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Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024; 74:264-285. [PMID: 38174605 DOI: 10.3322/caac.21825] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
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Cooke SF, Wright TA, Sin YY, Ling J, Kyurkchieva E, Phanthaphol N, Mcskimming T, Herbert K, Rebus S, Biankin AV, Chang DK, Baillie GS, Blair CM. Disruption of the pro-oncogenic c-RAF-PDE8A complex represents a differentiated approach to treating KRAS-c-RAF dependent PDAC. Sci Rep 2024; 14:8998. [PMID: 38637546 PMCID: PMC11026450 DOI: 10.1038/s41598-024-59451-3] [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: 12/21/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is considered the third leading cause of cancer mortality in the western world, offering advanced stage patients with few viable treatment options. Consequently, there remains an urgent unmet need to develop novel therapeutic strategies that can effectively inhibit pro-oncogenic molecular targets underpinning PDACs pathogenesis and progression. One such target is c-RAF, a downstream effector of RAS that is considered essential for the oncogenic growth and survival of mutant RAS-driven cancers (including KRASMT PDAC). Herein, we demonstrate how a novel cell-penetrating peptide disruptor (DRx-170) of the c-RAF-PDE8A protein-protein interaction (PPI) represents a differentiated approach to exploiting the c-RAF-cAMP/PKA signaling axes and treating KRAS-c-RAF dependent PDAC. Through disrupting the c-RAF-PDE8A protein complex, DRx-170 promotes the inactivation of c-RAF through an allosteric mechanism, dependent upon inactivating PKA phosphorylation. DRx-170 inhibits cell proliferation, adhesion and migration of a KRASMT PDAC cell line (PANC1), independent of ERK1/2 activity. Moreover, combining DRx-170 with afatinib significantly enhances PANC1 growth inhibition in both 2D and 3D cellular models. DRx-170 sensitivity appears to correlate with c-RAF dependency. This proof-of-concept study supports the development of DRx-170 as a novel and differentiated strategy for targeting c-RAF activity in KRAS-c-RAF dependent PDAC.
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Affiliation(s)
- Sean F Cooke
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Thomas A Wright
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Yuan Yan Sin
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Jiayue Ling
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Elka Kyurkchieva
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Nattaporn Phanthaphol
- Siriraj Centre of Research Excellence for Cancer Immunotherapy, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thomas Mcskimming
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Katharine Herbert
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Selma Rebus
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - George S Baillie
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Connor M Blair
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK.
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Agostini A, Piro G, Inzani F, Quero G, Esposito A, Caggiano A, Priori L, Larghi A, Alfieri S, Casolino R, Scaglione G, Tondolo V, Cammarota G, Ianiro G, Corbo V, Biankin AV, Tortora G, Carbone C. Identification of spatially-resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms. Nat Commun 2024; 15:2764. [PMID: 38553466 PMCID: PMC10980816 DOI: 10.1038/s41467-024-46994-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 03/08/2024] [Indexed: 04/02/2024] Open
Abstract
The existing Intraductal Papillary Mucinous Neoplasm (IPMN) risk stratification relies on clinical and histological factors, resulting in inaccuracies and leading to suboptimal treatment. This is due to the lack of appropriate molecular markers that can guide patients toward the best therapeutic options. Here, we assess and confirm subtype-specific markers for IPMN across two independent cohorts of patients using two Spatial Transcriptomics (ST) technologies. Specifically, we identify HOXB3 and ZNF117 as markers for Low-Grade Dysplasia, SPDEF and gastric neck cell markers in borderline cases, and NKX6-2 and gastric isthmus cell markers in High-Grade-Dysplasia Gastric IPMN, highlighting the role of TNFα and MYC activation in IPMN progression and the role of NKX6-2 in the specific Gastric IPMN progression. In conclusion, our work provides a step forward in understanding the gene expression landscapes of IPMN and the critical transcriptional networks related to PDAC progression.
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Affiliation(s)
- Antonio Agostini
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Geny Piro
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy.
| | - Frediano Inzani
- Department of Anatomic Pathology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giuseppe Quero
- Pancreatic Surgery Unit, Gemelli Pancreatic Advanced Research Center (CRMPG), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Digestive Surgery Unit, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Annachiara Esposito
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Alessia Caggiano
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Lorenzo Priori
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Alberto Larghi
- Digestive Endoscopy Unit, Fondazione Policlinico A. Gemelli IRCCS and Center for Endoscopic Research, Therapeutics and Training, Catholic University, Rome, Italy
| | - Sergio Alfieri
- Pancreatic Surgery Unit, Gemelli Pancreatic Advanced Research Center (CRMPG), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Digestive Surgery Unit, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Giulia Scaglione
- Department of Anatomic Pathology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Vincenzo Tondolo
- General Surgery, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, Gastroenterology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, Gastroenterology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, University of Verona, 37134, Verona, Italy
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Giampaolo Tortora
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Carmine Carbone
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
- Medical Oncology, Department of Translational Medicine, Catholic University of the Sacred Heart, Rome, Italy.
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4
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Topham JT, Lawlor RT, Lemaire D, Casolino R, Biankin AV. Data sharing in cancer research: perceived risks and the consequences of not sharing. Lancet Oncol 2024; 25:275-276. [PMID: 38423044 DOI: 10.1016/s1470-2045(24)00021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/02/2024]
Affiliation(s)
| | - Rita T Lawlor
- ARC-Net Research Centre and Department of Engineering for Innovative Medicine, University of Verona, Verona, Italy
| | - Diana Lemaire
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK.
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Canel M, Sławińska AD, Lonergan DW, Kallor AA, Upstill-Goddard R, Davidson C, von Kriegsheim A, Biankin AV, Byron A, Alfaro J, Serrels A. FAK suppresses antigen processing and presentation to promote immune evasion in pancreatic cancer. Gut 2023; 73:131-155. [PMID: 36977556 PMCID: PMC10715489 DOI: 10.1136/gutjnl-2022-327927] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/19/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVE Immunotherapy for the treatment of pancreatic ductal adenocarcinoma (PDAC) has shown limited efficacy. Poor CD8 T-cell infiltration, low neoantigen load and a highly immunosuppressive tumour microenvironment contribute to this lack of response. Here, we aimed to further investigate the immunoregulatory function of focal adhesion kinase (FAK) in PDAC, with specific emphasis on regulation of the type-II interferon response that is critical in promoting T-cell tumour recognition and effective immunosurveillance. DESIGN We combined CRISPR, proteogenomics and transcriptomics with mechanistic experiments using a KrasG12Dp53R172H mouse model of pancreatic cancer and validated findings using proteomic analysis of human patient-derived PDAC cell lines and analysis of publicly available human PDAC transcriptomics datasets. RESULTS Loss of PDAC cell-intrinsic FAK signalling promotes expression of the immunoproteasome and Major Histocompatibility Complex class-I (MHC-I), resulting in increased antigen diversity and antigen presentation by FAK-/- PDAC cells. Regulation of the immunoproteasome by FAK is a critical determinant of this response, optimising the physicochemical properties of the peptide repertoire for high affinity binding to MHC-I. Expression of these pathways can be further amplified in a STAT1-dependent manner via co-depletion of FAK and STAT3, resulting in extensive infiltration of tumour-reactive CD8 T-cells and further restraint of tumour growth. FAK-dependent regulation of antigen processing and presentation is conserved between mouse and human PDAC, but is lost in cells/tumours with an extreme squamous phenotype. CONCLUSION Therapies aimed at FAK degradation may unlock additional therapeutic benefit for the treatment of PDAC through increasing antigen diversity and promoting antigen presentation.
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Affiliation(s)
- Marta Canel
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - David W Lonergan
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ashwin Adrian Kallor
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Rosie Upstill-Goddard
- The Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Catherine Davidson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew V Biankin
- The Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Adam Byron
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alan Serrels
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
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6
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Golan T, Casolino R, Biankin AV, Hammel P, Whitaker KD, Hall MJ, Riegert-Johnson DL. Germline BRCA testing in pancreatic cancer: improving awareness, timing, turnaround, and uptake. Ther Adv Med Oncol 2023; 15:17588359231189127. [PMID: 37720496 PMCID: PMC10504836 DOI: 10.1177/17588359231189127] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/04/2023] [Indexed: 09/19/2023] Open
Abstract
Prognosis is generally poor for patients with pancreatic ductal adenocarcinoma. However, patients with germline BRCA1 or BRCA2 mutations (gBRCAm) may benefit from first-line platinum-based chemotherapy and maintenance therapy with the poly(adenosine diphosphate-ribose) polymerase inhibitor olaparib following at least 16 weeks of first-line platinum-based chemotherapy without disease progression. Germline breast cancer gene (BRCA) testing is therefore important to ensure that patients receive the most effective treatment. In addition, testing for other DNA damage response gene mutations beyond gBRCAm may also guide treatment decisions. However, clinical pathways for genetic testing are often suboptimal, leading to delays in treatment initiation or missed opportunities for personalized therapy. Barriers to testing include low rates of referral and uptake, delays to referral and slow result turnaround times, cost, and biopsy and assay limitations if somatic testing is performed, leading to the requirement for subsequent dedicated germline testing. Low rates of referral may result from lack of awareness among physicians of the clinical value of testing, coupled with low confidence in interpreting test results and poor availability of genetic counseling services. Among patients, barriers to uptake may include similar lack of awareness of the clinical value of testing, anxiety regarding the implications of test results, lack of insurance coverage, fear of negative insurance implications, and socioeconomic factors. Potential solutions include innovative approaches to testing pathways, including 'mainstreaming' of testing in which BRCA tests are routinely arranged by the treating oncologist, with the involvement of genetic counselors if a patient is found to have a gBRCAm. More recently, the utility of multigene panel analyses has also been explored. Access to genetic counseling may also be improved through initiatives such as having a genetic counseling appointment for all new patient visits and telemedicine approaches, including the use of telephone consultations or DVD-assisted counseling. Educational programs will also be beneficial, and cost effectiveness is likely to improve as the number of targeted treatments increases and when the earlier detection of tumors in family members following cascade testing is considered.
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Affiliation(s)
- Talia Golan
- Institute of Oncology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, University Paris-Saclay, Paul Brousse Hospital (AP-HP), Villejuif, France
| | - Kristen D. Whitaker
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J. Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
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7
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Chitty JL, Yam M, Perryman L, Parker AL, Skhinas JN, Setargew YFI, Mok ETY, Tran E, Grant RD, Latham SL, Pereira BA, Ritchie SC, Murphy KJ, Trpceski M, Findlay AD, Melenec P, Filipe EC, Nadalini A, Velayuthar S, Major G, Wyllie K, Papanicolaou M, Ratnaseelan S, Phillips PA, Sharbeen G, Youkhana J, Russo A, Blackwell A, Hastings JF, Lucas MC, Chambers CR, Reed DA, Stoehr J, Vennin C, Pidsley R, Zaratzian A, Da Silva AM, Tayao M, Charlton B, Herrmann D, Nobis M, Clark SJ, Biankin AV, Johns AL, Croucher DR, Nagrial A, Gill AJ, Grimmond SM, Pajic M, Timpson P, Jarolimek W, Cox TR. A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer. Nat Cancer 2023; 4:1326-1344. [PMID: 37640930 PMCID: PMC10518255 DOI: 10.1038/s43018-023-00614-y] [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] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/07/2023] [Indexed: 08/31/2023]
Abstract
The lysyl oxidase family represents a promising target in stromal targeting of solid tumors due to the importance of this family in crosslinking and stabilizing fibrillar collagens and its known role in tumor desmoplasia. Using small-molecule drug-design approaches, we generated and validated PXS-5505, a first-in-class highly selective and potent pan-lysyl oxidase inhibitor. We demonstrate in vitro and in vivo that pan-lysyl oxidase inhibition decreases chemotherapy-induced pancreatic tumor desmoplasia and stiffness, reduces cancer cell invasion and metastasis, improves tumor perfusion and enhances the efficacy of chemotherapy in the autochthonous genetically engineered KPC model, while also demonstrating antifibrotic effects in human patient-derived xenograft models of pancreatic cancer. PXS-5505 is orally bioavailable, safe and effective at inhibiting lysyl oxidase activity in tissues. Our findings present the rationale for progression of a pan-lysyl oxidase inhibitor aimed at eliciting a reduction in stromal matrix to potentiate chemotherapy in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jessica L Chitty
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle Yam
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Lara Perryman
- Pharmaxis, Frenchs Forest, New South Wales, Australia
| | - Amelia L Parker
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Joanna N Skhinas
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Yordanos F I Setargew
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Ellie T Y Mok
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Emmi Tran
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Rhiannon D Grant
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Sharissa L Latham
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Brooke A Pereira
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Shona C Ritchie
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Kendelle J Murphy
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Trpceski
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | | | - Pauline Melenec
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Elysse C Filipe
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Audrey Nadalini
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Sipiththa Velayuthar
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Gretel Major
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Kaitlin Wyllie
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Papanicolaou
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Shivanjali Ratnaseelan
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Phoebe A Phillips
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - George Sharbeen
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Janet Youkhana
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Alice Russo
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Antonia Blackwell
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Jordan F Hastings
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Morghan C Lucas
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Cecilia R Chambers
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Daniel A Reed
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Janett Stoehr
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Claire Vennin
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Ruth Pidsley
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Andrew M Da Silva
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Tayao
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | | | - David Herrmann
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Max Nobis
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- Intravital Imaging Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Susan J Clark
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Amber L Johns
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - David R Croucher
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Adnan Nagrial
- Department of Medical Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Anthony J Gill
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, VCCC, Melbourne, Victoria, Australia
| | - Marina Pajic
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Thomas R Cox
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
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8
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Nocini R, Tondulli L, D'Ambrosio C, Luchini C, Biankin AV, Casolino R, Scarpa A, Milella M, Lawlor RT. ICGC ARGO precision medicine: genomic profiling-informed prediction of immunotherapy response in two patients with metastatic head and neck squamous cell carcinoma. Lancet Oncol 2023; 24:851-853. [PMID: 37541270 DOI: 10.1016/s1470-2045(23)00241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 08/06/2023]
Affiliation(s)
- Riccardo Nocini
- Section of Ears, Nose and Throat, Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy
| | - Luca Tondulli
- UOC of Oncology, Verona University and Hospital Trust (Azienda Ospedaliera Universitaria Integrata-AOUI-Verona), Verona, Italy
| | - Consuelo D'Ambrosio
- Division of Medical Oncology A, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Claudio Luchini
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; ARC-Net Research Centre, University of Verona, Verona, Italy.
| | - Michele Milella
- Section of Innovative Biomedicine-Oncology Area, Department of Engineering for Innovative Medicine, University of Verona, Verona, Italy; UOC of Oncology, Verona University and Hospital Trust (Azienda Ospedaliera Universitaria Integrata-AOUI-Verona), Verona, Italy
| | - Rita T Lawlor
- ARC-Net Research Centre, University of Verona, Verona, Italy; Section of Innovative Biomedicine-Oncology Area, Department of Engineering for Innovative Medicine, University of Verona, Verona, Italy
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9
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Wood CS, Pennel KA, Leslie H, Legrini A, Cameron AJ, Melissourgou-Syka L, Quinn JA, van Wyk HC, Hay J, Roseweir AK, Nixon C, Roxburgh CS, McMillan DC, Biankin AV, Sansom OJ, Horgan PG, Edwards J, Steele CW, Jamieson NB. Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases. Cancer Res 2023; 83:1329-1344. [PMID: 37057593 PMCID: PMC10102851 DOI: 10.1158/0008-5472.can-22-2794] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/02/2022] [Revised: 11/11/2022] [Accepted: 02/07/2023] [Indexed: 04/15/2023]
Abstract
Strong immune responses in primary colorectal cancer correspond with better patient survival following surgery compared with tumors with predominantly stromal microenvironments. However, biomarkers to identify patients with colorectal cancer liver metastases (CRLM) with good prognosis following surgery for oligometastatic disease remain elusive. The aim of this study was to determine the practical application of a simple histological assessment of immune cell infiltration and stromal content in predicting outcome following synchronous resection of primary colorectal cancer and CRLM and to interrogate the underlying functional biology that drives disease progression. Samples from patients undergoing synchronous resection of primary colorectal cancer and CRLM were evaluated in detail through histological assessment, panel genomic and bulk transcriptomic assessment, IHC, and GeoMx spatial transcriptomics (ST) analysis. High immune infiltration of metastases was associated with improved cancer-specific survival. Bulk transcriptomic analysis was confounded by stromal content, but ST demonstrated that the invasive edge of the metastases of long-term survivors was characterized by adaptive immune cell populations enriched for type II IFN signaling and MHC-class II antigen presentation. In contrast, patients with poor prognosis demonstrated increased abundance of regulatory T cells and neutrophils with enrichment of Notch and TGFβ signaling pathways at the metastatic tumor center. In summary, histological assessment can stratify outcomes in patients undergoing synchronous resection of CRLM, suggesting that it has potential as a prognostic biomarker. Furthermore, ST analysis has revealed significant intratumoral and interlesional heterogeneity and identified the underlying transcriptomic programs driving each phenotype. SIGNIFICANCE Spatial transcriptomics uncovers heterogeneity between patients, between matched lesions in the same patient, and within individual lesions and identifies drivers of metastatic progression in colorectal cancer with reactive and suppressed immune microenvironments.
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Affiliation(s)
- Colin S. Wood
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Holly Leslie
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Assya Legrini
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J. Cameron
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Jean A. Quinn
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hester C. van Wyk
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jennifer Hay
- Glasgow Tissue Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | | | - Colin Nixon
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Campbell S.D. Roxburgh
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Donald C. McMillan
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Andrew V. Biankin
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Owen J. Sansom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Paul G. Horgan
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Joanne Edwards
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Colin W. Steele
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Nigel B. Jamieson
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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10
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Paiella S, Azzolina D, Gregori D, Malleo G, Golan T, Simeone DM, Davis MB, Vacca PG, Crovetto A, Bassi C, Salvia R, Biankin AV, Casolino R. A systematic review and meta-analysis of germline BRCA mutations in pancreatic cancer patients identifies global and racial disparities in access to genetic testing. ESMO Open 2023; 8:100881. [PMID: 36822114 PMCID: PMC10163165 DOI: 10.1016/j.esmoop.2023.100881] [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: 11/19/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Germline BRCA1 and BRCA2 mutations (gBRCAm) can inform pancreatic cancer (PC) risk and treatment but most of the available information is derived from white patients. The ethnic and geographic variability of gBRCAm prevalence and of germline BRCA (gBRCA) testing uptake in PC globally is largely unknown. MATERIALS AND METHODS We carried out a systematic review and prevalence meta-analysis of gBRCA testing and gBRCAm prevalence in PC patients stratified by ethnicity. The main outcome was the distribution of gBRCA testing uptake across diverse populations worldwide. Secondary outcomes included: geographic distribution of gBRCA testing uptake, temporal analysis of gBRCA testing uptake in ethnic groups, and pooled proportion of gBRCAm stratified by ethnicity. The study is listed under PROSPERO registration number #CRD42022311769. RESULTS A total of 51 studies with 16 621 patients were included. Twelve of the studies (23.5%) enrolled white patients only, 10 Asians only (19.6%), and 29 (56.9%) included mixed populations. The pooled prevalence of white, Asian, African American, and Hispanic patients tested per study was 88.7%, 34.8%, 3.6%, and 5.2%, respectively. The majority of included studies were from high-income countries (HICs) (64; 91.2%). Temporal analysis showed a significant increase only in white and Asians patients tested from 2000 to present (P < 0.001). The pooled prevalence of gBRCAm was: 3.3% in white, 1.7% in Asian, and negligible (<0.3%) in African American and Hispanic patients. CONCLUSIONS Data on gBRCA testing and gBRCAm in PC derive mostly from white patients and from HICs. This limits the interpretation of gBRCAm for treating PC across diverse populations and implies substantial global and racial disparities in access to BRCA testing in PC.
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Affiliation(s)
- S Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/Totuccio83
| | - D Azzolina
- Department of Environmental and Preventive Science, University of Ferrara, Ferrara
| | - D Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy. https://twitter.com/gregoriDario
| | - G Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/gimalleo
| | - T Golan
- Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - D M Simeone
- Department of Surgery, New York University, New York; Perlmutter Cancer Center, New York University, New York. https://twitter.com/MadameSurgeon
| | - M B Davis
- Department of Surgery and Surgical Oncology, Weill Cornell University, New York; Englander Institute of Precision Medicine, Weill Cornell University, New York, USA. https://twitter.com/MeliD32
| | - P G Vacca
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/pvhdfm
| | - A Crovetto
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/crovetto_a
| | - C Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona
| | - R Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/SalviaRobi
| | - A V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; Faculty of Medicine, South Western Sydney Clinical School, University of NSW, Liverpool, Australia.
| | - R Casolino
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow.
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11
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Dreyer SB, Rae S, Bisset K, Upstill-Goddard R, Gemenetzis G, Johns AL, Dickson EJ, Mittal A, Gill AJ, Duthie F, Pea A, Lawlor RT, Scarpa A, Salvia R, Pulvirenti A, Zerbi A, Marchesi F, McKay CJ, Biankin AV, Samra JS, Chang DK, Jamieson NB. The Impact of Molecular Subtyping on Pathological Staging of Pancreatic Cancer. Ann Surg 2023; 277:e396-e405. [PMID: 36745763 PMCID: PMC9831035 DOI: 10.1097/sla.0000000000005050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The long-term outcomes following surgical resection for pancreatic ductal adenocarcinoma (PDAC) remains poor, with only 20% of patients surviving 5 years after pancreatectomy. Patient selection for surgery remains suboptimal largely due to the absence of consideration of aggressive tumor biology. OBJECTIVE The aim of this study was to evaluate traditional staging criteria for PDAC in the setting of molecular subtypes. METHODS Clinicopathological data were obtained for 5 independent cohorts of consecutive unselected patients, totaling n = 1298, including n = 442 that underwent molecular subtyping. The main outcome measure was disease-specific survival following surgical resection for PDAC stratified according to the American Joint Commission for Cancer (TNM) staging criteria, margin status, and molecular subtype. RESULTS TNM staging criteria and margin status confers prognostic value only in tumors with classical pancreatic subtype. Patients with tumors that are of squamous subtype, have a poor outcome irrespective of favorable traditional pathological staging [hazard ratio (HR) 1.54, 95% confidence interval (CI) 1.04-2.28, P = 0.032]. Margin status has no impact on survival in the squamous subtype (16.0 vs 12.1 months, P = 0.374). There were no differences in molecular subtype or gene expression of tumors with positive resection margin status. CONCLUSIONS Aggressive tumor biology as measured by molecular subtype predicts poor outcome following pancreatectomy for PDAC and should be utilized to inform patient selection for surgery.
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Affiliation(s)
- Stephan B Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Sarah Rae
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
| | - Kirsty Bisset
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
| | - Georgios Gemenetzis
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Amber L Johns
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst and Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Euan J Dickson
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Anubhav Mittal
- Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Anthony J Gill
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst and Garvan Institute of Medical Research, 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
- Northern Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Fraser Duthie
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Antonio Pea
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy; Pancreatic Surgery Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | | | - Alessandro Zerbi
- University of Sydney, Sydney, NSW, Australia
- Department of Biomedical Sciences, Humanitas University, Pieve Emanule, Milan, Italy
| | - Federica Marchesi
- Department of Immunology, IRCCS Humanitas Research Hospital, Rozzano, Italy; and
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Colin J McKay
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jaswinder S Samra
- Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, NSW, Australia
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
- Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, NSW, Australia
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12
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Golder AM, Pennel KAF, Mansouri D, Horgan PG, Roxburgh CSD, Biankin AV, Edwards J, McMillan DC. The association between KRAS mutational status, clinicopathological factors including the preoperative systemic inflammatory response and outcomes in TNM stage I-III colon cancer. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.193] [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: 01/26/2023] Open
Abstract
193 Background: TNM Stage is the most significant prognostic indicator in colon cancer however other tumour and host factors (eg the systemic inflammatory response (SIR)) are associated with long-term outcomes. The relationship between the tumour and the host SIR remains poorly understood. KRAS mutations are associated with adverse outcomes in metastatic disease and have been reported to have an inflammatory phenotype however this has not been widely studied in non-metastatic disease. The present study investigates the association between KRAS mutations, clinicopathological factors including the SIR and outcomes in TNM I-III colon cancer. Methods: Two cohorts of patients (single centre–2000-2008 and regional-2011-2014) undergoing curative surgery for TNM I-III colon cancer in the West of Scotland were shown to be well-matched and combined. Mutational status was analysed retrospectively. The SIR was stratified using Systemic Inflammatory Grade (SIG). 3-year overall and cancer specific survival (OS and CSS) were measured from date of surgery until date of death. Results: 267 patients were identified, 45% with KRAS mutations. KRAS mutations were associated with: right sided (p=0.013), well differentiated (p=0.011), BRAF-wt (p<0.001), PIK3CA-wt (p=0.027) and P53-wt (p=0.002) tumours. A trend was seen between KRAS mutations and female sex (p=0.074) and increased SIG (p=0.072). No association was seen with age, deprivation, smoking, ASA Grade, TNM Stage or EMVI. KRAS mutant status was associated with adverse 3-year CSS (74% versus 82%, p=0.006) and OS (69% versus 78%, p=0.070). For CSS, TNM Stage (HR 2.92, p<0.001), KRAS mutant status (HR 1.64, p=0.050) and Systemic Inflammatory Grade (HR 1.34, p=0.004) were independently prognostic. For OS: age (HR 1.39, p=0.022), TNM Stage (HR 1.50, p=0.016) and SIG (HR 1.25, p=0.005) were independently prognostic. A trend was seen between KRAS mutant status and adverse OS (HR 1.47, p=0.079). Conclusions: The present results show an association between KRAS mutational status and SIG. Furthermore, both of these factors were associated with adverse oncological outcomes. Further investigation into the association between KRAS-mutant status and the local/systemic inflammatory response in TNM I-III colon cancer is warranted. While comprehensive genomic profiling is likely to become increasingly common place, staging the host (SIR) should also be routinely undertaken.
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Affiliation(s)
| | | | - David Mansouri
- Department of Surgery, University of Glasgow, Glasgow, United Kingdom
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13
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Casolino R, Johns AL, Courtot M, Lawlor RT, De Lorenzo F, Horgan D, Mateo J, Normanno N, Rubin M, Stein L, Subbiah V, Westphalen BC, Lawler M, Park K, Perdomo S, Yoshino T, Wu J, Biankin AV. Accelerating cancer omics and precision oncology in health care and research: a Lancet Oncology Commission. Lancet Oncol 2023; 24:123-125. [PMID: 36725142 DOI: 10.1016/s1470-2045(23)00007-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 02/01/2023]
Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
| | - Amber L Johns
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, Australia
| | | | - Rita T Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | | | - Denis Horgan
- European Alliance for Personalised Medicine, Brussels, Belgium
| | - Joaquin Mateo
- ESMO Translational Research and Precision Medicine Working Group, Lugano, Switzerland; Medical Oncology, Vall d'Hebron Institute of Oncology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Mark Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Vivek Subbiah
- ESMO Translational Research and Precision Medicine Working Group, Lugano, Switzerland; Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benedikt C Westphalen
- ESMO Translational Research and Precision Medicine Working Group, Lugano, Switzerland; Department of Medicine III and Comprehensive Cancer Center, University Hospital, LMU Munich, Munich, Germany
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Keunchil Park
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology and Division for the Promotion of Drug and Diagnostic Development, National Cancer Center Hospital East, Kashiwa, Japan
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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14
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, 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K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-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: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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16
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Kotani D, Nakamura Y, Fujisawa T, Bando H, Sakamoto N, Johns AL, Park K, Casolino R, Yoshino T, Biankin AV. ICGC-ARGO precision medicine: an update on targeted therapy based on longitudinal analysis of tumour heterogeneity and evolution in colorectal cancer. Lancet Oncol 2023; 24:20-21. [PMID: 36603918 DOI: 10.1016/s1470-2045(22)00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/17/2022] [Indexed: 01/04/2023]
Affiliation(s)
- Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Takao Fujisawa
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Department of Head and Neck Medical Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Hideaki Bando
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Naoya Sakamoto
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Amber L Johns
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, Australia
| | - Keunchil Park
- Division of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan.
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW, Australia
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17
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Tempero MA, Pelzer U, O'Reilly EM, Winter J, Oh DY, Li CP, Tortora G, Chang HM, Lopez CD, Bekaii-Saab T, Ko AH, Santoro A, Park JO, Noel MS, Frassineti GL, Shan YS, Dean A, Riess H, Van Cutsem E, Berlin J, Philip P, Moore M, Goldstein D, Tabernero J, Li M, Ferrara S, Le Bruchec Y, Zhang G, Lu B, Biankin AV, Reni M. Adjuvant nab-Paclitaxel + Gemcitabine in Resected Pancreatic Ductal Adenocarcinoma: Results From a Randomized, Open-Label, Phase III Trial. J Clin Oncol 2022; 41:2007-2019. [PMID: 36521097 PMCID: PMC10082313 DOI: 10.1200/jco.22.01134] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE This randomized, open-label trial compared the efficacy and safety of adjuvant nab-paclitaxel + gemcitabine with those of gemcitabine for resected pancreatic ductal adenocarcinoma (ClinicalTrials.gov identifier: NCT01964430 ). METHODS We assigned 866 treatment-naive patients with pancreatic ductal adenocarcinoma to nab-paclitaxel (125 mg/m2) + gemcitabine (1,000 mg/m2) or gemcitabine alone to one 30-40 infusion on days 1, 8, and 15 of six 28-day cycles. The primary end point was independently assessed disease-free survival (DFS). Additional end points included investigator-assessed DFS, overall survival (OS), and safety. RESULTS Two hundred eighty-seven of 432 patients and 310 of 434 patients completed nab-paclitaxel + gemcitabine and gemcitabine treatment, respectively. At primary data cutoff (December 31, 2018; median follow-up, 38.5 [interquartile range [IQR], 33.8-43 months), the median independently assessed DFS was 19.4 ( nab-paclitaxel + gemcitabine) versus 18.8 months (gemcitabine; hazard ratio [HR], 0.88; 95% CI, 0.729 to 1.063; P = .18). The median investigator-assessed DFS was 16.6 (IQR, 8.4-47.0) and 13.7 (IQR, 8.3-44.1) months, respectively (HR, 0.82; 95% CI, 0.694 to 0.965; P = .02). The median OS (427 events; 68% mature) was 40.5 (IQR, 20.7 to not reached) and 36.2 (IQR, 17.7-53.3) months, respectively (HR, 0.82; 95% CI, 0.680 to 0.996; P = .045). At a 16-month follow-up (cutoff, April 3, 2020; median follow-up, 51.4 months [IQR, 47.0-57.0]), the median OS (511 events; 81% mature) was 41.8 ( nab-paclitaxel + gemcitabine) versus 37.7 months (gemcitabine; HR, 0.82; 95% CI, 0.687 to 0.973; P = .0232). At the 5-year follow-up (cutoff, April 9, 2021; median follow-up, 63.2 months [IQR, 60.1-68.7]), the median OS (555 events; 88% mature) was 41.8 versus 37.7 months, respectively (HR, 0.80; 95% CI, 0.678 to 0.947; P = .0091). Eighty-six percent ( nab-paclitaxel + gemcitabine) and 68% (gemcitabine) of patients experienced grade ≥ 3 treatment-emergent adverse events. Two patients per study arm died of treatment-emergent adverse events. CONCLUSION The primary end point (independently assessed DFS) was not met despite favorable OS seen with nab-paclitaxel + gemcitabine.
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Affiliation(s)
- Margaret A. Tempero
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Uwe Pelzer
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | | | - Jordan Winter
- Thomas Jefferson University Hospital, Philadelphia, PA
| | - Do-Youn Oh
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Integrated Major in Innovative Medical Science, Seoul National University Graduate School, Seoul, South Korea
| | - Chung-Pin Li
- Division of Clinical Skills Training, Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Giampaolo Tortora
- Azienda Ospedaliera Universitaria, Verona, Italy
- Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Heung-Moon Chang
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Charles D. Lopez
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | | | - Andrew H. Ko
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Armando Santoro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Rozzano, Milan, Italy
| | - Joon Oh Park
- Division of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Marcus S. Noel
- Division of Hematology/Oncology, Georgetown Lombardi Cancer Center, Washington, DC
| | - Giovanni Luca Frassineti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Yan-Shen Shan
- Department of Surgery, Institute of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Andrew Dean
- Department of Medical Oncology, St John of God Subiaco Hospital, Subiaco, Western Australia, Australia
| | - Hanno Riess
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Eric Van Cutsem
- University Hospitals Gasthuisberg/Leuven and KU Leuven, Leuven, Belgium
| | | | - Philip Philip
- Karmanos Cancer Institute, Detroit, MI
- Henry Ford Cancer Institute, Detroit, MI
| | - Malcolm Moore
- Princess Margaret Hospital, Toronto, Ontario, Canada
| | - David Goldstein
- Nelune Cancer Center, Prince of Wales Hospital, University of New South Wales, Randwick, New South Wales, Australia
| | - Josep Tabernero
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), IOB-Quiron, UVic-UCC, Barcelona, Spain
| | | | - Stefano Ferrara
- Celgene Research SLU, a Bristol Myers Squibb Company, Boudry, Switzerland
| | - Yvan Le Bruchec
- Celgene Research SLU, a Bristol Myers Squibb Company, Boudry, Switzerland
| | | | - Brian Lu
- Bristol Myers Squibb, Princeton, NJ
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales, Australia
| | - Michele Reni
- IRCCS Ospedale San Raffaele Vita e Salute University, Milan, Italy
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Ho GY, Kyran EL, Bedo J, Wakefield MJ, Ennis DP, Mirza HB, Vandenberg CJ, Lieschke E, Farrell A, Hadla A, Lim R, Dall G, Vince JE, Chua NK, Kondrashova O, Upstill-Goddard R, Bailey UM, Dowson S, Roxburgh P, Glasspool RM, Bryson G, Biankin AV, Cooke SL, Ratnayake G, McNally O, Traficante N, DeFazio A, Weroha SJ, Bowtell DD, McNeish IA, Papenfuss AT, Scott CL, Barker HE. Epithelial-to-Mesenchymal Transition Supports Ovarian Carcinosarcoma Tumorigenesis and Confers Sensitivity to Microtubule Targeting with Eribulin. Cancer Res 2022; 82:4457-4473. [PMID: 36206301 PMCID: PMC9716257 DOI: 10.1158/0008-5472.can-21-4012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/22/2021] [Revised: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
Ovarian carcinosarcoma (OCS) is an aggressive and rare tumor type with limited treatment options. OCS is hypothesized to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analyzed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated that the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumors. Preclinical OCS models were used to test the efficacy of microtubule-targeting drugs, including eribulin, which has previously been shown to reverse EMT characteristics in breast cancers and induce differentiation in sarcomas. Vinorelbine and eribulin more effectively inhibited OCS growth than standard-of-care platinum-based chemotherapy, and treatment with eribulin reduced mesenchymal characteristics and N-MYC expression in OCS patient-derived xenografts. Eribulin treatment resulted in an accumulation of intracellular cholesterol in OCS cells, which triggered a downregulation of the mevalonate pathway and prevented further cholesterol biosynthesis. Finally, eribulin increased expression of genes related to immune activation and increased the intratumoral accumulation of CD8+ T cells, supporting exploration of immunotherapy combinations in the clinic. Together, these data indicate that EMT plays a key role in OCS tumorigenesis and support the conversion theory for OCS histogenesis. Targeting EMT using eribulin could help improve OCS patient outcomes. SIGNIFICANCE Genomic analyses and preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate antitumor immunity.
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Affiliation(s)
- Gwo Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
| | - Elizabeth L. Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Justin Bedo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- School of Computing and Information Systems, the University of Melbourne, Parkville, Victoria, Australia
| | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
| | - Darren P. Ennis
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Hasan B. Mirza
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Farrell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Anthony Hadla
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Genevieve Dall
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - James E. Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ngee Kiat Chua
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Rosanna Upstill-Goddard
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Ulla-Maja Bailey
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Suzanne Dowson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Patricia Roxburgh
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Rosalind M. Glasspool
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Gareth Bryson
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Andrew V. Biankin
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | - Susanna L. Cooke
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | - Orla McNally
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Nadia Traficante
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, Australia
| | - S. John Weroha
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - David D. Bowtell
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Iain A. McNeish
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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19
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Hendley AM, Urano A, Peng XL, Ashe S, Kerper NR, Phu TA, Ng M, Giacometti S, Berrios DI, Jang GH, Yeh JJ, Gallinger S, Chang DK, Biankin AV, Weaver VM, Kim GE, Dawson DW, Raffai RL, Hebrok M. Abstract C051: Ceramide signaling regulates PDA aggression through exosome reprogramming of the stroma. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c051] [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: 11/17/2022]
Abstract
Abstract
Ceramide is a bioactive lipid signaling molecule that regulates multiple cellular processes influencing pancreatic tumor progression and drug response. The pleiotropic role of ceramide signaling in cancer includes modulation of exosome biogenesis and secretion. Smpd3 encodes an enzyme that generates ceramide through hydrolysis of sphingomyelin. Employing the KPC mouse model of pancreatic cancer, we demonstrated that Smpd3 regulates exosome biogenesis in pancreatic ductal adenocarcinoma (PDA) cells and is pro-tumorigenic during PDA progression. Ablation of Smdp3 in KPC mice significantly extends survival by 19% when compared to KPC; Smpd3wt/wt controls. KPC; Smpd3f/f mice display significantly less PanIN and tumor burden compared to KPC; Smpd3wt/wt controls. Lipidomics analysis of epithelial cell lines generated from end-stage pancreatic tumors of KPC; Smpd3f/f and KPC; Smpd3wt/wt mice demonstrated an alteration in hundreds of lipid species including ceramides, triacylglycerides, sphingomyelins, and phosphatidylcholines. Analysis of RNA-seq data of these epithelial cell lines showed a switching of primary tumors from the predominant more aggressive basal-like subtype seen in KPC; Smpd3wt/wt mice to classical in KPC; Smpd3f/f mice. Pathways analysis of our RNA-seq dataset showed an enrichment for genes involved in cellular mechanics and regulation of the tumor microenvironment. To query if Smpd3-generated exosomes have a direct effect on pancreatic tumor progression, we injected KPC; Smpd3wt/wt and KPC; Smpd3f/f mice with exosomes isolated from KPC; Smpd3f/f and KPC; Smpd3wt/wt PDA cell lines. Injection of exosomes derived from KPC; Smpd3f/f mice significantly extended survival of both Smpd3wt/wt and KPC; Smpd3f/f mice when compared to injection of exosomes isolated from KPC; Smpd3wt/wt mice, suggesting an anti-tumorigenic effect of exosomes isolated from Smpd3-deficient PDA cell lines. We observed a decrease in extracellular matrix collagen abundance and fewer activated stellate cells and fibroblasts in KPC; Smpd3f/f compared to control KPC; Smpd3wt/wt pancreata. Abrogation of Smpd3 expression also affected immune cell infiltration, as demonstrated by a significant increase in iNOS+ F4/80+ double positive macrophages in KPC; Smpd3f/f pancreata when compared to KPC; Smpd3wt/wt pancreata. Loss of Smpd3 resulted in a significant reduction in CD31+ endothelial cells in pancreatic tumors of KPC; Smpd3f/f mice when compared to KPC; Smpd3wt/wt mice, which may influence the ability of chemotherapeutics to enter pancreatic tumors. Our patient data demonstrate that high SMPD3 expression in surgically resected, treatment naive PDA significantly correlated with longer patient survival when patients received adjuvant chemotherapy, more than 95% of which was gemcitabine. Collectively, our data show that ceramide-dependent exosomes promote tumorigenesis, specifically activation of stellate cells and fibroblasts – which may in turn induce a stiff, fibrotic, proinflammatory tumor microenvironment that also impedes vasculature formation.
Citation Format: Audrey M. Hendley, Atsushi Urano, Xianlu L. Peng, Sudipta Ashe, Natanya R. Kerper, Tuan A. Phu, Martin Ng, Simone Giacometti, David I. Berrios, Gun H. Jang, Jen J. Yeh, Steven Gallinger, David K. Chang, Andrew V. Biankin, Valerie M. Weaver, Grace E. Kim, David W. Dawson, Robert L. Raffai, Matthias Hebrok. Ceramide signaling regulates PDA aggression through exosome reprogramming of the stroma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C051.
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Affiliation(s)
| | - Atsushi Urano
- 1University of California San Francisco, San Francisco, CA,
| | | | - Sudipta Ashe
- 1University of California San Francisco, San Francisco, CA,
| | | | - Tuan A. Phu
- 1University of California San Francisco, San Francisco, CA,
| | - Martin Ng
- 1University of California San Francisco, San Francisco, CA,
| | | | | | | | - Jen J. Yeh
- 2University of North Carolina, Chapel Hill, NC,
| | | | | | | | | | - Grace E. Kim
- 1University of California San Francisco, San Francisco, CA,
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Canel M, Slawinska A, Lonergan DW, Kallor AA, Upstill-Goddard R, Davidson C, von Kriegsheim A, Biankin AV, Bryron A, Alfaro J, Serrels A. Abstract C019: FAK suppresses antigen processing and presentation to promote immune evasion in pancreatic cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c019] [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: 11/17/2022]
Abstract
Abstract
Immunotherapy for the treatment of Pancreatic Ductal Adenocarcinoma (PDAC) has shown limited efficacy. Poor CD8 T-cell infiltration, low neoantigen load and a highly immunosuppressive tumor microenvironment are key factors that contribute to this lack of response. Here, we identify a novel role for Focal Adhesion Kinase (FAK) in regulating type-II interferon signalling in human and murine PDAC cells and tumors, leading to suppression of antigen processing and presentation pathways critical for T-cell tumor recognition. We find that FAK loss promotes expression of the immunoproteasome and MHC-I, resulting in a significant increase in the diversity of antigens presented by FAK-/- PDAC cells. We show that regulation of the immunoproteasome subunit Psmb8 (β5i) is a critical determinant of this response, optimising the physicochemical properties of the peptide repertoire for high-affinity binding to MHC-I. Expression of the immunoproteasome and MHC-I can be further amplified in a STAT1-dependent manner via co-depletion of FAK and STAT3, leading to extensive CD8 T-cell infiltration into PDAC tumors and further restraint of tumor growth. Regulation of antigen processing and presentation by FAK preferentially occurs in human and murine PDAC cells and tumors of the classical/progenitor molecular subtype, further suggesting that precision medicine approaches based on molecular subtyping should be integrated into current and future clinical testing of FAK targeted therapies for the treatment of pancreatic cancer.
Citation Format: Marta Canel, Aleksandra Slawinska, David W. Lonergan, Ashwin A. Kallor, Rosie Upstill-Goddard, Catherine Davidson, Alex von Kriegsheim, Andrew V. Biankin, Adam Bryron, Javier Alfaro, Alan Serrels. FAK suppresses antigen processing and presentation to promote immune evasion in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C019.
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Affiliation(s)
- Marta Canel
- 1University of Edinburgh, Edinburgh, United Kingdom,
| | | | | | | | | | | | | | | | - Adam Bryron
- 1University of Edinburgh, Edinburgh, United Kingdom,
| | | | - Alan Serrels
- 1University of Edinburgh, Edinburgh, United Kingdom,
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Reiss DJ, Browne A, Fox B, Ratushnyy AV, Wang M, Biankin AV, Lila T. Abstract C085: Spatial arrangements of immune cells of the pancreatic ductal adenocarcinoma tumor microenvironment correlated with outcomes in the phase 3 APACT trial. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c085] [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: 11/17/2022]
Abstract
Abstract
Introduction The newly diagnosed pancreatic ductal adenocarcinoma (PDAC) population has a high unmet need for effective treatments, with median survival of < 1 year. The phase 3 APACT (Adjuvant Pancreatic Adenocarcinoma Clinical Trial) evaluated the use of adjuvant nab-paclitaxel plus gemcitabine vs. gemcitabine in 866 patients with surgically resected PDAC. We explored the tumor microenvironment (TME) of >500 baseline resected APACT tumors to identify TME features that are associated with adverse outcomes. Methods Biopsy analyses included RNA-seq, DNA-seq, and multiplexed immunohistochemistry (mIHC). We quantified, for 533 patient biopsies, via mIHC the spatial arrangement of 7 immune cell types and 2 checkpoint markers relative to tumor and nontumor regions, and pairwise colocalization relative to each other. We identified combinations of biomarkers that correlate significantly with molecular signatures, predefined patient subsets, and overall survival (OS). Hazard ratios (HR) and p-values were computed via a Cox proportional hazards regression model which included resection and lymph node status as covariates. Significantly differentially-expressed transcripts were associated with biomarkers derived from the mIHC via unpaired t-test. Results Higher densities of CD8+ T cells within tumor regions correlated with longer OS (hazard ratio HR=0.76; p=0.03), and higher overall densities of CD163+ macrophages correlated with shorter OS (HR=1.44; p=0.006). We furthermore identified a patient subset (n=72) with a combination of higher CD8+ T cell and lower CD163+ macrophage densities that had a strikingly significant decreased HR of 0.46 (p=0.009). Moreover, patients with a high degree of spatial colocalization between CD8+ T cells and dual-positive CMAF+CD163+ M2-like macrophages observed a significant increased HR of 1.51 (p=0.0006), a biomarker only surpassed by nodal status in significance of correlation with OS (HR=1.9; p=0.00015). While this cellular colocalization was computed to be independent of cell densities, we found that the association of this colocalized pair of cell types with shorter OS was most significant for patients with lower overall CD8+ T cell densities (HR=1.84; p=0.0004). We further identified differentially regulated transcripts associated with this interaction and found specific putative ligand-receptor pairs that were also associated with lower OS. Conclusion A combination of greater infiltration of CD8+ cytotoxic T cells and lower infiltration of macrophages is associated with longer OS in the APACT trial. Moreover, the spatial colocalization between CD8+ T cells and CMAF+ M2 macrophages is associated with shorter OS. These findings were observed across both treatment arms of the study. Future investigation of this apparent interaction, and associated differentially expressed transcripts, may inform management of patients with pancreatic adenocarcinoma and increase effectiveness of PDAC therapies.
Citation Format: David J. Reiss, Andrew Browne, Brian Fox, Alexander V. Ratushnyy, Maria Wang, Andrew V. Biankin, Thomas Lila. Spatial arrangements of immune cells of the pancreatic ductal adenocarcinoma tumor microenvironment correlated with outcomes in the phase 3 APACT trial [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C085.
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22
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Beer PA, Biankin AV. Bridging the implementation gap: delivering complex genomic analysis for routine cancer care. Ann Oncol 2022; 33:857-859. [PMID: 35931317 DOI: 10.1016/j.annonc.2022.06.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER UNITED KINGDOM; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool NSW 2170, AUSTRALIA
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Milella M, Lawlor RT, Luchini C, Johns AL, Casolino R, Yoshino T, Biankin AV, Scarpa A. ICGC-ARGO precision medicine: an update on familial matters in pancreatic cancer. Lancet Oncol 2022; 23:991-992. [DOI: 10.1016/s1470-2045(22)00448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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Casolino R, Corbo V, Beer P, Hwang CI, Paiella S, Silvestri V, Ottini L, Biankin AV. Germline Aberrations in Pancreatic Cancer: Implications for Clinical Care. Cancers (Basel) 2022; 14:3239. [PMID: 35805011 PMCID: PMC9265115 DOI: 10.3390/cancers14133239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis and represents a major public health issue, as both its incidence and mortality are expecting to increase steeply over the next years. Effective screening strategies are lacking, and most patients are diagnosed with unresectable disease precluding the only chance of cure. Therapeutic options for advanced disease are limited, and the treatment paradigm is still based on chemotherapy, with a few rare exceptions to targeted therapies. Germline variants in cancer susceptibility genes-particularly those involved in mechanisms of DNA repair-are emerging as promising targets for PDAC treatment and prevention. Hereditary PDAC is part of the spectrum of several syndromic disorders, and germline testing of PDAC patients has relevant implications for broad cancer prevention. Germline aberrations in BRCA1 and BRCA2 genes are predictive biomarkers of response to poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitor olaparib and platinum-based chemotherapy in PDAC, while mutations in mismatch repair genes identify patients suitable for immune checkpoint inhibitors. This review provides a timely and comprehensive overview of germline aberrations in PDAC and their implications for clinical care. It also discusses the need for optimal approaches to better select patients for PARP inhibitor therapy, novel therapeutic opportunities under clinical investigation, and preclinical models for cancer susceptibility and drug discovery.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK; (P.B.); (A.V.B.)
- Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
- NHS Greater Glasgow and Clyde, Glasgow G4 0SF, UK
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy;
| | - Philip Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK; (P.B.); (A.V.B.)
| | - Chang-il Hwang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA;
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA 95817, USA
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona Hospital Trust, 37134 Verona, Italy;
| | - Valentina Silvestri
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (V.S.); (L.O.)
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (V.S.); (L.O.)
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK; (P.B.); (A.V.B.)
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
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25
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Beer PA, Cooke SL, Li XS, Biankin AV. Abstract 1176: Leveraging the GENIE dataset to distinguish somatic cancer drivers from passenger events in routine oncology practice. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1176] [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
Distinguishing genomic events that drive cancer (drivers) from inconsequential damage (passengers) is key to matching patients with biomarker-associated therapies and clinical trials. Whilst population level genomic analyses can estimate the proportion of driver events within a given gene, they cannot categorize individual variants. Reliable annotation remains a significant barrier to unlocking the full utility of cancer genomics. GENIE (Genomics Evidence Neoplasia Information Exchange) data was used to generate codon recurrence scores (CRS) for known cancer genes. GENIE was parsed to remove duplicates, sequencing artefact (recurrent variants reported by one institution, invariably associated with amplicon-based sequencing) and hypermutated samples (>15 mutations per megabase). For missense mutations, a codon recurrence of ≥10 was used to classify driver mutations.
The table shows proportion of missense mutations classified as drivers by gene and cancer type, comparing population-based non-synonymous to synonymous mutation ratio; dN/dS (Martincorena 2017, PMID 29056346) with assessment of individual variants by CRS. This comparison demonstrates a high degree of concordance. For a few genes, CRS under called driver mutations (ie VHL in renal cancer) likely due to reduced power with small sample numbers. Importantly, CRS is able to assign driver status to individual missense mutations. Comparison with informatic analyses (PMIDs 28115009, 29247016, 30365005, 31034466) showed equivalent or superior performance of the GENIE approach. These findings demonstrate how a large (and expanding) real-world dataset can be used to predict the driver status of somatic missense mutations at the n=1 variant level. This process is amenable to implementation as a rules-based classification process for somatic missense mutations as part of an automated annotation pipeline.
+corrected dN/dS ratio not significantly different from one. Pan- cancer Breast cancer Renal cancer Lung adenocarcinoma Gene dN/dS CRS dN/dS CRS dN/dS CRS dN/dS CRS BRAF 91% 76% <50% 34% <50% 33% 88% 74% PIK3CA 94% 89% 97% 95% 65%+ 84% 86% 76% KRAS 97% 98% 90% 95% 80%+ 100% 99% 99% IDH1 96% 81% <50% 16% <50% n/a <50% 47% EGFR 52% 51% <50% 7% <50% 17% 88% 81% TP53 96% 96% 99% 97% 82%+ 89% 96% 95% PTEN 94% 54% 90% 59% <50% 47% 70% 32% VHL 80% 22% <50% 8% 99% 33% <50% 0% CDKN2A 50% 51% <50% 43% <50% n/a <50% 46% APC <50% 1% <50% 1% <50% n/a <50% 1% RB1 <50% 6% <50% 6% <50% 50% <50% 5% ARID1A <50% 3% <50% 2% <50% 6% <50% 2% KMT2C <50% 0% <50% 0% <50% n/a <50% 0%
Citation Format: Philip A. Beer, Susanna L. Cooke, Xuan Shirley Li, Andrew V. Biankin. Leveraging the GENIE dataset to distinguish somatic cancer drivers from passenger events in routine oncology practice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1176.
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Patel M, Pennel KAF, Quinn JA, Hood H, Chang DK, Biankin AV, Rebus S, Roseweir AK, Park JH, Horgan PG, McMillan DC, Edwards J. Spatial expression of IKK-alpha is associated with a differential mutational landscape and survival in primary colorectal cancer. Br J Cancer 2022; 126:1704-1714. [PMID: 35173303 PMCID: PMC9174220 DOI: 10.1038/s41416-022-01729-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/31/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND To understand the relationship between key non-canonical NF-κB kinase IKK-alpha(α), tumour mutational profile and survival in primary colorectal cancer. METHODS Immunohistochemical expression of IKKα was assessed in a cohort of 1030 patients who had undergone surgery for colorectal cancer using immunohistochemistry. Mutational tumour profile was examined using a customised gene panel. Immunofluorescence was used to identify the cellular location of punctate IKKα expression. RESULTS Two patterns of IKKα expression were observed; firstly, in the tumour cell cytoplasm and secondly as discrete 'punctate' areas in a juxtanuclear position. Although cytoplasmic expression of IKKα was not associated with survival, high 'punctate' IKKα expression was associated with significantly reduced cancer-specific survival on multivariate analysis. High punctate expression of IKKα was associated with mutations in KRAS and PDGFRA. Dual immunofluorescence suggested punctate IKKα expression was co-located with the Golgi apparatus. CONCLUSIONS These results suggest the spatial expression of IKKα is a potential biomarker in colorectal cancer. This is associated with a differential mutational profile highlighting possible distinct signalling roles for IKKα in the context of colorectal cancer as well as potential implications for future treatment strategies using IKKα inhibitors.
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Affiliation(s)
- Meera Patel
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Kathryn A F Pennel
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jean A Quinn
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Hannah Hood
- School of Medicine, Wolfson Medical School Building, University of Glasgow, Glasgow, UK
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Royal Infirmary, Glasgow, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Selma Rebus
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Antonia K Roseweir
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - James H Park
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Royal Infirmary, Glasgow, UK
| | - Paul G Horgan
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Royal Infirmary, Glasgow, UK
| | - Donald C McMillan
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Royal Infirmary, Glasgow, UK
| | - Joanne Edwards
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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Kotani D, Nakamura Y, Fujisawa T, Bando H, Sakamoto N, Johns AL, Park K, Casolino R, Yoshino T, Biankin AV. ICGC-ARGO precision medicine: targeted therapy according to longitudinal assessment of tumour heterogeneity in colorectal cancer. Lancet Oncol 2022; 23:463-464. [PMID: 35358454 DOI: 10.1016/s1470-2045(22)00142-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
Affiliation(s)
- Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Takao Fujisawa
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Department of Head and Neck Medical Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Hideaki Bando
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Naoya Sakamoto
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Amber L Johns
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, Australia
| | - Keunchil Park
- Division of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Raffaella Casolino
- Department of Medicine, University of Verona, and School of Medicine and University Hospital Trust of Verona (AOUI Verona), Verona, Italy; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan.
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW, Australia
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Jamieson NB, Legrini A, Leslie H, Dreyer S, Biankin AV, Chang DKF. High-plex proteomic prognostic marker discovery for patients with pancreatic cancer adenocarcinoma using digital spatial profiling. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.611] [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: 11/20/2022] Open
Abstract
611 Background: The long-term outcomes following surgical resection for Pancreatic Ductal Adenocarcinoma (PDAC) remain poor, with only 20% of patients surviving 5 years after pancreatectomy. With its immune-privileged nature, starting from the early pre-neoplastic state, it appears to escape easily from the antitumor immune response. Despite rationale for targeting immune pathways in PDAC, there has been little benefit observed at this point. The aim of the current study was to interrogate immune landscape of PDAC utilising the Nanostring GeoMx Digital Spatial Profiler (DSP), a state-of-the art analysis platform enabling Hi-plex proteomic characterisation whilst maintaining tumor microenvironment (TME) topographical features. Methods: We assessed Formalin Fixed Paraffin Embedded (FFPE) tumor samples from 28 treatment-naive PDAC cases represented in a multi-regional tissue microarray (TMA) for which extensive IHC, molecular, genomic characterisation and clinicopathological follow-up data is available. Following multiplex IHC staining for DAPI, panCK, aSMA and CD3 to guide region selection, we employed the GeoMx DSP system (NanoString) to select regions within multiple TMA cores. We quantified 60 immune markers simultaneously in multiple tissue compartments defined by immunofluorescence co-localization including (tumor [panCK+ve], immune stroma (PanCK-ve]. Data analysis was performed by a combination of DSP analysis suite and custom R pipeline. Results: The spatially informed variable assessment by DSP was validated by both regression and variable prognostication compared with IHC for stromal CD3, CD8 CD68 in near serial TMA PDAC sections. Unsupervised analysis of DSP proteome data in the panCK-negative regions identified an immune poor group associated with shorter Overall Survival (OS) (13.0 versus 31.1months, P = 0.005). When transcriptomic subtype was considered, the checkpoint inhibitor B7-H3 was significantly upregulated in the squamous subtype tumours versus the classical group (Log2: 1.63, P = 0.001). Patients with high B7-H3 expression, using a median expression cut-off, were associated with shorter OS on multivariate analysis (Hazard Ratio: 4.16, P = 0.01) including lymph node and resection margin status, a finding that was validated in an external cohort at the transcriptome level. Conclusions: This pilot scale discovery study shows the potential of the Nanostring DSP technology in the identification of spatially-informed biomarkers with prognostic relevance in biopsy sized samples from treatment-naive PDAC. We identified a number of relevant candidate immune predictors in spatial context that are currently undergoing validation in larger independent cohorts and the neoadjuvant setting. Future studies will apply this technology to pre- and post-treatment biopsy samples.
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Affiliation(s)
- Nigel Balfour Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Holly Leslie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, Glasgow, United Kingdom
| | - Stephan Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Kuang-Fu Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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Golder AM, Pennel KAF, Mansouri D, Horgan PG, Roxburgh CSD, Biankin AV, Edwards J, McMillan DC. The association between tumour sidedness, clinicopathological characteristics and outcomes in patients undergoing curative resection for colon cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.148] [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: 11/20/2022] Open
Abstract
148 Background: Right-sided colon cancer is associated with worse outcomes than left-sided disease, likely due to an association between tumour/host factors and tumour sidedness. The present study analyses the association between tumour sidedness, clinicopathological features and common mutations to better understand this discrepancy in outcomes. Methods: The association between tumour sidedness, clinicopathological characteristics and survival was examined within a cohort of patients undergoing curative surgery for TNM I-III colon cancer. Results: 3,419 patients were identified. 54% of cases were right-sided and associated with worse 3-year OS/CSS. On multivariate analysis for clinical factors: sex (OR 0.63), Systemic Inflammatory Grade (SIG), anaemia and differentiation (OR 0.80/0.31/0.57) were associated with T3 cancer sidedness and: sex, anaemia and differentiation (OR 0.61/0.46/0.57) were associated with T4 cancer sidedness. On further MVA including mutational factors anaemia/BRAF status remained significant in T3/T4 cancer respectively (OR 0.08/0.09). BRAF mutant status was associated with SIG in all patients/T3 disease (p=0.046/0.016). Conclusions: Worse outcomes seen in right-sided colon cancer are likely explained predominantly by factors including tumour stage, SIG, anaemia and BRAF mutational status. BRAF mutations are associated with the Systemic Inflammatory Response and further research is required to better understand this relationship taking into the tumour microenvironment, microsatellite instability.[Table: see text]
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Affiliation(s)
| | | | - David Mansouri
- Department of Surgery, University of Glasgow, Glasgow, United Kingdom
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Milella M, Luchini C, Lawlor RT, Johns AL, Casolino R, Yoshino T, Biankin AV, Biankin AV, Stein LD, Park K, Lawlor RT, Johns AL, Korbel JO, Zeps N, Rubin MA, Marra MA, Elemento O, Gallinger S, Tuveson D, Trumper L, Koch R, Scarpa A, Brennan P, Pilarsky C, Nikolaev S, Yoon SS, Lee ES, Shibata T, Wu X, Wu J, Zhan Q, Poon W, Yoshino T, Al-Kuraya KS, Eeles R, Fitzgerald R, Caldas C, Abraham J, Chang DK. ICGC-ARGO precision medicine: familial matters in pancreatic cancer. Lancet Oncol 2022; 23:25-26. [DOI: 10.1016/s1470-2045(21)00703-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
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Dreyer SB, Upstill-Goddard R, Legrini A, Biankin AV, Jamieson NB, Chang DK, Jamieson NB, Chang DK. Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence. Gastroenterology 2022; 162:320-324.e4. [PMID: 34534536 PMCID: PMC8721486 DOI: 10.1053/j.gastro.2021.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Stephan B Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom.
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom
| | - Assya Legrini
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom and West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom.
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom.
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom and West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom.
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom and West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom.
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Casolino R, Biankin AV, Corbo V, Upadhaya S, Xin YJ, Torroni L, Braconi C, Cappello P, Carbone C, Chang DK, Giovannetti E, Lovisa S, Martini M, Pea A, Piro G, Milella M, Scarpa A, Bassi C, Campbell J. Impact of COVID-19 on Pancreatic Cancer Research and the Path Forward. Gastroenterology 2021; 161:1758-1763. [PMID: 34389342 PMCID: PMC8424064 DOI: 10.1053/j.gastro.2021.06.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/07/2023]
Affiliation(s)
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, Australia.
| | | | - Vincenzo Corbo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Italy; ARC-Net Research Centre, University of Verona, Italy
| | - Samik Upadhaya
- Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA
| | - Yu Jia Xin
- Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA
| | - Lorena Torroni
- Department of Diagnostics and Public Health, Unit of Epidemiology and Medical Statistics, University and Hospital Trust of Verona, Italy
| | - Chiara Braconi
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, UK; Beatson West of Scotland Cancer centre, Glasgow, UK
| | - Paola Cappello
- Center for Experimental Research and Medical Studies (CERMS), AOU Città della Salute e della Scienza di Torino, University of Torino, Italy; Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center (MBC), University of Torino, Italy
| | - Carmine Carbone
- Comprehensive Cancer Center-Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Sara Lovisa
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (MI), Italy; Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), Italy
| | - Miriam Martini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center (MBC), University of Torino, Italy
| | - Antonio Pea
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Italy
| | - Geny Piro
- Comprehensive Cancer Center-Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Michele Milella
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Italy; ARC-Net Research Centre, University of Verona, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Italy
| | - Jay Campbell
- Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA
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Carotenuto P, Amato F, Lampis A, Rae C, Hedayat S, Previdi MC, Zito D, Raj M, Guzzardo V, Sclafani F, Lanese A, Parisi C, Vicentini C, Said-Huntingford I, Hahne JC, Hallsworth A, Kirkin V, Young K, Begum R, Wotherspoon A, Kouvelakis K, Azevedo SX, Michalarea V, Upstill-Goddard R, Rao S, Watkins D, Starling N, Sadanandam A, Chang DK, Biankin AV, Jamieson NB, Scarpa A, Cunningham D, Chau I, Workman P, Fassan M, Valeri N, Braconi C. Modulation of pancreatic cancer cell sensitivity to FOLFIRINOX through microRNA-mediated regulation of DNA damage. Nat Commun 2021; 12:6738. [PMID: 34795259 PMCID: PMC8602334 DOI: 10.1038/s41467-021-27099-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/06/2020] [Accepted: 10/29/2021] [Indexed: 01/17/2023] Open
Abstract
FOLFIRINOX, a combination of chemotherapy drugs (Fluorouracil, Oxaliplatin, Irinotecan -FOI), provides the best clinical benefit in pancreatic ductal adenocarcinoma (PDAC) patients. In this study we explore the role of miRNAs (MIR) as modulators of chemosensitivity to identify potential biomarkers of response. We find that 41 and 84 microRNA inhibitors enhance the sensitivity of Capan1 and MiaPaCa2 PDAC cells respectively. These include a MIR1307-inhibitor that we validate in further PDAC cell lines. Chemotherapy-induced apoptosis and DNA damage accumulation are higher in MIR1307 knock-out (MIR1307KO) versus control PDAC cells, while re-expression of MIR1307 in MIR1307KO cells rescues these effects. We identify binding of MIR1307 to CLIC5 mRNA through covalent ligation of endogenous Argonaute-bound RNAs cross-linking immunoprecipitation assay. We validate these findings in an in vivo model with MIR1307 disruption. In a pilot cohort of PDAC patients undergoing FOLFIRONX chemotherapy, circulating MIR1307 correlates with clinical outcome.
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Affiliation(s)
- Pietro Carotenuto
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
- TIGEM - Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Francesco Amato
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Colin Rae
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Somaieh Hedayat
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Maria C Previdi
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Domenico Zito
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Maya Raj
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | | | | | - Andrea Lanese
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - Claudia Parisi
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - Caterina Vicentini
- ARC-Net Research Centre and Department of Diagnostics and Public Health, Section of Pathology, , University of Verona, Verona, Italy
| | | | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Albert Hallsworth
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Vladimir Kirkin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Kate Young
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - Ruwaida Begum
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | | | | | | | | | | | - Sheela Rao
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - David Watkins
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | | | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - David K Chang
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Andrew V Biankin
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW, Australia
| | - Nigel B Jamieson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Aldo Scarpa
- ARC-Net Research Centre and Department of Diagnostics and Public Health, Section of Pathology, , University of Verona, Verona, Italy
| | | | - Ian Chau
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - Paul Workman
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padua, Italy
- Veneto Institute of Oncology (IOV-IRCCS), Padua, Italy
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Trust, London and Surrey, London, UK
| | - Chiara Braconi
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
- The Royal Marsden NHS Trust, London and Surrey, London, UK.
- Beatson West of Scotland Cancer Centre, Glasgow, UK.
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34
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Murphy KJ, Reed DA, Vennin C, Conway JRW, Nobis M, Yin JX, Chambers CR, Pereira BA, Lee V, Filipe EC, Trpceski M, Ritchie S, Lucas MC, Warren SC, Skhinas JN, Magenau A, Metcalf XL, Stoehr J, Major G, Parkin A, Bidanel R, Lyons RJ, Zaratzian A, Tayao M, Da Silva A, Abdulkhalek L, Gill AJ, Johns AL, Biankin AV, Samra J, Grimmond SM, Chou A, Goetz JG, Samuel MS, Lyons JG, Burgess A, Caldon CE, Horvath LG, Daly RJ, Gadegaard N, Wang Y, Sansom OJ, Morton JP, Cox TR, Pajic M, Herrmann D, Timpson P. Intravital imaging technology guides FAK-mediated priming in pancreatic cancer precision medicine according to Merlin status. Sci Adv 2021; 7:eabh0363. [PMID: 34586840 PMCID: PMC8480933 DOI: 10.1126/sciadv.abh0363] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/06/2021] [Indexed: 05/05/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic, chemoresistant malignancy and is characterized by a dense, desmoplastic stroma that modulates PDAC progression. Here, we visualized transient manipulation of focal adhesion kinase (FAK), which integrates bidirectional cell-environment signaling, using intravital fluorescence lifetime imaging microscopy of the FAK-based Förster resonance energy transfer biosensor in mouse and patient-derived PDAC models. Parallel real-time quantification of the FUCCI cell cycle reporter guided us to improve PDAC response to standard-of-care chemotherapy at primary and secondary sites. Critically, micropatterned pillar plates and stiffness-tunable matrices were used to pinpoint the contribution of environmental cues to chemosensitization, while fluid flow–induced shear stress assessment, patient-derived matrices, and personalized in vivo models allowed us to deconstruct how FAK inhibition can reduce PDAC spread. Last, stratification of PDAC patient samples via Merlin status revealed a patient subset with poor prognosis that are likely to respond to FAK priming before chemotherapy.
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Affiliation(s)
- Kendelle J. Murphy
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Daniel A. Reed
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Claire Vennin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Oncode Institute, Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - James R. W. Conway
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Max Nobis
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Julia X. Yin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Cecilia R. Chambers
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Brooke A. Pereira
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Victoria Lee
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Elysse C. Filipe
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael Trpceski
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Shona Ritchie
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Morghan C. Lucas
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sean C. Warren
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Joanna N. Skhinas
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Astrid Magenau
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Xanthe L. Metcalf
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Janett Stoehr
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Gretel Major
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Ashleigh Parkin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Romain Bidanel
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Ruth J. Lyons
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Anaiis Zaratzian
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Michael Tayao
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Andrew Da Silva
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Lea Abdulkhalek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Australian Pancreatic Genome Initiative (APGI)
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Oncode Institute, Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, NSW 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, NSW 2064, Australia
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
- Department of Anatomical Pathology, SydPath, Darlinghurst, NSW 2010, Australia
- INSERM UMR, Tumour Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Centre for Cancer Biology, SA Pathology and University of South Australia, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Dermatology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Cancer Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
- ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, Concord Clinical School, University of Sydney, Sydney, NSW 2000, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW 2006, Australia
- Cancer Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Australian Pancreatic Cancer Matrix Atlas (APMA)
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Oncode Institute, Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, NSW 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, NSW 2064, Australia
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
- Department of Anatomical Pathology, SydPath, Darlinghurst, NSW 2010, Australia
- INSERM UMR, Tumour Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Centre for Cancer Biology, SA Pathology and University of South Australia, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Dermatology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Cancer Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
- ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, Concord Clinical School, University of Sydney, Sydney, NSW 2000, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW 2006, Australia
- Cancer Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Anthony J. Gill
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, NSW 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, NSW 2064, Australia
| | - Amber L. Johns
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
| | - Andrew V. Biankin
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Jaswinder Samra
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Sean M. Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Angela Chou
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, NSW 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, NSW 2064, Australia
- Department of Anatomical Pathology, SydPath, Darlinghurst, NSW 2010, Australia
| | - Jacky G. Goetz
- INSERM UMR, Tumour Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Michael S. Samuel
- Centre for Cancer Biology, SA Pathology and University of South Australia, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - J. Guy Lyons
- Dermatology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Cancer Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew Burgess
- ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, Concord Clinical School, University of Sydney, Sydney, NSW 2000, Australia
| | - C. Elizabeth Caldon
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Lisa G. Horvath
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW 2006, Australia
| | - Roger J. Daly
- Cancer Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Nikolaj Gadegaard
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Yingxiao Wang
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Owen J. Sansom
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Jennifer P. Morton
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Thomas R. Cox
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Marina Pajic
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - David Herrmann
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
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35
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Casolino R, Biankin AV. COVID-19 provides an opportunity to transform cancer research. Cancer Cell 2021; 39:1169-1170. [PMID: 34433075 PMCID: PMC8318678 DOI: 10.1016/j.ccell.2021.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, UK; Department of Medicine, University and Hospital Trust of Verona, Italy.
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, Australia
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36
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Casolino R, Paiella S, Azzolina D, Beer PA, Corbo V, Lorenzoni G, Gregori D, Golan T, Braconi C, Froeling FEM, Milella M, Scarpa A, Pea A, Malleo G, Salvia R, Bassi C, Chang DK, Biankin AV. Homologous Recombination Deficiency in Pancreatic Cancer: A Systematic Review and Prevalence Meta-Analysis. J Clin Oncol 2021; 39:2617-2631. [PMID: 34197182 PMCID: PMC8331063 DOI: 10.1200/jco.20.03238] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [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: 11/02/2020] [Revised: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To analyze the prevalence of homologous recombination deficiency (HRD) in patients with pancreatic ductal adenocarcinoma (PDAC). MATERIALS AND METHODS We conducted a systematic review and meta-analysis of the prevalence of HRD in PDAC from PubMed, Scopus, and Cochrane Library databases, and online cancer genomic data sets. The main outcome was pooled prevalence of somatic and germline mutations in the better characterized HRD genes (BRCA1, BRCA2, PALB2, ATM, ATR, CHEK2, RAD51, and the FANC genes). The secondary outcomes were prevalence of germline mutations overall, and in sporadic and familial cases; prevalence of germline BRCA1/2 mutations in Ashkenazi Jewish (AJ); and prevalence of HRD based on other definitions (ie, alterations in other genes, genomic scars, and mutational signatures). Random-effects modeling with the Freeman-Tukey transformation was used for the analyses. PROSPERO registration number: (CRD42020190813). RESULTS Sixty studies with 21,842 participants were included in the systematic review and 57 in the meta-analysis. Prevalence of germline and somatic mutations was BRCA1: 0.9%, BRCA2: 3.5%, PALB2: 0.2%, ATM: 2.2%, CHEK2: 0.3%, FANC: 0.5%, RAD51: 0.0%, and ATR: 0.1%. Prevalence of germline mutations was BRCA1: 0.9% (2.4% in AJ), BRCA2: 3.8% (8.2% in AJ), PALB2: 0.2%, ATM: 2%, CHEK2: 0.3%, and FANC: 0.4%. No significant differences between sporadic and familial cases were identified. HRD prevalence ranged between 14.5%-16.5% through targeted next-generation sequencing and 24%-44% through whole-genome or whole-exome sequencing allowing complementary genomic analysis, including genomic scars and other signatures (surrogate markers of HRD). CONCLUSION Surrogate readouts of HRD identify a greater proportion of patients with HRD than analyses limited to gene-level approaches. There is a clear need to harmonize HRD definitions and to validate the optimal biomarker for treatment selection. Universal HRD screening including integrated somatic and germline analysis should be offered to all patients with PDAC.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Danila Azzolina
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
- Research Support Unit, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Philip A. Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Vincenzo Corbo
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Giulia Lorenzoni
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
| | - Dario Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
| | - Talia Golan
- The Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - Chiara Braconi
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Fieke E. M. Froeling
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michele Milella
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Antonio Pea
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Giuseppe Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
- Faculty of Medicine, South Western Sydney Clinical School, University of NSW, Liverpool, Australia
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Normanno N, Apostolides K, de Lorenzo F, Beer PA, Henderson R, Sullivan R, Biankin AV, Horgan D, Lawler M. Cancer Biomarkers in the era of precision oncology: Addressing the needs of patients and health systems. Semin Cancer Biol 2021; 84:293-301. [PMID: 34389490 DOI: 10.1016/j.semcancer.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 12/09/2020] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Cancer Biomarkers are the key to unlocking the promise of precision oncology, selecting which patients will respond to a more personalised treatment while sparing non-responders the therapy-related toxicity. In this paper, we highlight the primacy of cancer biomarkers, but focus on their importance to patients and to health systems. We also highlight how cancer biomarkers represent value for money. We emphasise the need for cancer biomarkers infrastructure to be embedded into European health systems. We also highlight the need to deploy multiple biomarker testing to deliver the optimal benefit for patients and health systems and consider cancer biomarkers from the perspective of cost, value and regulation. Cancer biomarkers must also be situated in the context of the upcoming In Vitro Diagnostics Regulation, which may pose certain challenges (e.g. non-compliance of laboratory developed tests, leading to cancer biomarker shortages and increased costs) that need to be overcome. Cancer biomarkers must be embedded in the real world of oncology delivery and testing must be implemented across Europe, with the intended aim of narrowing, not widening the inequity gap for patients. Cancer patients must be placed firmly at the centre of a cancer biomarker informed precision oncology care agenda.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - "Fondazione G. Pascale", Napoli, Italy
| | - Kathi Apostolides
- European Cancer Patient Coalition, Rue Montoyer 40, 1000, Brussels, Belgium
| | | | - Philip A Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Raymond Henderson
- Diaceutics PLC, Belfast, United Kingdom; Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom
| | - Richard Sullivan
- King's College London, Institute of Cancer Policy, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, United Kingdom; South Western Sydney Clinical School, Goulburn St, Liverpool, NSW, 2170, Australia
| | - Denis Horgan
- European Alliance for Personalised Medicine, Avenue de l'Armee Legerlaan 10, 1040, Brussels, Belgium
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom.
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Schwappacher R, Dieterich W, Reljic D, Pilarsky C, Mukhopadhyay D, Chang DK, Biankin AV, Siebler J, Herrmann HJ, Neurath MF, Zopf Y. Muscle-Derived Cytokines Reduce Growth, Viability and Migratory Activity of Pancreatic Cancer Cells. Cancers (Basel) 2021; 13:cancers13153820. [PMID: 34359731 PMCID: PMC8345221 DOI: 10.3390/cancers13153820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/13/2021] [Revised: 07/11/2021] [Accepted: 07/23/2021] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Pancreatic cancer (PC) is a highly fatal malignancy. A major reason for the poor prognosis of patients with PC is the insensitivity to most oncological treatment approaches. It is known that regular exercise reduces the cancer risk. We have already shown that serum from advanced prostate and colon cancer patients after exercise reduces growth and viability of cancer cells. The aim of this study was to identify exercise-induced cytokines in serum from patients with advanced-stage PC that regulate cancer cell proliferation and apoptosis. Our data suggest that a mild resistance exercise training in advanced PC patients induces the release of CXCL1, IL10 and CCL4 from contracting skeletal muscle. We demonstrate that these myokines inhibit growth and migration of PC cells, and induce PC cell death. With this report we provide new knowledge on the cancer-protective function of exercise in PC. Our data strongly support sport therapies for cancer patients. Abstract The evidence that regular physical exercise reduces the risk of developing cancer is well described. However, the interaction between physical exercise and cancer is not fully clarified yet. Several myokines released by skeletal muscle appear to have a direct anti-tumour function. There are few data on myokine secretion after exercise in patients with advanced tumours. Pancreatic cancer (PC) is a very aggressive and usually fatal cancer. To investigate the effects of exercise in PC, the blood of advanced-stage PC patients was analysed after 12 weeks of resistance training using whole-body electromyostimulation. After the 12-week training period, the patient serum inhibited the proliferation and the motility of PC cells and enhanced PC cell apoptosis. The impact of exercise training was also investigated in an exercise-mimicking in vitro model using electric pulse stimulation of human myotubes and revealed similar anti-tumour effects on PC cells, clearly indicating direct cancer-protective properties of activated skeletal muscle. Protein and gene expression analyses in plasma from exercise-trained patients and in myotube cultures after in vitro exercise showed that interleukin 10 (IL10), C-X-C motif ligand 1 (CXCL1) and C-C motif chemokine ligand 4 (CCL4) are myokines released from activated skeletal muscle. In accordance with the effects of serum from exercise-trained patients, the supplementation with recombinant IL10, CXCL1 and CCL4 impaired growth and migration of PC cells. Treatment of PC cells with these myokines upregulated caspase 3/7 expression and the cleavage of poly(ADP-ribose) polymerase, leading to enhanced PC cell death. The identification of myokines with anti-tumour properties in advanced-stage PC patients after exercise opens a new perspective in supportive therapy with sports and exercise for cancer patients.
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Affiliation(s)
- Raphaela Schwappacher
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Hector-Center for Nutrition, Exercise and Sports, Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Walburga Dieterich
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Hector-Center for Nutrition, Exercise and Sports, Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Dejan Reljic
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Hector-Center for Nutrition, Exercise and Sports, Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Christian Pilarsky
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
- Department of Surgery, Friedrich-Alexander University Erlangen-Nürnberg, Schwabachanlage 12, 91054 Erlangen, Germany
| | - Debabrata Mukhopadhyay
- Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 4500 San Pablo Road, Jacksonville, FL 32224, USA;
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate Switchback Road, Glasgow G61 1QH, UK; (D.K.C.); (A.V.B.)
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, 84 Castle Street, Glasgow G4 0SF, UK
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate Switchback Road, Glasgow G61 1QH, UK; (D.K.C.); (A.V.B.)
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, 84 Castle Street, Glasgow G4 0SF, UK
| | - Jürgen Siebler
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Hans J. Herrmann
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Hector-Center for Nutrition, Exercise and Sports, Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Markus F. Neurath
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
| | - Yurdagül Zopf
- Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; (R.S.); (W.D.); (D.R.); (J.S.); (H.J.H.); (M.F.N.)
- Hector-Center for Nutrition, Exercise and Sports, Medical Department 1, Friedrich-Alexander University Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Östliche Stadtmauerstraße 30, 91054 Erlangen, Germany;
- Correspondence: ; Tel.: +49-09131-8545218; Fax: +49-09131-8535228
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Ewing A, Meynert A, Churchman M, Grimes GR, Hollis RL, Herrington CS, Rye T, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Dowson S, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D, McMahon L, Matakidou A, Dougherty B, March R, Barrett JC, McNeish IA, Biankin AV, Roxburgh P, Gourley C, Semple CA. Structural Variants at the BRCA1/2 Loci are a Common Source of Homologous Repair Deficiency in High-grade Serous Ovarian Carcinoma. Clin Cancer Res 2021; 27:3201-3214. [PMID: 33741650 PMCID: PMC7610896 DOI: 10.1158/1078-0432.ccr-20-4068] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/29/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE The abundance and effects of structural variation at BRCA1/2 in tumors are not well understood. In particular, the impact of these events on homologous recombination repair deficiency (HRD) has yet to be demonstrated. EXPERIMENTAL DESIGN Exploiting a large collection of whole-genome sequencing data from high-grade serous ovarian carcinoma (N = 205) together with matched RNA sequencing for the majority of tumors (N = 150), we have comprehensively characterized mutation and expression at BRCA1/2. RESULTS In addition to the known spectrum of short somatic mutations (SSM), we discovered that multi-megabase structural variants (SV) were a frequent, unappreciated source of BRCA1/2 disruption in these tumors, and we found a genome-wide enrichment for large deletions at the BRCA1/2 loci across the cohort. These SVs independently affected a substantial proportion of patients (16%) in addition to those affected by SSMs (24%), conferring HRD and impacting patient survival. We also detail compound deficiencies involving SSMs and SVs at both loci, demonstrating that the strongest risk of HRD emerges from combined SVs at both BRCA1 and BRCA2 in the absence of SSMs. Furthermore, these SVs are abundant and disruptive in other cancer types. CONCLUSIONS These results extend our understanding of the mutational landscape underlying HRD, increase the number of patients predicted to benefit from therapies exploiting HRD, and suggest there is currently untapped potential in SV detection for patient stratification.
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Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Graeme R Grimes
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - C Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Edinburgh Pathology, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Tzyvia Rye
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Clare Bartos
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ian Croy
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Michelle Ferguson
- Department of Oncology, Ninewells Hospital, NHS Tayside, Dundee, Scotland, United Kingdom
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, Scotland, United Kingdom
| | - Mairi Lennie
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, Scotland, United Kingdom
| | - Trevor McGoldrick
- Department of Oncology, Aberdeen Royal Infirmary, Aberdeen, Scotland, United Kingdom
- Institute of Education for Medical and Dental Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Neil McPhail
- Department of Oncology, Raigmore Hospital, NHS Highland, Inverness, Scotland, United Kingdom
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
| | - Suzanne Dowson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Rosalind Glasspool
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Melanie Mackean
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, Scotland, United Kingdom
| | - Fiona Nussey
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, Scotland, United Kingdom
| | - Brian McDade
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Darren Ennis
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, England, United Kingdom
| | - Lynn McMahon
- Precision Medicine Scotland (PMS-IC), Queen Elizabeth University Hospital, Glasgow, Scotland, United Kingdom
| | - Athena Matakidou
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, England, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Ruth March
- Precision Medicine, Oncology R&D, AstraZeneca, Cambridge, England, United Kingdom
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Iain A McNeish
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, England, United Kingdom
| | - Andrew V Biankin
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
- South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, New South Wales, Australia
| | - Patricia Roxburgh
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Colin A Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Lakis V, Lawlor RT, Newell F, Patch AM, Mafficini A, Sadanandam A, Koufariotis LT, Johnston RL, Leonard C, Wood S, Rusev B, Corbo V, Luchini C, Cingarlini S, Landoni L, Salvia R, Milella M, Chang D, Bailey P, Jamieson NB, Duthie F, Gingras MC, Muzny DM, Wheeler DA, Gibbs RA, Milione M, Pederzoli P, Samra JS, Gill AJ, Johns AL, Pearson JV, Biankin AV, Grimmond SM, Waddell N, Nones K, Scarpa A. DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Commun Biol 2021; 4:155. [PMID: 33536587 PMCID: PMC7859232 DOI: 10.1038/s42003-020-01469-0] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.
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Affiliation(s)
- Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Borislav Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Cingarlini
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Baden-Württemberg, Germany
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of Pathology, Queen Elizabeth University Hospital, Greater Glasgow & Clyde NHS, Glasgow, G51 4TF, UK
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030-3411, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | | | - Anthony J Gill
- University of Sydney, Sydney, New South Wales, 2006, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia.
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy.
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy.
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41
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Casolino R, Braconi C, Malleo G, Paiella S, Bassi C, Milella M, Dreyer SB, Froeling FEM, Chang DK, Biankin AV, Golan T. Reshaping preoperative treatment of pancreatic cancer in the era of precision medicine. Ann Oncol 2021; 32:183-196. [PMID: 33248227 PMCID: PMC7840891 DOI: 10.1016/j.annonc.2020.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 10/09/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
This review summarises the recent evidence on preoperative therapeutic strategies in pancreatic cancer and discusses the rationale for an imminent need for a personalised therapeutic approach in non-metastatic disease. The molecular diversity of pancreatic cancer and its influence on prognosis and treatment response, combined with the failure of 'all-comer' treatments to significantly impact on patient outcomes, requires a paradigm shift towards a genomic-driven approach. This is particularly important in the preoperative, potentially curable setting, where a personalised treatment allocation has the substantial potential to reduce pancreatic cancer mortality.
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Affiliation(s)
- R Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, UK; Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - C Braconi
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, UK
| | - G Malleo
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - S Paiella
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - C Bassi
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - M Milella
- Department of Medicine, Medical Oncology, University and Hospital Trust of Verona, Verona (VR), Italy
| | - S B Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - F E M Froeling
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - D K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - A V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, NSW, Australia.
| | - T Golan
- Oncology Institute, Sheba Medical Center, Tel Hashomer, Israel
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42
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Griffith BGC, Upstill-Goddard R, Brunton H, Grimes GR, Biankin AV, Serrels B, Byron A, Frame MC. FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs. Sci Rep 2021; 11:229. [PMID: 33420223 PMCID: PMC7794255 DOI: 10.1038/s41598-020-80111-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/27/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Focal adhesion kinase (FAK) localizes to focal adhesions and is overexpressed in many cancers. FAK can also translocate to the nucleus, where it binds to, and regulates, several transcription factors, including MBD2, p53 and IL-33, to control gene expression by unknown mechanisms. We have used ATAC-seq to reveal that FAK controls chromatin accessibility at a subset of regulated genes. Integration of ATAC-seq and RNA-seq data showed that FAK-dependent chromatin accessibility is linked to differential gene expression, including of the FAK-regulated cytokine and transcriptional regulator interleukin-33 (Il33), which controls anti-tumor immunity. Analysis of the accessibility peaks on the Il33 gene promoter/enhancer regions revealed sequences for several transcription factors, including ETS and AP-1 motifs, and we show that c-Jun, a component of AP-1, regulates Il33 gene expression by binding to its enhancer in a FAK kinase-dependent manner. This work provides the first demonstration that FAK controls transcription via chromatin accessibility, identifying a novel mechanism by which nuclear FAK regulates biologically important gene expression.
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Affiliation(s)
- Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosanna Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- NanoString Technologies, Inc, Seattle, WA, 98109, USA.
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
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43
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Froeling FEM, Casolino R, Pea A, Biankin AV, Chang DK. Molecular Subtyping and Precision Medicine for Pancreatic Cancer. J Clin Med 2021; 10:E149. [PMID: 33406790 PMCID: PMC7794969 DOI: 10.3390/jcm10010149] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/25/2020] [Indexed: 12/12/2022] Open
Abstract
Substantial progress in recent years has dramatically increased our knowledge of the molecular basis of cancer, revealing new potential therapeutic targets and paving the way for effective personalised medicine for the treatment of many tumour types. However, pancreatic cancer has been lagging behind in this success and continues to be one of the most lethal solid malignancies. Its molecular heterogeneity and the unselected design of the majority of clinical trials to date can in part explain the reason for our failure to make a significant change in the survival outcomes for patients with pancreatic cancer. A changing paradigm in drug development is required to validate the new molecular taxonomy and to rapidly translate preclinical discovery into clinical trials. Here, we review the molecular subtyping of pancreatic cancer, the challenges in identifying effective treatment regimens according to defined low-prevalence molecular subgroups and we illustrate a new model of translational therapeutic development that was established in the U.K. (Precision-Panc) as a potentially effective solution to improve outcomes for patients with pancreatic cancer.
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Affiliation(s)
- Fieke E. M. Froeling
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; (F.E.M.F.); (R.C.); (A.P.); (A.V.B.)
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; (F.E.M.F.); (R.C.); (A.P.); (A.V.B.)
- Department of Medicine, University and Hospital Trust of Verona of Verona, Piazzale L.A. Scuro 10, 37134 Verona, Italy
| | - Antonio Pea
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; (F.E.M.F.); (R.C.); (A.P.); (A.V.B.)
- Department of Surgery, University and Hospital Trust of Verona, Piazzale L.A. Scuro 10, 37134 Verona, Italy
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; (F.E.M.F.); (R.C.); (A.P.); (A.V.B.)
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; (F.E.M.F.); (R.C.); (A.P.); (A.V.B.)
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
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44
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Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D, Galluzzo Z, Brunton H, Cunningham R, Tesson M, Nourse C, Bailey UM, Jones M, Moran-Jones K, Wright DW, Duthie F, Oien K, Evers L, McKay CJ, McGregor GA, Gulati A, Brough R, Bajrami I, Pettitt S, Dziubinski ML, Candido J, Balkwill F, Barry ST, Grützmann R, Rahib L, Johns A, Pajic M, Froeling FE, Beer P, Musgrove EA, Petersen GM, Ashworth A, Frame MC, Crawford HC, Simeone DM, Lord C, Mukhopadhyay D, Pilarsky C, Tuveson DA, Cooke SL, Jamieson NB, Morton JP, Sansom OJ, Bailey PJ, Biankin AV, Chang DK. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer. Gastroenterology 2021; 160:362-377.e13. [PMID: 33039466 PMCID: PMC8167930 DOI: 10.1053/j.gastro.2020.09.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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: 08/08/2019] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. METHODS We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. RESULTS Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency. CONCLUSIONS Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.
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Affiliation(s)
- Stephan B. Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Clara Paris
- Department of Pharmacological Faculty, Université Grenoble Alpes, Saint-Martin-d’Heres, France
| | - Eirini-Maria Lampraki
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Giuseppina Caligiuri
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Selma Rebus
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Zachary Galluzzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Richard Cunningham
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Mathias Tesson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Ulla-Maja Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Marc Jones
- Stratified Medicine Scotland, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Kim Moran-Jones
- College of Medicine, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Derek W. Wright
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Karin Oien
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom,Greater Glasgow and Clyde Bio-repository, Pathology Department, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Lisa Evers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Colin J. McKay
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Aditi Gulati
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Stephan Pettitt
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Michele L. Dziubinski
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Juliana Candido
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Frances Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Simon T. Barry
- Bioscience, Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Lola Rahib
- Pancreatic Cancer Action Network, Manhattan Beach, California
| | - Glasgow Precision Oncology Laboratory,AllisonSarah1BaileyPeter J.1BaileyUlla-Maja1BiankinAndrew V.1BeraldiDario1BruntonHolly1CaligiuriGiuseppina1CameronEuan1ChangDavid K.12CookeSusanna L.1CunninghamRichard1DreyerStephan12GrimwoodPaul1KellyShane1LamprakiEirini-Maria1MarshallJohn1MartinSancha1McDadeBrian1McElroyDaniel1MusgroveElizabeth A.1NourseCraig1Paulus-HockViola1RamsayDonna1Upstill-GoddardRosie1WrightDerek1JonesMarc D.1EversLisa1RebusSelma1RahibLola1SerrelsBryan1HairJane1JamiesonNigel B.12McKayColin J.12WestwoodPaul14WilliamsNicola14DuthieFraser13Glasgow Precision Oncology Laboratory, University of Glasgow, Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Glasgow, United KingdomWest of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United KingdomDepartment of Pathology, Southern General Hospital, Greater Glasgow and Clyde National Health Service, Glasgow, United KingdomWest of Scotland Genetic Services, National Health Service, Greater Glasgow and Clyde, Queen Elizabeth University Hospital Campus, Glasgow, United Kingdom
- Glasgow Precision Oncology Laboratory, Glasgow, United Kingdom
| | - Australian Pancreatic Cancer Genome InitiativeBiankinAndrew V.12JohnsAmber L.1MawsonAmanda1ChangDavid K.12ScarlettChristopher J.1BrancatoMary-Anne L.1RoweSarah J.1SimpsonSkye H.1Martyn-SmithMona1ThomasMichelle T.1ChantrillLorraine A.1ChinVenessa T.1ChouAngela1CowleyMark J.1HumphrisJeremy L.1JonesMarc D.12MeadR. Scott1NagrialAdnan M.1PajicMarina1PettitJessica1PineseMark1RoomanIlse1WuJianmin1TaoJiang1DiPietroRenee1WatsonClare1SteinmannAngela1LeeHong Ching1WongRachel1PinhoAndreia V.1Giry-LaterriereMarc1DalyRoger J.1MusgroveElizabeth A.12SutherlandRobert L.1GrimmondSean M.3WaddellNicola3KassahnKarin S.3MillerDavid K.3WilsonPeter J.3PatchAnn-Marie3SongSarah3HarliwongIvon3IdrisogluSenel3NourseCraig3NourbakhshEhsan3ManningSuzanne3WaniShivangi3GongoraMilena3AndersonMatthew3HolmesOliver3LeonardConrad3TaylorDarrin3WoodScott3XuChristina3NonesKatia3FinkJ. Lynn3ChristAngelika3BruxnerTim3CloonanNicole3NewellFelicity3PearsonJohn V.3BaileyPeter3QuinnMichael3NagarajShivashankar3KazakoffStephen3WaddellNick3KrisnanKeerthana3QuekKelly3WoodDavid3SamraJaswinder S.4GillAnthony J.4PavlakisNick4GuminskiAlex4ToonChristopher4AsghariRay5MerrettNeil D.5PaveyDarren5DasAmitabha5CosmanPeter H.6IsmailKasim6O’ConnnorChelsie6LamVincent W.7McLeodDuncan7PleassHenry C.7RichardsonArthur7JamesVirginia7KenchJames G.8CooperCaroline L.8JosephDavid8SandroussiCharbel8CrawfordMichael8GallagherJames8TexlerMichael9ForestCindy9LaycockAndrew9EpariKrishna P.9BallalMo9FletcherDavid R.9MukhedkarSanjay9SpryNigel A.10DeBoerBastiaanChaiMingZepsNikolajs11BeilinMaria11FeeneyKynan11NguyenNan Q.12RuszkiewiczAndrew R.12WorthleyChris12TanChuan P.12DebrenciniTamara12ChenJohn13Brooke-SmithMark E.13PapangelisVirginia13TangHenry14BarbourAndrew P.14CloustonAndrew D.15MartinPatrick15O’RourkeThomas J.16ChiangAmy16FawcettJonathan W.16SlaterKellee16YeungShinn16HatzifotisMichael16HodgkinsonPeter16ChristophiChristopher17NikfarjamMehrdad17MountainAngela17BiobankVictorian Cancer18EshlemanJames R.19HrubanRalph H.19MaitraAnirban19Iacobuzio-DonahueChristine A.19SchulickRichard D.19WolfgangChristopher L.19MorganRichard A.19HodginMary19ScarpaAldo20LawlorRita T.20BeghelliStefania20CorboVincenzo20ScardoniMaria20BassiClaudio20TemperoMargaret A.21BiankinAndrew V.1222GrimmondSean M.23ChangDavid K.1222MusgroveElizabeth A.2JonesMarc D.12NourseCraig23JamiesonNigel B.222GrahamJanet S.222BiankinAndrew V.1222ChangDavid K.1222JamiesonNigel B.222GrahamJanet S.222The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, AustraliaWolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United KingdomQueensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, AustraliaRoyal North Shore Hospital, St Leonards, New South Wales, AustraliaBankstown Hospital, Bankstown, New South Wales, AustraliaLiverpool Hospital, Liverpool, New South Wales, AustraliaWestmead Hospital, Westmead, New South Wales, AustraliaRoyal Prince Alfred Hospital, Camperdown, New South Wales, AustraliaFremantle Hospital, Fremantle, Western Australia, AustraliaSir Charles Gairdner Hospital, Nedlands, Western Australia, AustraliaSt John of God Healthcare, Subiaco, Western Australia, AustraliaRoyal Adelaide Hospital, Adelaide, South Australia, AustraliaFlinders Medical Centre, Bedford Park, South Australia, AustraliaGreenslopes Private Hospital, Greenslopes, Queensland, AustraliaEnvoi Pathology, Herston, Queensland, AustraliaPrincess Alexandria Hospital, Woolloongabba, Queensland, AustraliaAustin Hospital, Heidelberg, Victoria, AustraliaVictorian Cancer Biobank, Carlton, Victoria, AustraliaJohns Hopkins Medical Institute, Baltimore, MarylandARC-NET Center for Applied Research on Cancer, University of Verona, Verona, ItalyUniversity of California, San Francisco, San Francisco, CaliforniaGreater Glasgow and Clyde National Health Service, Glasgow, United Kingdom
- Australian Pancreas Genome, Darlinghurst, Australia
| | - Amber Johns
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Fieke E.M. Froeling
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York,Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Phillip Beer
- Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Elizabeth A. Musgrove
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Alan Ashworth
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom,University of California–San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Margaret C. Frame
- Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Howard C. Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Diane M. Simeone
- Pancreatic Cancer Center, Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Chris Lord
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, Florida
| | | | - David A. Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Susanna L. Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Nigel B. Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jennifer P. Morton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Owen J. Sansom
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Peter J. Bailey
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom,South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia,Andrew V. Biankin, MD, PhD, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom fax: +44 141 330 5834.
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom,West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom,South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia,Correspondence Address correspondence to: David K. Chang, MD, PhD, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom fax: +44 141 330 5834.
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Biankin AV. Abstract IA-12: Precision oncology for pancreatic cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.panca20-ia-12] [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
Pancreatic cancer presents distinct challenges in advancing more contemporary therapeutic approaches that target specific molecular aberrations within subgroups of patients. This “precision oncology” approach requires: 1. The ability to define targetable molecular pathology and the characteristics of molecular subtypes which harbour vulnerabilities and build preclinical platforms of evidence that support the testing of therapeutic strategies in clinical trials.2. The capability and capacity to accurately select subgroups of participants and provide feasible opportunities for clinical trials of novel therapeutic strategies in the real world.3. The ability to robustly aggregate data from clinical trials and cohorts to inform the evolution of novel therapeutic approaches.
To achieve these goals, the Glasgow Precision Oncology Laboratory has endeavoured to define molecular vulnerabilities and build the systems that enable the above 3 requirements.
The Glasgow Cancer Test
The GPOL team have created a new suite of tests that not only covers what is already known about cancer, but also allows for new information to be assimilated. The content of the GCTs is carefully curated to include genomic features for which there is high-quality objective evidence for a biological role in cancer. These genomic features are tiered by clinical actionability and confidence to generate a nested set of cancer assays to accommodate different clinical or scientific requirements and financial and infrastructure constraints so as to meet increasing demand, especially in cancers of unmet need.
Precision-panc
Precision-Panc was designed to be the evolution of clinical trial platforms that involved molecular profiling for difficult to treat cancers, typically not a priority for commercial therapeutic development. It was developed in partnership with, and has significant funding support from industry. In order to institute a step change for pancreatic cancer, it was necessary to transform pancreatic cancer therapeutic development into a more competitive arena so as to secure greater investment from pharmaceutical companies. Essential to this strategy is the concept that molecular profiling of all cancer patients should be performed for clinical trials (Reasons to be testing: the dawn of complex molecular profiling in routine oncology practice. Beer et al. Ann Oncol. 2019 30:1691-1694). In the area of human data science, extremely accurate information from digital pathology and digital imaging necessitates the molecular profiling of cancer coupled with accurate clinical data at scale and is the long-term goal of the processes developed through Precision-Panc.
From commencement of funding, the first site was open within 8 months, with the first randomisation a month after that. From first randomisation, after 2 years, 26 sites have been opened, 277 participants have entered the platform, 216 registered for studies and 113 proceeded to a trial. Current rate of participant entry into Precision-Panc is 15 - 20 per month. Of the 6 specific trials currently on the platform, one has completed, 5 continue with more in development in order to accommodate all therapeutic opportunities (eg:metastatic, 2nd-line, local advanced, resectable disease).
ICGC-ARGO
The International Cancer Genome Consortium’s new initiative called ARGO (Accelerating Research in Genomic Oncology) designed and led by GPOL aims to deliver a Million patient years of precision oncology knowledge. Platforms such as Precision-panc will contribute data to ICGC-ARGO to enable pooled analysis of granular standardised datasets across and between different cancer types.
Citation Format: Andrew V. Biankin. Precision oncology for pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr IA-12.
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Affiliation(s)
- Andrew V. Biankin
- Regius Professor of Surgery Director, Wolfson Wohl Cancer Research Centre, Executive Director, International Cancer Genome Consortium, Director, Glasgow Precision Oncology Laboratory, Chair, Precision-Panc Therapeutic Development Platform Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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Beer PA, Cooke SL, Chang DK, Biankin AV. Defining the clinical genomic landscape for real-world precision oncology. Genomics 2020; 112:5324-5330. [PMID: 33144218 PMCID: PMC7758710 DOI: 10.1016/j.ygeno.2020.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 07/06/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]
Abstract
Through the delivery of large international projects including ICGC and TCGA, knowledge of cancer genomics is reaching saturation point. Enabling this to improve patient outcomes now requires embedding comprehensive genomic profiling into routine oncology practice. Towards this goal, this study defined the biologically and clinically relevant genomic features of adult cancer through detailed curation and analysis of large genomic datasets, accumulated literature and biomarker-driven therapeutics in clinic and development. The characteristics and prevalence of these features were then interrogated in 2348 whole genome sequences, covering 21 solid tumour types, generated by the PCAWG project. This analysis highlights the predominant contribution of copy number alterations and identifies a critical role for disruptive structural variants in the inactivation of clinically important tumour suppressor genes, including PTEN and RB1, which are not currently captured by diagnostic assays. This study defines a set of essential genomic features for the characterisation of common adult cancers.
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Affiliation(s)
- Philip A Beer
- Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1QH, United Kingdom
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1QH, United Kingdom
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom; South Western Sydney Clinical School, Goulburn, St, Liverpool NSW, 2170, Australia.
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Pan C, Otsuka Y, Sridharan B, Woo M, Leiton CV, Babu S, Torrente Gonçalves M, Kawalerski RR, K. Bai JD, Chang DK, Biankin AV, Scampavia L, Spicer T, Escobar‐Hoyos LF, Shroyer KR. An unbiased high-throughput drug screen reveals a potential therapeutic vulnerability in the most lethal molecular subtype of pancreatic cancer. Mol Oncol 2020; 14:1800-1816. [PMID: 32533886 PMCID: PMC7400780 DOI: 10.1002/1878-0261.12743] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 01/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related deaths in the United States by 2020, due in part to innate resistance to widely used chemotherapeutic agents and limited knowledge about key molecular factors that drive tumor aggression. We previously reported a novel negative prognostic biomarker, keratin 17 (K17), whose overexpression in cancer results in shortened patient survival. In this study, we aimed to determine the predictive value of K17 and explore the therapeutic vulnerability in K17-expressing PDAC, using an unbiased high-throughput drug screen. Patient-derived data analysis showed that K17 expression correlates with resistance to gemcitabine (Gem). In multiple in vitro and in vivo models of PDAC, spanning human and murine PDAC cells, and orthotopic xenografts, we determined that the expression of K17 results in a more than twofold increase in resistance to Gem and 5-fluorouracil, key components of current standard-of-care chemotherapeutic regimens. Furthermore, through an unbiased drug screen, we discovered that podophyllotoxin (PPT), a microtubule inhibitor, showed significantly higher sensitivity in K17-positive compared to K17-negative PDAC cell lines and animal models. In the clinic, another microtubule inhibitor, paclitaxel (PTX), is used in combination with Gem as a first-line chemotherapeutic regimen for PDAC. Surprisingly, we found that when combined with Gem, PPT, but not PTX, was synergistic in inhibiting the viability of K17-expressing PDAC cells. Importantly, in preclinical models, PPT in combination with Gem effectively decreased tumor growth and enhanced the survival of mice bearing K17-expressing tumors. This provides evidence that PPT and its derivatives could potentially be combined with Gem to enhance treatment efficacy for the ~ 50% of PDACs that express high levels of K17. In summary, we reported that K17 is a novel target for developing a biomarker-based personalized treatment for PDAC.
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Affiliation(s)
- Chun‐Hao Pan
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Molecular and Cellular Biology Graduate ProgramStony Brook UniversityNYUSA
| | | | | | - Melissa Woo
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Simons Summer Research ProgramStony Brook UniversityNYUSA
| | - Cindy V. Leiton
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - Sruthi Babu
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Department of Family, Population & Preventive MedicineRenaissance School of MedicineStony Brook UniversityNYUSA
| | | | - Ryan R. Kawalerski
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - Ji Dong K. Bai
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - David K. Chang
- Wolfson Wohl Cancer Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
- West of Scotland Pancreatic UnitGlasgow Royal InfirmaryUK
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
- West of Scotland Pancreatic UnitGlasgow Royal InfirmaryUK
| | | | | | - Luisa F. Escobar‐Hoyos
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Department of Therapeutic RadiologySchool of MedicineYale UniversityNew HavenCTUSA
- David M. Rubenstein Center for Pancreatic Cancer ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Genetic Toxicology and Cytogenetics Research GroupDepartment of BiologySchool of Natural Sciences and EducationUniversidad del CaucaPopayánColombia
| | - Kenneth R. Shroyer
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
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Muthalagu N, Monteverde T, Raffo-Iraolagoitia X, Wiesheu R, Whyte D, Hedley A, Laing S, Kruspig B, Upstill-Goddard R, Shaw R, Neidler S, Rink C, Karim SA, Gyuraszova K, Nixon C, Clark W, Biankin AV, Carlin LM, Coffelt SB, Sansom OJ, Morton JP, Murphy DJ. Repression of the Type I Interferon Pathway Underlies MYC- and KRAS-Dependent Evasion of NK and B Cells in Pancreatic Ductal Adenocarcinoma. Cancer Discov 2020; 10:872-887. [PMID: 32200350 PMCID: PMC7611248 DOI: 10.1158/2159-8290.cd-19-0620] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [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: 05/30/2019] [Revised: 02/07/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022]
Abstract
MYC is implicated in the development and progression of pancreatic cancer, yet the precise level of MYC deregulation required to contribute to tumor development has been difficult to define. We used modestly elevated expression of human MYC, driven from the Rosa26 locus, to investigate the pancreatic phenotypes arising in mice from an approximation of MYC trisomy. We show that this level of MYC alone suffices to drive pancreatic neuroendocrine tumors, and to accelerate progression of KRAS-initiated precursor lesions to metastatic pancreatic ductal adenocarcinoma (PDAC). Our phenotype exposed suppression of the type I interferon (IFN) pathway by the combined actions of MYC and KRAS, and we present evidence of repressive MYC-MIZ1 complexes binding directly to the promoters of the genes encodiing the type I IFN regulators IRF5, IRF7, STAT1, and STAT2. Derepression of IFN regulator genes allows pancreatic tumor infiltration by B and natural killer (NK) cells, resulting in increased survival. SIGNIFICANCE: We define herein a novel mechanism of evasion of NK cell-mediated immunity through the combined actions of endogenously expressed mutant KRAS and modestly deregulated expression of MYC, via suppression of the type I IFN pathway. Restoration of IFN signaling may improve outcomes for patients with PDAC.This article is highlighted in the In This Issue feature, p. 747.
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Affiliation(s)
| | - Tiziana Monteverde
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Robert Wiesheu
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Declan Whyte
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Ann Hedley
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Sarah Laing
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Björn Kruspig
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Rosanna Upstill-Goddard
- Wolfson Wohl Translational Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Robin Shaw
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Sarah Neidler
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Curtis Rink
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Saadia A Karim
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Katarina Gyuraszova
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Colin Nixon
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - William Clark
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Translational Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Leo M Carlin
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Seth B Coffelt
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Owen J Sansom
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jennifer P Morton
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Daniel J Murphy
- CRUK Beatson Institute, Glasgow, Scotland, United Kingdom.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
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Brunton H, Caligiuri G, Cunningham R, Upstill-Goddard R, Bailey UM, Garner IM, Nourse C, Dreyer S, Jones M, Moran-Jones K, Wright DW, Paulus-Hock V, Nixon C, Thomson G, Jamieson NB, McGregor GA, Evers L, McKay CJ, Gulati A, Brough R, Bajrami I, Pettitt SJ, Dziubinski ML, Barry ST, Grützmann R, Brown R, Curry E, Pajic M, Musgrove EA, Petersen GM, Shanks E, Ashworth A, Crawford HC, Simeone DM, Froeling FEM, Lord CJ, Mukhopadhyay D, Pilarsky C, Grimmond SE, Morton JP, Sansom OJ, Chang DK, Bailey PJ, Biankin AV, Chang DK, Cooke SL, Dreyer S, Grimwood P, Kelly S, Marshall J, McDade B, McElroy D, Ramsay D, Upstill-Goddard R, Rebus S, Hair J, Jamieson NB, McKay CJ, Westwood P, Williams N, Duthie F, Biankin AV, Johns AL, Mawson A, Chang DK, Scarlett CJ, Brancato MAL, Rowe SJ, Simpson SH, Martyn-Smith M, Thomas MT, Chantrill LA, Chin VT, Chou A, Cowley MJ, Humphris JL, Mead RS, Nagrial AM, Pajic M, Pettit J, Pinese M, Rooman I, Wu J, Tao J, DiPietro R, Watson C, Steinmann A, Lee HC, Wong R, Pinho AV, Giry-Laterriere M, Daly RJ, Musgrove EA, Sutherland RL, Grimmond SM, Waddell N, Kassahn KS, Miller DK, Wilson PJ, Patch AM, Song S, Harliwong I, Idrisoglu S, Nourbakhsh E, Manning S, Wani S, Gongora M, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu C, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Newell F, Pearson JV, Quinn M, Nagaraj S, Kazakoff S, Waddell N, Krisnan K, Quek K, Wood D, Samra JS, Gill AJ, Pavlakis N, Guminski A, Toon C, Asghari R, Merrett ND, Pavey D, Das A, Cosman PH, Ismail K, O’Connnor C, Lam VW, McLeod D, Pleass HC, Richardson A, James V, Kench JG, Cooper CL, Joseph D, Sandroussi C, Crawford M, Gallagher J, Texler M, Forest C, Laycock A, Epari KP, Ballal M, Fletcher DR, Mukhedkar S, Spry NA, DeBoer B, Chai M, Zeps N, Beilin M, Feeney K, Nguyen NQ, Ruszkiewicz AR, Worthley C, Tan CP, Debrencini T, Chen J, Brooke-Smith ME, Papangelis V, Tang H, Barbour AP, Clouston AD, Martin P, O’Rourke TJ, Chiang A, Fawcett JW, Slater K, Yeung S, Hatzifotis M, Hodgkinson P, Christophi C, Nikfarjam M, Mountain A, Eshleman JR, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Hodgin M, Scarpa A, Lawlor RT, Beghelli S, Corbo V, Scardoni M, Bassi C, Tempero MA, Nourse C, Jamieson NB, Graham JS. HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer. Cell Rep 2020; 31:107625. [PMID: 32402285 PMCID: PMC9511995 DOI: 10.1016/j.celrep.2020.107625] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 07/24/2019] [Revised: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC.
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Affiliation(s)
- Holly Brunton
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Giuseppina Caligiuri
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Richard Cunningham
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Rosie Upstill-Goddard
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Ulla-Maja Bailey
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Ian M Garner
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Stephan Dreyer
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Marc Jones
- Stratified Medicine Scotland Innovation Centre, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Kim Moran-Jones
- Stratified Medicine Scotland Innovation Centre, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Derek W Wright
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Viola Paulus-Hock
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gemma Thomson
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Nigel B Jamieson
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Grant A McGregor
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lisa Evers
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Colin J McKay
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ilirjana Bajrami
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Michele L Dziubinski
- Department of Molecular and Integrative Physiology, University of Michigan, 4304 Rogel Cancer Center Drive, Ann Arbor, MI 48109, USA
| | - Simon T Barry
- Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Robert Brown
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Edward Curry
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | | | | | - Marina Pajic
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth A Musgrove
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | | | - Emma Shanks
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Alan Ashworth
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, 4304 Rogel Cancer Center Drive, Ann Arbor, MI 48109, USA
| | - Diane M Simeone
- Pancreatic Cancer Center, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Fieke E M Froeling
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL 32224, USA
| | | | - Sean E Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne 3010, VIC, Australia
| | - Jennifer P Morton
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Owen J Sansom
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David K Chang
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Peter J Bailey
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Department of General Surgery, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andrew V Biankin
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, 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Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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