SUPER Solving Cancer of Unknown Primary

A diagnosis of ‘Cancer of Unknown Primary’ CUP is made when a patient presents with metastatic disease for which no primary cancer can be identified despite extensive clinical assessment, imaging, and pathological evaluation. Currently, there is little information available to clinicians to help guide diagnostic, treatment, or supportive care practices for patients with CUP. 

SUPER is a cohort study that was initiated by a multidisciplinary research team to address the difficulties that both clinicians and patients face when dealing with a diagnosis of CUP. 

Professor Linda Mileshkin is the clinical lead for the SUPER studies, and works closely with Dr Richard Tothill (genomics lead) from the University of Melbourne and Professor Penelope Schofield (behavioural science lead) from Peter MacCallum Cancer Centre and Swinburne University of Technology 

SUPER established a ‘bio and information bank’ which is a national information resource of clinical, molecular, and patient questionnaire information that is currently being used to identify the supportive care and psychosocial needs of CUP patients, understand the clinical and molecular characteristics of CUP, as well as improving the diagnostic assessment of CUP patients.  

We have manuscripts in preparation exploring patient experiences throughout their CUP diagnosis and treatment journey. We have identified differences in needs between patients residing in metropolitan versus rural/regional areas and compared the economic, quality of life and psychosocial needs of CUP patients to other patients diagnosed with advanced cancer of a known primary. Some of the work we have already presented/published is listed below. 

SUPER recruited patients from 11 metropolitan sites nationally in Victoria, New South Wales, South Australia, Northern Territory and Australian Capital Territory and well exceeded the target recruitment of 300 participants. To our knowledge, we are the only translational, cross-disciplinary research group in Australia investigating CUP. 

SUPER-NEXT Complete Whole Genome Sequencing for Cancer of Unknown Primary

SUPER-NEXT is a prospective clinical study involving 16 sites nationally and an extension of the successful SUPER study. We hope to recruit an additional 200 patients to the study, collect clinical and patient reported outcome data and biospecimen (fresh or archival tumour material and a blood sample). 

Our goal is to develop and rapidly deploy genomics and precision medicine for CUP patients. SUPER-NEXT will generate a comprehensive molecular genomics report for individual patients that will be used to make recommendations for molecularly targeted therapy, immunotherapy, or site-specific therapy, as well as help to correctly diagnose primary tissue of origin. 

Molecular Tests for CUP patients

As part of the SUPER team’s larger body of work, we currently offer participants two molecular tests; a targeted gene sequencing panel (Illumina TSO500) test, as well as whole genome and transcriptome sequencing. 

Both test reports are prepared simultaneously at the Peter MacCallum Cancer Centre (PMCC) and University of Melbourne Centre for Cancer Research (UMCCR)and results are fed back to clinicians within four to six weeks (about one and a half months) from receipt of tissue at Peter Mac. 

See SUPER-NEXT: Solving Unknown Primary Cancer for more information. 

The TSO500 panel is reported by the Peter Mac molecular pathology team and contains a select set of genes or gene regions that are implicated in a range of cancer types, some of which may be targets of newer types of precision therapies. 

This test can also provide information on whether the genome is unstable (microsatellite instability) and quantify the mutations present across the genome (tumour mutation burden), both of which are biomarkers of potential response to immune-based therapies. 

Whole genome sequencing analyses all the genome, including both germline and somatic genes and non-coding regions and measures their complete expression/activity. This= provides a deeper understanding of the genomic and gene expression landscape and reveals extra details not covered by targeted sequencing. This information can be harnessed so that unknown primary cancers can be matched to tumours of known origin. Whole Genome sequenciung also reveals mutational and gene expression signatures which may suggest the tissue of origin of cancer and response to therapy. For example, a ‘UV signature’ may indicate sun exposure and a likely origin from the skin. 

Figure 1. Patients will be consented, diagnostic tissues sourced from pathology archives and blood taken for germline DNA and ctDNA extraction. SUPER-NEXT will incorporate WGS and WTS and comparative targeted gene-panel testing. Targeted DNA sequencing of ctDNA will also be applied. Novel methods for detection of mutational signatures and tissue of origin classification will be developed. Curation of WGS/WTS and ctDNA data will be done through the VCCC (Victorian Comprehensive Cancer Centre) Precision Oncology Program at University of Melbourne and Peter Mac. Results including driver gene mutations, mutational signatures, tissue of origin prediction and immune/stromal signatures will be discussed at the VCCC Molecular Tumour Board, together with any additional information from pathology review (including validation IHC stains and FISH (Fluorescence in situ hybridisation). 

Recruitment sites

Victoria

Peter MacCallum Cancer Centre, VIC (Coordinating Centre) 
South West Healthcare – Warrnambool 
Bendigo Cancer Centre 
Alfred Hospital 
Box Hill Hospital 
Frankston Hospital – Peninsula Health 
Geelong Hospital – Barwon Health 

Queensland

Royal Brisbane and Women’s Hospital

New South Wales

Blacktown Mount Druitt Hospital 
Border Medical Oncology 

Northern Territory

Royal Darwin Hospital

Tasmania

Launceston General Hospital 

Primary Objectives

• Demonstrate that WGS/WTS in CUP can assist diagnosis and provide evidence-based therapeutic leads superior to current targeted DNA panel testing 
• Demonstrate circulating tumour DNA from CUP patients facilitates rapid mutation testing 

Secondary Objectives

This project has two long-term objectives:

1. To establish a biobank for analysis of CUP patient tumour and blood samples including establishment of organoid and patient-derived xenograft (PDX) models 
2. Describe the clinical characteristics and outcomes of CUP patients receiving genomic testing. 

Sponsor

Peter MacCallum Cancer Centre

Funding 

The project has received 4 sources of grant funding:

1. ‘SUPER’ was funded by Cancer Australia. This study established a ‘biobank’ of 120 CUP patients, and 120 non-CUP patients which is a resource of clinical, molecular, and patient questionnaire information for future studies. The study is based in New South Wales, South Australia, and Melbourne Victoria. 

2. ‘SUPER plus’ is funded by the Victorian Cancer Agency. This study expanded SUPER by increasing patient numbers and expanding recruitment sites across regional Victoria. In addition, clinical questionnaires were included here to assess whether receiving timely molecular profiling results would alter patient management and treatment choice. 

3. ‘Recuperate’ is funded by Cancer Australia, and compliments ‘SUPER plus’ by expanding the study nationally to include Northern Territory and the Australia Capital Territory. In addition, Recuperate also is assessing the costs associated with a diagnosis of CUP. 

4. ‘SUPER-NEXT’ is funded by the MRFF (Medical Research Future Fund) Genomics Health Future Mission and extends the very sucessful SUPER study, bringing recent innovations in the use of whole genome (WGS) and whole transcriptome (WTS) sequencing to increase our sensitivity to detect therapeutic targets in CUP patients and help to correctly diagnose primary tissue of origin. 

Principal Investigator/s

• SUPER - CIA: Prof Penelope Schofield, CIB: Prof David Bowtell, CIC: Prof Linda Mileshkin 
• SUPER plus - CIA: Prof Linda Mileshkin, CIB: Prof Penelope Schofield, CIC: Prof David Bowtell 
• Recuperate - CIA: Prof Linda Mileshkin, CIB: Prof David Bowtell; CIC: Prof Penelope Schofield 
• SUPER-NEXT – Co-le by A/Prof Richard Tothill, CProf Linda Mileshkin, Prof Penelope Schofield 

Contact details

SUPER-NEXT Project Coordinator
Smitha Sithara  
T: 03 855 97952  
E: [email protected] 

Research Assistant 
Christine Dijkstra  
T: (03) 8559 8499  
E: [email protected]

Genomics Coordinator 
Wendy Ip 
University of Melbourne  
E: [email protected] 

PROJECT STATUS 

• Open and Recruiting (SUPER-NEXT)