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Nenclares P, Larkeryd A, Manodoro F, Lee JY, Lalondrelle S, Gilbert DC, Punta M, O’Leary B, Rullan A, Sadanandam A, Chain B, Melcher A, Harrington KJ, Bhide SA. T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies. Front Oncol 2024; 13:1296948. [PMID: 38234396 PMCID: PMC10791873 DOI: 10.3389/fonc.2023.1296948] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Background The effect of chemoradiation on the anti-cancer immune response is being increasingly acknowledged; however, its clinical implications in treatment responses are yet to be fully understood. Human papillomavirus (HPV)-driven malignancies express viral oncogenic proteins which may serve as tumor-specific antigens and represent ideal candidates for monitoring the peripheral T-cell receptor (TCR) changes secondary to chemoradiotherapy (CRT). Methods We performed intra-tumoral and pre- and post-treatment peripheral TCR sequencing in a cohort of patients with locally-advanced HPV16-positive cancers treated with CRT. An in silico computational pipeline was used to cluster TCR repertoire based on epitope-specificity and to predict affinity between these clusters and HPV16-derived epitopes. Results Intra-tumoral repertoire diversity, intra-tumoral and post-treatment peripheral CDR3β similarity clustering were predictive of response. In responders, CRT triggered an increase peripheral TCR clonality and clonal relatedness. Post-treatment expansion of baseline peripheral dominant TCRs was associated with response. Responders showed more baseline clustered structures of TCRs maintained post-treatment and displayed significantly more maintained clustered structures. When applying clustering by TCR-specificity methods, responders displayed a higher proportion of intra-tumoral TCRs predicted to recognise HPV16 peptides. Conclusions Baseline TCR characteristics and changes in the peripheral T-cell clones triggered by CRT are associated with treatment outcome. Maintenance and boosting of pre-existing clonotypes are key elements of an effective anti-cancer immune response driven by CRT, supporting a paradigm in which the immune system plays a central role in the success of CRT in current standard-of-care protocols.
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Affiliation(s)
- Pablo Nenclares
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Adrian Larkeryd
- Bioinformatics Unit, The Centre for Translational Immunotherapy, The Institute of Cancer Research, London, United Kingdom
| | - Floriana Manodoro
- Genomics Facility, The Institute of Cancer Research, London, United Kingdom
| | - Jen Y. Lee
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Susan Lalondrelle
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Duncan C. Gilbert
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom
| | - Marco Punta
- Unit of Immunogenetic, Leukemia Genomics and Immunobiology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ben O’Leary
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Antonio Rullan
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Anguraj Sadanandam
- Systems and Precision Cancer Medicine Team, The Institute of Cancer Research, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Alan Melcher
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Kevin J. Harrington
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Shreerang A. Bhide
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
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Wagner S, Vlachogiannis G, De Haven Brandon A, Valenti M, Box G, Jenkins L, Mancusi C, Self A, Manodoro F, Assiotis I, Robinson P, Chauhan R, Rust AG, Matthews N, Eason K, Khan K, Starling N, Cunningham D, Sadanandam A, Isacke CM, Kirkin V, Valeri N, Whittaker SR. Correction: Suppression of interferon gene expression overcomes resistance to MEK inhibition in KRAS-mutant colorectal cancer. Oncogene 2019; 38:5746. [PMID: 31147600 PMCID: PMC7608239 DOI: 10.1038/s41388-019-0835-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Steve Wagner
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | | | | | - Melanie Valenti
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Gary Box
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Liam Jenkins
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Caterina Mancusi
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Annette Self
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | | | - Ioannis Assiotis
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Penny Robinson
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Ritika Chauhan
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Alistair G Rust
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Kate Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Khurum Khan
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Naureen Starling
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - David Cunningham
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Clare M Isacke
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Vladimir Kirkin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.,Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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Wagner S, Vlachogiannis G, De Haven Brandon A, Valenti M, Box G, Jenkins L, Mancusi C, Self A, Manodoro F, Assiotis I, Robinson P, Chauhan R, Rust AG, Matthews N, Eason K, Khan K, Starling N, Cunningham D, Sadanandam A, Isacke CM, Kirkin V, Valeri N, Whittaker SR. Suppression of interferon gene expression overcomes resistance to MEK inhibition in KRAS-mutant colorectal cancer. Oncogene 2019; 38:1717-1733. [PMID: 30353166 PMCID: PMC6462854 DOI: 10.1038/s41388-018-0554-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 03/13/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022]
Abstract
Despite showing clinical activity in BRAF-mutant melanoma, the MEK inhibitor (MEKi) trametinib has failed to show clinical benefit in KRAS-mutant colorectal cancer. To identify mechanisms of resistance to MEKi, we employed a pharmacogenomic analysis of MEKi-sensitive versus MEKi-resistant colorectal cancer cell lines. Strikingly, interferon- and inflammatory-related gene sets were enriched in cell lines exhibiting intrinsic and acquired resistance to MEK inhibition. The bromodomain inhibitor JQ1 suppressed interferon-stimulated gene (ISG) expression and in combination with MEK inhibitors displayed synergistic effects and induced apoptosis in MEKi-resistant colorectal cancer cell lines. ISG expression was confirmed in patient-derived organoid models, which displayed resistance to trametinib and were resensitized by JQ1 co-treatment. In in vivo models of colorectal cancer, combination treatment significantly suppressed tumor growth. Our findings provide a novel explanation for the limited response to MEK inhibitors in KRAS-mutant colorectal cancer, known for its inflammatory nature. Moreover, the high expression of ISGs was associated with significantly reduced survival of colorectal cancer patients. Excitingly, we have identified novel therapeutic opportunities to overcome intrinsic and acquired resistance to MEK inhibition in colorectal cancer.
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Affiliation(s)
- Steve Wagner
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | | | | | - Melanie Valenti
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Gary Box
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Liam Jenkins
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Caterina Mancusi
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Annette Self
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | | | - Ioannis Assiotis
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Penny Robinson
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Ritika Chauhan
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Alistair G Rust
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Kate Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Khurum Khan
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Naureen Starling
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - David Cunningham
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Clare M Isacke
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Vladimir Kirkin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, Royal Marsden NHS Foundation Trust, London, UK
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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Wilkins A, Chauhan R, Rust A, Pearson A, Daley F, Manodoro F, Fenwick K, Bliss J, Yarnold J, Somaiah N. FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment. Breast Cancer Res Treat 2018; 170:573-581. [PMID: 29700676 PMCID: PMC6022520 DOI: 10.1007/s10549-018-4798-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/19/2018] [Indexed: 11/29/2022]
Abstract
Background Bio-banked formalin-fixed paraffin-embedded (FFPE) tissues provide an excellent opportunity for translational genomic research. Historically matched blood has not always been collected as a source of germline DNA. This project aimed to establish if normal FFPE breast tissue could be used as an alternative to blood. Methods Exome sequencing was carried out on matched tumour tissue, normal breast tissue and blood on five patients in the START trial. Retrieved samples had been archived at different centres for at least 13 years. Following tissue macro-dissection and DNA extraction, targeted exome capture was performed using SureSelect Human All Exome v5 reagents (Agilent). Illumina paired-end libraries were prepared from the captured target regions and sequenced on a HiSeq2500 (Illumina) acquiring 2 × 75 bp reads. Somatic variants were called using the MuTect software analysis tool and copy number abnormalities (CNA) were identified using CNVkit. Targeted sequencing and droplet digital PCR were used to validate somatic variants and CNA, respectively. Results Overlap of somatic variants and CNA called on tumour versus blood and tumour versus normal breast tissue was good. Agreement in somatic variant calling ranged from 76.9 to 93.6%. Variants with an allele frequency lower than 10% were more difficult to validate irrespective of the type of germline DNA used. Pearson’s correlation coefficients for paired comparisons of CNA using blood or normal tissue as reference ranged from 0.70 to 0.94. Conclusions There is good correlation between the somatic mutations and CNA called using archived blood or normal breast tissue as germline reference material. Electronic supplementary material The online version of this article (10.1007/s10549-018-4798-7) contains supplementary material, which is available to authorised users.
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Affiliation(s)
- Anna Wilkins
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK.,The Institute of Cancer Research Clinical Trials and Statistics Unit, London, UK.,The Royal Marsden Hospital, Downs Road, Sutton, SM2 5PT, UK
| | - Ritika Chauhan
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Alistair Rust
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Alex Pearson
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Frances Daley
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | | | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Judith Bliss
- The Institute of Cancer Research Clinical Trials and Statistics Unit, London, UK
| | - John Yarnold
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK.,The Royal Marsden Hospital, Downs Road, Sutton, SM2 5PT, UK
| | - Navita Somaiah
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK. .,The Royal Marsden Hospital, Downs Road, Sutton, SM2 5PT, UK.
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