University of Melbourne – Lead Investigator Dr. Richard Tothill

A5 SDHB Genomics Study

The A5 SDHB Genomics study is an ambitious multi-national research project involving comprehensive analysis of metastatic SDHB-associated pheochromocytoma and paraganglioma (PCPG).

The study has these key objectives:

1. To elucidate the biology of SDHB PC/PGL by characterizing recurrently altered genes, gene pathways and cell types in tumors.
2. To identify either single biomarkers or biomarker gene sets that can predict the likelihood of metastatic progression.
3. To identify new therapeutic targets representing single genes, proteins or signalling pathways.

The team is led by A/Prof Richard Tothill at the University of Melbourne, and patient samples and clinical data have been accrued from 12 institutions across six countries. A/Prof Tothill’s team has applied genome-wide multi-omics analysis to more than 100 PCPG tumors including whole-genome DNA sequencing, DNA methylation profiling and cutting-edge single cell analysis. The work has been generously funded by the National Health and Medical Research Council (Australia), Pheo-Para Coalition (USA), Pheo-Para Alliance (USA) and Paradifference (Sweden).

A recent study published by the team in the journal Nature Communications described analysis of PCPG tumors using single-cell genomics. The method enabled simultaneous gene-expression analysis in thousands of individual cells from patient tumor samples. The study involved analysis of 30 PCPG tumors representing diverse genetic backgrounds (including SDHB carriers) as well as two normal adrenal tissues totalling more than 109,000 cells.

Key findings from the single-cell genomics study included an elevation of normal cell types associated with blood vessel formation in tumors, which is linked to aberrant hypoxia pathway signalling with some unexpected observations made in PCPG carrying MAML3-fusions, that also have some of these features. Other cell types of interest included immune cells such as macrophages that were abundant in some tumors. A support cell type called a sustentactular cell, commonly seen in PCPG tumors and normal adrenal tissues, were also characterised in great detail. A comparison of cancerous cells found in tumors to normal healthy adrenal chromaffin cells showed associations between tumor genotype and developmental stages in the adrenal gland but that tumor cells also have very unique transcriptional changes based on underlying mutated genes. The team also combined their single-cell analysis with data from 735 tumors profiled using “bulk tissue” analysis to conduct the largest single analysis of its kind to date. The data was used to refine molecular subtypes of PCPG and find gene-expression changes associated with metastatic progression in SDHB-associated PCPG. Finally, promising new diagnostic and therapeutic targets were identified, including the G-protein couple receptor GPR139, that had elevated expression in pseudohypoxic PCPG including metastatic SDHB-associated PCPG.

Further analysis of the other data types generated during the A5 SDHB Genomics Study is still underway and currently being finalised for preparation of manuscripts. The data will be valuable resource made available to other researchers once published. Indeed, the single cell genomics data has already been made publicly available to other research groups for their own analysis.