ORCID Profile
0000-0002-1933-505X
Current Organisation
University of Melbourne
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Publisher: Springer Science and Business Media LLC
Date: 21-10-2022
DOI: 10.1038/S41467-022-34011-3
Abstract: Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors associated with autonomic nerves. Here we use single-nuclei RNA-seq and bulk-tissue gene-expression data to characterize the cellular composition of PCPG and normal adrenal tissues, refine tumor gene-expression subtypes and make clinical and genotypic associations. We confirm seven PCPG gene-expression subtypes with significant genotype and clinical associations. Tumors with mutations in VHL , SDH-encoding genes ( SDHx ) or MAML3 -fusions are characterized by hypoxia-inducible factor signaling and neoangiogenesis. PCPG have few infiltrating lymphocytes but abundant macrophages. While neoplastic cells transcriptionally resemble mature chromaffin cells, early chromaffin and neuroblast markers are also features of some PCPG subtypes. The gene-expression profile of metastatic SDHx -related PCPG indicates these tumors have elevated cellular proliferation and a lower number of non-neoplastic Schwann-cell-like cells, while GPR139 is a potential theranostic target. Our findings therefore clarify the erse transcriptional programs and cellular composition of PCPG and identify biomarkers of potential clinical significance.
Publisher: American Association for Cancer Research (AACR)
Date: 08-2015
DOI: 10.1158/1538-7445.AM2015-2175
Abstract: Background/Aims: Pheochromocytoma (PCC) is a neoplastic growth of adrenal or extra-adrenal chromaffin cells. PCC is one of the most heritable cancers with up to 35% of cases attributed to a germline mutation in one of 13 or more genes. Previous microarray gene-expression studies have observed that PCC clusters into two or more subtypes corresponding to the underlying mutations that cause either dysregulation of hypoxia inducible factor (HIF) (e.g. VHL, SDHx) or constitutive activation of receptor tyrosine kinase (RTK) signalling (e.g. RET, NF1). The aim of this study was to conduct an unbiased assessment of the number of gene-expression subtypes of PCC using a compendium of published gene-expression data. Furthermore, we aimed to design a gene-expression based diagnostic assay to accurately classify tumours as an adjunct to clinical mutation analysis and for research purposes. Methods: Consensus clustering was applied to a gene-expression compendium of 253 s les to assess the most stable number of subtypes. Differential gene-expression analysis was performed to identify genes specific to each class. The expression of these genes in the microarray data was used to train a cross-platform k-NN classifier. The classifier was tested on an independent RNA-seq dataset to assess accuracy. Forty-seven genes (plus five control genes) were selected for Nanostring gene-expression analysis. The Nanostring assay was performed on RNA isolated from FFPE blocks corresponding to s les in the RNA-seq dataset to assess concordance and accuracy of the cross platform classifier. Results: Consensus clustering identified six robust PCC subtypes. Based on clinical annotation from the published data, four classes belong to the RTK signalling group, three of which (annotated RTK1 to 3) contain a mixture of NF1, RET, RAS, and TMEM127 gene mutations, and a fourth (annotated MAX-like) containing s les with mutations in the MAX gene.The remaining two classes belong to the HIF signalling group, one representing s les with a VHL mutation and the other mutations in one of the SDHx subunits. Applying the classifier we were able to classify RNA-seq data for s les with RET (6), NF1 (6), RAS (2), and TMEM127 (1) as belonging to the RTK 1-3 groups. Accurate classification of nine of eleven VHL s les and two SDHx s les was achieved. Classification of corresponding Nanostring data provided concordant classification for eleven of twelve s les. Conclusion: PCC can be ided into six biological classes indicative of the underlying driver mutation. The ability to accurately classify s les from FFPE material would provide a valuable adjunct to current practices in genetic testing laboratories, providing corroboration for known mutations and guidance on s les with mutations of unknown significance in PCC genes. Furthermore, the classifier can be used for research purposes to subtype tumours with unknown driver mutations for the interpretation of candidate driver genes. Citation Format: Aidan Flynn, Diana Benn, Roderick Clifton-Bligh, Joshy George, Anthony J. Gill, Rodney J. Hicks, Richard W. Tothill. A diagnostic gene expression assay for the classification of pheochromocytoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research 2015 Apr 18-22 Philadelphia, PA. Philadelphia (PA): AACR Cancer Res 2015 (15 Suppl):Abstract nr 2175. doi:10.1158/1538-7445.AM2015-2175
Publisher: Bioscientifica
Date: 2017
DOI: 10.1530/ERC-17-0306
Abstract: Pheochromocytomas (PC) and paragangliomas (PGL) are endocrine tumors for which the genetic and clinicopathological features of metastatic progression remain incompletely understood. As a result, the risk of metastasis from a primary tumor cannot be predicted. Early diagnosis of in iduals at high risk of developing metastases is clinically important and the identification of new biomarkers that are predictive of metastatic potential is of high value. Activation of TERT has been associated with a number of malignant tumors, including PC/PGL. However, the mechanism of TERT activation in the majority of PC/PGL remains unclear. As TERT promoter mutations occur rarely in PC/PGL, we hypothesized that other mechanisms – such as structural variations – may underlie TERT activation in these tumors. From 35 PC and four PGL, we identified three primary PCs that developed metastases with elevated TERT expression, each of which lacked TERT promoter mutations and promoter DNA methylation. Using whole genome sequencing, we identified somatic structural alterations proximal to the TERT locus in two of these tumors. In both tumors, the genomic rearrangements led to the positioning of super-enhancers proximal to the TERT promoter, that are likely responsible for the activation of the normally tightly repressed TERT expression in chromaffin cells
Publisher: Wiley
Date: 02-02-2015
DOI: 10.1002/PATH.4503
Publisher: Wiley
Date: 13-05-2017
DOI: 10.1002/PATH.4900
Abstract: Hereditary endocrine neoplasias, including phaeochromocytoma araganglioma and medullary thyroid cancer, are caused by autosomal dominant mutations in several familial cancer genes. A common feature of these diseases is the presentation of multiple primary tumours, or multifocal disease representing independent tumour clones that have arisen from the same initiating genetic lesion, but have undergone independent clonal evolution. Such tumours provide an opportunity to discover common cooperative changes required for tumourigenesis, while controlling for the genetic background of the in idual. We performed genomic analysis of synchronous and metachronous tumours from five patients bearing germline mutations in the genes SDHB, RET, and MAX. Using whole exome sequencing and high-density single-nucleotide polymorphism arrays, we analysed two to four primary tumours from each patient. We also applied multi-region s ling, to assess intratumoural heterogeneity and clonal evolution, in two cases involving paraganglioma and medullary thyroid cancer, respectively. Heterogeneous patterns of genomic change existed between synchronous or metachronous tumours, with evidence of branching evolution. We observed striking ex les of evolutionary convergence involving the same rare somatic copy-number events in synchronous primary phaeochromocytoma araganglioma. Convergent events also occurred during clonal evolution of metastatic medullary thyroid cancer. These observations suggest that genetic or epigenetic changes acquired early within precursor cells, or pre-existing within the genetic background of the in idual, create contingencies that determine the evolutionary trajectory of the tumour. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Publisher: The Endocrine Society
Date: 03-2016
DOI: 10.1210/JC.2015-3889
Abstract: Pheochromocytomas and paragangliomas (PPGLs) are heritable neoplasms that can be classified into gene-expression subtypes corresponding to their underlying specific genetic drivers. This study aimed to develop a diagnostic and research tool (Pheo-type) capable of classifying PPGL tumors into gene-expression subtypes that could be used to guide and interpret genetic testing, determine surveillance programs, and aid in elucidation of PPGL biology. A compendium of published microarray data representing 205 PPGL tumors was used for the selection of subtype-specific genes that were then translated to the Nanostring gene-expression platform. A support vector machine was trained on the microarray dataset and then tested on an independent Nanostring dataset representing 38 familial and sporadic cases of PPGL of known genotype (RET, NF1, TMEM127, MAX, HRAS, VHL, and SDHx). Different classifier models involving between three and six subtypes were compared for their discrimination potential. A gene set of 46 genes and six endogenous controls was selected representing six known PPGL subtypes RTK1–3 (RET, NF1, TMEM127, and HRAS), MAX-like, VHL, and SDHx. Of 38 test cases, 34 (90%) were correctly predicted to six subtypes based on the known genotype to gene-expression subtype association. Removal of the RTK2 subtype from training, characterized by an admixture of tumor and normal adrenal cortex, improved the classification accuracy (35/38). Consolidation of RTK and pseudohypoxic PPGL subtypes to four- and then three-class architectures improved the classification accuracy for clinical application. The Pheo-type gene-expression assay is a reliable method for predicting PPGL genotype using routine diagnostic tumor s les.
Publisher: Wiley
Date: 25-06-2021
Abstract: Treatment of glioblastoma (GBM) remains a challenging task, with limited treatment options, none offering a cure. Immune therapy has proven effective across different cancers with remarkable response rates. Tumor mutational burden (TMB) is a marker of response, but technical and methodological differences in TMB estimates have made a proper assessment and comparison challenging. Here, we analyzed a prospective collection of paired s les from 35 patients with newly diagnosed GBM, all of whom were wild‐type (WT) for isocitrate dehydrogenase, before and after treatment with radiotherapy and temozolomide. Seven patients (20%) had O6‐methylguanine‐DNA methyltransferase‐methylated tumors. Six patients (17%) had two relapse surgeries, and tissue from all three surgeries was collected. We found that accurate evaluation of TMB was confounded by high variability in the cancer cell fraction of relapse s les. To ameliorate this, we developed a model to adjust for tumor purity based on the relative density distribution of variant allele frequencies in each primary–relapse pair. Additionally, we examined the mutation spectra of shared and private mutations. After tumor purity adjustment, we found TMB comparison reliable in tumors with tumor purity between 15% and 40%, resulting in 27/35 patients (77.1%). TMB remained unchanged from 0.65 mutations per megabase (Mb) to 0.67/Mb before and after treatment, respectively. Examination of the mutation spectra revealed a dominance of C T transitions at CpG sites in both shared and relapse‐private mutations, consistent with cytosine deamination and the clock‐like mutational signature 1. We present and apply a cellularity correction approach that enables more accurate assessment of TMB in paired tumor s les. We did not find a significant increase in TMB after correcting for cancer cell fraction. Our study raises significant concerns when determining TMB. Although a small s le size, corrected TMB can have a clinical significance when stratifying patients to experimental treatment, for ex le, immune checkpoint therapy.
Location: Denmark
No related grants have been discovered for Aidan Flynn.