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Ellis R, Tang D, Nasr B, Greenwood A, McConnell A, Anagnostou M, Elias M, Verykiou S, Bajwa D, Ewen T, Reynolds N, Barrett P, Carling E, Watson G, Armstrong J, Allen A, Horswell S, Labus M, Lovat P. 测量两种蛋白质, 帮助评估哪种黑色素瘤最有可能传播. Br J Dermatol 2020. [DOI: 10.1111/bjd.18675] [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] [Indexed: 11/29/2022]
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Ellis R, Tang D, Nasr B, Greenwood A, McConnell A, Anagnostou M, Elias M, Verykiou S, Bajwa D, Ewen T, Reynolds N, Barrett P, Carling E, Watson G, Armstrong J, Allen A, Horswell S, Labus M, Lovat P. Measuring two proteins to help assess which melanomas are most likely to spread. Br J Dermatol 2020. [DOI: 10.1111/bjd.18658] [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] [Indexed: 11/28/2022]
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Au L, Litchfield K, Rowan A, Horswell S, Byrne F, Nicol D, Fotiadis N, Salgado R, Hazell S, Lopez J, Hatipoglu E, Del Rosario L, Pickering L, Gore M, Chain B, Quezada S, Larkin J, Swanton C, Turajlic S. ADAPTeR: A phase II study of anti-PD1 (nivolumab) therapy as pre- and post-operative therapy in metastatic renal cell carcinoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz249.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ellis R, Tang D, Nasr B, Greenwood A, McConnell A, Anagnostou ME, Elias M, Verykiou S, Bajwa D, Ewen T, Reynolds NJ, Barrett P, Carling E, Watson G, Armstrong J, Allen AJ, Horswell S, Labus M, Lovat PE. Epidermal autophagy and beclin 1 regulator 1 and loricrin: a paradigm shift in the prognostication and stratification of the American Joint Committee on Cancer stage I melanomas. Br J Dermatol 2019; 182:156-165. [PMID: 31056744 PMCID: PMC6973157 DOI: 10.1111/bjd.18086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND The updated American Joint Committee on Cancer (AJCC) staging criteria for melanoma remain unable to identify high-risk stage I tumour subsets. OBJECTIVES To determine the utility of epidermal autophagy and beclin 1 regulator 1 (AMBRA1)/loricrin (AMLo) expression as a prognostic biomarker for AJCC stage I cutaneous melanoma. METHODS Peritumoral AMBRA1 expression was evaluated in a retrospective discovery cohort of 76 AJCC stage I melanomas. AMLo expression was correlated with clinical outcomes up to 12 years in two independent powered, retrospective validation and qualification cohorts comprising 379 AJCC stage I melanomas. RESULTS Decreased AMBRA1 expression in the epidermis overlying primary melanomas in a discovery cohort of 76 AJCC stage I tumours was associated with a 7-year disease-free survival (DFS) rate of 81·5% vs. 100% survival with maintained AMBRA1 (P < 0·081). Following an immunohistochemistry protocol for semi-quantitative analysis of AMLo, analysis was undertaken in validation (n = 218) and qualification cohorts (n = 161) of AJCC stage I melanomas. Combined cohort analysis revealed a DFS rate of 98·3% in the AMLo low-risk group (n = 239) vs. 85·4% in the AMLo high-risk cohort (n = 140; P < 0·001). Subcohort multivariate analysis revealed that an AMLo hazard ratio (HR) of 4·04 [95% confidence interval (CI) 1·69-9·66; P = 0·002] is a stronger predictor of DFS than Breslow depth (HR 2·97, 95% CI 0·93-9·56; P = 0·068) in stage IB patients. CONCLUSIONS Loss of AMLo expression in the epidermis overlying primary AJCC stage I melanomas identifies high-risk tumour subsets independently of Breslow depth. What's already known about this topic? There is an unmet clinical need for biomarkers of early-stage melanoma. Autophagy and beclin 1 regulator 1 (AMBRA1) is a proautophagy regulatory protein with known roles in cell proliferation and differentiation, and is a known tumour suppressor. Loricrin is a marker of epidermal terminal differentiation. What does this study add? AMBRA1 has a functional role in keratinocyte/epidermal proliferation and differentiation. The combined decrease/loss of peritumoral AMBRA1 and loricrin is associated with a significantly increased risk of metastatic spread in American Joint Committee on Cancer (AJCC) stage I tumours vs. melanomas, in which peritumoral AMBRA1 and loricrin are maintained, independently of Breslow depth. What is the translational message? The integration of peritumoral epidermal AMBRA1/loricrin biomarker expression into melanoma care guidelines will facilitate more accurate, personalized risk stratification for patients with AJCC stage I melanomas, thereby facilitating stratification for appropriate follow-up and informing postdiagnostic investigations, including sentinel lymph node biopsy, ultimately resulting in improved disease outcomes and rationalization of healthcare costs.
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Affiliation(s)
- R Ellis
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K.,Department of Dermatology, James Cook University Hospital, Middlesbrough, U.K
| | - D Tang
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K.,Department of Dermatology, James Cook University Hospital, Middlesbrough, U.K
| | - B Nasr
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K.,Department of Pathology, University of North Durham Hospital, Durham, U.K
| | - A Greenwood
- Department of Pathology, James Cook University Hospital, Middlesbrough, U.K
| | - A McConnell
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - M E Anagnostou
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - M Elias
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - S Verykiou
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - D Bajwa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - T Ewen
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - N J Reynolds
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - P Barrett
- Department of Pathology, University of North Durham Hospital, Durham, U.K
| | - E Carling
- Department of Pathology, St James's University Hospital, Leeds, U.K
| | - G Watson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K.,Department of Pathology, James Cook University Hospital, Middlesbrough, U.K
| | - J Armstrong
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, U.K
| | - A J Allen
- NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle University, Newcastle upon Tyne, U.K
| | - S Horswell
- Bioinformatics and Bio Statistics Group, The Francis Crick Institute, London, U.K
| | - M Labus
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - P E Lovat
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
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Ellis R, McConnell A, Tang D, Nasr B, Greenwood A, Watson G, Barrett P, Horswell S, Labus M, Lovat P. 996 Epidermal AMBRA1 and Loricrin; A paradigm shift in prognostication and stratification of AJCC stage I melanoma. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.03.1072] [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] [Indexed: 10/27/2022]
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Zecchin D, Howell M, Horswell S, Downward J. 20 Identification of combinatorial therapies with inhibitors of the PI3K pathway in PTEN-null tumours. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.20] [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] [Indexed: 11/04/2022] Open
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Molina-Arcas M, Moore C, Rana S, Van Maldegem F, Horswell S, Hancock D, Downward J. 15 Identification of new combination therapies for lung cancer tumours harbouring KRAS mutations. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Molina-Arcas M, Hancock D, Moore C, Horswell S, Matthews N, Downward J. Identification of new combination therapies for NSCLC tumours harbouring KRAS mutations. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61193-0] [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] [Indexed: 11/17/2022]
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Jamal-Hanjani M, Wilson GA, Horswell S, Mitter R, Sakarya O, Constantin T, Salari R, Kirkizlar E, Sigurjonsson S, Pelham R, Kareht S, Zimmermann B, Swanton C. Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer. Ann Oncol 2016; 27:862-7. [PMID: 26823523 DOI: 10.1093/annonc/mdw037] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [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: 11/08/2015] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The aim of this pilot study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in cell-free DNA (cfDNA) from patients with early-stage non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS Three stage I and one stage II primary NSCLC tumors were subjected to multiregion whole-exome sequencing (WES) and validated with AmpliSeq. A subset of ubiquitous and heterogeneous single-nucleotide variants (SNVs) were chosen. Multiplexed PCR using custom-designed primers, coupled with next-generation sequencing (mPCR-NGS), was used to detect these SNVs in both tumor DNA and cfDNA isolated from plasma obtained before surgical resection of the tumors. The limit of detection for each assay was determined using cfDNA from 48 presumed-normal healthy volunteers. RESULTS Tumor DNA and plasma-derived cfDNA was successfully amplified and sequenced for 37/50 (74%) SNVs using the mPCR-NGS method. Twenty-five (68%) were ubiquitous and 12 (32%) were heterogeneous SNVs. Variant detection by mPCR-NGS and WES-AmpliSeq in tumor tissue was well correlated (R(2) = 0.8722, P < 0.0001). Sixteen (43%) out of 37 SNVs were detected in cfDNA. Twelve of these were ubiquitous SNVs with a variant allele frequency (VAF) range of 0.15-23.25%, and four of these were heterogeneous SNVs with a VAF range of 0.28-1.71%. There was a statistically significant linear relationship between the VAFs for tumor and cfDNA (R(2) = 0.5144; P = 0.0018). For all four patients, at least two variants were detected in plasma. The estimated number of copies of variant DNA present in each sample ranged from 5 to 524. The average number of variant copies required for detection (VCRD) was 3.16 (range: 0.2-7.6 copies). CONCLUSIONS The mPCR-NGS method revealed intratumor heterogeneity in early-stage NSCLC tumors, and was able to detect both ubiquitous and heterogeneous SNVs in cfDNA. Further validation of mPCR-NGS in cfDNA is required to define its potential use in clinical practice.
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Affiliation(s)
- M Jamal-Hanjani
- Translational Cancer Therapeutics Laboratory, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - G A Wilson
- Translational Cancer Therapeutics Laboratory, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London
| | - S Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - R Mitter
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - O Sakarya
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | | | | | | | | | | | | | | | - C Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London
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Haywood MEK, Rose SJ, Horswell S, Lees MJ, Fu G, Walport MJ, Morley BJ. Overlapping BXSB congenic intervals, in combination with microarray gene expression, reveal novel lupus candidate genes. Genes Immun 2007; 7:250-63. [PMID: 16541099 DOI: 10.1038/sj.gene.6364294] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The BXSB mouse strain is an important model of glomerulonephritis observed in systemic lupus erythematosus (SLE). Linkage studies have successfully identified disease-susceptibility intervals; however, extracting the identity of the susceptibility gene(s) in such regions is the crucial next step. Congenic mouse strains present a defined genetic resource that is highly amenable to microarray analysis. We have performed microarray analysis using a series of chromosome 1 BXSB congenic mice with partially overlapping disease-susceptibility intervals. Simultaneous comparison of the four congenic lines allowed the identification of expression differences associated with both the initiation and progression of disease. Thus, we have identified a number of novel SLE disease gene candidates and have confirmed the identity of Ifi202 as a disease candidate in the BXSB strain. Sequencing of the promoter regions of Gas5 has revealed polymorphisms in the BXSB strain, which may account for the differential expression profile. Furthermore, the combination of the microarray results with the different phenotypes of these mice has allowed the identification of a number of expression differences that do not necessarily map to the congenic interval, but may be implicated in disease pathways.
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Affiliation(s)
- M E K Haywood
- Rheumatology Section, Division of Medicine, Imperial College Faculty of Medicine, London, UK
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