartonicek, N., Hou, R., Torpy, J.R., Junankar, S., Chan, C.L., Lam, C.E., Hui, M.N., Gluch, L., Beith, J., Parker, A., Robbins, E., Segara, D., Mak, C., Cooper, C., Warrier, S., Forrest, A., Powell, J., O'Toole, S., Cox, T.R., Timpson, P., Lim, E., Liu, X.S., Swarbrick, A.

2020 Stromal cell diversity associated with immune evasion in human triple-negative breast cancer. EMBO J 1 (39): e104063.

IF – 11.6 / Citations - 96 / FWCI – 8.14 / Altmetric - 238

This was the first study to report a comprehensive cellular profile of triple negative breast cancer, a particularly poor-prognosis subset. We discovered novel subsets of stromal cells and inferred a role for them in suppressing anti-tumor immunity. 

This manuscript was featured on the cover of this edition and in a news and views article by Kalluri et al “A map of human breast cancer: new players in stromal-immune crosstalkEMBO J 2020.


3) Singh, M., Al-Eryani, G., Carswell, S., Ferguson, J.M., Blackburn, J., Barton, K., Roden, D., Luciani, F., Giang Phan, T., Junankar, S., Jackson, K., Goodnow, C.C., Smith, M.A., Swarbrick, A. 2019 High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat Commun. 10 (1): 3120.

IF - 17.8 /  Citations 158 / FWCI - 6.48 / Altmetric - 173 / Accesses > 45,000

We solved a technical challenge of how to affordably and rapidly profile gene expression in tandem with full-length single molecule mRNA sequencing from thousands of cells. We developed this method to permit deep profiling of lymphocyte gene expression and receptor expression. We use it to show clonal expansion and trafficking of lymphocytes from the lymph node to tumour, and unique gene expression features of clonal populations. We are now extending this method to enable very deep cellular characterisation of molecular features such as splicing, recombination, mutations and gene fusions in cancer cell populations.

Examples of scientific commentaries:


4) Cazet, A.S., Hui, M.N., Elsworth, B.L., Wu, S.Z., Roden, D., Chan, C.L., Skhinas, J.N., Collot, R., Yang, J., Harvey, K., Johan, M.Z., Cooper, C., Nair, R., Herrmann, D., McFarland, A., Deng, N., Ruiz-Borrego, M., Rojo, F., Trigo, J.M., Bezares, S., Caballero, R., Lim, E., Timpson, P., O'Toole, S., Watkins, D.N., Cox, T.R., Samuel, M.S., Martin, M., Swarbrick, A. 2018 Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer. Nat Commun. 9 (1): 2897.

IF – 17.8 / Citations - 225 / FWCI - 10.09 / Altmetric - 82 / Accesses - 13,000

This manuscript is a key demonstration of the influence of the tumour microenvironment in driving cancer cell plasticity during drug treatment. Fundamental discoveries and preclinical modeling by my lab drove the development of a Phase I trial of an anti-neoplastic (docetaxel) + an anti-stromal (smoothened/hedgehog inhibitor) combination therapy for metastatic TNBC, in which 3/11 women experienced clinical benefit, including one complete response. While small patient numbers, this is early evidence for clinical response to a stromal-directed therapy. Larger clinical trials are in development.


A full listing of Dr Swarbrick’s publications

More Garvan Publications