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Westphalen CB, Federer-Gsponer J, Pauli C, Karapetyan AR, Chalabi N, Durán-Pacheco G, Beringer A, Bochtler T, Cook N, Höglander E, Jin DX, Losa F, Mileshkin L, Moch H, Ross JS, Sokol ES, Tothill RW, Krämer A. Baseline mutational profiles of patients with carcinoma of unknown primary origin enrolled in the CUPISCO study. ESMO Open 2023; 8:102035. [PMID: 37922692 PMCID: PMC10774891 DOI: 10.1016/j.esmoop.2023.102035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Patients with unfavorable carcinoma of unknown primary origin (CUP) have an extremely poor prognosis of ∼1 year or less, stressing the need for more tailored treatments, which are currently being tested in clinical trials. CUPISCO (NCT03498521) was a phase II randomized study of targeted therapy/cancer immunotherapy versus platinum-based chemotherapy in patients with previously untreated, unfavorable CUP, defined as per the European Society for Medical Oncology guidelines. We present a preliminary, descriptive molecular analysis of 464 patients with stringently diagnosed, unfavorable CUP enrolled in the CUPISCO study. MATERIALS AND METHODS Genomic profiling was carried out on formalin-fixed, paraffin-embedded tissue to detect genomic alterations and assess tumor mutational burden and microsatellite instability. RESULTS Overall, ∼32% of patients carried a potentially targetable genomic alteration, including PIK3CA, FGFR2, ERBB2, BRAFV600E, EGFR, MET, NTRK1, ROS1, and ALK. Using hierarchical clustering of co-mutational profiles, 10 clusters were identified with specific genomic alteration co-occurrences, with some mirroring defined tumor entities. CONCLUSIONS Results reveal the molecular heterogeneity of patients with unfavorable CUP and suggest that genomic profiling may be used as part of informed decision-making to identify the potential primary tumor and targeted treatment options. Whether stringently diagnosed patients with unfavorable CUP benefit from targeted therapies in a similar manner to those with matched known primaries will be a key learning from CUPISCO.
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Affiliation(s)
- C B Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - C Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zürich, Switzerland
| | | | | | | | | | - T Bochtler
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and University of Heidelberg, Heidelberg; Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - N Cook
- The University of Manchester and the Christie NHS Foundation Trust, Manchester, UK
| | | | - D X Jin
- Foundation Medicine, Inc., Cambridge, USA
| | - F Losa
- Hospital de Sant Joan Despí-Moisès Broggi, ICO-Hospitalet, Barcelona, Spain
| | - L Mileshkin
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - H Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zürich, Switzerland
| | - J S Ross
- Foundation Medicine, Inc., Cambridge, USA; SUNY Upstate Medical University, Syracuse, USA
| | - E S Sokol
- Foundation Medicine, Inc., Cambridge, USA
| | - R W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Australia
| | - A Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and University of Heidelberg, Heidelberg.
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2
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Waldeck K, Van Zuylekom J, Cullinane C, Gulati T, Simpson KJ, Tothill RW, Blyth B, Hicks RJ. A genome-wide CRISPR/Cas9 screen identifies DNA-PK as a sensitiser to 177Lutetium-DOTA-octreotate radionuclide therapy. Theranostics 2023; 13:4745-4761. [PMID: 37771787 PMCID: PMC10526672 DOI: 10.7150/thno.84628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/17/2023] [Indexed: 09/30/2023] Open
Abstract
Peptide receptor radionuclide therapy (PRRT) using 177Lutetium-DOTA-octreotate (LuTate) for neuroendocrine tumours (NET) is now an approved treatment available in many countries, though primary or secondary resistance continue to limit its effectiveness or durability. We hypothesised that a genome-wide CRISPR/Cas9 screen would identify key mediators of response to LuTate and gene targets that might offer opportunities for novel combination therapies for NET patients. Methods: We utilised a genome-wide CRISPR-Cas9 screen in LuTate-treated cells to identify genes that impact on the sensitivity or resistance of cells to LuTate. Hits were validated through single-gene knockout. LuTate-resistant cells were assessed to confirm LuTate uptake and retention, and persistence of somatostatin receptor 2 (SSTR2) expression. Gene knockouts conferring LuTate sensitivity were further characterised by pharmacological sensitisation using specific inhibitors and in vivo analysis of the efficacy of these inhibitors in combination with LuTate. Results: The CRISPR-Cas9 screen identified several potential targets for both resistance and sensitivity to PRRT. Two gene knockouts which conferred LuTate resistance in vitro, ARRB2 and MVP, have potential mechanisms related to LuTate binding and retention, and modulation of DNA-damage repair (DDR) pathways, respectively. The screen showed that sensitivity to LuTate treatment in vitro can be conferred by the loss of a variety of genes involved in DDR pathways, with loss of genes involved in Non-Homologous End-Joining (NHEJ) being the most lethal. Loss of the key NHEJ gene, PRKDC (DNA-PK), either by gene loss or inhibition by two different inhibitors, resulted in significantly reduced cell survival upon exposure of cells to LuTate. In SSTR2-positive xenograft-bearing mice, the combination of nedisertib (a DNA-PK specific inhibitor) and LuTate produced a more robust control of tumour growth and increased survival compared to LuTate alone. Conclusions: DDR pathways are critical for sensing and repairing radiation-induced DNA damage, and our study shows that regulation of DDR pathways may be involved in both resistance and sensitivity to PRRT. Additionally, the use of a DNA-PK inhibitor in combination with LuTate PRRT significantly improves the efficacy of the treatment in pre-clinical models, providing further evidence for the clinical efficacy of this combination.
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Affiliation(s)
- Kelly Waldeck
- Models of Cancer Translational Research Centre, Research Division, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Jessica Van Zuylekom
- Models of Cancer Translational Research Centre, Research Division, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Carleen Cullinane
- Models of Cancer Translational Research Centre, Research Division, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Twishi Gulati
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
| | - Kaylene J. Simpson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Richard W. Tothill
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
- Department of Clinical Pathology and University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Benjamin Blyth
- Models of Cancer Translational Research Centre, Research Division, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Rodney J. Hicks
- St Vincent's Hospital Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia, 3010
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3
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van Mourik A, Tonkin-Hill G, O'Farrell J, Waller S, Tan L, Tothill RW, Bowtell D, Fox S, Fellowes A, Fedele C, Schofield P, Sivakumaran T, Wong HL, Mileshkin L. Six-year experience of Australia's first dedicated cancer of unknown primary clinic. Br J Cancer 2023; 129:301-308. [PMID: 37225894 PMCID: PMC10338450 DOI: 10.1038/s41416-023-02254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Diagnosis and management of cancers of unknown primary (CUP) remain challenging. This study examines the referral patterns, management and outcomes of patients referred to Australia's first dedicated CUP clinic. METHODS Retrospective medical record review was conducted for patients seen at the Peter MacCallum Cancer Centre CUP clinic between July 2014 and August 2020. Overall survival (OS) was analysed for patients with a CUP diagnosis where treatment information was available. RESULTS Of 361 patients referred, fewer than half had completed diagnostic work-up at the time of referral. A diagnosis of CUP was established in 137 (38%), malignancy other than CUP in 177 (49%) and benign pathology in 36 (10%) patients. Genomic testing was successfully completed in 62% of patients with initial provisional CUP and impacted management in 32% by identifying a tissue of origin or actionable genomic alteration. The use of site-specific, targeted therapy or immunotherapy was independently associated with longer OS compared to empirical chemotherapy. CONCLUSION Our specialised CUP clinic facilitated diagnostic work-up among patients with suspected malignancy and provided access to genomic testing and clinical trials for patients with a CUP diagnosis, all of which are important to improve outcomes in this patient population.
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Affiliation(s)
- Arielle van Mourik
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Gina Tonkin-Hill
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - John O'Farrell
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Shohei Waller
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lavinia Tan
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia
| | - David Bowtell
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen Fox
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Fellowes
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Penelope Schofield
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Psychology, and Iverson Health Innovation Research Institute Swinburne University, Melbourne, VIC, Australia
- Behavioural Sciences Unit, Health Services Research and Implementation Sciences, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tharani Sivakumaran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Hui-Li Wong
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
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4
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Kong G, Boehm E, Prall O, Murray WK, Tothill RW, Michael M. Integrating Functional Imaging and Molecular Profiling for Optimal Treatment Selection in Neuroendocrine Neoplasms (NEN). Curr Oncol Rep 2023; 25:465-478. [PMID: 36826704 PMCID: PMC10110720 DOI: 10.1007/s11912-023-01381-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE OF REVIEW Gastroenteropancreatic NEN (GEP-NEN) are group of malignancies with significant clinical, anatomical and molecular heterogeneity. High-grade GEP-NEN in particular present unique management challenges. RECENT FINDINGS In the current era, multidisciplinary management with access to a combination of functional imaging and targeted molecular profiling can provide important disease characterisation, guide individualised management and improve patient outcome. Multiple treatment options are now available, and combination and novel therapies are being explored in clinical trials. Precision medicine is highly relevant for a heterogenous disease like NEN. The integration of dual-tracer functional PET/CT imaging, molecular histopathology and genomic data has the potential to be used to gain a more comprehensive understanding of an individual patient's disease biology for precision diagnosis, prognostication and optimal treatment allocation.
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Affiliation(s)
- Grace Kong
- Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia. .,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
| | - Emma Boehm
- Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Owen Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - William K Murray
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Michael Michael
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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5
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Wolyniec K, O'Callaghan C, Fisher K, Jessica S, Tothill RW, Bowtell D, Linda M, Schofield P, Wolyniec K, O'Callaghan C, Fisher K, Sharp J, Tothill R, Bowtell D, Mileshkin L, Schofield P. A qualitative study of patients with Cancer of Unknown Primary: Perceptions of communication, understanding of diagnosis and genomic testing, and information needs. Psychooncology 2023; 32:589-596. [PMID: 36690922 DOI: 10.1002/pon.6104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Patients with Cancer of Unknown Primary (CUP) commonly report poor understanding of their illness and high levels of psychological distress. Despite the potential benefits to CUP patients, there is a paucity of research exploring the reasons behind poor understanding of a CUP diagnosis. The aim of this study was to understand patients' experiences of communication with doctors, their understanding of diagnosis and the role of genomic testing, as well as their information needs. METHODS Semi-structured interviews explored CUP patients' perceptions of communication with their doctors, understanding of their illness, and their needs regarding medical information. Qualitative inductive thematic analysis of transcribed audio-recordings was employed. SETTING/PARTICIPANTS Nineteen patients were recruited from within a prospective cohort study involving routine genomic testing of CUP patients. RESULTS CUP patients had varied perceptions of communication with doctors as well as different levels of need, readiness, and capacity for information. Some patients felt well understood and supported by their doctors while others did not. Many patients reported feeling overwhelmed and shocked when receiving their cancer diagnosis and emphasized the importance of family support in receiving and understanding medical information. While patients understood the implications of genomic testing for treatment and diagnosis, few had a detailed understanding of genomic testing. CONCLUSIONS Patients' experience of communication and understanding of CUP could be potentially improved by clinicians' assessment of the communication style preferred by each patient and their family and the development of online resources to meet their evolving information needs.
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Affiliation(s)
- Kamil Wolyniec
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Clare O'Callaghan
- Caritas Christi and Psychosocial Cancer Care, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia.,Department of Medicine, St Vincent's Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Krista Fisher
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sharp Jessica
- Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Department of Clinical Pathology and University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mileshkin Linda
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Penelope Schofield
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kamil Wolyniec
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Clare O'Callaghan
- Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Krista Fisher
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jessica Sharp
- Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Richard Tothill
- St Vincent's Hospital Melbourne, Caritas Christi and Psychosocial Cancer Care, Victoria, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Penelope Schofield
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Psychological Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
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Zethoven M, Martelotto L, Pattison A, Bowen B, Balachander S, Flynn A, Rossello FJ, Hogg A, Miller JA, Frysak Z, Grimmond S, Fishbein L, Tischler AS, Gill AJ, Hicks RJ, Dahia PLM, Clifton-Bligh R, Pacak K, Tothill RW. Author Correction: Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment. Nat Commun 2023; 14:123. [PMID: 36624099 PMCID: PMC9829661 DOI: 10.1038/s41467-022-35751-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Magnus Zethoven
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Luciano Martelotto
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Andrew Pattison
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Blake Bowen
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Shiva Balachander
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Aidan Flynn
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Fernando J. Rossello
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Annette Hogg
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Julie A. Miller
- grid.416153.40000 0004 0624 1200Department of Surgery, Royal Melbourne Hospital, Parkville, VIC Australia ,grid.414539.e0000 0001 0459 5396Department of Surgery, Epworth Hospital, Richmond, VIC Australia
| | - Zdenek Frysak
- grid.10979.360000 0001 1245 39533rd Department of Internal Medicine—Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Sean Grimmond
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia
| | - Lauren Fishbein
- grid.430503.10000 0001 0703 675XDepartment of Medicine, Division of Endocrinology, Metabolism, Diabetes, University of Colorado, Aurora, CO USA
| | | | - Anthony J. Gill
- grid.1013.30000 0004 1936 834XSydney Medical School, University of Sydney, Sydney, NSW Australia ,grid.412703.30000 0004 0587 9093Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW Australia ,grid.412703.30000 0004 0587 9093NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW Australia
| | - Rodney J. Hicks
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Patricia L. M. Dahia
- grid.267309.90000 0001 0629 5880Div. Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, TX USA
| | - Roderick Clifton-Bligh
- grid.1013.30000 0004 1936 834XSydney Medical School, University of Sydney, Sydney, NSW Australia ,grid.412703.30000 0004 0587 9093Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW Australia
| | - Karel Pacak
- grid.420089.70000 0000 9635 8082Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD USA
| | - Richard W. Tothill
- grid.1008.90000 0001 2179 088XCentre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
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7
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Gordon LG, Wood C, Tothill RW, Webb PM, Schofield P, Mileshkin L. Healthcare Costs Before and After Diagnosis of Cancer of Unknown Primary Versus Ovarian Cancer in Australia. Pharmacoecon Open 2023; 7:111-120. [PMID: 36253664 PMCID: PMC9929003 DOI: 10.1007/s41669-022-00371-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Little is known about the healthcare resource usage and costs for patients with cancer of unknown primary (CUP). OBJECTIVE The aim of this study was to describe and quantify healthcare resource use and costs in Australia, 6 months prior to and after a diagnosis of CUP, and compare to those of women with ovarian cancer. METHODS Individual-level data combining baseline surveys, clinical records and Medicare Benefits Schedule (MBS) claim records were analysed for 149 patients with CUP and 480 patients with ovarian cancer from two prospective cohort studies. MBS data were aggregated for the period 6 months prior to diagnosis date and 6 months after diagnosis. Data included doctor consultations, pathology, diagnostics, therapeutic procedures, imaging, allied health and medicines. Generalised linear models were used to evaluate the cost differences between CUP and ovarian cancer using gamma family and log link functions. Models were adjusted for age, employment, marital status, surgery, chemotherapy and number of comorbidities. RESULTS The mean healthcare costs in the 6 months prior to diagnosis of CUP were Australian (AU) $3903 versus AU$1327 for ovarian cancer (adjusted cost ratio 2.94, 95% confidence interval [CI] 2.08-4.15). Mean healthcare costs 6 months post-diagnosis were higher for patients with CUP versus ovarian cancer (AU$20,339 vs AU$13,819, adjusted cost ratio 1.47, 95% CI 1.13-1.92). Higher costs for patients with CUP were driven by imaging (AU$1937 vs AU$1387), procedures (AU$5403 vs AU$2702) and prescribed medicines for all conditions (AU$10,111 vs AU$6717). CONCLUSIONS Pre-diagnosis costs for patients with CUP are nearly triple those for ovarian cancer. Six months after diagnosis, healthcare costs for CUP remained higher than for ovarian cancer due to imaging, procedures and medicines.
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Affiliation(s)
- Louisa G Gordon
- QIMR Berghofer Medical Research Institute, Population Health Department, Locked Bag 2000, Royal Brisbane Hospital, Herston, Brisbane, Australia.
- Queensland University of Technology (QUT), School of Nursing, Kelvin Grove, Australia.
- The University of Queensland, School of Medicine, Herston, Brisbane, Australia.
| | - C Wood
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - R W Tothill
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - P M Webb
- QIMR Berghofer Medical Research Institute, Population Health Department, Locked Bag 2000, Royal Brisbane Hospital, Herston, Brisbane, Australia
| | | | - L Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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8
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Posner A, Prall OW, Sivakumaran T, Etemadamoghadam D, Thio N, Pattison A, Balachander S, Fisher K, Webb S, Wood C, DeFazio A, Wilcken N, Gao B, Karapetis CS, Singh M, Collins IM, Richardson G, Steer C, Warren M, Karanth N, Wright G, Williams S, George J, Hicks RJ, Boussioutas A, Gill AJ, Solomon BJ, Xu H, Fellowes A, Fox SB, Schofield P, Bowtell D, Mileshkin L, Tothill RW. A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary. J Pathol 2023; 259:81-92. [PMID: 36287571 PMCID: PMC10099529 DOI: 10.1002/path.6022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/02/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high-medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs - 80% had high-medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high-medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Owen Wj Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tharani Sivakumaran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | | | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Krista Fisher
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Samantha Webb
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Colin Wood
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna DeFazio
- The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia.,The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Nicholas Wilcken
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia
| | - Bo Gao
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia
| | - Christos S Karapetis
- Department of Medical Oncology, Flinders University and Flinders Medical Centre, Adelaide, SA, Australia
| | - Madhu Singh
- Department of Medical Oncology, Barwon Health Cancer Services, Geelong, VIC, Australia
| | - Ian M Collins
- Department of Medical Oncology, SouthWest HealthCare, Warrnambool and Deakin University, Geelong, VIC, Australia
| | - Gary Richardson
- Department of Medical Oncology, Cabrini Health, Melbourne, VIC, Australia
| | - Christopher Steer
- Border Medical Oncology, Albury Wodonga Regional Cancer Centre, Albury, NSW, Australia
| | - Mark Warren
- Department of Medical Oncology, Bendigo Health, Bendigo, VIC, Australia
| | - Narayan Karanth
- Division of Medicine, Alan Walker Cancer Centre, Darwin, NT, Australia
| | - Gavin Wright
- Department of Cardiothoracic Surgery, St Vincent's Hospital, Melbourne, VIC, Australia
| | - Scott Williams
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Joshy George
- Department of Computational Sciences, The Jackson Laboratory, Farmington, Connecticut, USA
| | - Rodney J Hicks
- The St Vincent's Hospital Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Alex Boussioutas
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical, Research and Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Penelope Schofield
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Psychology, and Iverson Health Innovation Research Institute, Swinburne University, Melbourne, VIC, Australia.,Behavioural Sciences Unit, Health Services Research and Implementation Sciences, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David Bowtell
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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9
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M Silva S, Langley DP, Cossins LR, Samudra AN, Quigley AF, Kapsa RMI, Tothill RW, Greene GW, Moulton SE. Rapid Point-of-Care Electrochemical Sensor for the Detection of Cancer Tn Antigen Carbohydrate in Whole Unprocessed Blood. ACS Sens 2022; 7:3379-3388. [PMID: 36374944 DOI: 10.1021/acssensors.2c01460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Improving outcomes for cancer patients during treatment and monitoring for cancer recurrence requires personalized care which can only be achieved through regular surveillance for biomarkers. Unfortunately, routine detection for blood-based biomarkers is cost-prohibitive using currently specialized laboratories. Using a rapid self-assembly sensing interface amenable to methods of mass production, we demonstrate the ability to detect and quantify a small carbohydrate-based cancer biomarker, Tn antigen (αGalNAc-Ser/Thr) in a small volume of blood, using a test format strip reminiscent of a blood glucose test. The detection of Tn antigen at picomolar levels is achieved through a new transduction mechanism based on the impact of Tn antigen interactions on the molecular dynamic motion of a lectin cross-linked lubricin antifouling brush. In tests performed on retrospective blood plasma samples from patients presenting three different tumor types, differentiation between healthy and diseased patients was achieved, highlighting the clinical potential for cancer monitoring.
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Affiliation(s)
- Saimon M Silva
- ARC Centre of Excellence for Electromaterials Science, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn3122, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia.,Iverson Health Innovation Research Institute, Swinburne University of Technology, Hawthorn3122, Victoria, Australia
| | | | | | | | - Anita F Quigley
- School of Electrical and Biomedical Engineering, RMIT University, Melbourne3001, Victoria, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne3065, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia
| | - Robert M I Kapsa
- School of Electrical and Biomedical Engineering, RMIT University, Melbourne3001, Victoria, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne3065, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia
| | - Richard W Tothill
- Peter MacCallum Cancer Centre, Department of Clinical Pathology, University of Melbourne, Melbourne3010, Victoria, Australia
| | - George W Greene
- Institute for Frontier Materials and ARC Centre of Excellence for Electromaterials Science, Deakin University, Waurn Ponds3216, Victoria, Australia
| | - Simon E Moulton
- ARC Centre of Excellence for Electromaterials Science, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn3122, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia.,Iverson Health Innovation Research Institute, Swinburne University of Technology, Hawthorn3122, Victoria, Australia
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10
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Wolyniec K, Sharp J, Fisher K, Tothill RW, Bowtell D, Mileshkin L, Schofield P. Psychological distress, understanding of cancer and illness uncertainty in patients with Cancer of Unknown Primary. Psychooncology 2022; 31:1869-1876. [PMID: 35765251 PMCID: PMC9796856 DOI: 10.1002/pon.5990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 06/22/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Patients diagnosed with Cancer of Unknown Primary (CUP) experience high levels of psychological distress and report poor understanding of their cancer. We aimed to investigate: (1) if CUP patients with poorer understanding of their cancer diagnosis and testing experience more symptoms of psychological distress than those with better understanding; (2) if the relationship between patients' understanding of their cancer and psychological distress is mediated by illness uncertainty; and (3) explore whether patients' degree of understanding of their cancer can be predicted by clinical and socio-demographic factors. METHODS 209 CUP patients completed a questionnaire measuring anxiety, depression, illness uncertainty, fatigue, pain, sleep and understanding of their cancer. Using an apriori theoretical framework, we employed structural equation modelling to investigate predictors of patient's understanding of their cancer and psychological distress and the relationships between understanding, illness uncertainty and distress. RESULTS The structural equation model displayed good fit indices and supported the hypothesised relationship of patient's understanding of their cancer and the extent of psychological distress, which was mediated via illness uncertainty. Physical symptoms were positively associated with psychological distress and illness uncertainty. Younger age was predictive of lower patient's understanding of their cancer and higher levels of psychological distress. CONCLUSIONS Patients with CUP, particularly those who are younger and experiencing more physical symptoms, report higher levels of psychological distress and may require additional mental health support. Our findings highlight a need to improve CUP patient's understanding about their illness, which could help reduce their illness uncertainty and alleviate psychological distress.
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Affiliation(s)
- Kamil Wolyniec
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia,Department of Psychological SciencesSwinburne University of TechnologyMelbourneVictoriaAustralia
| | - Jessica Sharp
- Department of Psychological SciencesSwinburne University of TechnologyMelbourneVictoriaAustralia
| | - Krista Fisher
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | - Richard W. Tothill
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneMelbourneVictoriaAustralia,Department of Clinical PathologyUniversity of Melbourne Centre for Cancer ResearchMelbourneVictoriaAustralia
| | - David Bowtell
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | | | - Penelope Schofield
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia,Department of Psychological SciencesSwinburne University of TechnologyMelbourneVictoriaAustralia
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11
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Zethoven M, Martelotto L, Pattison A, Bowen B, Balachander S, Flynn A, Rossello FJ, Hogg A, Miller JA, Frysak Z, Grimmond S, Fishbein L, Tischler AS, Gill AJ, Hicks RJ, Dahia PLM, Clifton-Bligh R, Pacak K, Tothill RW. Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment. Nat Commun 2022; 13:6262. [PMID: 36271074 PMCID: PMC9587261 DOI: 10.1038/s41467-022-34011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 10/10/2022] [Indexed: 01/13/2023] Open
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 diverse transcriptional programs and cellular composition of PCPG and identify biomarkers of potential clinical significance.
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Affiliation(s)
| | - Luciano Martelotto
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Pattison
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Blake Bowen
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Shiva Balachander
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Aidan Flynn
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Fernando J Rossello
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Annette Hogg
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Julie A Miller
- Department of Surgery, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Surgery, Epworth Hospital, Richmond, VIC, Australia
| | - Zdenek Frysak
- 3rd Department of Internal Medicine - Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Lauren Fishbein
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, University of Colorado, Aurora, CO, USA
| | | | - Anthony J Gill
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW, Australia.,NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Patricia L M Dahia
- Div. Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, TX, USA
| | - Roderick Clifton-Bligh
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Richard W Tothill
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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12
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Mweempwa A, Xu H, Vissers JHA, Tothill RW, Pattison AD, Fellowes AP, Thomas DM, Richardson G, Hicks RJ, Grimmond SM, Fox SB, Luen SJ, Desai J, Solomon BJ. Novel RET Fusion RET-SEPTIN9 Predicts Response to Selective RET Inhibition With Selpercatinib in Malignant Pheochromocytoma. JCO Precis Oncol 2022; 5:1160-1165. [PMID: 34994633 DOI: 10.1200/po.21.00127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Angela Mweempwa
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Richard W Tothill
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew D Pattison
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew P Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Gary Richardson
- Cabrini Health, Department of Medical Oncology, Malvern, Victoria, Australia
| | - Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.,Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sean M Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen J Luen
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jayesh Desai
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
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13
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Guerra GR, Kong JC, Millen RM, Read M, Liu DS, Roth S, Sampurno S, Sia J, Bernardi MP, Chittleborough TJ, Behrenbruch CC, Teh J, Xu H, Haynes NM, Yu J, Lupat R, Hawkes D, Di Costanzo N, Tothill RW, Mitchell C, Ngan SY, Heriot AG, Ramsay RG, Phillips WA. Molecular and genomic characterisation of a panel of human anal cancer cell lines. Cell Death Dis 2021; 12:959. [PMID: 34663790 PMCID: PMC8523722 DOI: 10.1038/s41419-021-04141-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/20/2022]
Abstract
Anal cancer is a rare disease that has doubled in incidence over the last four decades. Current treatment and survival of patients with this disease has not changed substantially over this period of time, due, in part, to a paucity of preclinical models to assess new therapeutic options. To address this hiatus, we set-out to establish, validate and characterise a panel of human anal squamous cell carcinoma (ASCC) cell lines by employing an explant technique using fresh human ASCC tumour tissue. The panel of five human ASCC cell lines were validated to confirm their origin, squamous features and tumourigenicity, followed by molecular and genomic (whole-exome sequencing) characterisation. This panel recapitulates the genetic and molecular characteristics previously described in ASCC including phosphoinositide-3-kinase (PI3K) mutations in three of the human papillomavirus (HPV) positive lines and TP53 mutations in the HPV negative line. The cell lines demonstrate the ability to form tumouroids and retain their tumourigenic potential upon xenotransplantation, with varied inducible expression of major histocompatibility complex class I (MHC class I) and Programmed cell death ligand 1 (PD-L1). We observed differential responses to standard chemotherapy, radiotherapy and a PI3K specific molecular targeted agent in vitro, which correlated with the clinical response of the patient tumours from which they were derived. We anticipate this novel panel of human ASCC cell lines will form a valuable resource for future studies into the biology and therapeutics of this rare disease.
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Affiliation(s)
- Glen R Guerra
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Joseph C Kong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rosemary M Millen
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Matthew Read
- Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David S Liu
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- UGI Surgery Unit, Austin Hospital, 145 Studley Road, Heidelberg, Victoria, 3084, Australia
| | - Sara Roth
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shienny Sampurno
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Joseph Sia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Maria-Pia Bernardi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Timothy J Chittleborough
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Corina C Behrenbruch
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jiasian Teh
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Huiling Xu
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Nicole M Haynes
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jiaan Yu
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Richard Lupat
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - David Hawkes
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
- VCS Foundation, Carlton, VIC, 3053, Australia
- Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia
| | - Natasha Di Costanzo
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Catherine Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Samuel Y Ngan
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Alexander G Heriot
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robert G Ramsay
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia.
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14
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Gherardin NA, Waldeck K, Caneborg A, Martelotto LG, Balachander S, Zethoven M, Petrone PM, Pattison A, Wilmott JS, Quiñones-Parra SM, Rossello F, Posner A, Wong A, Weppler AM, Shannon KF, Hong A, Ferguson PM, Jakrot V, Raleigh J, Hatzimihalis A, Neeson PJ, Deleso P, Johnston M, Chua M, Becker JC, Sandhu S, McArthur GA, Gill AJ, Scolyer RA, Hicks RJ, Godfrey DI, Tothill RW. γδ T Cells in Merkel Cell Carcinomas Have a Proinflammatory Profile Prognostic of Patient Survival. Cancer Immunol Res 2021; 9:612-623. [PMID: 33674358 DOI: 10.1158/2326-6066.cir-20-0817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/14/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022]
Abstract
Merkel cell carcinomas (MCC) are immunogenic skin cancers associated with viral infection or UV mutagenesis. To study T-cell infiltrates in MCC, we analyzed 58 MCC lesions from 39 patients using multiplex-IHC/immunofluorescence (m-IHC/IF). CD4+ or CD8+ T cells comprised the majority of infiltrating T lymphocytes in most tumors. However, almost half of the tumors harbored prominent CD4/CD8 double-negative (DN) T-cell infiltrates (>20% DN T cells), and in 12% of cases, DN T cells represented the majority of T cells. Flow cytometric analysis of single-cell suspensions from fresh tumors identified DN T cells as predominantly Vδ2- γδ T cells. In the context of γδ T-cell inflammation, these cells expressed PD-1 and LAG3, which is consistent with a suppressed or exhausted phenotype, and CD103, which indicates tissue residency. Furthermore, single-cell RNA sequencing (scRNA-seq) identified a transcriptional profile of γδ T cells suggestive of proinflammatory potential. T-cell receptor (TCR) analysis confirmed clonal expansion of Vδ1 and Vδ3 clonotypes, and functional studies using cloned γδ TCRs demonstrated restriction of these for CD1c and MR1 antigen-presenting molecules. On the basis of a 13-gene γδ T-cell signature derived from scRNA-seq analysis, gene-set enrichment on bulk RNA-seq data showed a positive correlation between enrichment scores and DN T-cell infiltrates. An improved disease-specific survival was evident for patients with high enrichment scores, and complete responses to anti-PD-1/PD-L1 treatment were observed in three of four cases with high enrichment scores. Thus, γδ T-cell infiltration may serve as a prognostic biomarker and should be explored for therapeutic interventions.See related Spotlight on p. 600.
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Affiliation(s)
- Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Kelly Waldeck
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alex Caneborg
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano G Martelotto
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Pasquale M Petrone
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sergio M Quiñones-Parra
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando Rossello
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Annie Wong
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison M Weppler
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Angela Hong
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeanette Raleigh
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Athena Hatzimihalis
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul J Neeson
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paolo Deleso
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Meredith Johnston
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Liverpool Hospital, Sydney, New South Wales, Australia
| | - Margaret Chua
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Juergen C Becker
- German Cancer Consortium (DKTK), Translational Skin Cancer Research, University Medicine Essen, Essen and DKFZ, Heidelberg, Germany
| | - Shahneen Sandhu
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical, Research and The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Cancer Imaging Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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15
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IJzerman MJ, de Boer J, Azad A, Degeling K, Geoghegan J, Hewitt C, Hollande F, Lee B, To YH, Tothill RW, Wright G, Tie J, Dawson SJ. Towards Routine Implementation of Liquid Biopsies in Cancer Management: It Is Always Too Early, until Suddenly It Is Too Late. Diagnostics (Basel) 2021; 11:103. [PMID: 33440749 PMCID: PMC7826562 DOI: 10.3390/diagnostics11010103] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Blood-based liquid biopsies are considered a new and promising diagnostic and monitoring tool for cancer. As liquid biopsies only require a blood draw, they are non-invasive, potentially more rapid and assumed to be a less costly alternative to genomic analysis of tissue biopsies. A multi-disciplinary workshop (n = 98 registrations) was organized to discuss routine implementation of liquid biopsies in cancer management. Real-time polls were used to engage with experts' about the current evidence of clinical utility and the barriers to implementation of liquid biopsies. Clinical, laboratory and health economics presentations were given to illustrate the opportunities and current levels of evidence, followed by three moderated break-out sessions to discuss applications. The workshop concluded that tumor-informed assays using next-generation sequencing (NGS) or PCR-based genotyping assays will most likely provide better clinical utility than tumor-agnostic assays, yet at a higher cost. For routine application, it will be essential to determine clinical utility, to define the minimum quality standards and performance of testing platforms and to ensure their use is integrated into current clinical workflows including how they complement tissue biopsies and imaging. Early health economic models may help identifying the most viable application of liquid biopsies. Alternative funding models for the translation of complex molecular diagnostics, such as liquid biopsies, may also be explored if clinical utility has been demonstrated and when their use is recommended in multi-disciplinary consensus guidelines.
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Affiliation(s)
- Maarten J. IJzerman
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, Melbourne School of Population and Global Health, Parkville, VIC 3053, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
| | - Jasper de Boer
- Victorian Comprehensive Cancer Centre, Parkville, VIC 3050, Australia;
| | - Arun Azad
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
| | - Koen Degeling
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, Melbourne School of Population and Global Health, Parkville, VIC 3053, Australia
| | | | - Chelsee Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia;
| | - Frédéric Hollande
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
| | - Belinda Lee
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
- Department of Medical Oncology, Northern Health, Epping, VIC 3076, Australia
| | - Yat Ho To
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
| | - Richard W. Tothill
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
| | - Gavin Wright
- Department of Surgery, St. Vincents Hospital, Melbourne, VIC 3065, Australia;
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
- Department of Medical Oncology, Western Health, St. Albans, VIC 3021, Australia
| | - Sarah-Jane Dawson
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
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16
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Hicks RJ, Roselt PJ, Kallur KG, Tothill RW, Mileshkin L. FAPI PET/CT: Will It End the Hegemony of 18F-FDG in Oncology? J Nucl Med 2020; 62:296-302. [PMID: 33277397 DOI: 10.2967/jnumed.120.256271] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
For over 40 years, 18F-FDG has been the dominant PET tracer in neurology, cardiology, inflammatory diseases, and, most particularly, oncology. Combined with the ability to perform whole-body scanning, 18F-FDG has revolutionized the evaluation of cancer and has stifled the adoption of other tracers, except in situations where low avidity or high background activity limits diagnostic performance. The strength of 18F-FDG has generally been its ability to detect disease in the absence of structural abnormality, thereby enhancing diagnostic sensitivity, but its simultaneous weakness has been a lack of specificity due to diverse pathologies with enhanced glycolysis. Radiotracers that leverage other hallmarks of cancer or specific cell-surface targets are gradually finding a niche in the diagnostic armamentarium. However, none have had sufficient sensitivity to realistically compete with 18F-FDG for evaluation of the broad spectrum of malignancies. Perhaps, this situation is about to change with development of a class of tracers targeting fibroblast activation protein that have low uptake in almost all normal tissues but high uptake in most cancer types. In this review, the development and exciting preliminary clinical data relating to various fibroblast activation protein-specific small-molecule inhibitor tracers in oncology will be discussed along with potential nononcologic applications.
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Affiliation(s)
- Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter J Roselt
- Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Linda Mileshkin
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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17
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Zhao Y, Pan Z, Namburi S, Pattison A, Posner A, Balachander S, Paisie CA, Reddi HV, Rueter J, Gill AJ, Fox S, Raghav KPS, Flynn WF, Tothill RW, Li S, Karuturi RKM, George J. CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence. EBioMedicine 2020; 61:103030. [PMID: 33039710 PMCID: PMC7553237 DOI: 10.1016/j.ebiom.2020.103030] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cancer of unknown primary (CUP), representing approximately 3-5% of all malignancies, is defined as metastatic cancer where a primary site of origin cannot be found despite a standard diagnostic workup. Because knowledge of a patient's primary cancer remains fundamental to their treatment, CUP patients are significantly disadvantaged and most have a poor survival outcome. Developing robust and accessible diagnostic methods for resolving cancer tissue of origin, therefore, has significant value for CUP patients. METHODS We developed an RNA-based classifier called CUP-AI-Dx that utilizes a 1D Inception convolutional neural network (1D-Inception) model to infer a tumor's primary tissue of origin. CUP-AI-Dx was trained using the transcriptional profiles of 18,217 primary tumours representing 32 cancer types from The Cancer Genome Atlas project (TCGA) and International Cancer Genome Consortium (ICGC). Gene expression data was ordered by gene chromosomal coordinates as input to the 1D-CNN model, and the model utilizes multiple convolutional kernels with different configurations simultaneously to improve generality. The model was optimized through extensive hyperparameter tuning, including different max-pooling layers and dropout settings. For 11 tumour types, we also developed a random forest model that can classify the tumour's molecular subtype according to prior TCGA studies. The optimised CUP-AI-Dx tissue of origin classifier was tested on 394 metastatic samples from 11 tumour types from TCGA and 92 formalin-fixed paraffin-embedded (FFPE) samples representing 18 cancer types from two clinical laboratories. The CUP-AI-Dx molecular subtype was also independently tested on independent ovarian and breast cancer microarray datasets FINDINGS: CUP-AI-Dx identifies the primary site with an overall top-1-accuracy of 98.54% in cross-validation and 96.70% on a test dataset. When applied to two independent clinical-grade RNA-seq datasets generated from two different institutes from the US and Australia, our model predicted the primary site with a top-1-accuracy of 86.96% and 72.46% respectively. INTERPRETATION The CUP-AI-Dx predicts tumour primary site and molecular subtype with high accuracy and therefore can be used to assist the diagnostic work-up of cancers of unknown primary or uncertain origin using a common and accessible genomics platform. FUNDING NIH R35 GM133562, NCI P30 CA034196, Victorian Cancer Agency Australia.
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Affiliation(s)
- Yue Zhao
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ziwei Pan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia
| | - Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia
| | - Carolyn A Paisie
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Honey V Reddi
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
| | - Jens Rueter
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales 2065 Australia; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065 Australia; Department of Anatomical Pathology, Douglass Hanly Moir Pathology, Macquarie Park, New South Wales 2113 Australia; University of Sydney, Sydney, New South Wales 2006 Australia
| | - Stephen Fox
- Peter MacCallum Cancer Centre, Department of Pathology, University of Melbourne, Victoria, Australia
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William F Flynn
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia; Peter MacCallum Cancer Centre, Parkville, Melbourne, Australia.
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA; Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
| | - R Krishna Murthy Karuturi
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA; Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
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18
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Powers JF, Cochran B, Baleja JD, Sikes HD, Pattison AD, Zhang X, Lomakin I, Shepard-Barry A, Pacak K, Moon SJ, Langford TF, Stein KT, Tothill RW, Ouyang Y, Tischler AS. A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/- rats. Endocr Relat Cancer 2020; 27:X9-X10. [PMID: 32861212 PMCID: PMC8133318 DOI: 10.1530/erc-19-0474e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- James F Powers
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
- Correspondence should be addressed to J F Powers:
| | - Brent Cochran
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - James D Baleja
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew D Pattison
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Xue Zhang
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Inna Lomakin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Annette Shepard-Barry
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver Division National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Troy F Langford
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kassi Taylor Stein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard W Tothill
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
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19
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Weppler AM, Pattison A, Bhave P, De Ieso P, Raleigh J, Hatzimihalis A, Gill AJ, Balachander S, Callahan J, Chua M, Au-Yeung G, McArthur GA, Hicks RJ, Tothill RW, Sandhu S. Clinical, FDG-PET and molecular markers of immune checkpoint inhibitor response in patients with metastatic Merkel cell carcinoma. J Immunother Cancer 2020; 8:e000700. [PMID: 33060145 PMCID: PMC7566424 DOI: 10.1136/jitc-2020-000700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Metastatic Merkel cell carcinoma (mMCC) is an aggressive neuroendocrine malignancy of the skin with a poor prognosis. Immune checkpoint inhibitors (ICIs) have shown substantial efficacy and favorable safety in clinical trials. METHODS Medical records of patients (pts) with mMCC treated with ICIs from August 2015 to December 2018 at Peter MacCallum Cancer Centre in Australia were analyzed. Response was assessed with serial imaging, the majority with FDG-PET/CT scans. RNA sequencing and immunohistochemistry for PD-L1, CD3 and Merkel cell polyomavirus (MCPyV) on tumor samples was performed. RESULTS 23 pts with mMCC were treated with ICIs. A median of 8 cycles (range 1 to 47) were administered, with treatment ongoing in 6 pts. Objective responses (OR) were observed in 14 pts (61%): 10 (44%) complete responses (CR) and 4 (17%) partial responses (PR). Median time to response was 8 weeks (range 6 to 12) and 12-month progression-free survival rate was 39%. Increased OR were seen in pts aged less than 75 (OR 80% vs 46%), no prior history of chemotherapy (OR 64% vs 50%), patients with an immune-related adverse event (OR 100% vs 43%) and in MCPyV-negative tumors (OR 69% vs 43%). Pts with a CR had lower mean metabolic tumor volume on baseline FDG-PET/CT scan (CR: 35.7 mL, no CR: 187.8 mL, p=0.05). There was no correlation between PD-L1 positivity and MCPyV status (p=0.764) or OR (p=0.245). 10 pts received radiation therapy (RT) during ICI: 4 pts started RT concurrently (OR 75%, CR 50%), 3 pts had isolated ICI-resistant lesions successfully treated with RT and 3 pts with multisite progression continued to progress despite RT. Overall, 6 pts (26%) had grade 1-2 immune-related adverse events. CONCLUSION ICIs showed efficacy and safety in mMCC consistent with trial data. Clinical and imaging predictors of response were identified.
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Affiliation(s)
- Alison M Weppler
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Prachi Bhave
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paolo De Ieso
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jeanette Raleigh
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Athena Hatzimihalis
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Department of Anatomical Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Callahan
- Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Margaret Chua
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - George Au-Yeung
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Rodney J Hicks
- Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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20
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Cullinane C, Waldeck K, Kirby L, Rogers BE, Eu P, Tothill RW, Hicks RJ. Enhancing the anti-tumour activity of 177Lu-DOTA-octreotate radionuclide therapy in somatostatin receptor-2 expressing tumour models by targeting PARP. Sci Rep 2020; 10:10196. [PMID: 32576907 PMCID: PMC7311440 DOI: 10.1038/s41598-020-67199-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/02/2020] [Indexed: 01/25/2023] Open
Abstract
Peptide receptor radionuclide therapy (PRRT) is an important treatment option for patients with somatostatin receptor-2 (SSTR2)-expressing neuroendocrine tumour (NET) though tumour regression occurs in only a minority of patients. Therefore, novel PRRT regimens with improved therapeutic activity are needed. Radiation induced DNA damage repair is an attractive therapeutic target to increase PRRT efficacy and consequently, we have characterised a panel of preclinical models for their SSTR2 expression, in vivo growth properties and response to 177Lu-DOTA-octreotate (LuTate) PRRT to identify models with features suitable for evaluating novel therapeutic combinations. In vitro studies using the SSTR2 expressing AR42J model demonstrate that the combination of LuTate and the small molecule Poly(ADP-ribose) polymerase-1 (PARP) inhibitor, talazoparib led to increased DNA double strand breaks, as assessed by γ-H2AX foci formation, as compared to LuTate alone. Furthermore, using the AR42J tumour model in vivo we demonstrate that the combination of LuTate and talazoparib significantly improved the anti-tumour efficacy of LuTate alone. These findings support the clinical evaluation of the combination of LuTate and PARP inhibition in SSTR2-expressing NET.
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Affiliation(s)
- Carleen Cullinane
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
| | - Kelly Waldeck
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura Kirby
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Buck E Rogers
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Peter Eu
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Richard W Tothill
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | - Rodney J Hicks
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
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21
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Powers JF, Cochran B, Baleja JD, Sikes HD, Pattison AD, Zhang X, Lomakin I, Shepard-Barry A, Pacak K, Moon SJ, Langford TF, Stein KT, Tothill RW, Ouyang Y, Tischler AS. A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/- rats. Endocr Relat Cancer 2020; 27:337-354. [PMID: 32252027 PMCID: PMC7219221 DOI: 10.1530/erc-19-0474] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
Abstract
Tumors caused by loss-of-function mutations in genes encoding TCA cycle enzymes have been recently discovered and are now of great interest. Mutations in succinate dehydrogenase (SDH) subunits cause pheochromocytoma/paraganglioma (PCPG) and syndromically associated tumors, which differ phenotypically and clinically from more common SDH-intact tumors of the same types. Consequences of SDH deficiency include rewired metabolism, pseudohypoxic signaling and altered redox balance. PCPG with SDHB mutations are particularly aggressive, and development of treatments has been hampered by lack of valid experimental models. Attempts to develop mouse models have been unsuccessful. Using a new strategy, we developed a xenograft and cell line model of SDH-deficient pheochromocytoma from rats with a heterozygous germline Sdhb mutation. The genome, transcriptome and metabolome of this model, called RS0, closely resemble those of SDHB-mutated human PCPGs, making it the most valid model now available. Strategies employed to develop RS0 may be broadly applicable to other SDH-deficient tumors.
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Affiliation(s)
- James F Powers
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
- Correspondence should be addressed to J F Powers:
| | - Brent Cochran
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - James D Baleja
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew D Pattison
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Xue Zhang
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Inna Lomakin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Annette Shepard-Barry
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver Division National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Troy F Langford
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kassi Taylor Stein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard W Tothill
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
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22
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Le Nours J, Gherardin NA, Ramarathinam SH, Awad W, Wiede F, Gully BS, Khandokar Y, Praveena T, Wubben JM, Sandow JJ, Webb AI, von Borstel A, Rice MT, Redmond SJ, Seneviratna R, Sandoval-Romero ML, Li S, Souter MNT, Eckle SBG, Corbett AJ, Reid HH, Liu L, Fairlie DP, Giles EM, Westall GP, Tothill RW, Davey MS, Berry R, Tiganis T, McCluskey J, Pellicci DG, Purcell AW, Uldrich AP, Godfrey DI, Rossjohn J. A class of γδ T cell receptors recognize the underside of the antigen-presenting molecule MR1. Science 2020; 366:1522-1527. [PMID: 31857486 DOI: 10.1126/science.aav3900] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/20/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022]
Abstract
T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I-like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity to the monomorphic MHC-related protein 1 (MR1). The crystal structure of a γδTCR-MR1-antigen complex starkly contrasts with all other TCR-MHC and TCR-MHC-I-like complex structures. Namely, the γδTCR binds underneath the MR1 antigen-binding cleft, where contacts are dominated by the MR1 α3 domain. A similar pattern of reactivity was observed for diverse MR1-restricted γδTCRs from multiple individuals. Accordingly, we simultaneously report MR1 as a ligand for human γδ T cells and redefine the parameters for TCR recognition.
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Affiliation(s)
- Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Florian Wiede
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Yogesh Khandokar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - T Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jacinta M Wubben
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michael T Rice
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Rebecca Seneviratna
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Maria L Sandoval-Romero
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Ligong Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward M Giles
- Department of Paediatrics, Monash University, and Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medicine, Clayton, Victoria 3168, Australia
| | - Glen P Westall
- Lung Transplant Service, Alfred Hospital, Melbourne, Victoria 3004, Australia.,Department of Medicine, Monash University, Clayton, Victoria 3800, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Victoria 3052, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Martin S Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Tiganis
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Adam P Uldrich
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
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23
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Burr ML, Sparbier CE, Chan KL, Chan YC, Kersbergen A, Lam EYN, Azidis-Yates E, Vassiliadis D, Bell CC, Gilan O, Jackson S, Tan L, Wong SQ, Hollizeck S, Michalak EM, Siddle HV, McCabe MT, Prinjha RK, Guerra GR, Solomon BJ, Sandhu S, Dawson SJ, Beavis PA, Tothill RW, Cullinane C, Lehner PJ, Sutherland KD, Dawson MA. An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer. Cancer Cell 2019; 36:385-401.e8. [PMID: 31564637 PMCID: PMC6876280 DOI: 10.1016/j.ccell.2019.08.008] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/26/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022]
Abstract
Loss of MHC class I (MHC-I) antigen presentation in cancer cells can elicit immunotherapy resistance. A genome-wide CRISPR/Cas9 screen identified an evolutionarily conserved function of polycomb repressive complex 2 (PRC2) that mediates coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP), promoting evasion of T cell-mediated immunity. MHC-I APP gene promoters in MHC-I low cancers harbor bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine-induced upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological MHC-I silencing highlights a conserved mechanism by which cancers arising from these primitive tissues exploit PRC2 activity to enable immune evasion.
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Affiliation(s)
- Marian L Burr
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - Christina E Sparbier
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kah Lok Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Ariena Kersbergen
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Omer Gilan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Susan Jackson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Lavinia Tan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sebastian Hollizeck
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Ewa M Michalak
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hannah V Siddle
- Department of Biological Sciences, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Michael T McCabe
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Rab K Prinjha
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA; Epigenetics Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Glen R Guerra
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Benjamin J Solomon
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia
| | - Paul A Beavis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard W Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia.
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24
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McEvoy CR, Xu H, Smith K, Etemadmoghadam D, San Leong H, Choong DY, Byrne DJ, Iravani A, Beck S, Mileshkin L, Tothill RW, Bowtell DD, Bates BM, Nastevski V, Browning J, Bell AH, Khoo C, Desai J, Fellowes AP, Fox SB, Prall OW. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion. J Clin Invest 2019; 129:1940-1945. [PMID: 30835257 PMCID: PMC6486352 DOI: 10.1172/jci123089] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
BRAF and CRAF are critical components of the MAPK signaling pathway which is activated in many cancer types. In approximately 1% of melanomas, BRAF or CRAF are activated through structural arrangements. We describe here a metastatic melanoma with a GOLGA4-RAF1 fusion and pathogenic variants in CTNNB1 and CDKN2A. Anti-CTLA4/anti-PD1 combination immunotherapy failed to control tumor progression. In the absence of other actionable variants the patient was administered MEK inhibitor therapy on the basis of its potential action against RAF1 fusions. This resulted in a profound and clinically significant response. We demonstrated that GOLGA4-RAF1 expression was associated with ERK activation, elevated expression of the RAS/RAF downstream co-effector ETV5, and a high Ki67 index. These findings provide a rationale for the dramatic response to targeted therapy. This study shows that thorough molecular characterization of treatment-resistant cancers can identify therapeutic targets and personalize management, leading to improved patient outcomes.
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Affiliation(s)
- Christopher R. McEvoy
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Huiling Xu
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | | | | | | | | | | | - Amir Iravani
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sophie Beck
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Linda Mileshkin
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Richard W. Tothill
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - David D. Bowtell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | | | | | | | | | - Chloe Khoo
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jayesh Desai
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Department of Surgery, St Vincent’s Hospital, Fitzroy, Australia
- Clinical School, Austin Health, Heidelberg, Australia
- Department of Surgery, Royal Melbourne Hospital, Parkville, Australia
| | - Andrew P. Fellowes
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen B. Fox
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
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25
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Flores SK, Cheng Z, Jasper AM, Natori K, Okamoto T, Tanabe A, Gotoh K, Shibata H, Sakurai A, Nakai T, Wang X, Zethoven M, Balachander S, Aita Y, Young W, Zheng S, Takekoshi K, Nakamura E, Tothill RW, Aguiar RCT, Dahia PLM. A synonymous VHL variant in exon 2 confers susceptibility to familial pheochromocytoma and von Hippel-Lindau disease. J Clin Endocrinol Metab 2019; 104:3826-3834. [PMID: 30946460 PMCID: PMC6660912 DOI: 10.1210/jc.2019-00235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/29/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT von Hippel-Lindau disease, comprising renal cancer, hemangioblastoma and/or pheochromocytoma (PHEO) is caused by missense or truncating variants of the VHL tumor suppressor gene, which is involved in degradation of hypoxia inducible factors (HIFs). However, the role of synonymous VHL variants in the disease is unclear. OBJECTIVE We evaluated a synonymous VHL variant in patients with familial PHEO or VHL disease without a detectable pathogenic VHL mutation. DESIGN We performed genetic and transcriptional analyses of leukocytes and/or tumors from affected and unaffected individuals and evaluated VHL splicing in existing cancer databases. RESULTS We identified a synonymous VHL variant(c.414A>G, p.Pro138Pro) as the driver event in five independent individuals/families with PHEOs or VHL syndrome. This variant promotes exon 2 skipping and, hence, abolishes expression of the full-length VHL transcript. Exon 2 spans the HIF binding domain, required for HIF degradation by VHL. Accordingly, PHEOs carrying this variant display HIF hyperactivation typical of VHL loss. Moreover, other exon 2 VHL variants from the TCGA pan-cancer datasets are biased toward expression of a VHL transcript that excludes this exon, supporting a broader impact of this spliced variant. CONCLUSION A recurrent synonymous VHL variant (c.414A>G, p.Pro138Pro) confers susceptibility to PHEO and VHL disease through splice disruption, leading to VHL dysfunction. This finding indicates that certain synonymous VHL variants may be clinically relevant and should be considered in genetic testing and surveillance settings. The observation that other coding VHL variants can exclude exon 2 suggests that dysregulated splicing may be an underappreciated mechanism in VHL-mediated tumorigenesis.
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Affiliation(s)
- Shahida K Flores
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas San Antonio, San Antonio, Texas
| | - Ziming Cheng
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas San Antonio, San Antonio, Texas
| | - Angela M Jasper
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas San Antonio, San Antonio, Texas
| | - Keiko Natori
- Department of Breast and Endocrine Surgery, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo, Japan
| | - Takahiro Okamoto
- Department of Breast and Endocrine Surgery, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo, Japan
| | - Akiyo Tanabe
- Department of Diabetes, Endocrinology and Metabolism, National Center for Global Health and Medicine, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Koro Gotoh
- Department of Endocrinology, Metabolism, Rheumatology and Nephrology, Faculty of Medicine, Oita University, Oita, Japan
| | - Hirotaka Shibata
- Department of Endocrinology, Metabolism, Rheumatology and Nephrology, Faculty of Medicine, Oita University, Oita, Japan
| | - Akihiro Sakurai
- Department of Medical Genetics and Genomics, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Takuya Nakai
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Xiaojing Wang
- Greehey Children’s Cancer Research Institute, University of Texas San Antonio, San Antonio, Texas
| | - Magnus Zethoven
- Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Shiva Balachander
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuichi Aita
- Division of Sports Medicine and Laboratory Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - William Young
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Mayo Clinic, Rochester, Minnesota
| | - Siyuan Zheng
- Greehey Children’s Cancer Research Institute, University of Texas San Antonio, San Antonio, Texas
| | - Kazuhiro Takekoshi
- Division of Sports Medicine and Laboratory Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eijiro Nakamura
- DSK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Richard W Tothill
- Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ricardo C T Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas San Antonio, San Antonio, Texas
- Greehey Children’s Cancer Research Institute, University of Texas San Antonio, San Antonio, Texas
- Audie Murphy VA Hospital, San Antonio, South Texas Veterans Health Care System, San Antonio, Texas
| | - Patricia L M Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas San Antonio, San Antonio, Texas
- Greehey Children’s Cancer Research Institute, University of Texas San Antonio, San Antonio, Texas
- Correspondence and Reprint Requests: Patricia L. M. Dahia, MD, PhD, Department of Medicine, University of Texas Health San Antonio, Mail Code 7880, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900. E-mail:
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26
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Benn DE, Zhu Y, Andrews KA, Wilding M, Duncan EL, Dwight T, Tothill RW, Burgess J, Crook A, Gill AJ, Hicks RJ, Kim E, Luxford C, Marfan H, Richardson AL, Robinson B, Schlosberg A, Susman R, Tacon L, Trainer A, Tucker K, Maher ER, Field M, Clifton-Bligh RJ. Bayesian approach to determining penetrance of pathogenic SDH variants. J Med Genet 2018; 55:729-734. [PMID: 30201732 PMCID: PMC6252366 DOI: 10.1136/jmedgenet-2018-105427] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND Until recently, determining penetrance required large observational cohort studies. Data from the Exome Aggregate Consortium (ExAC) allows a Bayesian approach to calculate penetrance, in that population frequencies of pathogenic germline variants should be inversely proportional to their penetrance for disease. We tested this hypothesis using data from two cohorts for succinate dehydrogenase subunits A, B and C (SDHA-C) genetic variants associated with hereditary pheochromocytoma/paraganglioma (PC/PGL). METHODS Two cohorts were 575 unrelated Australian subjects and 1240 unrelated UK subjects, respectively, with PC/PGL in whom genetic testing had been performed. Penetrance of pathogenic SDHA-C variants was calculated by comparing allelic frequencies in cases versus controls from ExAC (removing those variants contributed by The Cancer Genome Atlas). RESULTS Pathogenic SDHA-C variants were identified in 106 subjects (18.4%) in cohort 1 and 317 subjects (25.6%) in cohort 2. Of 94 different pathogenic variants from both cohorts (seven in SDHA, 75 in SDHB and 12 in SDHC), 13 are reported in ExAC (two in SDHA, nine in SDHB and two in SDHC) accounting for 21% of subjects with SDHA-C variants. Combining data from both cohorts, estimated lifetime disease penetrance was 22.0% (95% CI 15.2% to 30.9%) for SDHB variants, 8.3% (95% CI 3.5% to 18.5%) for SDHC variants and 1.7% (95% CI 0.8% to 3.8%) for SDHA variants. CONCLUSION Pathogenic variants in SDHB are more penetrant than those in SDHC and SDHA. Our findings have important implications for counselling and surveillance of subjects carrying these pathogenic variants.
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Affiliation(s)
- Diana E Benn
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Ying Zhu
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia,Department of Cancer Services, Northern Sydney Local Health District Familial Cancer Service, Royal North Shore Hospital, Saint Leonards, New South Wales, Australia
| | - Katrina A Andrews
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre and Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Mathilda Wilding
- Department of Cancer Services, Northern Sydney Local Health District Familial Cancer Service, Royal North Shore Hospital, Saint Leonards, New South Wales, Australia
| | - Emma L Duncan
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia,Department of Endocrinology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - Trisha Dwight
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Richard W Tothill
- Department of Oncology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - John Burgess
- Faculty of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Ashley Crook
- Department of Cancer Services, Northern Sydney Local Health District Familial Cancer Service, Royal North Shore Hospital, Saint Leonards, New South Wales, Australia
| | - Anthony J Gill
- Department of Medicine, University of Sydney, Sydney, New South Wales, Australia,Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Rodney J Hicks
- Department of Oncology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Edward Kim
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Catherine Luxford
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - Anne Louise Richardson
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Bruce Robinson
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia,Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, USA
| | - Arran Schlosberg
- Department of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - Lyndal Tacon
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia,Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, USA
| | - Alison Trainer
- Department of Oncology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Katherine Tucker
- Department of Clinical Genetics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre and Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Michael Field
- Department of Cancer Services, Northern Sydney Local Health District Familial Cancer Service, Royal North Shore Hospital, Saint Leonards, New South Wales, Australia
| | - Roderick J Clifton-Bligh
- Hormones and Cancer, Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, St Leonards, New South Wales, Australia,Department of Medicine, University of Sydney, Sydney, New South Wales, Australia,Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, USA
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27
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Fan K, Ritter C, Nghiem P, Blom A, Verhaegen ME, Dlugosz A, Ødum N, Woetmann A, Tothill RW, Hicks RJ, Sand M, Schrama D, Schadendorf D, Ugurel S, Becker JC. Circulating Cell-Free miR-375 as Surrogate Marker of Tumor Burden in Merkel Cell Carcinoma. Clin Cancer Res 2018; 24:5873-5882. [PMID: 30061360 DOI: 10.1158/1078-0432.ccr-18-1184] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/15/2018] [Accepted: 07/24/2018] [Indexed: 01/10/2023]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is an aggressive skin cancer with neuroendocrine differentiation. There is an unmet need for MCC-specific blood-based surrogate biomarkers of tumor burden; circulating cell-free miRNA may serve this purpose. EXPERIMENTAL DESIGN Expression of miR-375 was quantified in 24 MCC and 23 non-MCC cell lines, 67 MCC and 58 non-MCC tumor tissues, sera of 2 preclinical MCC models, and sera of 109 patients with MCC and 30 healthy controls by nCounter human-v2-miRNA expression or miR-375-specific real-time PCR assays. The patients' sera consisted of two retrospective (discovery and training) and two prospective (validation) cohorts. RESULTS miR-375 expression was high in MCC cell lines and tissues compared with non-MCCs. It was readily detected in MCC-conditioned medium and sera of preclinical models bearing MCC xenografts. miR-375 levels were higher in sera from tumor-bearing patients with MCC than in tumor-free patients or healthy controls (P < 0.0005). Moreover, miR-375 serum levels correlated with tumor stage in tumor-bearing (P = 0.037) but not in tumor-free (P = 0.372) patients with MCC. miR-375 serum level showed high diagnostic accuracy to discriminate tumor-bearing and tumor-free patients with MCC as demonstrated by ROC curve analysis in the retrospective cohorts (AUC = 0.954 and 0.800) as well as in the prospective cohorts (AUC = 0.929 and 0.959). miR-375 serum level reflected dynamic changes in tumor burden of patients with MCC during therapeutic interventions. CONCLUSIONS Circulating cell-free miR-375 proved as a surrogate marker for tumor burden in MCC without restriction to polyomavirus positivity; it thus appears to be useful for therapy monitoring and the follow-up of patients with MCC.
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Affiliation(s)
- Kaiji Fan
- Department of Dermatology, Medical University of Graz, Graz, Austria.,Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cathrin Ritter
- Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Nghiem
- Department of Dermatology/Medicine, University of Washington, Seattle, Washington
| | - Astrid Blom
- Department of Dermatology/Medicine, University of Washington, Seattle, Washington
| | | | - Andrzej Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Niels Ødum
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Richard W Tothill
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia.,Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Michael Sand
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - David Schrama
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schadendorf
- German Cancer Consortium (DKTK), Essen, Germany.,Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Jürgen C Becker
- Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany. .,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, University Hospital Essen, Essen, Germany
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28
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Becker JC, Stang A, Hausen AZ, Fischer N, DeCaprio JA, Tothill RW, Lyngaa R, Hansen UK, Ritter C, Nghiem P, Bichakjian CK, Ugurel S, Schrama D. Epidemiology, biology and therapy of Merkel cell carcinoma: conclusions from the EU project IMMOMEC. Cancer Immunol Immunother 2018; 67:341-351. [PMID: 29188306 PMCID: PMC6015651 DOI: 10.1007/s00262-017-2099-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/24/2017] [Indexed: 01/23/2023]
Abstract
Merkel cell carcinoma (MCC) is a highly aggressive, often lethal neuroendocrine cancer. Its carcinogenesis may be either caused by the clonal integration of the Merkel cell polyomavirus into the host genome or by UV-induced mutations. Notably, virally-encoded oncoproteins and UV-induced mutations affect comparable signaling pathways such as RB restriction of cell cycle progression or p53 inactivation. Despite its low incidence, MCC recently received much attention based on its exquisite immunogenicity and the resulting major success of immune modulating therapies. Here, we summarize current knowledge on epidemiology, biology and therapy of MCC as conclusion of the project 'Immune Modulating strategies for treatment of Merkel Cell Carcinoma', which was funded over a 5-year period by the European Commission to investigate innovative immunotherapies for MCC.
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Affiliation(s)
- Jürgen C Becker
- Translational Skin Cancer Research (tscr), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, S05 T05 B, 45141, Essen, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Dermatology, University Hospital of Essen, Essen, Germany.
| | - Andreas Stang
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center of Clinical Epidemiology; c/o Institute of Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Axel Zur Hausen
- Department of Pathology, Academisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James A DeCaprio
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Rikke Lyngaa
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Ulla Kring Hansen
- George F. Odland Endowed Chair in Dermatology, University of Washington, Seattle, WA, USA
| | - Cathrin Ritter
- Translational Skin Cancer Research (tscr), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, S05 T05 B, 45141, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Nghiem
- George F. Odland Endowed Chair in Dermatology, University of Washington, Seattle, WA, USA
| | | | - Selma Ugurel
- Department of Dermatology, University Hospital of Essen, Essen, Germany
| | - David Schrama
- Department of Dermatology, University Hospital Wuerzburg, Würzburg, Germany
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29
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Dwight T, Flynn A, Amarasinghe K, Benn DE, Lupat R, Li J, Cameron DL, Hogg A, Balachander S, Candiloro ILM, Wong SQ, Robinson BG, Papenfuss AT, Gill AJ, Dobrovic A, Hicks RJ, Clifton-Bligh RJ, Tothill RW. TERT structural rearrangements in metastatic pheochromocytomas. Endocr Relat Cancer 2018; 25:1-9. [PMID: 28974544 DOI: 10.1530/erc-17-0306] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/03/2017] [Indexed: 12/21/2022]
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 individuals 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.
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Affiliation(s)
- Trisha Dwight
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Aidan Flynn
- The Finsen LaboratoryRigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC)University of Copenhagen, Copenhagen N, Denmark
| | | | - Diana E Benn
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Richard Lupat
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Jason Li
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Daniel L Cameron
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical BiologyUniversity of Melbourne, Melbourne, Victoria, Australia
| | - Annette Hogg
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Shiva Balachander
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Ida L M Candiloro
- Olivia Newton-John Cancer Research InstituteHeidelberg, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
| | - Stephen Q Wong
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Bruce G Robinson
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Anthony T Papenfuss
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical BiologyUniversity of Melbourne, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
- The Department of Mathematics and StatisticsUniversity of Melbourne, Parkville, Victoria, Australia
| | - Anthony J Gill
- The University of SydneySydney, New South Wales, Australia
- Cancer Diagnosis and Pathology GroupKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Alexander Dobrovic
- Olivia Newton-John Cancer Research InstituteHeidelberg, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
- School of Cancer MedicineLa Trobe University, Bundoora, Victoria, Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
| | - Roderick J Clifton-Bligh
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
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30
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Flynn A, Dwight T, Benn D, Deb S, Colebatch AJ, Fox S, Harris J, Duncan EL, Robinson B, Hogg A, Ellul J, To H, Duong C, Miller JA, Yates C, James P, Trainer A, Gill AJ, Clifton-Bligh R, Hicks RJ, Tothill RW. Cousins not twins: intratumoural and intertumoural heterogeneity in syndromic neuroendocrine tumours. J Pathol 2017; 242:273-283. [PMID: 28369925 DOI: 10.1002/path.4900] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/01/2017] [Accepted: 03/23/2017] [Indexed: 12/23/2022]
Abstract
Hereditary endocrine neoplasias, including phaeochromocytoma/paraganglioma 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 individual. 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 sampling, 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 examples of evolutionary convergence involving the same rare somatic copy-number events in synchronous primary phaeochromocytoma/paraganglioma. 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 individual, 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.
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Affiliation(s)
- Aidan Flynn
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Trisha Dwight
- Cancer Genetics, Kolling Institute, Royal North Shore Hospital, Sydney, NSW, Australia.,University of Sydney, Sydney, NSW, Australia
| | - Diana Benn
- Cancer Genetics, Kolling Institute, Royal North Shore Hospital, Sydney, NSW, Australia.,University of Sydney, Sydney, NSW, Australia
| | - Siddhartha Deb
- Anatomical Pathology, Anatpath, Melbourne, Victoria, Australia
| | - Andrew J Colebatch
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Fox
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica Harris
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Emma L Duncan
- Queensland University of Technology, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Department of Endocrinology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Bruce Robinson
- Cancer Genetics, Kolling Institute, Royal North Shore Hospital, Sydney, NSW, Australia.,University of Sydney, Sydney, NSW, Australia
| | - Annette Hogg
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jason Ellul
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henry To
- Department of Surgery, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Cuong Duong
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Julie A Miller
- Department of Surgery, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Surgery, Epworth Hospital, Melbourne, Victoria, Australia
| | - Christopher Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Diabetes and Endocrinology, Western Health, Melbourne, Victoria, Australia
| | - Paul James
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Trainer
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony J Gill
- University of Sydney, Sydney, NSW, Australia.,Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics, Kolling Institute, Royal North Shore Hospital, Sydney, NSW, Australia.,University of Sydney, Sydney, NSW, Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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31
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Wong SQ, Tothill RW, Dawson SJ, Hicks RJ. Wet or Dry? Do Liquid Biopsy Techniques Compete with or Complement PET for Disease Monitoring in Oncology? J Nucl Med 2017; 58:869-870. [PMID: 28450568 DOI: 10.2967/jnumed.117.190116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 03/27/2017] [Indexed: 11/16/2022] Open
Affiliation(s)
- Stephen Q Wong
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia; and
| | - Richard W Tothill
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia; and.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia; and.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia; and .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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32
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Lefebure M, Tothill RW, Kruse E, Hawkins ED, Shortt J, Matthews GM, Gregory GP, Martin BP, Kelly MJ, Todorovski I, Doyle MA, Lupat R, Li J, Schroeder J, Wall M, Craig S, Poortinga G, Cameron D, Bywater M, Kats L, Gearhart MD, Bardwell VJ, Dickins RA, Hannan RD, Papenfuss AT, Johnstone RW. Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene. Nat Commun 2017; 8:14581. [PMID: 28262675 PMCID: PMC5343491 DOI: 10.1038/ncomms14581] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 01/12/2017] [Indexed: 01/05/2023] Open
Abstract
The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor. These findings challenge the assumed two-hit model of Eμ-Myc lymphoma and demonstrate a functional in vivo role for Bcor in suppressing tumorigenesis. The Eμ-Myc lymphoma mouse model has been invaluable in the study of this disease. Here, the authors use multiple sequencing strategies to analyse the tumours in these mice and find recurrent inactivating mutations in Bcor, suggesting that this gene has a negative role in Myc signalling.
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Affiliation(s)
- Marcus Lefebure
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Elizabeth Kruse
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Edwin D Hawkins
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Jake Shortt
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing &Health Sciences, Clayton, Victoria 3168, Australia
| | | | - Gareth P Gregory
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Benjamin P Martin
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Madison J Kelly
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Richard Lupat
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jan Schroeder
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia.,Department of Medicine, St Vincent's Hospital, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Stuart Craig
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Don Cameron
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Megan Bywater
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lev Kats
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Micah D Gearhart
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Vivian J Bardwell
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, AMREP Building, Commercial Road, The Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Ross D Hannan
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Cancer Biology and Therapeutics Department, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Anthony T Papenfuss
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
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Kader T, Goode DL, Wong SQ, Connaughton J, Rowley SM, Devereux L, Byrne D, Fox SB, Mir Arnau G, Tothill RW, Campbell IG, Gorringe KL. Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue. Genome Med 2016; 8:121. [PMID: 27846907 PMCID: PMC5111221 DOI: 10.1186/s13073-016-0375-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Abstract
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.
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Affiliation(s)
- Tanjina Kader
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - David L Goode
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Stephen Q Wong
- Molecular Biomarkers and Translational Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Jacquie Connaughton
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Lisa Devereux
- LifePool, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - David Byrne
- Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Gisela Mir Arnau
- Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Molecular Imaging and Targeted Therapeutics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Kylie L Gorringe
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia. .,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. .,Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
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Chang CA, Pattison DA, Tothill RW, Kong G, Akhurst TJ, Hicks RJ, Hofman MS. (68)Ga-DOTATATE and (18)F-FDG PET/CT in Paraganglioma and Pheochromocytoma: utility, patterns and heterogeneity. Cancer Imaging 2016; 16:22. [PMID: 27535829 PMCID: PMC4989291 DOI: 10.1186/s40644-016-0084-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/12/2016] [Indexed: 12/24/2022] Open
Abstract
Background Pheochromocytomas (PCC) and paragangliomas (PGL) are neuroendocrine tumours arising from pluripotent neural crest stem cells and are associated with neurons of the autonomic nervous system. PCCs/PGLs are often hereditary and multifocal, and their biologic behaviour and metabolic activity vary making imaging of these tumours challenging. The imaging gold standard has been I-123 MIBG complemented by CT or MRI. PGLs being neuroendocrine tumours express somatostatin receptors enabling imaging with Ga-68 DOTA-coupled peptides such as DOTATATE. Imaging with F-18 FDG also provides additional information regarding metabolic activity and biologic aggressiveness of these tumours, or, in some situations, reflecting metabolic reprogramming of these tumours. We report our experience using both Ga-68 DOTATATE and F-18 FDG PET/CT imaging in patients with PGLs and PCCs. Methods This was a retrospective review of 23 patients with proven PGL/PCC who underwent both DOTATATE and FDG PET/CT. Seven patients also had I-123 MIBG SPECT/CT and 1 patient had I-124 MIBG PET/CT. Lesional intensity and patterns of uptake were analysed. Results DOTATATE and FDG were positive at most sites of disease (96.2 % vs 91.4 %), although uptake intensity was significantly higher on DOTATATE with a median SUV of 21 compared to 12.5 for FDG (p < 0.001). SUVmax on F-18 FDG was significantly higher (p < 0.001) in clinically aggressive cases. I-123/I-124 MIBG detected fewer lesions (30.4 %). Conclusion Overall, Ga-68 DOTATATE PET/CT detected similar number but has significantly greater lesion-to-background contrast compared to F-18 FDG PET/CT. Combined with high specificity, patient convenience and relatively low cost, DOTATATE PET/CT should be considered the ideal first line investigation for imaging PGL/PCC. Depending on DOTATATE findings and the clinical question, FDG and MIBG remain useful and, in selected cases, may provide more accurate staging, disease characterisation and guide treatment choices.
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Affiliation(s)
- Chian A Chang
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia
| | - David A Pattison
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Endocrinology Service, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Richard W Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Grace Kong
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia
| | - Tim J Akhurst
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Rodney J Hicks
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Michael S Hofman
- Cancer Imaging, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
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Gao B, Lindemann K, Anderson L, Fereday S, Hung J, Alsop K, Tothill RW, Gebski V, Kennedy C, Balleine RL, Harnett PR, Bowtell DDL, DeFazio A. Serous ovarian and primary peritoneal cancers: A comparative analysis of clinico-pathological features, molecular subtypes and treatment outcome. Gynecol Oncol 2016; 142:458-64. [PMID: 27444035 DOI: 10.1016/j.ygyno.2016.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/23/2016] [Accepted: 06/30/2016] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Primary peritoneal cancer is rare and considered equivalent to stage III/IV ovarian cancer, but questions remain concerning its underlying biology, prognosis and optimal management. METHODS Clinico-pathological and treatment details of primary peritoneal (n=120) and ovarian cancer (n=635) were obtained on women recruited to the Australian Ovarian Cancer Study. Log-rank test was used to compare survival and cox proportional hazards models were fitted to obtain hazard ratios and 95% confidence intervals, both unadjusted and adjusted for age, grade, FIGO stage, residual disease and treatment with neoadjuvant chemotherapy. Molecular subtype was determined by gene expression profiling using published data. RESULTS Compared with advanced serous ovarian cancer, primary peritoneal cancer patients were older (mean age 65.5 vs. 60.2years, p<0.001), more often treated with neoadjuvant chemotherapy (38.4% vs. 11.4%, p<0.001). Gene expression profiling classified a substantially higher proportion of primary peritoneal carcinomas as C1 (mesenchymal, reactive stromal infiltration) subtype (70.6% vs. 32.1%, p=0.029), which was associated with lower complete surgical resection rate. Women with primary peritoneal cancer had significantly shorter progression-free (11.6 vs. 13.6months, p=0.007) and overall survival (31.7 vs. 39.8months, p=0.012). In multivariate analysis, residual disease and neoadjuvant chemotherapy were both independently associated with increased risk of progression and death. CONCLUSIONS Primary peritoneal cancer patients were more frequently treated with neoadjuvant chemotherapy and had inferior survival. Different tumor biology characterized by activated stromal fibrosis in primary peritoneal cancer may underlie the differences in treatment and clinical outcome.
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Affiliation(s)
- Bo Gao
- Crown Princess Mary Cancer Care Centre, Westmead Hospital, Sydney, NSW, Australia; The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Kristina Lindemann
- Crown Princess Mary Cancer Care Centre, Westmead Hospital, Sydney, NSW, Australia; NHMRC Clinical Trials Centre, Sydney, NSW, Australia; Department of Gynecological Cancer, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jillian Hung
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia; Department of Gynecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Val Gebski
- NHMRC Clinical Trials Centre, Sydney, NSW, Australia
| | - Catherine Kennedy
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia; Department of Gynecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Rosemary L Balleine
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia; Pathology West ICPMR, Westmead, NSW, Australia
| | | | - Paul R Harnett
- Crown Princess Mary Cancer Care Centre, Westmead Hospital, Sydney, NSW, Australia; The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, UK; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Anna DeFazio
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia; Department of Gynecological Oncology, Westmead Hospital, Sydney, NSW, Australia.
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36
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Hogg SJ, Newbold A, Vervoort SJ, Cluse LA, Martin BP, Gregory GP, Lefebure M, Vidacs E, Tothill RW, Bradner JE, Shortt J, Johnstone RW. BET Inhibition Induces Apoptosis in Aggressive B-Cell Lymphoma via Epigenetic Regulation of BCL-2 Family Members. Mol Cancer Ther 2016; 15:2030-41. [PMID: 27406984 DOI: 10.1158/1535-7163.mct-15-0924] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 06/22/2016] [Indexed: 11/16/2022]
Abstract
Targeting BET bromodomain proteins using small molecules is an emerging anticancer strategy with clinical evaluation of at least six inhibitors now underway. Although MYC downregulation was initially proposed as a key mechanistic property of BET inhibitors, recent evidence suggests that additional antitumor activities are important. Using the Eμ-Myc model of B-cell lymphoma, we demonstrate that BET inhibition with JQ1 is a potent inducer of p53-independent apoptosis that occurs in the absence of effects on Myc gene expression. JQ1 skews the expression of proapoptotic (Bim) and antiapoptotic (BCL-2/BCL-xL) BCL-2 family members to directly engage the mitochondrial apoptotic pathway. Consistent with this, Bim knockout or Bcl-2 overexpression inhibited apoptosis induction by JQ1. We identified lymphomas that were either intrinsically resistant to JQ1-mediated death or acquired resistance following in vivo exposure. Strikingly, in both instances BCL-2 was strongly upregulated and was concomitant with activation of RAS pathways. Eμ-Myc lymphomas engineered to express activated Nras upregulated BCL-2 and acquired a JQ1 resistance phenotype. These studies provide important information on mechanisms of apoptosis induction and resistance to BET-inhibition, while providing further rationale for the translation of BET inhibitors in aggressive B-cell lymphomas. Mol Cancer Ther; 15(9); 2030-41. ©2016 AACR.
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Affiliation(s)
- Simon J Hogg
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrea Newbold
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephin J Vervoort
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Leonie A Cluse
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Benjamin P Martin
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Gareth P Gregory
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia. Monash Hematology, Monash Health, Clayton, Victoria, Australia
| | - Marcus Lefebure
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eva Vidacs
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jake Shortt
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia. Monash Hematology, Monash Health, Clayton, Victoria, Australia. School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
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Waldeck K, Cullinane C, Ardley K, Shortt J, Martin B, Tothill RW, Li J, Johnstone RW, McArthur GA, Hicks RJ, Wood PJ. Long term, continuous exposure to panobinostat induces terminal differentiation and long term survival in the TH-MYCN neuroblastoma mouse model. Int J Cancer 2016; 139:194-204. [PMID: 26914605 DOI: 10.1002/ijc.30056] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/12/2016] [Indexed: 01/10/2023]
Abstract
Neuroblastoma is the most common extra-cranial malignancy in childhood and accounts for ∼15% of childhood cancer deaths. Amplification of MYCN in neuroblastoma is associated with aggressive disease and predicts for poor prognosis. Novel therapeutic approaches are therefore essential to improving patient outcomes in this setting. The histone deacetylases are known to interact with N-Myc and regulate numerous cellular processes via epigenetic modulation, including differentiation. In this study, we used the TH-MYCN mouse model of neuroblastoma to investigate the antitumor activity of the pan-HDAC inhibitor, panobinostat. In particular we sought to explore the impact of long term, continuous panobinostat exposure on the epigenetically driven differentiation process. Continuous treatment of tumor bearing TH-MYCN transgenic mice with panobinostat for nine weeks led to a significant improvement in survival as compared with mice treated with panobinostat for a three-week period. Panobinostat induced rapid tumor regression with no regrowth observed following a nine-week treatment period. Initial tumor response was associated with apoptosis mediated via upregulation of BMF and BIM. The process of terminal differentiation of neuroblastoma into benign ganglioneuroma, with a characteristic increase in S100 expression and reduction of N-Myc expression, occurred following prolonged exposure to the drug. RNA-sequencing analysis of tumors from treated animals confirmed significant upregulation of gene pathways associated with apoptosis and differentiation. Together our data demonstrate the potential of panobinostat as a novel therapeutic strategy for high-risk neuroblastoma patients.
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Affiliation(s)
- Kelly Waldeck
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kerry Ardley
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Gene Regulation Laboratory, East Melbourne, VIC, Australia.,School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Ben Martin
- Peter MacCallum Cancer Centre, Gene Regulation Laboratory, East Melbourne, VIC, Australia
| | - Richard W Tothill
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia
| | - Jason Li
- Peter MacCallum Cancer Centre, Bioinformatics Core Facility, East Melbourne, VIC, Australia
| | - Ricky W Johnstone
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Gene Regulation Laboratory, East Melbourne, VIC, Australia
| | - Grant A McArthur
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Department of Medicine, St.Vincent's Hospital, Fitzroy, VIC, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Paul J Wood
- Peter MacCallum Cancer Centre, Translational Research Laboratory, East Melbourne, VIC, Australia.,Children's Cancer Centre, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
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Flynn A, Dwight T, Harris J, Benn D, Zhou L, Hogg A, Catchpoole D, James P, Duncan EL, Trainer A, Gill AJ, Clifton-Bligh R, Hicks RJ, Tothill RW. Pheo-Type: A Diagnostic Gene-expression Assay for the Classification of Pheochromocytoma and Paraganglioma. J Clin Endocrinol Metab 2016; 101:1034-43. [PMID: 26796762 DOI: 10.1210/jc.2015-3889] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT Pheochromocytomas and paragangliomas (PPGLs) are heritable neoplasms that can be classified into gene-expression subtypes corresponding to their underlying specific genetic drivers. OBJECTIVE 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. DESIGN 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. RESULTS 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. CONCLUSIONS The Pheo-type gene-expression assay is a reliable method for predicting PPGL genotype using routine diagnostic tumor samples.
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Affiliation(s)
- Aidan Flynn
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Trisha Dwight
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Jessica Harris
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Diana Benn
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Li Zhou
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Annette Hogg
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Daniel Catchpoole
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Paul James
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Emma L Duncan
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Alison Trainer
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Anthony J Gill
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Roderick Clifton-Bligh
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
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Wong SQ, Waldeck K, Vergara IA, Schröder J, Madore J, Wilmott JS, Colebatch AJ, De Paoli-Iseppi R, Li J, Lupat R, Semple T, Arnau GM, Fellowes A, Leonard JH, Hruby G, Mann GJ, Thompson JF, Cullinane C, Johnston M, Shackleton M, Sandhu S, Bowtell DDL, Johnstone RW, Fox SB, McArthur GA, Papenfuss AT, Scolyer RA, Gill AJ, Hicks RJ, Tothill RW. UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas. Cancer Res 2015; 75:5228-34. [PMID: 26627015 DOI: 10.1158/0008-5472.can-15-1877] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/01/2015] [Indexed: 11/16/2022]
Abstract
Merkel cell carcinoma (MCC) is an uncommon, but highly malignant, cutaneous tumor. Merkel cell polyoma virus (MCV) has been implicated in a majority of MCC tumors; however, viral-negative tumors have been reported to be more prevalent in some geographic regions subject to high sun exposure. While the impact of MCV and viral T-antigens on MCC development has been extensively investigated, little is known about the etiology of viral-negative tumors. We performed targeted capture and massively parallel DNA sequencing of 619 cancer genes to compare the gene mutations and copy number alterations in MCV-positive (n = 13) and -negative (n = 21) MCC tumors and cell lines. We found that MCV-positive tumors displayed very low mutation rates, but MCV-negative tumors exhibited a high mutation burden associated with a UV-induced DNA damage signature. All viral-negative tumors harbored mutations in RB1, TP53, and a high frequency of mutations in NOTCH1 and FAT1. Additional mutated or amplified cancer genes of potential clinical importance included PI3K (PIK3CA, AKT1, PIK3CG) and MAPK (HRAS, NF1) pathway members and the receptor tyrosine kinase FGFR2. Furthermore, looking ahead to potential therapeutic strategies encompassing immune checkpoint inhibitors such as anti-PD-L1, we also assessed the status of T-cell-infiltrating lymphocytes (TIL) and PD-L1 in MCC tumors. A subset of viral-negative tumors exhibited high TILs and PD-L1 expression, corresponding with the higher mutation load within these cancers. Taken together, this study provides new insights into the underlying biology of viral-negative MCC and paves the road for further investigation into new treatment opportunities.
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Affiliation(s)
- Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kelly Waldeck
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Jan Schröder
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Walter Eliza Hall Institute, Melbourne, Victoria, Australia. Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Madore
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - Andrew J Colebatch
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ricardo De Paoli-Iseppi
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - Jason Li
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard Lupat
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Timothy Semple
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Andrew Fellowes
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - J Helen Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - George Hruby
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - Graham J Mann
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - John F Thompson
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | | | | | - Mark Shackleton
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony T Papenfuss
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Walter Eliza Hall Institute, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia and the University of Sydney, Sydney, New South Wales, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Research Group Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia.
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Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MCJ, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, Leong HS, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Arnau GM, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJC, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DDL. Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer. Nature 2015; 527:398. [PMID: 26503049 DOI: 10.1038/nature15716] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wong SQ, Waldeck K, Vergara IA, Li J, Lupat R, Semple T, Cullinane C, Mir Arnau G, Johnston M, Hogg A, Papenfuss AT, Fox S, McArthur G, Gill A, Hicks RJ, Tothill RW. Abstract 3875: Merkel cell carcinomas in Australia have distinct mutation profiles reflecting viral etiology and UV-related DNA damage. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background/Aims: Merkel cell carcinoma (MCC) is rare but aggressive cutaneous high-grade neuroendocrine cancer. Viral infection and sun-exposure are known risk factors for development of MCC, the latter being important in Australia, which has the highest reported incidence of MCC worldwide. There is growing evidence to suggest that MCC associated with the Merkel cell polyoma virus (MCPyV) is clinically, biologically and genetically distinct to those tumors without viral infection. We aimed to assess mutations arising in MCC in the Australian population by targeted massively-parallel sequencing (MPS) to gain new biological insight and identify novel therapeutic opportunities in this disease.
Methods: MCPyV was detected in tumours by PCR amplification of large-T antigen coding DNA. The tumor cohort was comprised of seven MCPyV-positive and 16 MCPyV-negative tumors reflecting the reported prevalence of these subtypes in the Australian population. We also sequenced two viral negative MCC cell lines. Hybridization-based DNA capture was used for enrichment of 625 cancer genes for high-depth MPS of tumor and the matching germline DNA, where available. Single nucleotide variants and small insertions and deletions were detected using GATK and muTect variant calling tools and annotated using ENSEMBL variant effect predictor. Somatic variants were enriched in the data by filtering out any variants found in matching germline samples or population-based polymorphism databases
Results: High mutation burden was found exclusively in the MCPyV-negative cases with the hallmark signature of UV induced DNA damage. Somatic mutations were identified in known cancer genes specific to the MCPyV-negative tumors. Deleterious RB1 and TP53 mutations were found in 17 and 16 of the MCPyV-negative cases, respectively. Canonical mutations were identified in PIK3CA, HRAS as well as truncating NF1 mutations, indicating that activation of the PI3K and RAS-MAPK pathways are important for pathogenesis of MCPyV-negative tumors. Treatment of two cell lines harboring either PIK3CA or HRAS mutations, respectively, showed in vitro sensitivity to the dual PI3K/mTOR inhibitor PF-04691502.
Conclusions: The identification of a UV-induced DNA damage signature and mutations in PI3K and MAPK pathways specific to viral negative tumors confirms the distinct routes to pathogenesis in this disease subtype. This study provides new insight into the biology of viral negative MCC and potential opportunities for the deployment of targeted therapies in this patient group.
Citation Format: Stephen Q. Wong, Kelly Waldeck, Ismael A. Vergara, Jason Li, Richard Lupat, Timothy Semple, Carleen Cullinane, Gisela Mir Arnau, Meredith Johnston, Annette Hogg, Anthony T. Papenfuss, Stephen Fox, Grant McArthur, Anthony Gill, Rodney J. Hicks, Richard W. Tothill. Merkel cell carcinomas in Australia have distinct mutation profiles reflecting viral etiology and UV-related DNA damage. [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;75(15 Suppl):Abstract nr 3875. doi:10.1158/1538-7445.AM2015-3875
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Affiliation(s)
| | - Kelly Waldeck
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Jason Li
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Richard Lupat
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | | | - Annette Hogg
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Stephen Fox
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
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Ryland GL, Doyle MA, Goode D, Boyle SE, Choong DYH, Rowley SM, Li J, Bowtell DDL, Tothill RW, Campbell IG, Gorringe KL. Loss of heterozygosity: what is it good for? BMC Med Genomics 2015; 8:45. [PMID: 26231170 PMCID: PMC4522148 DOI: 10.1186/s12920-015-0123-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Loss of heterozygosity (LOH) is a common genetic event in cancer development, and is known to be involved in the somatic loss of wild-type alleles in many inherited cancer syndromes. The wider involvement of LOH in cancer is assumed to relate to unmasking a somatically mutated tumour suppressor gene through loss of the wild type allele. METHODS We analysed 86 ovarian carcinomas for mutations in 980 genes selected on the basis of their location in common regions of LOH. RESULTS We identified 36 significantly mutated genes, but these could only partly account for the quanta of LOH in the samples. Using our own and TCGA data we then evaluated five possible models to explain the selection for non-random accumulation of LOH in ovarian cancer genomes: 1. Classic two-hit hypothesis: high frequency biallelic genetic inactivation of tumour suppressor genes. 2. Epigenetic two-hit hypothesis: biallelic inactivation through methylation and LOH. 3. Multiple alternate-gene biallelic inactivation: low frequency gene disruption. 4. Haplo-insufficiency: Single copy gene disruption. 5. Modified two-hit hypothesis: reduction to homozygosity of low penetrance germline predisposition alleles. We determined that while high-frequency biallelic gene inactivation under model 1 is rare, regions of LOH (particularly copy-number neutral LOH) are enriched for deleterious mutations and increased promoter methylation, while copy-number loss LOH regions are likely to contain under-expressed genes suggestive of haploinsufficiency. Reduction to homozygosity of cancer predisposition SNPs may also play a minor role. CONCLUSION It is likely that selection for regions of LOH depends on its effect on multiple genes. Selection for copy number neutral LOH may better fit the classic two-hit model whereas selection for copy number loss may be attributed to its effect on multi-gene haploinsufficiency. LOH mapping alone is unlikely to be successful in identifying novel tumour suppressor genes; a combined approach may be more effective.
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Affiliation(s)
- Georgina L Ryland
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. .,Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
| | - Maria A Doyle
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - David Goode
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - Samantha E Boyle
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - David Y H Choong
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - Jason Li
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | | | - David D L Bowtell
- Cancer Genomics and Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - Richard W Tothill
- Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. .,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia.
| | - Kylie L Gorringe
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. .,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia.
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Flynn A, Benn D, Clifton-Bligh R, George J, Gill AJ, Hicks RJ, Tothill RW. Abstract 2175: A diagnostic gene expression assay for the classification of pheochromocytoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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 samples 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 samples 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 samples with mutations in the MAX gene.The remaining two classes belong to the HIF signalling group, one representing samples 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 samples 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 samples and two SDHx samples was achieved. Classification of corresponding Nanostring data provided concordant classification for eleven of twelve samples.
Conclusion:
PCC can be divided into six biological classes indicative of the underlying driver mutation. The ability to accurately classify samples from FFPE material would provide a valuable adjunct to current practices in genetic testing laboratories, providing corroboration for known mutations and guidance on samples 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;75(15 Suppl):Abstract nr 2175. doi:10.1158/1538-7445.AM2015-2175
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Affiliation(s)
- Aidan Flynn
- 1Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Diana Benn
- 2Kolling Institute of Medical Research, Sydney, Australia
| | | | - Joshy George
- 3Jackson Laboratory for Genomic Medicine, Farmington, CT
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44
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Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MCJ, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, Leong HS, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Arnau GM, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJC, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DDL. Whole-genome characterization of chemoresistant ovarian cancer. Nature 2015; 521:489-94. [PMID: 26017449 DOI: 10.1038/nature14410] [Citation(s) in RCA: 1050] [Impact Index Per Article: 116.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/16/2015] [Indexed: 12/12/2022]
Abstract
Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- Cohort Studies
- Cyclin E/genetics
- Cystadenocarcinoma, Serous/drug therapy
- Cystadenocarcinoma, Serous/genetics
- DNA Methylation
- DNA Mutational Analysis
- DNA-Binding Proteins/genetics
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Genes, BRCA1
- Genes, BRCA2
- Genes, Neurofibromatosis 1
- Genome, Human/genetics
- Germ-Line Mutation/genetics
- Humans
- Mutagenesis/genetics
- Oncogene Proteins/genetics
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- PTEN Phosphohydrolase/genetics
- Promoter Regions, Genetic/genetics
- Retinoblastoma Protein/genetics
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Affiliation(s)
- Ann-Marie Patch
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | | | - Dariush Etemadmoghadam
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030, USA
| | - Sian Fereday
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Katia Nones
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Prue Cowin
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Peter J Bailey
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Karin S Kassahn
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia 5000, Australia
| | - Felicity Newell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Michael C J Quinn
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Stephen Kazakoff
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Kelly Quek
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Charlotte Wilhelm-Benartzi
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Ed Curry
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Huei San Leong
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Anne Hamilton
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Medicine, University of Melbourne, Parkville, Victoria 3052, Australia [3] The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Linda Mileshkin
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - George Au-Yeung
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Catherine Kennedy
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Jillian Hung
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Yoke-Eng Chiew
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Paul Harnett
- Crown Princess Mary Cancer Centre and University of Sydney at Westmead Hospital, Westmead, Sydney, New South Wales 2145, Australia
| | - Michael Friedlander
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2031, Australia
| | - Michael Quinn
- The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Jan Pyman
- The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Stephen Cordner
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Patricia O'Brien
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Jodie Leditschke
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Greg Young
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Kate Strachan
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Paul Waring
- Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Walid Azar
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Chris Mitchell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Joy Hendley
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Heather Thorne
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Mark Shackleton
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David K Miller
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Gisela Mir Arnau
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Richard W Tothill
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | | | - Timothy Semple
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Craig Nourse
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Ehsan Nourbakhsh
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Suzanne Manning
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Senel Idrisoglu
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Timothy J C Bruxner
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Angelika N Christ
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Barsha Poudel
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Oliver Holmes
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Matthew Anderson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Conrad Leonard
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Andrew Lonie
- Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - Nathan Hall
- La Trobe Institute for Molecular Science, Bundoora, Victoria 3083, Australia
| | - Scott Wood
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Darrin F Taylor
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Qinying Xu
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - J Lynn Fink
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Ronny Drapkin
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115-5450, USA
| | - Euan Stronach
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Robert Brown
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | | | - Shivashankar H Nagaraj
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Emma Markham
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Peter J Wilson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Jason Ellul
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Orla McNally
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Maria A Doyle
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | | | - Collin Stewart
- The University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - John V Pearson
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Nicola Waddell
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Anna deFazio
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Sean M Grimmond
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - David D L Bowtell
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia [4] Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK [5] Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia
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45
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Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MCJ, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, Leong HS, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Arnau GM, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJC, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DDL. Whole-genome characterization of chemoresistant ovarian cancer. Nature 2015. [PMID: 26017449 DOI: 10.1038/nature14410] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.
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Affiliation(s)
- Ann-Marie Patch
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | | | - Dariush Etemadmoghadam
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030, USA
| | - Sian Fereday
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Katia Nones
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Prue Cowin
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Peter J Bailey
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Karin S Kassahn
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia 5000, Australia
| | - Felicity Newell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Michael C J Quinn
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Stephen Kazakoff
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Kelly Quek
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Charlotte Wilhelm-Benartzi
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Ed Curry
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Huei San Leong
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | | | - Anne Hamilton
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Medicine, University of Melbourne, Parkville, Victoria 3052, Australia [3] The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Linda Mileshkin
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - George Au-Yeung
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Catherine Kennedy
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Jillian Hung
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Yoke-Eng Chiew
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Paul Harnett
- Crown Princess Mary Cancer Centre and University of Sydney at Westmead Hospital, Westmead, Sydney, New South Wales 2145, Australia
| | - Michael Friedlander
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2031, Australia
| | - Michael Quinn
- The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Jan Pyman
- The Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Stephen Cordner
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Patricia O'Brien
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Jodie Leditschke
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Greg Young
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Kate Strachan
- Victorian Institute of Forensic Medicine, Southbank, Victoria 3006, Australia
| | - Paul Waring
- Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Walid Azar
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Chris Mitchell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Joy Hendley
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Heather Thorne
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Mark Shackleton
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David K Miller
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Gisela Mir Arnau
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Richard W Tothill
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | | | - Timothy Semple
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Craig Nourse
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Ehsan Nourbakhsh
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Suzanne Manning
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Senel Idrisoglu
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Timothy J C Bruxner
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Angelika N Christ
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Barsha Poudel
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Oliver Holmes
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Matthew Anderson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Conrad Leonard
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Andrew Lonie
- Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - Nathan Hall
- La Trobe Institute for Molecular Science, Bundoora, Victoria 3083, Australia
| | - Scott Wood
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Darrin F Taylor
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Qinying Xu
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - J Lynn Fink
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Ronny Drapkin
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115-5450, USA
| | - Euan Stronach
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | - Robert Brown
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK
| | | | - Shivashankar H Nagaraj
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Emma Markham
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Peter J Wilson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Jason Ellul
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Orla McNally
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Maria A Doyle
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | | | - Collin Stewart
- The University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - John V Pearson
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Nicola Waddell
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Anna deFazio
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Sean M Grimmond
- 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia [2] WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - David D L Bowtell
- 1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia [4] Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK [5] Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia
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Flynn A, Benn D, Clifton-Bligh R, Robinson B, Trainer AH, James P, Hogg A, Waldeck K, George J, Li J, Fox SB, Gill AJ, McArthur G, Hicks RJ, Tothill RW. The genomic landscape of phaeochromocytoma. J Pathol 2015; 236:78-89. [DOI: 10.1002/path.4503] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/19/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Aidan Flynn
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
- The Department of Pathology; University of Melbourne; Parkville VIC Australia
| | - Diana Benn
- Cancer Genetics; Kolling Institute of Medical Research, Royal North Shore Hospital; Sydney NSW Australia
- University of Sydney; Sydney NSW Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics; Kolling Institute of Medical Research, Royal North Shore Hospital; Sydney NSW Australia
- University of Sydney; Sydney NSW Australia
| | - Bruce Robinson
- Cancer Genetics; Kolling Institute of Medical Research, Royal North Shore Hospital; Sydney NSW Australia
- University of Sydney; Sydney NSW Australia
| | - Alison H Trainer
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
- Royal Melbourne Hospital and Department of Medicine; University of Melbourne; Parkville VIC Australia
| | - Paul James
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
| | - Annette Hogg
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
| | - Kelly Waldeck
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
| | - Joshy George
- Jackson Laboratory for Genomic Medicine; Farmington CT 06030 USA
| | - Jason Li
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
| | - Stephen B Fox
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
| | - Anthony J Gill
- University of Sydney; Sydney NSW Australia
- Cancer Diagnosis and Pathology Group; Kolling Institute of Medical Research and Department of Anatomical Pathology, Royal North Shore Hospital; Sydney NSW Australia
| | - Grant McArthur
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
- The Sir Peter MacCallum Department of Oncology; University of Melbourne; Parkville VIC Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
- The Sir Peter MacCallum Department of Oncology; University of Melbourne; Parkville VIC Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre; East Melbourne VIC Australia
- The Department of Pathology; University of Melbourne; Parkville VIC Australia
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47
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Xu H, Yan Y, Deb S, Rangasamy D, Germann M, Malaterre J, Eder NC, Ward RL, Hawkins NJ, Tothill RW, Chen L, Mortensen NJ, Fox SB, McKay MJ, Ramsay RG. Cohesin Rad21 mediates loss of heterozygosity and is upregulated via Wnt promoting transcriptional dysregulation in gastrointestinal tumors. Cell Rep 2014; 9:1781-1797. [PMID: 25464844 DOI: 10.1016/j.celrep.2014.10.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 08/29/2014] [Accepted: 10/27/2014] [Indexed: 01/22/2023] Open
Abstract
Loss of heterozygosity (LOH) of the adenomatous polyposis coli (APC) gene triggers a series of molecular events leading to intestinal adenomagenesis. Haploinsufficiency of the cohesin Rad21 influences multiple initiating events in colorectal cancer (CRC). We identify Rad21 as a gatekeeper of LOH and a β-catenin target gene and provide evidence that Wnt pathway activation drives RAD21 expression in human CRC. Genome-wide analyses identified Rad21 as a key transcriptional regulator of critical CRC genes and long interspersed element (LINE-1 or L1) retrotransposons. Elevated RAD21 expression tracks with reactivation of L1 expression in human sporadic CRC, implicating cohesin-mediated L1 expression in global genomic instability and gene dysregulation in cancer.
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Affiliation(s)
- Huiling Xu
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Yuqian Yan
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia
| | - Siddhartha Deb
- Pathology Department, PMCC, East Melbourne, VIC 3002, Australia; Victorian Cancer Biobank, Carlton, VIC 3053, Australia
| | - Danny Rangasamy
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Markus Germann
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Jordane Malaterre
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Noreen C Eder
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia
| | - Robyn L Ward
- Prince of Wales Clinical School, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | | | - Richard W Tothill
- Cancer Therapeutics Program, Cancer Research Division, PMCC, East Melbourne, VIC 3002, Australia
| | - Long Chen
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Neil J Mortensen
- Department of Colorectal Surgery, Oxford University Hospitals, Oxford Cancer Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Stephen B Fox
- Department of Pathology, The University of Melbourne, Parkville, VIC 3000, Australia; Pathology Department, PMCC, East Melbourne, VIC 3002, Australia
| | - Michael J McKay
- University of Sydney and North Coast Cancer Institute, Lismore, NSW 2480, Australia
| | - Robert G Ramsay
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia.
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Abstract
The future of cancer treatment lies in personalized strategies designed to specifically target tumorigenic cell populations present in an individual. Although recent advances in directed therapies have greatly improved patient outcomes in some cancers, intuitive drug design is proving more difficult than expected owing largely to the complexity of human cancers. Intratumoral heterogeneity, the presence of multiple genotypically and/or phenotypically distinct cell subpopulations within a single tumor, is a likely cause of drug resistance. Advances in systems biology are helping to unravel the mysteries of cancer progression. In this issue of Cancer Discovery, Zhao and colleagues define a path for functional validation of computational modeling in the context of heterogeneous tumor populations and their potential for drug response and resistance.
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Affiliation(s)
- Clare Fedele
- 1Cancer Therapeutics Program, Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne; 2Sir Peter MacCallum Department of Oncology and 3Department of Pathology, University of Melbourne, Parkville; and 4Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
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49
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Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW. Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment. PLoS One 2014; 9:e95217. [PMID: 24752294 PMCID: PMC3994043 DOI: 10.1371/journal.pone.0095217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.
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Affiliation(s)
- Jason Li
- Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia
| | - Maria A. Doyle
- Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Isaam Saeed
- Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia
- YourGene Biosciences Australia, Southbank, VIC, Australia
| | - Stephen Q. Wong
- Molecular Pathology Research and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Victoria Mar
- Victorian Melanoma Service, Alfred Hospital, Prahran, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Clayton, VIC, Australia
- Molecular Oncology Laboratory, Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - David L. Goode
- Sarcoma Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Franco Caramia
- Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Ken Doig
- Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Georgina L. Ryland
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Ella R. Thompson
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Sally M. Hunter
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Saman K. Halgamuge
- Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia
| | - Jason Ellul
- Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Alexander Dobrovic
- Molecular Pathology Research and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Translational Genomics & Epigenomics Laboratory, Ludwig Institute for Cancer Research, Heidelberg, VIC, Australia
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Anthony T. Papenfuss
- Bioinformatics division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Grant A. McArthur
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Molecular Oncology Laboratory, Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Translational Research Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Department of Medicine, St. Vincent’s Hospital, Fitzroy, VIC, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Richard W. Tothill
- Translational Research Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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Tothill RW, Li J, Mileshkin L, Doig K, Siganakis T, Cowin P, Fellowes A, Semple T, Fox S, Byron K, Kowalczyk A, Thomas D, Schofield P, Bowtell DD. Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary. J Pathol 2014; 231:413-23. [PMID: 24037760 DOI: 10.1002/path.4251] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/22/2013] [Accepted: 08/28/2013] [Indexed: 12/30/2022]
Abstract
The clinical management of patients with cancer of unknown primary (CUP) is hampered by the absence of a definitive site of origin. We explored the utility of massively-parallel (next-generation) sequencing for the diagnosis of a primary site of origin and for the identification of novel treatment options. DNA enrichment by hybridization capture of 701 genes of clinical and/or biological importance, followed by massively-parallel sequencing, was performed on 16 CUP patients who had defied attempts to identify a likely site of origin. We obtained high quality data from both fresh-frozen and formalin-fixed, paraffin-embedded samples, demonstrating accessibility to routine diagnostic material. DNA copy-number obtained by massively-parallel sequencing was comparable to that obtained using oligonucleotide microarrays or quantitatively hybridized fluorescently tagged oligonucleotides. Sequencing to an average depth of 458-fold enabled detection of somatically acquired single nucleotide mutations, insertions, deletions and copy-number changes, and measurement of allelic frequency. Common cancer-causing mutations were found in all cancers. Mutation profiling revealed therapeutic gene targets and pathways in 12/16 cases, providing novel treatment options. The presence of driver mutations that are enriched in certain known tumour types, together with mutational signatures indicative of exposure to sunlight or smoking, added to clinical, pathological, and molecular indicators of likely tissue of origin. Massively-parallel DNA sequencing can therefore provide comprehensive mutation, DNA copy-number, and mutational signature data that are of significant clinical value for a majority of CUP patients, providing both cumulative evidence for the diagnosis of primary site and options for future treatment.
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Affiliation(s)
- Richard W Tothill
- The Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; The Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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