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Nulsen J, Hussain N, Al-Deka A, Yap J, Uddin K, Yau C, Ahmed AA. Correction: Completing a genomic characterisation of microscopic tumour samples with copy number. BMC Bioinformatics 2024; 25:20. [PMID: 38216884 PMCID: PMC10785409 DOI: 10.1186/s12859-024-05642-8] [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] [Indexed: 01/14/2024] Open
Affiliation(s)
- Joel Nulsen
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Nosheen Hussain
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Aws Al-Deka
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Jason Yap
- University of Birmingham, Birmingham, UK
| | | | - Christopher Yau
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Health Data Research UK, London, UK
| | - Ahmed Ashour Ahmed
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK.
- Singula Bio Ltd., Oxford, UK.
- Oxford Biomedical Research Centre, National Institute of Health Research, Oxford, UK.
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Nulsen J, Hussain N, Al-Deka A, Yap J, Uddin K, Yau C, Ahmed AA. Completing a genomic characterisation of microscopic tumour samples with copy number. BMC Bioinformatics 2023; 24:453. [PMID: 38036971 PMCID: PMC10688092 DOI: 10.1186/s12859-023-05576-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/11/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples. RESULTS Here, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations from picogram quantities of tumour DNA. We find that PicoCNV provides exactly accurate copy number in 84% of the genome for even the smallest samples, and demonstrate its clinical potential in maintenance therapy. CONCLUSIONS PicoCNV complements our existing platform, allowing for accurate and comprehensive genomic characterisations of cancers in settings where only microscopic samples are available.
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Affiliation(s)
- Joel Nulsen
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Nosheen Hussain
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Aws Al-Deka
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Jason Yap
- University of Birmingham, Birmingham, UK
| | | | - Christopher Yau
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Health Data Research UK, London, UK
| | - Ahmed Ashour Ahmed
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK.
- Singula Bio Ltd., Oxford, UK.
- Oxford Biomedical Research Centre, National Institute of Health Research, Oxford, UK.
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Mukherjee D, Romano E, Walshaw R, Zeef LAH, Banyard A, Kitcatt SJ, Cheadle EJ, Tuomela K, Pendharkar S, Al-Deka A, Salerno B, Raby S, Mills IG, Honeychurch J, Illidge TM. Reprogramming the immunosuppressive tumor microenvironment results in successful clearance of tumors resistant to radiation therapy and anti-PD-1/PD-L1. Oncoimmunology 2023; 12:2223094. [PMID: 37332616 PMCID: PMC10274532 DOI: 10.1080/2162402x.2023.2223094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023] Open
Abstract
Despite breakthroughs in immune checkpoint inhibitors (ICI), the majority of tumors, including those poorly infiltrated by CD8+ T cells or heavily infiltrated by immunosuppressive immune effector cells, are unlikely to result in clinically meaningful tumor responses. Radiation therapy (RT) has been combined with ICI to potentially overcome this resistance and improve response rates but reported clinical trial results have thus far been disappointing. Novel approaches are required to overcome this resistance and reprogram the immunosuppressive tumor microenvironment (TME) and address this major unmet clinical need. Using diverse preclinical tumor models of prostate and bladder cancer, including an autochthonous prostate tumor (Pten-/-/trp53-/-) that respond poorly to radiation therapy (RT) and anti-PD-L1 combinations, the key drivers of this resistance within the TME were profiled and used to develop rationalized combination therapies that simultaneously enhance activation of anti-cancer T cell responses and reprogram the immunosuppressive TME. The addition of anti-CD40mAb to RT resulted in an increase in IFN-y signaling, activation of Th-1 pathways with an increased infiltration of CD8+ T-cells and regulatory T-cells with associated activation of the CTLA-4 signaling pathway in the TME. Anti-CTLA-4mAb in combination with RT further reprogrammed the immunosuppressive TME, resulting in durable, long-term tumor control. Our data provide novel insights into the underlying mechanisms of the immunosuppressive TME that result in resistance to RT and anti-PD-1 inhibitors and inform therapeutic approaches to reprogramming the immune contexture in the TME to potentially improve tumor responses and clinical outcomes.
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Affiliation(s)
- Debayan Mukherjee
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Erminia Romano
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Richard Walshaw
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Leo A. H. Zeef
- Bioinformatics Core Facility, Michael Smith Building, The University of Manchester, Manchester, UK
| | - Antonia Banyard
- Mass and Flow Cytometry Core Facility, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Stephen J. Kitcatt
- Scientific Computing Core Facility, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Eleanor J. Cheadle
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Karoliina Tuomela
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Swati Pendharkar
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Aws Al-Deka
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Beatrice Salerno
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Sophie Raby
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Patrick G. Johnston Centre for Cancer Research, Queen’s University of Belfast, Belfast, UK
| | - Jamie Honeychurch
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Tim M. Illidge
- Targeted Therapy Group, Division of Cancer Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
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