ORCID Profile
0000-0002-3594-5851
Current Organisations
The Univeristy of Melbourne
,
Walter and Eliza Hall Institute of Medical Research
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Oxford University Press (OUP)
Date: 21-12-2011
DOI: 10.1093/NAR/GKQ1205
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-04-2021
DOI: 10.1126/SCIIMMUNOL.ABF4432
Abstract: DC-SCRIPT is a key transcription factor controlling type 1 conventional dendritic cell fate and function.
Publisher: Cold Spring Harbor Laboratory
Date: 17-06-2022
DOI: 10.1101/2022.06.17.496207
Abstract: Inflammation is a key driver of cystic fibrosis (CF) lung disease, not addressed by current standard care. Improved understanding of the mechanisms leading to aberrant inflammation may assist the development of effective anti-inflammatory therapy. Single-cell RNA sequencing (scRNA-seq) allows profiling of cell composition and function at previously unprecedented resolution. Herein, we seek to use multimodal single-cell analysis to comprehensively define immune cell phenotypes, proportions and functional characteristics in preschool children with CF. We analyzed 42,658 cells from bronchoalveolar lavage of 11 preschool children with CF and a healthy control using scRNA-seq and parallel assessment of 154 cell surface proteins. Validation of cell types identified by scRNA-seq was achieved by assessment of s les by spectral flow cytometry. Analysis of transcriptome expression and cell surface protein expression, combined with functional pathway analysis, revealed 41 immune and epithelial cell populations in BAL. Spectral flow cytometry analysis of over 256,000 cells from a subset of the same patients revealed high correlation in major cell type proportions across the two technologies. Macrophages consisted of 13 functionally distinct sub populations, including previously undescribed populations enriched for markers of vesicle production and regulatory/repair functions. Other novel cell populations included CD4 T cells expressing inflammatory IFNα/β and NFκB signalling genes. Our work provides a comprehensive cellular analysis of the pediatric lower airway in preschool children with CF, reveals novel cell types and provides a reference for investigation of inflammation in early life CF.
Publisher: Oxford University Press (OUP)
Date: 30-04-2018
Publisher: Springer Science and Business Media LLC
Date: 30-06-2014
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/0008-5472.22422093.V1
Abstract: Supplementary File comprising of Supplementary Material and Methods, Supplementary References and Supplementary Figures S1-S7. Figure S1: IHC of melanoma and proliferation markers Figure S2: Images of fish used for bulk RNA-seq, Figure S3: Heatmaps of most variable genes and MITF target genes Figure S4: describes transcriptome comparison of the three melanoma models Figure S5: apoptosis at the site of melanoma regression Figure S6: fish used for low cell number and single cell RNA-seq Figure S7: MITF-independent cells present in residual disease and primary tumour.
Publisher: Springer Science and Business Media LLC
Date: 04-2018
DOI: 10.1038/S41586-018-0040-3
Abstract: In cancer, the epithelial-to-mesenchymal transition (EMT) is associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However, there is no direct in vivo evidence for this idea. Here we screen a large panel of cell surface markers in skin and mammary primary tumours, and identify the existence of multiple tumour subpopulations associated with different EMT stages: from epithelial to completely mesenchymal states, passing through intermediate hybrid states. Although all EMT subpopulations presented similar tumour-propagating cell capacity, they displayed differences in cellular plasticity, invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes identify the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulate EMT transition states.
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/0008-5472.22422090
Abstract: Supplementary file comprising Supplementary Tables S1-S8. Table S1: list of antibodies used in this study Table S2: gene set from literature used for pathway analysis Table S3: list of significantly enriched pathways from GSEA analysis between primary tumour and regression site (low cell number RNA-seq) Table S4: qPCR primers used in this study Tables S5: list of shared upregulated pathways in superficial melanoma and low MITF patients Table S6: list of shared upregulated pathways in nodular melanoma and high MITF patients Table S7: list of pathways upregulated in paired comparison of zebrafish melanoma models Table S8: list of upregulated pathways from pairwise comparison between in idual clusters in single cell RNA-seq analysis.
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.YEXCR.2018.12.010
Abstract: Glioblastoma (GBM) tumor cells exhibit drug resistance and are highly infiltrative. GBM stem cells (GSCs), which have low proliferative capacity are thought to be one of the sources of resistant cells which result in relapse/recurrence. However, the molecular mechanisms regulating quiescent-specific tumor cell biology are not well understood. Using human GBM cell lines and patient-derived GBM cells, Oregon Green dye retention was used to identify and isolate the slow-cycling, quiescent-like cell subpopulation from the more proliferative cells in culture. Sensitivity of cell subpopulations to temozolomide and radiation, as well as the migration and invasive potential were measured. Differential expression analysis following RNAseq identified genes enriched in the quiescent cell subpopulation. Orthotopic transplantation of cells into mice was used to compare the in vivo malignancy and invasive capacity of the cells. Proliferative quiescence correlated with better TMZ resistance and enhanced cell invasion, in vitro and in vivo. RNAseq expression analysis identified genes involved in the regulation cell invasion/migration and a three-gene signature, TGFBI, IGFBP3, CHI3L1, overexpressed in quiescent cells which correlates with poor GBM patient survival.
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.CELL.2018.06.025
Abstract: Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD, we applied single-cell RNA sequencing to malignant cells isolated from BRAF mutant patient-derived xenograft melanoma cohorts exposed to concurrent RAF/MEK-inhibition. We identified distinct drug-tolerant transcriptional states, varying combinations of which co-occurred within MRDs from PDXs and biopsies of patients on treatment. One of these exhibited a neural crest stem cell (NCSC) transcriptional program largely driven by the nuclear receptor RXRG. An RXR antagonist mitigated accumulation of NCSCs in MRD and delayed the development of resistance. These data identify NCSCs as key drivers of resistance and illustrate the therapeutic potential of MRD-directed therapy. They also highlight how gene regulatory network architecture reprogramming may be therapeutically exploited to limit cellular heterogeneity, a key driver of disease progression and therapy resistance.
Publisher: Cold Spring Harbor Laboratory
Date: 13-01-2023
DOI: 10.1101/2023.01.13.521174
Abstract: Single-cell multi-omics methods are enabling the study of cell state ersity, which is largely determined by the interplay of the genome, epigenome, and transcriptome. Here, we describe Gtag& T-seq, a genome-and-transcriptome sequencing (G& T-seq) protocol of the same single cells that omits whole-genome lification (WGA) by using direct genomic tagmentation (Gtag). Gtag drastically decreases the cost and improves coverage uniformity at both the single-cell and pseudo-bulk level when compared to WGA-based G& T-seq. We also show that transcriptome-based DNA copy number inference has limited resolution and accuracy, underlining the importance of affordable multi-omic approaches. Moreover, applying Gtag& T-seq to a melanoma xenograft model before treatment and at minimal residual disease revealed differential cell state plasticity and treatment response between cancer subclones. In summary, Gtag& T-seq is a low-cost and accurate single-cell multi-omics method enabling the exploration of genetic alterations and their functional consequences in single cells at scale.
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/0008-5472.C.6511122.V1
Abstract: Abstract The melanocyte-inducing transcription factor (MITF)–low melanoma transcriptional signature is predictive of poor outcomes for patients, but little is known about its biological significance, and animal models are lacking. Here, we used zebrafish genetic models with low activity of Mitfa (MITF-low) and established that the MITF-low state is causal of melanoma progression and a predictor of melanoma biological subtype. MITF-low zebrafish melanomas resembled human MITF-low melanomas and were enriched for stem and invasive (mesenchymal) gene signatures. MITF-low activity coupled with a p53 mutation was sufficient to promote superficial growth melanomas, whereas BRAF sup V600E /sup accelerated MITF-low melanoma onset and further promoted the development of MITF-high nodular growth melanomas. Genetic inhibition of MITF activity led to rapid regression recurrence occurred following reactivation of MITF. At the regression site, there was minimal residual disease that was resistant to loss of MITF activity (termed MITF-independent cells) with very low-to-no MITF activity or protein. Transcriptomic analysis of MITF-independent residual disease showed enrichment of mesenchymal and neural crest stem cell signatures similar to human therapy-resistant melanomas. Single-cell RNA sequencing revealed MITF-independent residual disease was heterogeneous depending on melanoma subtype. Further, there was a shared subpopulation of residual disease cells that was enriched for a neural crest G sub /sub -like state that preexisted in the primary tumor and remained present in recurring melanomas. These findings suggest that invasive and stem-like programs coupled with cellular heterogeneity contribute to poor outcomes for MITF-low melanoma patients and that MITF-independent subpopulations are an important therapeutic target to achieve long-term survival outcomes. Significance: This study provides a useful model for MITF-low melanomas and MITF-independent cell populations that can be used to study the mechanisms that drive these tumors as well as identify potential therapeutic options. /
Publisher: Springer Science and Business Media LLC
Date: 18-02-2021
DOI: 10.1038/S41467-021-21297-Y
Abstract: Regulatory CD4 + T cells (Treg) prevent tumor clearance by conventional T cells (Tconv) comprising a major obstacle of cancer immune-surveillance. Hitherto, the mechanisms of Treg repertoire formation in human cancers remain largely unclear. Here, we analyze Treg clonal origin in breast cancer patients using T-Cell Receptor and single-cell transcriptome sequencing. While Treg in peripheral blood and breast tumors are clonally distinct, Tconv clones, including tumor-antigen reactive effectors (Teff), are detected in both compartments. Tumor-infiltrating CD4 + cells accumulate into distinct transcriptome clusters, including early activated Tconv, uncommitted Teff, Th1 Teff, suppressive Treg and pro-tumorigenic Treg. Trajectory analysis suggests early activated Tconv differentiation either into Th1 Teff or into suppressive and pro-tumorigenic Treg. Importantly, Tconv, activated Tconv and Treg share highly-expanded clones contributing up to 65% of intratumoral Treg. Here we show that Treg in human breast cancer may considerably stem from antigen-experienced Tconv converting into secondary induced Treg through intratumoral activation.
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/0008-5472.22422090.V1
Abstract: Supplementary file comprising Supplementary Tables S1-S8. Table S1: list of antibodies used in this study Table S2: gene set from literature used for pathway analysis Table S3: list of significantly enriched pathways from GSEA analysis between primary tumour and regression site (low cell number RNA-seq) Table S4: qPCR primers used in this study Tables S5: list of shared upregulated pathways in superficial melanoma and low MITF patients Table S6: list of shared upregulated pathways in nodular melanoma and high MITF patients Table S7: list of pathways upregulated in paired comparison of zebrafish melanoma models Table S8: list of upregulated pathways from pairwise comparison between in idual clusters in single cell RNA-seq analysis.
Publisher: Cold Spring Harbor Laboratory
Date: 30-05-2017
DOI: 10.1101/143388
Abstract: Hyperactivation of the PI3K signaling is common in human cancers, including gliomas, but the precise role of the pathway in glioma biology remains to be determined. Some limited understanding of PI3K signaling in brain cancer come from studies on neural stem rogenitor cells (NSPCs) where signals transmitted via the PI3K pathway cooperate with other intracellular pathways and downstream transcription factors to regulate NSPC proliferation. To investigate the role for the PI3K pathway in glioma initiation and development, we generated a mouse model targeting the inducible expression of a Pik3ca H1047A oncogenic mutation and simultaneous deletion of the PI3K negative regulator, Pten, in NSPCs. We show that the expression of a Pik3ca H1047A was sufficient to initiate tumorigenesis but that simultaneous loss of Pten, was required for the development of invasive, high-grade glioma. Mutant NSPCs exhibited enhanced neurosphere forming capacity which correlated with increased Wnt signaling. We also show that loss of CREB in Pik3ca-PTEN tumors led to a longer symptom-free survival in mice. Taken together, our findings present a novel mouse model for high-grade glioma with which we demonstrate that the PI3K pathway is important for initiation of tumorigenesis and that disruption of downstream CREB signaling attenuates tumor expansion.
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/0008-5472.22422093
Abstract: Supplementary File comprising of Supplementary Material and Methods, Supplementary References and Supplementary Figures S1-S7. Figure S1: IHC of melanoma and proliferation markers Figure S2: Images of fish used for bulk RNA-seq, Figure S3: Heatmaps of most variable genes and MITF target genes Figure S4: describes transcriptome comparison of the three melanoma models Figure S5: apoptosis at the site of melanoma regression Figure S6: fish used for low cell number and single cell RNA-seq Figure S7: MITF-independent cells present in residual disease and primary tumour.
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.IMMUNI.2022.08.004
Abstract: To optimize immunity to pathogens, B lymphocytes generate plasma cells with functionally erse antibody isotypes. By lineage tracing single cells within differentiating B cell clones, we identified the heritability of discrete fate controlling mechanisms to inform a general mathematical model of B cell fate regulation. Founder cells highly influenced clonal plasma-cell fate, whereas class switch recombination (CSR) was variegated within clones. In turn, these CSR patterns resulted from independent all-or-none expression of both activation-induced cytidine deaminase (AID) and IgH germline transcription (GLT), with the latter being randomly re-expressed after each cell ision. A stochastic model premised on these molecular transition rules accurately predicted antibody switching outcomes under varied conditions in vitro and during an immune response in vivo. Thus, the generation of functionally erse antibody types follows rules of autonomous cellular programming that can be adapted and modeled for the rational control of antibody classes for potential therapeutic benefit.
Publisher: Elsevier BV
Date: 10-2022
Publisher: Wiley
Date: 18-09-2023
DOI: 10.1111/IMCB.12689
Publisher: Springer Science and Business Media LLC
Date: 21-05-2018
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2023
DOI: 10.1101/2023.06.20.544880
Abstract: Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of s le multiplexing reagents can impact data quality and experimental outcomes. In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across erse s le types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate s le types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are critical to optimal performance. We also compared the performance of fixed scRNA-Seq kits and highlight the advantages of the Parse Biosciences kit for fragile s les. Highly multiplexed scRNA-Seq experiments require more sequencing resources, therefore we evaluated CRISPR-based destruction of non-informative genes to enhance sequencing value. Our comprehensive analysis provides insights into the selection of appropriate s le multiplexing reagents and protocols for scRNASeq experiments, facilitating more accurate and cost-effective studies.
Publisher: American Association for Cancer Research (AACR)
Date: 08-2011
DOI: 10.1158/1535-7163.MCT-11-0240
Abstract: The phosphatidylinositol 3-kinase (PI3K)/Akt pathway is commonly dysregulated in human cancer, making it an attractive target for novel anticancer therapeutics. We have used a mouse model of ovarian cancer generated by KrasG12D activation and Pten deletion in the ovarian surface epithelium for the preclinical assessment of a novel PI3K/mTOR inhibitor PF-04691502. To enable higher throughput studies, we developed an orthotopic primary transplant model from these mice and evaluated therapeutic response to PF-04691502 using small-animal ultrasound and FDG-PET imaging. PF-04691502 inhibited tumor growth at 7 days by 72% ± 9. FDG-PET imaging revealed that PF-04691502 reduced glucose metabolism dramatically, suggesting FDG-PET may be exploited as an imaging biomarker of target inhibition by PF-04691502. Tissue biomarkers of PI3K/mTOR pathway activity, p-AKT (S473), and p-RPS6 (S240/244), were also dramatically inhibited following PF-04691502 treatment. However, as a single agent, PF-04691502 did not induce tumor regression and the long-term efficacy was limited, with tumor proliferation continuing in the presence of drug treatment. We hypothesized that tumor progression was because of concomitant activation of the mitogen-activated protein kinase pathway downstream of KrasG12D expression promoting cell survival and that the therapeutic effect of PF-04691502 would be enhanced by combinatory inhibition of MEK using PD-0325901. This combination induced striking tumor regression, apoptosis associated with upregulation of Bim and downregulation of Mcl-1, and greatly improved duration of survival. These data suggest that contemporaneous MEK inhibition enhances the cytotoxicity associated with abrogation of PI3K/mTOR signaling, converting tumor growth inhibition to tumor regression in a mouse model of ovarian cancer driven by PTEN loss and mutant K-Ras. Mol Cancer Ther 10(8) 1440–9. ©2011 AACR.
Publisher: IMR Press
Date: 2014
DOI: 10.2741/4264
Abstract: The understanding of how cancer stem cells (CSCs) or tumor-initiating cells (TICs) behave is important in understanding how tumors are initiated and how they recur following initial treatment. More specifically to understand how CSCs behave, the different signaling mechanisms orchestrating their growth, cell cycle dynamics, differentiation, trans-differentiation and survival following cytotoxic challenges need to be deciphered. Ultimately this will advance the ability to predict how these cells will behave in in idual patients and under different therapeutic conditions. Second or next-generation sequencing (NGS) capabilities have provided researchers a window into the molecular and genetic clockwork of CSCs at an unprecedented resolution and depth, with throughput capabilities allowing sequencing of hundreds of s les in relatively short timeframes and at relatively modest costs More specifically NGS gives us the ability to accurately determine the genomic and transcriptomic nature of CSCs. These technologies and the publicly available cancer genome databases, together with the ever increasing computing power available to researchers locally or via cloud-based servers are changing the way biomedical cancer research is approached.
Publisher: Public Library of Science (PLoS)
Date: 27-02-2017
Publisher: American Association for Cancer Research (AACR)
Date: 15-11-2019
DOI: 10.1158/0008-5472.CAN-19-0037
Abstract: This study provides a useful model for MITF-low melanomas and MITF-independent cell populations that can be used to study the mechanisms that drive these tumors as well as identify potential therapeutic options.
Location: Australia
Start Date: 2016
End Date: 2018
Funder: Belgian Federal Science Policy Office
View Funded Activity