1
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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. Res Sq 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [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] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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2
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Nissanka-Jayasuriya EH, Fenton TR, Rose-Zerilli MJJ. Molecular landscape of proliferative verrucous leukoplakia: a systematic review. Br J Oral Maxillofac Surg 2024; 62:118-127. [PMID: 38296711 DOI: 10.1016/j.bjoms.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024]
Abstract
Proliferative verrucous leukoplakia (PVL) is a rare oral potentially malignant disorder characterised by multifocal origin and unpredictable long-term evolution to oral squamous cell carcinoma (OSCC) or oral verrucous carcinoma (OVC). Currently no predictive biomarkers are in clinical use. We aimed to explore the genomic profile of PVL. A total of 685 cases in 26 studies were included in this review. Genomic data were presented in 15% of studies and biomarker analysis was reported in 85% of studies. At first clinical presentation, PVL is characterised by a high loss of heterozygosity (LOH), similar to OSCC, and low copy number alterations (CNA). As these progress, more CNAs and mutations in CDKN2A and alterations to ELAVL1 expression are noted, but no TP53 mutations are identified. There is significantly lower LOH at 17p in early PVL compared with OSCC (p = 0.037). Deletions in chromosomal loci 17q12, 5q31.1 and amplifications in 7q11.2, 7q22 are shared between early lesions and OVC. PVL shows CNAs at 11q31. WNT signalling pathway genes (SUZ12, CTTN and FOLR3) are enriched in CN-altered regions. PVL stroma shows significantly lower α-SMA and higher CD34 expression than OVC and OSCC. The exact genomic landscape is currently unclear, and further studies are necessary to unravel this mystery.
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Affiliation(s)
- Eranga H Nissanka-Jayasuriya
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Department of Histopathology, William Harvey Hospital, East Kent Hospitals University NHS Trust, Ashford, Kent, UK.
| | - Tim R Fenton
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; School of Biosciences, University of Kent, Canterbury, UK
| | - Matthew J J Rose-Zerilli
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
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3
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Reddin IG, Fenton TR, Wass MN, Michaelis M. Large inherent variability in data derived from highly standardised cell culture experiments. Pharmacol Res 2023; 188:106671. [PMID: 36681368 DOI: 10.1016/j.phrs.2023.106671] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
Cancer drug development is hindered by high clinical attrition rates, which are blamed on weak predictive power by preclinical models and limited replicability of preclinical findings. However, the technically feasible level of replicability remains unknown. To fill this gap, we conducted an analysis of data from the NCI60 cancer cell line screen (2.8 million compound/cell line experiments), which is to our knowledge the largest depository of experiments that have been repeatedly performed over decades. The findings revealed profound intra-laboratory data variability, although all experiments were executed following highly standardised protocols that avoid all known confounders of data quality. All compound/ cell line combinations with > 100 independent biological replicates displayed maximum GI50 (50% growth inhibition) fold changes (highest/ lowest GI50) > 5% and 70.5% displayed maximum fold changes > 1000. The highest maximum fold change was 3.16 × 1010 (lowest GI50: 7.93 ×10-10 µM, highest GI50: 25.0 µM). FDA-approved drugs and experimental agents displayed similar variation. Variability remained high after outlier removal, when only considering experiments that tested drugs at the same concentration range, and when only considering NCI60-provided quality-controlled data. In conclusion, high variability is an intrinsic feature of anti-cancer drug testing, even among standardised experiments in a world-leading research environment. Awareness of this inherent variability will support realistic data interpretation and inspire research to improve data robustness. Further research will have to show whether the inclusion of a wider variety of model systems, such as animal and/ or patient-derived models, may improve data robustness.
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Affiliation(s)
- Ian G Reddin
- School of Biosciences, University of Kent, Canterbury, UK; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, UK.
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4
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Chakravarthy A, Reddin I, Henderson S, Dong C, Kirkwood N, Jeyakumar M, Rodriguez DR, Martinez NG, McDermott J, Su X, Egawa N, Fjeldbo CS, Skingen VE, Lyng H, Halle MK, Krakstad C, Soleiman A, Sprung S, Lechner M, Ellis PJI, Wass M, Michaelis M, Fiegl H, Salvesen H, Thomas GJ, Doorbar J, Chester K, Feber A, Fenton TR. Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance. Nat Commun 2022; 13:5818. [PMID: 36207323 PMCID: PMC9547055 DOI: 10.1038/s41467-022-33544-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
Human papillomavirus (HPV)-associated cervical cancer is a leading cause of cancer deaths in women. Here we present an integrated multi-omic analysis of 643 cervical squamous cell carcinomas (CSCC, the most common histological variant of cervical cancer), representing patient populations from the USA, Europe and Sub-Saharan Africa and identify two CSCC subtypes (C1 and C2) with differing prognosis. C1 and C2 tumours can be driven by either of the two most common HPV types in cervical cancer (16 and 18) and while HPV16 and HPV18 are overrepresented among C1 and C2 tumours respectively, the prognostic difference between groups is not due to HPV type. C2 tumours, which comprise approximately 20% of CSCCs across these cohorts, display distinct genomic alterations, including loss or mutation of the STK11 tumour suppressor gene, increased expression of several immune checkpoint genes and differences in the tumour immune microenvironment that may explain the shorter survival associated with this group. In conclusion, we identify two therapy-relevant CSCC subtypes that share the same defining characteristics across three geographically diverse cohorts. Human papillomavirus (HPV) is a known cause of cervical cancer. Here, the authors perform a multi-omic analysis using published cervical squamous cell carcinoma cohorts from the USA, Europe, and SubSaharan Africa and identify two cervical squamous cell carcinoma subtypes that display prognostic differences.
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Affiliation(s)
- Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ian Reddin
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Stephen Henderson
- UCL Cancer Institute, Bill Lyons Informatics Centre, University College London, London, UK
| | - Cindy Dong
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Nerissa Kirkwood
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Maxmilan Jeyakumar
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | | | | | | | | | - Nagayasau Egawa
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Heidi Lyng
- Department of Radiation Biology, Oslo University Hospital, Oslo, Norway.,Department of Physics, University of Oslo, Oslo, Norway
| | - Mari Kyllesø Halle
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Camilla Krakstad
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Afschin Soleiman
- INNPATH, Institute of Pathology, Tirol Kliniken Innsbruck, Innsbruck, Austria
| | - Susanne Sprung
- Institute of Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matt Lechner
- UCL Cancer Institute, University College London, London, UK
| | - Peter J I Ellis
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Mark Wass
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Martin Michaelis
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Heidi Fiegl
- Department of Obstetrics and Gynaecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helga Salvesen
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gareth J Thomas
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Kerry Chester
- UCL Cancer Institute, University College London, London, UK.
| | - Andrew Feber
- Centre for Molecular Pathology, Royal Marsden Hospital Trust, London, UK. .,Division of Surgery and Interventional Science, University College London, London, UK.
| | - Tim R Fenton
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK. .,School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK. .,Institute for Life Sciences, University of Southampton, Southampton, UK.
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5
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Lechner M, Takahashi Y, Turri-Zanoni M, Ferrari M, Liu J, Counsell N, Mattavelli D, Rampinelli V, Vermi W, Lombardi D, Saade R, Park KW, Schartinger VH, Franchi A, Facco C, Sessa F, Battocchio S, Fenton TR, Vaz FM, O'Flynn P, Howard D, Stimpson P, Wang S, Hannan SA, Unadkat S, Hughes J, Dwivedi R, Forde CT, Randhawa P, Gane S, Joseph J, Andrews PJ, Dave M, Fleming JC, Thomson D, Zhu T, Teschendorff A, Royle G, Steele C, Jimenez JE, Laco J, Wang EW, Snyderman C, Lacy PD, Woods R, O'Neill JP, Saraswathula A, Kaur RP, Zhao T, Ramanathan M, Gallia GL, London NR, Le QT, West RB, Patel ZM, Nayak JV, Hwang PH, Hermsen M, Llorente J, Facchetti F, Nicolai P, Bossi P, Castelnuovo P, Jay A, Carnell D, Forster MD, Bell DM, Lund VJ, Hanna EY. International Multicenter Study of Clinical Outcomes of Sinonasal Melanoma Shows Survival Benefit for Patients Treated with Immune Checkpoint Inhibitors and Potential Improvements to the Current TNM Staging System. J Neurol Surg B Skull Base 2022. [DOI: 10.1055/s-0042-1750178] [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: 10/17/2022] Open
Abstract
Abstract
Objectives Sinonasal mucosal melanoma (SNMM) is an extremely rare and challenging sinonasal malignancy with a poor prognosis. Standard treatment involves complete surgical resection, but the role of adjuvant therapy remains unclear. Crucially, our understanding of its clinical presentation, course, and optimal treatment remains limited, and few advancements in improving its management have been made in the recent past.
Methods We conducted an international multicenter retrospective analysis of 505 SNMM cases from 11 institutions across the United States, United Kingdom, Ireland, and continental Europe. Data on clinical presentation, diagnosis, treatment, and clinical outcomes were assessed.
Results One-, three-, and five-year recurrence-free and overall survival were 61.4, 30.6, and 22.0%, and 77.6, 49.2, and 38.3%, respectively. Compared with disease confined to the nasal cavity, sinus involvement confers significantly worse survival; based on this, further stratifying the T3 stage was highly prognostic (p < 0.001) with implications for a potential modification to the current TNM staging system. There was a statistically significant survival benefit for patients who received adjuvant radiotherapy, compared with those who underwent surgery alone (hazard ratio [HR] = 0.74, 95% confidence interval [CI]: 0.57–0.96, p = 0.021). Immune checkpoint blockade for the management of recurrent or persistent disease, with or without distant metastasis, conferred longer survival (HR = 0.50, 95% CI: 0.25–1.00, p = 0.036).
Conclusions We present findings from the largest cohort of SNMM reported to date. We demonstrate the potential utility of further stratifying the T3 stage by sinus involvement and present promising data on the benefit of immune checkpoint inhibitors for recurrent, persistent, or metastatic disease with implications for future clinical trials in this field.
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Affiliation(s)
- Matt Lechner
- UCL Cancer Institute, University College London, London, United Kingdom
- UCL Division of Surgery and Interventional Science, University College London, London, United Kingdom
- Department of ENT, Barts Health NHS Trust, London, United Kingdom
| | - Yoko Takahashi
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Mario Turri-Zanoni
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Ferrari
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padova, Padova, Italy
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Nicholas Counsell
- Cancer Research UK and UCL Cancer Trials Centre, University College London, London, United Kingdom
| | - Davide Mattavelli
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Vittorio Rampinelli
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - William Vermi
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Davide Lombardi
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Rami Saade
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
- Department of Otolaryngology—Head and Neck Surgery, Lebanese American University, Beirut, Lebanon
| | - Ki Wan Park
- Rhinology and Endoscopic Skull Base Surgery, Department of Otolaryngology—Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, United States
| | - Volker H. Schartinger
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Carla Facco
- Unit of Pathology, ASST Sette Laghi, University of Insubria, Varese, Italy
| | - Fausto Sessa
- Unit of Pathology, ASST Sette Laghi, University of Insubria, Varese, Italy
| | - Simonetta Battocchio
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Tim R. Fenton
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, United Kingdom
| | - Francis M. Vaz
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Paul O'Flynn
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - David Howard
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Paul Stimpson
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Simon Wang
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S. Alam Hannan
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Samit Unadkat
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Jonathan Hughes
- Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Raghav Dwivedi
- Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Cillian T. Forde
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Premjit Randhawa
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Simon Gane
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Jonathan Joseph
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Peter J. Andrews
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Manas Dave
- Division of Dentistry, University of Manchester, Manchester, United Kingdom
| | - Jason C. Fleming
- Liverpool Head & Neck Centre, University of Liverpool, Liverpool, United Kingdom
| | - David Thomson
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Liverpool Head & Neck Centre, University of Liverpool, Liverpool, United Kingdom
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Gary Royle
- UCL Cancer Institute, University College London, London, United Kingdom
| | | | - Joaquin E. Jimenez
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, United States
| | - Jan Laco
- The Fingerland Department of Pathology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Czech Republic
| | - Eric W. Wang
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, United States
- Center for Cranial Base Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Carl Snyderman
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, United States
- Center for Cranial Base Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Peter D. Lacy
- Department of Otolaryngology—Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland
| | - Robbie Woods
- Department of Otolaryngology—Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland
| | - James P. O'Neill
- Department of Otolaryngology—Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland
- The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Anirudh Saraswathula
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, United States
| | - Raman Preet Kaur
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, United States
| | - Tianna Zhao
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Murugappan Ramanathan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, United States
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Gary L. Gallia
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, United States
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Nyall R. London
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, United States
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
- Sinonasal and Skull Base Tumor Program—Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California, United States
| | - Robert B. West
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California, United States
| | - Zara M. Patel
- Rhinology and Endoscopic Skull Base Surgery, Department of Otolaryngology—Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, United States
| | - Jayakar V. Nayak
- Rhinology and Endoscopic Skull Base Surgery, Department of Otolaryngology—Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, United States
| | - Peter H. Hwang
- Rhinology and Endoscopic Skull Base Surgery, Department of Otolaryngology—Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, United States
| | - Mario Hermsen
- Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Jose Llorente
- Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Fabio Facchetti
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Piero Nicolai
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padova, Padova, Italy
| | - Paolo Bossi
- Medical Oncology, Department of Medical and Surgical Specialities, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Paolo Castelnuovo
- Unit of Otorhinolaryngology—Head and Neck Surgery, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Amrita Jay
- Department of Histopathology, University College London Hospitals NHS Trust, London, United Kingdom
| | - Dawn Carnell
- Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Martin D. Forster
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Diana M. Bell
- Disease Team Alignment: Head and Neck, City of Hope Medical Center, Duarte, California, United States
| | - Valerie J. Lund
- Royal National ENT Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, United Kingdom
| | - Ehab Y. Hanna
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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6
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Melake MJ, Smith HG, Mansfield D, Davies E, Dillon MT, Wilkins AC, Patin EC, Pedersen M, Buus R, Melcher AA, Thway K, Miah AB, Zaidi SH, Hayes AJ, Fenton TR, Harrington KJ, McLaughlin M. OX40 and 4-1BB delineate distinct immune profiles in sarcoma. Oncoimmunology 2022; 11:2066050. [PMID: 35558159 PMCID: PMC9090286 DOI: 10.1080/2162402x.2022.2066050] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/08/2023] Open
Abstract
Systemic relapse after radiotherapy and surgery is the major cause of disease-related mortality in sarcoma patients. Combining radiotherapy and immunotherapy is under investigation as a means to improve response rates. However, the immune contexture of sarcoma is understudied. Here, we use a retrospective cohort of sarcoma patients, treated with neoadjuvant radiotherapy, and TCGA data. We explore therapeutic targets of relevance to sarcoma, using genomics and multispectral immunohistochemistry to provide insights into the tumor immune microenvironment across sarcoma subtypes. Differential gene expression between radioresponsive myxoid liposarcoma (MLPS) and more radioresistant undifferentiated pleomorphic sarcoma (UPS) indicated UPS contained higher transcript levels of a number of immunotherapy targets (CD73/NT5E, CD39/ENTPD1, CD25/IL2RA, and 4-1BB/TNFRSF9). We focused on 4-1BB/TNFRSF9 and other costimulatory molecules. In TCGA data, 4-1BB correlated to an inflamed and exhausted phenotype. OX40/TNFRSF4 and 4-1BB/TNFRSF9 were highly expressed in sarcoma subtypes versus other cancers. Despite OX40 and 4-1BB being described as Treg markers, we identified that they delineate distinct tumor immune profiles. This was true for sarcoma and other cancers. While only a limited number of samples could be analyzed, spatial analysis of OX40 expression identified two diverse phenotypes of OX40+ Tregs, one associated with and one independent of tertiary lymphoid structures (TLSs). Patient stratification is of intense interest for immunotherapies. We provide data supporting the viewpoint that a cohort of sarcoma patients, appropriately selected, are promising candidates for immunotherapies. Spatial profiling of OX40+ Tregs, in relation to TLSs, could be an additional metric to improve future patient stratification.
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Affiliation(s)
- MJ Melake
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - HG Smith
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- Digestive Disease Center, Bispebjerg and Frederiksberg Hospital, University of Copenhagen, Denmark
| | - D Mansfield
- Translational Immunotherapy Team, The Institute of Cancer Research, London, UK
| | - E Davies
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - MT Dillon
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | | | - EC Patin
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - M Pedersen
- Translational Immunotherapy Team, The Institute of Cancer Research, London, UK
| | - R Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - AA Melcher
- Translational Immunotherapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - K Thway
- The Royal Marsden Hospital, London, UK
| | - AB Miah
- The Royal Marsden Hospital, London, UK
| | - SH Zaidi
- The Royal Marsden Hospital, London, UK
| | - AJ Hayes
- The Royal Marsden Hospital, London, UK
| | - TR Fenton
- University of Southampton, Somers Cancer Research Building MP824, Southampton General Hospital, Southampton, UK
| | - KJ Harrington
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - M McLaughlin
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
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7
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Baker SC, Mason AS, Slip RG, Skinner KT, Macdonald A, Masood O, Harris RS, Fenton TR, Periyasamy M, Ali S, Southgate J. Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer. Oncogene 2022; 41:2139-2151. [PMID: 35194151 PMCID: PMC8862006 DOI: 10.1038/s41388-022-02235-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/10/2021] [Accepted: 02/04/2022] [Indexed: 12/29/2022]
Abstract
Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. Mutational signatures show the anti-viral apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC) enzymes are responsible for the preponderance of mutations in bladder tumour genomes, but no causative viral agent has been identified. BK polyomavirus (BKPyV) is a common childhood infection that remains latent in the adult kidney, where reactivation leads to viruria. This study provides missing mechanistic evidence linking reactivated BKPyV-infection to bladder cancer risk. We used a mitotically-quiescent, functionally-differentiated model of normal human urothelium to examine BKPyV-infection. BKPyV-infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry from G0 into the cell cycle through inhibition of retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, with cells arresting in G2. The single-stranded DNA displacement loops formed in urothelial cells during BKPyV-infection interacted with LT-Ag to provide a substrate for APOBEC3-activity. Addition of interferon gamma (IFNγ) to infected urothelium suppressed expression of the viral genome. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations.
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Affiliation(s)
- Simon C Baker
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.
| | - Andrew S Mason
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Raphael G Slip
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Katie T Skinner
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Andrew Macdonald
- Faculty of Biological Sciences, School of Molecular and Cellular Pathology, University of Leeds, Leeds, UK
| | - Omar Masood
- Leeds Kidney Unit, St James's University Hospital, Leeds, UK
| | - Reuben S Harris
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Manikandan Periyasamy
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London, UK
- Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cell Biology (IMCB), 8A Biomedical Grove, Neuros/Immunos, #06-04/05, Singapore, 138648, Singapore
| | - Simak Ali
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Jennifer Southgate
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
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8
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Lechner M, Liu J, Masterson L, Fenton TR. Reply to ‘HPV-associated oropharyngeal cancer — discussion points’. Nat Rev Clin Oncol 2022; 19:422-423. [DOI: 10.1038/s41571-022-00627-z] [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: 11/09/2022]
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9
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Lechner M, Takahashi Y, Turri-Zanoni M, Liu J, Counsell N, Hermsen M, Kaur RP, Zhao T, Ramanathan M, Schartinger VH, Emanuel O, Helman S, Varghese J, Dudas J, Riechelmann H, Sprung S, Haybaeck J, Howard D, Engel NW, Stewart S, Brooks L, Pickles JC, Jacques TS, Fenton TR, Williams L, Vaz FM, O'Flynn P, Stimpson P, Wang S, Hannan SA, Unadkat S, Hughes J, Dwivedi R, Forde CT, Randhawa P, Gane S, Joseph J, Andrews PJ, Royle G, Franchi A, Maragliano R, Battocchio S, Bewicke-Copley H, Pipinikas C, Webster A, Thirlwell C, Ho D, Teschendorff A, Zhu T, Steele CD, Pillay N, Vanhaesebroeck B, Mohyeldin A, Fernandez-Miranda J, Park KW, Le QT, West RB, Saade R, Manes RP, Omay SB, Vining EM, Judson BL, Yarbrough WG, Sansovini M, Silvia N, Grassi I, Bongiovanni A, Capper D, Schüller U, Thavaraj S, Sandison A, Surda P, Hopkins C, Ferrari M, Mattavelli D, Rampinelli V, Facchetti F, Nicolai P, Bossi P, Henriquez OA, Magliocca K, Solares CA, Wise SK, Llorente JL, Patel ZM, Nayak JV, Hwang PH, Lacy PD, Woods R, O'Neill JP, Jay A, Carnell D, Forster MD, Ishii M, London NR, Bell DM, Gallia GL, Castelnuovo P, Severi S, Lund VJ, Hanna EY. Clinical outcomes, Kadish-INSICA staging and therapeutic targeting of somatostatin receptor 2 in olfactory neuroblastoma. Eur J Cancer 2022; 162:221-236. [PMID: 34980502 PMCID: PMC9554673 DOI: 10.1016/j.ejca.2021.09.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 09/12/2021] [Accepted: 09/28/2021] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Olfactory neuroblastoma (ONB) is a rare cancer of the sinonasal region. We provide a comprehensive analysis of this malignancy with molecular and clinical trial data on a subset of our cohort to report on the potential efficacy of somatostatin receptor 2 (SSTR2)-targeting imaging and therapy. METHODS We conducted a retrospective analysis of 404 primary, locally recurrent, and metastatic olfactory neuroblastoma (ONB) patients from 12 institutions in the United States of America, United Kingdom and Europe. Clinicopathological characteristics and treatment approach were evaluated. SSTR2 expression, SSTR2-targeted imaging and the efficacy of peptide receptor radionuclide therapy [PRRT](177Lu-DOTATATE) were reported in a subset of our cohort (LUTHREE trial; NCT03454763). RESULTS Dural infiltration at presentation was a significant predictor of overall survival (OS) and disease-free survival (DFS) in primary cases (n = 278). Kadish-Morita staging and Dulguerov T-stage both had limitations regarding their prognostic value. Multivariable survival analysis demonstrated improved outcomes with lower stage and receipt of adjuvant radiotherapy. Prophylactic neck irradiation significantly reduces the rate of nodal recurrence. 82.4% of the cohort were positive for SSTR2; treatment of three metastatic cases with SSTR2-targeted peptide-radionuclide receptor therapy (PRRT) in the LUTHREE trial was well-tolerated and resulted in stable disease (SD). CONCLUSIONS This study presents pertinent clinical data from the largest dataset, to date, on ONB. We identify key prognostic markers and integrate these into an updated staging system, highlight the importance of adjuvant radiotherapy across all disease stages, the utility of prophylactic neck irradiation and the potential efficacy of targeting SSTR2 to manage disease.
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Affiliation(s)
- Matt Lechner
- UCL Cancer Institute, University College London, London, UK; Academic Head and Neck Centre, UCL Division of Surgery and Interventional Science, University College London, London, UK; ENT Department, Barts Health NHS Trust, London, United Kingdom; Rhinology & Endoscopic Skull Base Surgery, Department of Otolaryngology-H&N Surgery, Stanford University School of Medicine, Palo Alto, USA.
| | - Yoko Takahashi
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Mario Turri-Zanoni
- Unit of Otorhinolaryngology and Head & Neck Surgery, Department of Biotechnology and Life Sciences, ASST Sette Laghi, University of Insubria, Varese, Italy
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, London, UK
| | - Nicholas Counsell
- Cancer Research UK & UCL Cancer Trials Centre, University College London, London, UK
| | - Mario Hermsen
- Department of Head and Neck Oncology, Instituto de Investigacio´n Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncologı´a Del Principado de Asturias (IUOPA), Centro de Investigacio´n Biome´dica en Red (CIBER-ONC), Oviedo, Spain
| | - Raman Preet Kaur
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, USA
| | - Tianna Zhao
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Murugappan Ramanathan
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, USA
| | - Volker H Schartinger
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Oscar Emanuel
- UCL Cancer Institute, University College London, London, UK
| | - Sam Helman
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, USA
| | - Jordan Varghese
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, USA
| | - Jozsef Dudas
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Riechelmann
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Susanne Sprung
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria; Diagnostic & Research Center for Molecular BioMedicine, Institute of Pathology, Medical University Graz, Graz, Austria
| | - David Howard
- Head and Neck Cancer Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Nils Wolfgang Engel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Stewart
- Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Laura Brooks
- Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Jessica C Pickles
- Department of Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Department of Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK; School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Luke Williams
- UCL Division of Surgery and Interventional Science, University College London, London, UK
| | - Francis M Vaz
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Paul O'Flynn
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Paul Stimpson
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Simon Wang
- Institute of Nuclear Medicine, University College London, London, UK
| | - S Alam Hannan
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Samit Unadkat
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Jonathan Hughes
- Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Raghav Dwivedi
- Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Cillian T Forde
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Premjit Randhawa
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Simon Gane
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Jonathan Joseph
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Peter J Andrews
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Gary Royle
- UCL Cancer Institute, University College London, London, UK
| | | | - Roberta Maragliano
- Department of Medicine and Surgery, Unit of Pathology, University of Insubria, Varese, Italy
| | - Simonetta Battocchio
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | | | | | - Amy Webster
- UCL Cancer Institute, University College London, London, UK
| | - Chrissie Thirlwell
- UCL Cancer Institute, University College London, London, UK; College of Medicine and Health and Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Debbie Ho
- Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China
| | - Christopher D Steele
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | | | - Ahmed Mohyeldin
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, USA
| | | | - Ki Wan Park
- Rhinology & Endoscopic Skull Base Surgery, Department of Otolaryngology-H&N Surgery, Stanford University School of Medicine, Palo Alto, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, USA
| | - Robert B West
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, USA
| | - Rami Saade
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Peter Manes
- Department of Neurosurgery, Yale School of Medicine, New Haven, USA
| | | | - Eugenia M Vining
- Department of Neurosurgery, Yale School of Medicine, New Haven, USA
| | | | - Wendell G Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, Chapel Hill, NC, USA
| | - Maddalena Sansovini
- Therapeutic Nuclear Medicine, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Nicolini Silvia
- Therapeutic Nuclear Medicine, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Ilaria Grassi
- Therapeutic Nuclear Medicine, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center (CDO-TR), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - David Capper
- Department of Neuropathology, Charite - Universitatsmedizin Berlin, Corporate Member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, Institute of Neuropathology, And Research Institute Children's Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Selvam Thavaraj
- Centre for Clinical, Oral & Translational Science, King's College London, Department of Head and Neck Pathology, Guy's Hospital, London, UK
| | - Ann Sandison
- Department of Head and Neck Pathology, Guy's Hospital, London, UK
| | | | | | - Marco Ferrari
- Section of Otorhinolaryngology - Head and Neck Surgery, Department of Neurosciences, University of Padova, Italy
| | - Davide Mattavelli
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialities, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Vittorio Rampinelli
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialities, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Fabio Facchetti
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Piero Nicolai
- Section of Otorhinolaryngology - Head and Neck Surgery, Department of Neurosciences, University of Padova, Italy
| | - Paolo Bossi
- Medical Oncology, Department of Medical and Surgical Specialities, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Oswaldo A Henriquez
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, USA
| | - Kelly Magliocca
- Department of Pathology, Emory University School of Medicine, Atlanta, USA
| | - C Arturo Solares
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, USA
| | - Sarah K Wise
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, USA
| | - Jose L Llorente
- Dept Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Zara M Patel
- Rhinology & Endoscopic Skull Base Surgery, Department of Otolaryngology-H&N Surgery, Stanford University School of Medicine, Palo Alto, USA
| | - Jayakar V Nayak
- Rhinology & Endoscopic Skull Base Surgery, Department of Otolaryngology-H&N Surgery, Stanford University School of Medicine, Palo Alto, USA
| | - Peter H Hwang
- Rhinology & Endoscopic Skull Base Surgery, Department of Otolaryngology-H&N Surgery, Stanford University School of Medicine, Palo Alto, USA
| | - Peter D Lacy
- Department of Otolaryngology, Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland
| | - Robbie Woods
- Department of Otolaryngology, Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland
| | - James P O'Neill
- Department of Otolaryngology, Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland; The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Amrita Jay
- Department of Histopathology, University College London Hospitals NHS Trust, London, UK
| | - Dawn Carnell
- Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Martin D Forster
- UCL Cancer Institute, University College London, London, UK; Academic Head and Neck Centre, UCL Division of Surgery and Interventional Science, University College London, London, UK; Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Masaru Ishii
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, USA
| | - Nyall R London
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA; Sinonasal and Skull Base Tumor Program, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Diana M Bell
- Department of Pathology, The University of Texas MD Anderson Cancer Center Houston, USA; Division of Anatomic Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Gary L Gallia
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Paolo Castelnuovo
- Unit of Otorhinolaryngology and Head & Neck Surgery, Department of Biotechnology and Life Sciences, ASST Sette Laghi, University of Insubria, Varese, Italy
| | - Stefano Severi
- Therapeutic Nuclear Medicine, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Valerie J Lund
- Royal National Ear, Nose and Throat Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK.
| | - Ehab Y Hanna
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA.
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10
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Fenton TR. Accumulation of host cell genetic errors following high-risk HPV infection. Curr Opin Virol 2021; 51:1-8. [PMID: 34543805 DOI: 10.1016/j.coviro.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Tim R Fenton
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK; School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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11
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Venkatesan S, Angelova M, Puttick C, Zhai H, Caswell DR, Lu WT, Dietzen M, Galanos P, Evangelou K, Bellelli R, Lim EL, Watkins TB, Rowan A, Teixeira VH, Zhao Y, Chen H, Ngo B, Zalmas LP, Bakir MA, Hobor S, Gronroos E, Pennycuick A, Nigro E, Campbell BB, Brown WL, Akarca AU, Marafioti T, Wu MY, Howell M, Boulton SJ, Bertoli C, Fenton TR, de Bruin RA, Maya-Mendoza A, Santoni-Rugiu E, Hynds RE, Gorgoulis VG, Jamal-Hanjani M, McGranahan N, Harris RS, Janes SM, Bartkova J, Bakhoum SF, Bartek J, Kanu N, Swanton C. Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution. Cancer Discov 2021; 11:2456-2473. [PMID: 33947663 PMCID: PMC8487921 DOI: 10.1158/2159-8290.cd-20-0725] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 05/21/2020] [Revised: 12/08/2020] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive non-small cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution. SIGNIFICANCE: This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.This article is highlighted in the In This Issue feature, p. 2355.
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Affiliation(s)
- Subramanian Venkatesan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Haoran Zhai
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
| | - Deborah R. Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Panagiotis Galanos
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Roberto Bellelli
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Emilia L. Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
| | - Thomas B.K. Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bryan Ngo
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | | | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sebastijan Hobor
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Eva Gronroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Ersilia Nigro
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Brittany B. Campbell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - William L. Brown
- Masonic Cancer Center, Minneapolis, USA; Institute for Molecular Virology, Minneapolis, USA; Center for Genome Engineering, Minneapolis, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA
| | - Ayse U. Akarca
- Department of Histopathology, University College London, London, United Kingdom
| | - Teresa Marafioti
- Department of Histopathology, University College London, London, United Kingdom
| | - Mary Y. Wu
- High Throughput Screening Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Simon J. Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Tim R. Fenton
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Robertus A.M. de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Robert E. Hynds
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
| | - Vassilis G. Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Reuben S. Harris
- Masonic Cancer Center, Minneapolis, USA; Institute for Molecular Virology, Minneapolis, USA; Center for Genome Engineering, Minneapolis, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, USA
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jirina Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
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12
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Filipski K, Scherer M, Zeiner KN, Bucher A, Kleemann J, Jurmeister P, Hartung TI, Meissner M, Plate KH, Fenton TR, Walter J, Tierling S, Schilling B, Zeiner PS, Harter PN. DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma. J Immunother Cancer 2021; 9:jitc-2020-002226. [PMID: 34281986 PMCID: PMC8291310 DOI: 10.1136/jitc-2020-002226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background Therapies based on targeting immune checkpoints have revolutionized the treatment of metastatic melanoma in recent years. Still, biomarkers predicting long-term therapy responses are lacking. Methods A novel approach of reference-free deconvolution of large-scale DNA methylation data enabled us to develop a machine learning classifier based on CpG sites, specific for latent methylation components (LMC), that allowed for patient allocation to prognostic clusters. DNA methylation data were processed using reference-free analyses (MeDeCom) and reference-based computational tumor deconvolution (MethylCIBERSORT, LUMP). Results We provide evidence that DNA methylation signatures of tumor tissue from cutaneous metastases are predictive for therapy response to immune checkpoint inhibition in patients with stage IV metastatic melanoma. Conclusions These results demonstrate that LMC-based segregation of large-scale DNA methylation data is a promising tool for classifier development and treatment response estimation in cancer patients under targeted immunotherapy.
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Affiliation(s)
- Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Michael Scherer
- Department of Genetics, University of Saarland, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saabrücken, Germany
| | - Kim N Zeiner
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Andreas Bucher
- Department of Radiology, University Hospital, Frankfurt am Main, Germany
| | - Johannes Kleemann
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Tabea I Hartung
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany
| | - Markus Meissner
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Karl H Plate
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Tim R Fenton
- School of Biosciences, University of Kent, Kent, UK
| | - Jörn Walter
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Sascha Tierling
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Pia S Zeiner
- German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.,Dr. Senckenberg Institute of Neurooncology, University Hospital, Frankfurt am Main, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany .,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
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13
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Lechner M, Schartinger VH, Steele CD, Nei WL, Ooft ML, Schreiber LM, Pipinikas CP, Chung GTY, Chan YY, Wu F, To KF, Tsang CM, Pearce W, Morelli D, Philpott M, Masterson L, Nibhani R, Wells G, Bell CG, Koller J, Delecluse S, Yip YL, Liu J, Forde CT, Forster MD, Jay A, Dudás J, Krapp A, Wan S, Uprimny C, Sprung S, Haybaeck J, Fenton TR, Chester K, Thirlwell C, Royle G, Marafioti T, Gupta R, Indrasari SR, Herdini C, Slim MAM, Indrawati I, Sutton L, Fles R, Tan B, Yeong J, Jain A, Han S, Wang H, Loke KSH, He W, Xu R, Jin H, Cheng Z, Howard D, Hwang PH, Le QT, Tay JK, West RB, Tsao SW, Meyer T, Riechelmann H, Oppermann U, Delecluse HJ, Willems SM, Chua MLK, Busson P, Lo KW, Wollmann G, Pillay N, Vanhaesebroeck B, Lund VJ. Somatostatin receptor 2 expression in nasopharyngeal cancer is induced by Epstein Barr virus infection: impact on prognosis, imaging and therapy. Nat Commun 2021; 12:117. [PMID: 33402692 PMCID: PMC7785735 DOI: 10.1038/s41467-020-20308-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal cancer (NPC), endemic in Southeast Asia, lacks effective diagnostic and therapeutic strategies. Even in high-income countries the 5-year survival rate for stage IV NPC is less than 40%. Here we report high somatostatin receptor 2 (SSTR2) expression in multiple clinical cohorts comprising 402 primary, locally recurrent and metastatic NPCs. We show that SSTR2 expression is induced by the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) via the NF-κB pathway. Using cell-based and preclinical rodent models, we demonstrate the therapeutic potential of SSTR2 targeting using a cytotoxic drug conjugate, PEN-221, which is found to be superior to FDA-approved SSTR2-binding cytostatic agents. Furthermore, we reveal significant correlation of SSTR expression with increased rates of survival and report in vivo uptake of the SSTR2-binding 68Ga-DOTA-peptide radioconjugate in PET-CT scanning in a clinical trial of NPC patients (NCT03670342). These findings reveal a key role in EBV-associated NPC for SSTR2 in infection, imaging, targeted therapy and survival.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Epstein-Barr Virus Infections/drug therapy
- Epstein-Barr Virus Infections/genetics
- Epstein-Barr Virus Infections/mortality
- Epstein-Barr Virus Infections/virology
- Gene Expression Regulation, Neoplastic
- Herpesvirus 4, Human/drug effects
- Herpesvirus 4, Human/growth & development
- Herpesvirus 4, Human/pathogenicity
- Host-Pathogen Interactions/genetics
- Lymphatic Metastasis
- Mice, Nude
- Molecular Targeted Therapy
- Nasopharyngeal Carcinoma/drug therapy
- Nasopharyngeal Carcinoma/genetics
- Nasopharyngeal Carcinoma/mortality
- Nasopharyngeal Carcinoma/virology
- Nasopharyngeal Neoplasms/drug therapy
- Nasopharyngeal Neoplasms/genetics
- Nasopharyngeal Neoplasms/mortality
- Nasopharyngeal Neoplasms/virology
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/virology
- NF-kappa B/genetics
- NF-kappa B/metabolism
- Octreotide/pharmacology
- Positron Emission Tomography Computed Tomography
- Receptors, Somatostatin/antagonists & inhibitors
- Receptors, Somatostatin/genetics
- Receptors, Somatostatin/metabolism
- Signal Transduction
- Survival Analysis
- Viral Matrix Proteins/antagonists & inhibitors
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Matt Lechner
- UCL Cancer Institute, University College London, London, UK.
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA.
- Barts Health NHS Trust, London, UK.
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK.
| | - Volker H Schartinger
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Wen Long Nei
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Marc Lucas Ooft
- King´s College Hospitals, NHS Foundation Trust, London, UK
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Liesa-Marie Schreiber
- Institute of Virology and Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Grace Tin-Yun Chung
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuk Yu Chan
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wu
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Man Tsang
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wayne Pearce
- UCL Cancer Institute, University College London, London, UK
| | | | | | - Liam Masterson
- Department of Otolaryngology, Addenbrooke's Hospital, Cambridge, UK
| | - Reshma Nibhani
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Graham Wells
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Julia Koller
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Susanne Delecluse
- German Cancer Research Centre (DKFZ) and Inserm, Unit F100/U1074, Heidelberg, Germany
| | - Yim Ling Yip
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, London, UK
| | - Cillian T Forde
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Martin D Forster
- UCL Cancer Institute, University College London, London, UK
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Amrita Jay
- Department of Histopathology, University College London Hospitals NHS Trust, Euston Road, London, UK
| | - József Dudás
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Annika Krapp
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Simon Wan
- Institute of Nuclear Medicine, University College Hospital, Euston Road, London, UK
| | - Christian Uprimny
- Department of Nuclear Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Susanne Sprung
- Department of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Haybaeck
- Department of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK
| | - Kerry Chester
- UCL Cancer Institute, University College London, London, UK
| | - Christina Thirlwell
- UCL Cancer Institute, University College London, London, UK
- University of Exeter College of Medicine and Health, Exeter, UK
| | - Gary Royle
- UCL Cancer Institute, University College London, London, UK
| | | | - Rajeev Gupta
- UCL Cancer Institute, University College London, London, UK
| | - Sagung Rai Indrasari
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Camelia Herdini
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Mohd Afiq Mohd Slim
- Department of Ear, Nose and Throat, University Hospital Crosshouse, Crosshouse, Kilmarnock, UK
| | - I Indrawati
- Department of Anatomical Pathology, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | | | - Renske Fles
- Department of Head and Neck Surgery and Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bing Tan
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
- Department of ENT/Head and Neck Surgery, Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
| | - Joe Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Haitao Wang
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Kelvin S H Loke
- Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, Singapore, Singapore
| | - Wan He
- Department of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Hongtao Jin
- Department of Pathology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Zhiqiang Cheng
- Department of Pathology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - David Howard
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
- ENT Department, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Joshua K Tay
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sai Wah Tsao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Tim Meyer
- UCL Cancer Institute, University College London, London, UK
| | - Herbert Riechelmann
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Udo Oppermann
- Botnar Research Centre, University of Oxford, Oxford, UK
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79085, Freiburg, Germany
| | | | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Melvin L K Chua
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Pierre Busson
- CNRS-UMR 9018-METSY, Gustave Roussy and Université Paris-Saclay, Villejuif, France
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Guido Wollmann
- Institute of Virology and Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Nischalan Pillay
- UCL Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | | | - Valerie J Lund
- UCL Cancer Institute, University College London, London, UK.
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK.
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14
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Rothenburger T, McLaughlin KM, Herold T, Schneider C, Oellerich T, Rothweiler F, Feber A, Fenton TR, Wass MN, Keppler OT, Michaelis M, Cinatl J. SAMHD1 is a key regulator of the lineage-specific response of acute lymphoblastic leukaemias to nelarabine. Commun Biol 2020; 3:324. [PMID: 32581304 PMCID: PMC7314829 DOI: 10.1038/s42003-020-1052-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
The nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), is effective against T-cell acute lymphoblastic leukaemia (T-ALL) but not against B-cell ALL (B-ALL). The underlying mechanisms have remained elusive. Here, data from pharmacogenomics studies and a panel of ALL cell lines reveal an inverse correlation between nelarabine sensitivity and the expression of SAMHD1, which can hydrolyse and inactivate triphosphorylated nucleoside analogues. Lower SAMHD1 abundance is detected in T-ALL than in B-ALL in cell lines and patient-derived leukaemic blasts. Mechanistically, T-ALL cells display increased SAMHD1 promoter methylation without increased global DNA methylation. SAMHD1 depletion sensitises B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induces AraG resistance. SAMHD1 has a larger impact on nelarabine/AraG than on cytarabine in ALL cells. Opposite effects are observed in acute myeloid leukaemia cells, indicating entity-specific differences. In conclusion, SAMHD1 promoter methylation and, in turn, SAMHD1 expression levels determine ALL cell response to nelarabine.
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Affiliation(s)
- Tamara Rothenburger
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | | | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistraße 15, 81377, Munich, Germany
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Feodor-Lynenstraße 21, 81377, Munich, Germany
| | - Constanze Schneider
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Cancer Consortium/German Cancer Research Center, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Rothweiler
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Oliver T Keppler
- Faculty of Medicine, Max von Pettenkofer Institute, Virology, LMU München, Pettenkoferstraße 9a, 80336, Munich, Germany
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Jindrich Cinatl
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany.
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15
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Ford K, Hanley CJ, Mellone M, Szyndralewiez C, Heitz F, Wiesel P, Wood O, Machado M, Lopez MA, Ganesan AP, Wang C, Chakravarthy A, Fenton TR, King EV, Vijayanand P, Ottensmeier CH, Al-Shamkhani A, Savelyeva N, Thomas GJ. NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors. Cancer Res 2020; 80:1846-1860. [PMID: 32122909 PMCID: PMC7611230 DOI: 10.1158/0008-5472.can-19-3158] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 10/10/2019] [Revised: 12/13/2019] [Accepted: 02/04/2020] [Indexed: 01/01/2023]
Abstract
Determining mechanisms of resistance to αPD-1/PD-L1 immune-checkpoint immunotherapy is key to developing new treatment strategies. Cancer-associated fibroblasts (CAF) have many tumor-promoting functions and promote immune evasion through multiple mechanisms, but as yet, no CAF-specific inhibitors are clinically available. Here we generated CAF-rich murine tumor models (TC1, MC38, and 4T1) to investigate how CAFs influence the immune microenvironment and affect response to different immunotherapy modalities [anticancer vaccination, TC1 (HPV E7 DNA vaccine), αPD-1, and MC38] and found that CAFs broadly suppressed response by specifically excluding CD8+ T cells from tumors (not CD4+ T cells or macrophages); CD8+ T-cell exclusion was similarly present in CAF-rich human tumors. RNA sequencing of CD8+ T cells from CAF-rich murine tumors and immunochemistry analysis of human tumors identified significant upregulation of CTLA-4 in the absence of other exhaustion markers; inhibiting CTLA-4 with a nondepleting antibody overcame the CD8+ T-cell exclusion effect without affecting Tregs. We then examined the potential for CAF targeting, focusing on the ROS-producing enzyme NOX4, which is upregulated by CAF in many human cancers, and compared this with TGFβ1 inhibition, a key regulator of the CAF phenotype. siRNA knockdown or pharmacologic inhibition [GKT137831 (Setanaxib)] of NOX4 "normalized" CAF to a quiescent phenotype and promoted intratumoral CD8+ T-cell infiltration, overcoming the exclusion effect; TGFβ1 inhibition could prevent, but not reverse, CAF differentiation. Finally, NOX4 inhibition restored immunotherapy response in CAF-rich tumors. These findings demonstrate that CAF-mediated immunotherapy resistance can be effectively overcome through NOX4 inhibition and could improve outcome in a broad range of cancers. SIGNIFICANCE: NOX4 is critical for maintaining the immune-suppressive CAF phenotype in tumors. Pharmacologic inhibition of NOX4 potentiates immunotherapy by overcoming CAF-mediated CD8+ T-cell exclusion. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/9/1846/F1.large.jpg.See related commentary by Hayward, p. 1799.
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Affiliation(s)
- Kirsty Ford
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christopher J Hanley
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Massimiliano Mellone
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | | | | | - Oliver Wood
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Maria Machado
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | | | - Chuan Wang
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ankur Chakravarthy
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK
| | - Emma V King
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | | | - Aymen Al-Shamkhani
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Natalia Savelyeva
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK.
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16
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Yoo S, Chen Q, Wang L, Wang W, Chakravarthy A, Busuttil R, Boussioutas A, Fenton TR, Zhang J, Fan X, Leung SY, Zhu J. Abstract B103: Molecular heterogeneity of gastric cancer explained by methylation-driven key regulators. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-b103] [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
Gastric cancer (GC) is a heterogeneous disease in which diverse genetic, genomic, and epigenetic alterations can accumulate in different molecular and histologic subtypes. Tumor microenvironment (TME) also contributes to the heterogeneity of GC. To investigate what molecular features of tumor cells drive GC heterogeneity, we developed an integrative causal model, called Integrative Sequential Causality Test (ISCT), to identify key regulators of GC by integrating DNA methylation, copy number variation, and transcriptomic data. Applying ISCT to three GC cohorts that contain methylation, CNV, and gene expression data, 11 common methylation-driven key regulators were identified: ADHFE1, CDO1, CRYAB, FSTL1, GTP, PKP3, PTPRCAP, RAB25, RHOH, SFN, and SORD. Based on these 11 genes, gastric tumors resolved into three groups that were associated with known molecular subtypes, Lauren classification, tumor stage, and patient survival, suggesting significance of the methylation-driven key regulators in molecular and histologic heterogeneity of GC. We also investigated the relationship between TME and the methylation-driven key regulators and showed that both immune/stromal proportions in TME and tumor cell genomics variations contributed to expression variations of the methylation-driven key regulators. Especially, FSTL1, significantly associated with patient survival and tumor progression as well as stromal proportion in TME, was expressed at high level in both stromal and cancer cells, indicating its potential role in mediating tumor-stroma interactions. In summary, this study suggests that genetic, genomic, and epigenetic alterations as well as their interactions with TME contribute to heterogeneity of GC.
Citation Format: Seungyeul Yoo, Quan Chen, Li Wang, Wenhui Wang, Ankur Chakravarthy, Rita Busuttil, Alex Boussioutas, Tim R. Fenton, Jiangwen Zhang, Xiaodan Fan, Seut-Yi Leung, Jun Zhu. Molecular heterogeneity of gastric cancer explained by methylation-driven key regulators [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B103.
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Affiliation(s)
- Seungyeul Yoo
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
| | - Quan Chen
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
| | - Li Wang
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
| | - Wenhui Wang
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
| | - Ankur Chakravarthy
- 2Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada,
| | - Rita Busuttil
- 3University of Melbourne, Parkville, VIC, Australia,
| | | | | | | | - Xiaodan Fan
- 6Chinese University of Hong Kong, Hong Kong, China
| | | | - Jun Zhu
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
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17
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Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 36:690-691. [PMID: 31821785 PMCID: PMC6946119 DOI: 10.1016/j.ccell.2019.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 35:816. [PMID: 31085179 PMCID: PMC8717880 DOI: 10.1016/j.ccell.2019.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Abstract
The interaction between human papillomaviruses (HPV) and the apolipoprotein-B mRNA-editing catalytic polypeptide-like (APOBEC)3 (A3) genes has garnered increasing attention in recent years, with considerable efforts focused on understanding their apparent roles in both viral editing and in HPV-driven carcinogenesis. Here, we review these developments and highlight several outstanding questions in the field. We consider whether editing of the virus and mutagenesis of the host are linked or whether both are essentially separate events, coincidentally mediated by a common or distinct A3 enzymes. We discuss the viral mechanisms and cellular signalling pathways implicated in A3 induction in virally infected cells and examine which of the A3 enzymes might play the major role in HPV-associated carcinogenesis and in the development of therapeutic resistance. We consider the parallels between A3 induction in HPV-infected cells and what might be causing aberrant A3 activity in HPV-independent cancers such as those arising in the bladder, lung and breast. Finally, we discuss the implications of ongoing A3 activity in tumours under treatment and the therapeutic opportunities that this may present.
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Affiliation(s)
- Nicola J Smith
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, UK
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20
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Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 35:504-518.e7. [PMID: 30827889 PMCID: PMC6424615 DOI: 10.1016/j.ccell.2019.01.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [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: 06/08/2018] [Revised: 11/10/2018] [Accepted: 01/28/2019] [Indexed: 11/21/2022]
Abstract
Ionizing radiation (IR) and chemotherapy are standard-of-care treatments for glioblastoma (GBM) patients and both result in DNA damage, however, the clinical efficacy is limited due to therapeutic resistance. We identified a mechanism of such resistance mediated by phosphorylation of PTEN on tyrosine 240 (pY240-PTEN) by FGFR2. pY240-PTEN is rapidly elevated and bound to chromatin through interaction with Ki-67 in response to IR treatment and facilitates the recruitment of RAD51 to promote DNA repair. Blocking Y240 phosphorylation confers radiation sensitivity to tumors and extends survival in GBM preclinical models. Y240F-Pten knockin mice showed radiation sensitivity. These results suggest that FGFR-mediated pY240-PTEN is a key mechanism of radiation resistance and is an actionable target for improving radiotherapy efficacy.
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Affiliation(s)
- Jianhui Ma
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jorge A Benitez
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jie Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shunichiro Miki
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Claudio Ponte de Albuquerque
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Thais Galatro
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Laura Orellana
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Ciro Zanca
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Rachel Reed
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Antonia Boyer
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Tomoyuki Koga
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Nissi M Varki
- Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Suely Kazue Nagahashi Marie
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil; Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil
| | - Erik Lindahl
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Timothy C Gahman
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Andrew K Shiau
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - John DeGroot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P Sulman
- Departments of Radiation Oncology, Translational Molecular Pathology, and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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21
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Chakravarthy A, Furness A, Joshi K, Ghorani E, Ford K, Ward MJ, King EV, Lechner M, Marafioti T, Quezada SA, Thomas GJ, Feber A, Fenton TR. Author Correction: Pan-cancer deconvolution of tumour composition using DNA methylation. Nat Commun 2018; 9:4642. [PMID: 30389940 PMCID: PMC6214991 DOI: 10.1038/s41467-018-07155-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in Figure 4. In panel a, the colour code for hot and cold clusters was inadvertently inverted. In the correct version of panel a, the hot clusters are blue and the cold clusters are yellow. This error has now been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Ankur Chakravarthy
- Department of Oncology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Princess Margaret Cancer Centre, Toronto, ON M5G 2C4, Canada
| | - Andrew Furness
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Kroopa Joshi
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Ehsan Ghorani
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Kirsty Ford
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Matthew J Ward
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Emma V King
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Matt Lechner
- Department of Oncology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Teresa Marafioti
- Department of Pathology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Sergio A Quezada
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, London WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.
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22
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Chakravarthy A, Furness A, Joshi K, Ghorani E, Ford K, Ward MJ, King EV, Lechner M, Marafioti T, Quezada SA, Thomas GJ, Feber A, Fenton TR. Pan-cancer deconvolution of tumour composition using DNA methylation. Nat Commun 2018; 9:3220. [PMID: 30104673 PMCID: PMC6089972 DOI: 10.1038/s41467-018-05570-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [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: 03/09/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: 'immune hot' and 'immune cold', which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to cytotoxic T-lymphocyte infiltration, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations, potentially explaining the heterogeneity of immunotherapy response and prognosis seen within this group. Finally, we define a catalogue of mediators of active antitumour immunity, deriving candidate biomarkers and potential targets for precision immunotherapy.
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Affiliation(s)
- Ankur Chakravarthy
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
- Princess Margaret Cancer Centre, Toronto, ON, M5G 2C4, Canada
| | - Andrew Furness
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kroopa Joshi
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Ehsan Ghorani
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kirsty Ford
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matthew J Ward
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Emma V King
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matt Lechner
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Teresa Marafioti
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Sergio A Quezada
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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23
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Lechner M, Chakravarthy AR, Walter V, Masterson L, Feber A, Jay A, Weinberger PM, McIndoe RA, Forde CT, Chester K, Kalavrezos N, O'Flynn P, Forster M, Jones TM, Vaz FM, Hayes DN, Fenton TR. Frequent HPV-independent p16/INK4A overexpression in head and neck cancer. Oral Oncol 2018; 83:32-37. [DOI: 10.1016/j.oraloncology.2018.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/13/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
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24
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Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, Navaratnam N, Pálinkás HL, Vértessy BG, Fenton TR, Doorbar J, Fuller-Pace F, Meek DW, Coombes RC, Buluwela L, Ali S. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res 2017; 45:11056-11069. [PMID: 28977491 PMCID: PMC5737468 DOI: 10.1093/nar/gkx721] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022] Open
Abstract
Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.
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Affiliation(s)
- Manikandan Periyasamy
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Anup K. Singh
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Carolina Gemma
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Christian Kranjec
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Raed Farzan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Damien A. Leach
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Naveenan Navaratnam
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hajnalka L. Pálinkás
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Beata G. Vértessy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Tim R. Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - John Doorbar
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Frances Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - David W. Meek
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - R. Charles Coombes
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Laki Buluwela
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
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25
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Chakravarthy A, Henderson S, Thirdborough SM, Ottensmeier CH, Su X, Lechner M, Feber A, Thomas GJ, Fenton TR. Human Papillomavirus Drives Tumor Development Throughout the Head and Neck: Improved Prognosis Is Associated With an Immune Response Largely Restricted to the Oropharynx. J Clin Oncol 2016; 34:4132-4141. [PMID: 27863190 PMCID: PMC5477823 DOI: 10.1200/jco.2016.68.2955] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [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] [Indexed: 12/19/2022] Open
Abstract
Purpose In squamous cell carcinomas of the head and neck (HNSCC), the increasing incidence of oropharyngeal squamous cell carcinomas (OPSCCs) is attributable to human papillomavirus (HPV) infection. Despite commonly presenting at late stage, HPV-driven OPSCCs are associated with improved prognosis compared with HPV-negative disease. HPV DNA is also detectable in nonoropharyngeal (non-OPSCC), but its pathogenic role and clinical significance are unclear. The objectives of this study were to determine whether HPV plays a causal role in non-OPSCC and to investigate whether HPV confers a survival benefit in these tumors. Methods Meta-analysis was used to build a cross-tissue gene-expression signature for HPV-driven cancer. Classifiers trained by machine-learning approaches were used to predict the HPV status of 520 HNSCCs profiled by The Cancer Genome Atlas project. DNA methylation data were similarly used to classify 464 HNSCCs and these analyses were integrated with genomic, histopathology, and survival data to permit a comprehensive comparison of HPV transcript-positive OPSCC and non-OPSCC. Results HPV-driven tumors accounted for 4.1% of non-OPSCCs. Regardless of anatomic site, HPV+ HNSCCs shared highly similar gene expression and DNA methylation profiles; nonkeratinizing, basaloid histopathological features; and lack of TP53 or CDKN2A alterations. Improved overall survival, however, was largely restricted to HPV-driven OPSCCs, which were associated with increased levels of tumor-infiltrating lymphocytes compared with HPV-driven non-OPSCCs. Conclusion Our analysis identified a causal role for HPV in transcript-positive non-OPSCCs throughout the head and neck. Notably, however, HPV-driven non-OPSCCs display a distinct immune microenvironment and clinical behavior compared with HPV-driven OPSCCs.
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Affiliation(s)
- Ankur Chakravarthy
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen Henderson
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen M. Thirdborough
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christian H. Ottensmeier
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiaoping Su
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matt Lechner
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Feber
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gareth J. Thomas
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tim R. Fenton
- Ankur Chakravarthy, Stephen Henderson, Matt Lechner, Andrew Feber, and Tim R. Fenton, UCL Cancer Institute, University College London, London; Stephen M. Thirdborough, Christian H. Ottensmeier, and Gareth J. Thomas, University of Southampton, Southampton, United Kingdom; Xiaoping Su, The University of Texas MD Anderson Cancer Center, Houston, TX
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Affiliation(s)
- T R Fenton
- Department of Community Health Sciences, Institute of Public Health, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada.
| | - C J Fenton
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
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Lechner M, Fenton TR. The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease. Adv Genet 2016; 93:1-56. [PMID: 26915269 DOI: 10.1016/bs.adgen.2015.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis.
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Affiliation(s)
- M Lechner
- Head and Neck Centre, University College London Hospital, London, UK; UCL Cancer Institute, University College London, London, United Kingdom
| | - T R Fenton
- UCL Cancer Institute, University College London, London, United Kingdom
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Henderson S, Chakravarthy A, Su X, Boshoff C, Fenton TR. Abstract 3169: APOBEC-mediated cytosine deamination is a prominent mutagenic mechanism in human papillomavirus-driven cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3169] [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
APOBEC3B cytosine deaminase activity has recently emerged as a significant mutagenic factor in human cancer. APOBEC activity is induced in virally infected cells and APOBEC signature mutations occur at high frequency in cervical cancers, over 99% of which are caused by high risk variants of Human Papillomavirus (HPV). We tested the hypothesis that APOBEC-mediated mutagenesis plays a particularly important role in HPV-associated cancer by analysing head and neck squamous cell carcinoma (HNSCC), a tumor type for which exome sequence data from The Cancer Genome Atlas project are available from both HPV+ and HPV- variants. We show that HPV+ tumors express more APOBEC3B and harbor a higher proportion of APOBEC signature mutations than HPV- tumors. The APOBEC mutational signature is absent from hepatitis virus-associated hepatocellular carcinoma, indicating it is not simply a consequence of the immune response to persistent viral infection. We also uncover a strong linear relationship between APOBEC signature mutations and APOBEC-independent mutations in both HNSCC and in breast cancer, such that in high APOBEC subsets (HPV+ HNSCC and HER2-amplified breast cancer), the proportion of mutations due to APOBEC activity is consistently increased, regardless of the overall mutational burden in the tumor. Finally, HPV+ HNSCC and cervical cancer show particularly strong enrichment for APOBEC signature mutations in known cancer genes, implicating APOBEC activity as a key driver of HPV-induced transformation.
Citation Format: Stephen Henderson, Ankur Chakravarthy, Xiaoping Su, Chris Boshoff, Tim R. Fenton. APOBEC-mediated cytosine deamination is a prominent mutagenic mechanism in human papillomavirus-driven cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3169. doi:10.1158/1538-7445.AM2014-3169
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Affiliation(s)
| | | | - Xiaoping Su
- 2University of Texas MD Anderson Cancer Center, Houston, TX
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Read RD, Fenton TR, Gomez GG, Wykosky J, Vandenberg SR, Babic I, Iwanami A, Yang H, Cavenee WK, Mischel PS, Furnari FB, Thomas JB. A kinome-wide RNAi screen in Drosophila Glia reveals that the RIO kinases mediate cell proliferation and survival through TORC2-Akt signaling in glioblastoma. PLoS Genet 2013; 9:e1003253. [PMID: 23459592 PMCID: PMC3573097 DOI: 10.1371/journal.pgen.1003253] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [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: 06/06/2012] [Accepted: 12/04/2012] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma, the most common primary malignant brain tumor, is incurable with current therapies. Genetic and molecular analyses demonstrate that glioblastomas frequently display mutations that activate receptor tyrosine kinase (RTK) and Pi-3 kinase (PI3K) signaling pathways. In Drosophila melanogaster, activation of RTK and PI3K pathways in glial progenitor cells creates malignant neoplastic glial tumors that display many features of human glioblastoma. In both human and Drosophila, activation of the RTK and PI3K pathways stimulates Akt signaling along with other as-yet-unknown changes that drive oncogenesis. We used this Drosophila glioblastoma model to perform a kinome-wide genetic screen for new genes required for RTK- and PI3K-dependent neoplastic transformation. Human orthologs of novel kinases uncovered by these screens were functionally assessed in mammalian glioblastoma models and human tumors. Our results revealed that the atypical kinases RIOK1 and RIOK2 are overexpressed in glioblastoma cells in an Akt-dependent manner. Moreover, we found that overexpressed RIOK2 formed a complex with RIOK1, mTor, and mTor-complex-2 components, and that overexpressed RIOK2 upregulated Akt signaling and promoted tumorigenesis in murine astrocytes. Conversely, reduced expression of RIOK1 or RIOK2 disrupted Akt signaling and caused cell cycle exit, apoptosis, and chemosensitivity in glioblastoma cells by inducing p53 activity through the RpL11-dependent ribosomal stress checkpoint. These results imply that, in glioblastoma cells, constitutive Akt signaling drives RIO kinase overexpression, which creates a feedforward loop that promotes and maintains oncogenic Akt activity through stimulation of mTor signaling. Further study of the RIO kinases as well as other kinases identified in our Drosophila screen may reveal new insights into defects underlying glioblastoma and related cancers and may reveal new therapeutic opportunities for these cancers. Glioblastomas, the most common primary brain tumor, harbor mutations in receptor tyrosine kinases (RTKs), such as EGFR, and components of the Pi-3 kinase (PI3K) signaling pathway. However, the genes that act downstream of RTK and PI3K signaling to drive glioblastoma remain unclear. To investigate the genetic and molecular basis of this disease, we created a glioblastoma model in the fruit fly Drosophila melanogaster. To identify new genes involved in glioblastoma development, we performed a screen for the genes required for tumor cell proliferation using our Drosophila glioblastoma model and then functionally assessed the activity of human versions of novel genes identified in this screen. Our results revealed that the RIO kinases become overexpressed in human glioblastomas but not in normal human glial or neuronal cells. We found that overexpression of the RIO kinases promotes and maintains signals that drive tumor cell proliferation and survival in RTK- and PI3K-dependent human glioblastoma, and reduction of RIO kinase expression decreased proliferation and prompted cell death and chemosensitivity in glioblastoma cells. Therefore, disruption of the RIO kinases may provide new therapeutic opportunities to target glioblastoma and other RTK- or PI3K-dependent cancers.
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Affiliation(s)
- Renee D Read
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA.
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Fenton TR, Gout IT. Functions and regulation of the 70kDa ribosomal S6 kinases. Int J Biochem Cell Biol 2010; 43:47-59. [PMID: 20932932 DOI: 10.1016/j.biocel.2010.09.018] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/17/2010] [Accepted: 09/23/2010] [Indexed: 01/01/2023]
Abstract
The 70kDa ribosomal protein S6 kinases, S6K1 and S6K2 are two highly homologous serine/threonine kinases that are activated in response to growth factors, cytokines and nutrients. The S6 kinases have been linked to diverse cellular processes, including protein synthesis, mRNA processing, glucose homeostasis, cell growth and survival. Studies in model organisms have highlighted the roles that S6K activity plays in a number of pathologies, including obesity, diabetes, ageing and cancer. The importance of S6K function in human diseases has led to the development of S6K-specific inhibitors by a number of companies, offering the promise of improved tools with which to study these enzymes and potentially the effective targeting of deregulated S6K signalling in patients. Here we review the current literature on the role of S6Ks in the regulation of cell growth, survival and proliferation downstream of various signalling pathways and how their dysregulation contributes to the pathogenesis of human diseases.
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Affiliation(s)
- Tim R Fenton
- Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0660, USA
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Fenton TR, Gwalter J, Cramer R, Gout IT. S6K1 is acetylated at lysine 516 in response to growth factor stimulation. Biochem Biophys Res Commun 2010; 398:400-5. [PMID: 20599721 DOI: 10.1016/j.bbrc.2010.06.081] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 06/20/2010] [Indexed: 10/19/2022]
Abstract
The 70kDa ribosomal protein S6 kinase 1 (S6K1) plays important roles in the regulation of protein synthesis, cell growth and metabolism. S6K1 is activated by the phosphorylation of multiple serine and threonine residues in response to stimulation by a variety of growth factors and cytokines. In addition to phosphorylation, we have recently shown that S6K1 is also targeted by lysine acetylation. Here, using tandem mass spectrometry we have mapped acetylation of S6K1 to lysine 516, a site close to the C-terminus of the kinase that is highly conserved amongst vertebrate S6K1 orthologues. Using acetyl-specific K516 antibodies, we show that acetylation of endogenous S6K1 at this site is potently induced upon growth factor stimulation. Although S6K1 acetylation and phosphorylation are both induced by growth factor stimulation, these events appear to be functionally independent. Indeed, experiments using inhibitors of S6K1 activation and exposure of cells to various stresses indicate that S6K1 acetylation can occur in the absence of phosphorylation and vice versa. We propose that K516 acetylation may serve to modulate important kinase-independent functions of S6K1 in response to growth factor signalling.
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Affiliation(s)
- Tim R Fenton
- Department of Structural and Molecular Biology, University College London, Gower Street, Darwin Building, London WC1E 6BT, UK
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Fenton TR, Gwalter J, Ericsson J, Gout IT. Histone acetyltransferases interact with and acetylate p70 ribosomal S6 kinases in vitro and in vivo. Int J Biochem Cell Biol 2009; 42:359-66. [PMID: 19961954 DOI: 10.1016/j.biocel.2009.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 11/12/2009] [Accepted: 11/24/2009] [Indexed: 12/27/2022]
Abstract
The 70kDa ribosomal protein S6 kinases (S6K1 and S6K2) play important roles in the regulation of protein synthesis, cell growth and survival. S6Ks are activated in response to mitogen stimulation and nutrient sufficiency by the phosphorylation of conserved serine and threonine residues. Here we show for the first time, that in addition to phosphorylation, S6Ks are also targeted by lysine acetylation. Following mitogen stimulation, S6Ks interact with the p300 and p300/CBP-associated factor (PCAF) acetyltransferases. S6Ks can be acetylated by p300 and PCAF in vitro and S6K acetylation is detected in cells expressing p300. Furthermore, it appears that the acetylation sites targeted by p300 lie within the divergent C-terminal regulatory domains of both S6K1 and S6K2. Acetylation of S6K1 and 2 is increased upon the inhibition of class I/II histone deacetylases (HDACs) by trichostatin-A, while the enhancement of S6K1 acetylation by nicotinamide suggests the additional involvement of sirtuin deacetylases in S6K deacetylation. Both expression of p300 and HDAC inhibition cause increases in S6K protein levels, and we have shown that S6K2 is stabilized in cells treated with HDAC inhibitors. The finding that S6Ks are targeted by histone acetyltransferases uncovers a novel mode of crosstalk between mitogenic signalling pathways and the transcriptional machinery and reveals additional complexity in the regulation of S6K function.
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Affiliation(s)
- T R Fenton
- Research Department of Structural and Molecular Biology, University College London, London, United Kingdom
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Abstract
OBJECTIVES The use of exact percentiles and z-scores permit optimal assessment of infants' growth. In addition, z-scores allow the precise description of size outside of the 3rd and 97th percentiles of a growth reference. To calculate percentiles and z-scores, health professionals require the LMS parameters (Lambda for the skew, Mu for the median, and Sigma for the generalized coefficient of variation; Cole, 1990). The objective of this study was to calculate the LMS parameters for the Fenton preterm growth chart (2003). DESIGN Secondary data analysis of the Fenton preterm growth chart data. METHODS The Cole methods were used to produce the LMS parameters and to smooth the L parameter. New percentiles were generated from the smooth LMS parameters, which were then compared with the original growth chart percentiles. RESULTS The maximum differences between the original percentile curves and the percentile curves generated from the LMS parameters were: for weight; a difference of 66 g (2.9%) at 32 weeks along the 90th percentile; for head circumference; some differences of 0.3 cm (0.6-1.0%); and for length; a difference of 0.5 cm (1.6%) at 22 weeks on the 97th percentile. CONCLUSION The percentile curves generated from the smoothed LMS parameters for the Fenton growth chart are similar to the original curves. These LMS parameters for the Fenton preterm growth chart facilitate the calculation of z-scores, which will permit the more precise assessment of growth of infants who are born preterm.
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Affiliation(s)
- T R Fenton
- Department of Community Health Sciences, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.
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Fenton TR. Not all osmolality is created equal. Arch Dis Child Fetal Neonatal Ed 2006; 91:F234. [PMID: 16632657 PMCID: PMC2672716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Abstract
BACKGROUND The ideal quantity of dietary protein for formula-fed low birth weight infants < 2.5 kilograms is still a matter of controversy and debate. In premature infants, the protein intake must be sufficient to achieve normal growth without negative effects such as acidosis, uremia, and elevated levels of circulating amino acids (e.g. phenylalanine levels). This systematic review evaluates the benefits and risks of higher (>= 3.0 g/kg/day) versus lower (< 3.0 g/kg/day) protein intakes during the initial hospital stay of formula-fed preterm infants < 2.5 kilograms. OBJECTIVES To determine whether higher (>= 3.0 g/kg/day) versus lower (< 3.0 g/kg/day) protein intakes during the initial hospital stay of formula-fed preterm infants < 2.5 kilograms result in improved growth and neurodevelopmental outcomes without evidence of short and long-term morbidity. SEARCH STRATEGY Two review authors searched MEDLINE (1966 - May 2005), CINAHL (1982 - May 2005), PubMed (1966 - May 2005), EMBASE (1980 - May 2005), the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 2, 2005), abstracts, conferences and symposia proceedings from Society of Pediatric Research, and American Academy of Pediatrics. Cross references were reviewed independently for additional relevant titles and abstracts for articles up to fifty years old. SELECTION CRITERIA Randomized controlled trials contrasting levels of formula protein intakes as low (< 3.0 g/kg/day), high (=> 3.0 g/kg/day but < 4.0 g/kg/day), or very high protein intake (=> 4.0 g/kg/day) during hospitalization of neonates less than 2.5 kilograms at birth who were formula-fed. Studies were not included if infants received partial parenteral nutrition during the study period or were fed formula as a supplement to human milk. Given the small number of studies that met all inclusion criteria, studies in which nutrients other than protein also varied (> 10% relative difference) were added in a post-facto analysis. DATA COLLECTION AND ANALYSIS Two review authors used standard methods of the Cochrane Collaboration and of the Cochrane Neonatal Review Group to independently assess trial eligibility and quality, and extracted data. In a 3-arm trial where two groups fell within the same predesignated protein intake group, weighted means and pooled standard deviations were calculated. MAIN RESULTS The literature search identified 37 studies, of which five met all the inclusion criteria. All five studies compared low (< 3.0 g/kg/day) to high protein intakes (=> 3.0 g/kg/day but < 4.0 g/kg/day). The overall analysis revealed an improved weight gain (WMD 2.36 g/kg/day, 95% CI 1.31, 3.40) and higher nitrogen accretion (WMD 143.7 mg/kg/day, 95% CI 128.7, 158.8) in infants receiving formula with higher protein content while other nutrients were kept constant. None of the studies reported IQ or Bayley scores at 18 months or later. No significant differences were seen in rates of necrotizing enterocolitis, sepsis or diarrhea. Of three studies included in the post-facto analysis, only one could be included in the meta-analysis. The post-facto analysis revealed further improvement in all growth parameters in infants receiving formula with higher protein content (weight gain: WMD 2.53 g/kg/day, 95% CI 1.62, 3.45, linear growth: WMD 0.16 cm/week, 95% CI 0.03, 0.30, and head growth: WMD 0.23, 95% CI 0.12, 0.35). There was no significant difference (WMD 0.25, 95% CI -0.20, 0.70) in the concentration of plasma phenylalanine between the high and low protein intake groups. One study (Goldman 1969) in the post-facto analysis documented a significantly increased incidence of low IQ scores, below 90, in infants of birth weight less than 1300 grams who received a very high protein intake (6 to 7.2 g/kg/day). AUTHORS' CONCLUSIONS This systematic review suggests that higher protein intake (=> 3.0 g/kg/day but < 4.0 g/kg/day) from formula accelerates weight gain. Based on increased nitrogen accretion rates, this most likely indicates an increase in lean body mass. Although accelerated weight gain is considered to be a positive effect, increase in other outcome measures examined may represent a negative or ambivalent effect. These include elevated blood urea nitrogen levels and increased metabolic acidosis. Limited information was available regarding the impact of higher formula protein intakes on long term outcomes such as neurodevelopmental abnormalities. As determined in this review, existing research literature on this topic is not adequate to make specific recommendations regarding the provision of very high protein intake (> 4.0 g/kg/day) from formula.
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Affiliation(s)
- S S Premji
- University of Calgary, Faculty of Nursing, 2500 University Dr NW, Calgary, Alberta, Canada, T2N 1N4.
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Fordham-Skelton AP, Chilley P, Lumbreras V, Reignoux S, Fenton TR, Dahm CC, Pages M, Gatehouse JA. A novel higher plant protein tyrosine phosphatase interacts with SNF1-related protein kinases via a KIS (kinase interaction sequence) domain. Plant J 2002; 29:705-715. [PMID: 12148529 DOI: 10.1046/j.1365-313x.2002.01250.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A novel protein phosphatase in Arabidopsis thaliana was identified by database searching. This protein, designated AtPTPKIS1, contains a protein tyrosine phosphatase (PTP) catalytic domain and a kinase interaction sequence (KIS) domain. It is predicted to interact with plant SNF1-related kinases (SnRKs), representing central regulators of metabolic and stress responses. AtPTPKIS1 has close homologues in other plant species, both dicots and monocots, but is not found in other kingdoms. The tomato homologue of AtPTPKIS1 was expressed as a recombinant protein and shown to hydrolyse a generic phosphatase substrate, and phosphotyrosine residues in synthetic peptides. The KIS domain of AtPTPKIS1 was shown to interact with the plant SnRK AKIN11 both in vivo in the yeast two-hybrid system, and in vitro in a GST-fusion 'pull down' assay. The genomes of Arabidopsis and other plants contain further predicted proteins related to AtPTPKIS1, which could also interact with SnRKs and act in novel regulatory and signalling pathways.
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Abstract
Breast milk supplementation is frequently used to improve preterm infant growth and to achieve satisfactory intakes of minerals and vitamins. In the North American market there are commercial preparations: two powders and a liquid. The nutritional data available suggest these products are similar and their utilization is based on healthcare team choice. Parental perception about supplementation has not been previously evaluated although parental attitudes are known to impact on lactation success. The objectives of this paper are to determine parental preference and breastfeeding duration for very-low-birth-weight infants given commercial breast milk enrichment products. The study design is a randomized clinical trial with parental interviews. Sixty-three families with 71 infants were enrolled. Parents expressed their preference for the addition of a powder over a liquid preparation (p<0.01). Those mothers whose infants received the liquid enrichment had a shorter lactation relative to their goal, compared with the mothers of the infants who received the powder (p = 0.017). Parents prefer a powder product for breast milk supplementation and this choice positively impacts on the duration of breastfeeding for very-low-birth-weight infants.
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Affiliation(s)
- T R Fenton
- Clinical Nutrition Services, Foothills Medical Centre, Calgary Regional Health Authority, Alberta, Canada
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Abstract
Normative triglyceride levels were obtained from eighty-five infants weighing < 1500 g. At least 80% of their nutritional intake was their own mother's breast milk. Triglyceride levels did not correlate with birth weight, gestational age, volume of milk fed, age in days, or use of milk fortifier. The 95th percentile triglyceride value was 2.5 mmol/L. Assuming that breast milk-fed infants have triglyceride in the normal range, the acceptable limit of triglyceride values in very-low-birth-weight infants receiving i.v. lipids could be revised upward to 2.5 mmol/L.
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Affiliation(s)
- T R Fenton
- Clinical Nutrition Services, Foothills Hospital, Calgary, Alberta, Canada
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Fenton TR, Thirsk JE. Twin pregnancy: the distribution of maternal weight gain of non-smoking normal weight women. Can J Public Health 1994; 85:37-40. [PMID: 8180922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We documented the pattern and distribution of weight gain through twin pregnancies of healthy non-smoking women with good birth outcomes. The mean birthweight was 2621 g and the mean gestational age at delivery was 37.6 weeks. As few of the women were weighed after 34 weeks, the weight gain graph was drawn to this point. The sample was separated into subgroups based on birthweights and gender of the infants. Weight gains, parity, income, first measured weight, BMI and Apgars were not different between the subgroups. The only difference between those with infants that were small for gestational age (SGA), over 3 kg, or intermediate in weight was gestational age. For the groups divided by infant gender, the only differences were maternal age and infant birthweight. The mean, median and 80% confidence limits for weight gain at 34 weeks were 14.1, 13.6, and between 8.5 and 19.4 kg, respectively. There was a wide range of weight gained by these women carrying twin pregnancies.
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Affiliation(s)
- T R Fenton
- Clinical Nutrition Services, Foothills Hospital, Calgary, AB
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Fenton TR, McMillan DD, Sauve RS. Nutrition and growth analysis of very low birth weight infants. Pediatrics 1990; 86:378-83. [PMID: 2117742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The growth and nutrition of 220 very low birth weight infants were reviewed after comprehensive data on all infants in the hospital were entered into the Neonatal Intensive Care Unit Audit Data Base for 2 years prospectively. Fluid and energy (parenteral and oral) intakes were compared in four birth weight categories (1, less than or equal to 750 g; 2, 751 to 1000 g; 3, 1001 to 1250 g; 4, 1251 to 1500 g). Parenteral nutrition was the major source of first nutrition for the small infants, but seldom did it alone provide adequate nutrition for very low birth weight infants. The age of the first nutrition (parenteral and/or oral nutrition other than dextrose) decreased with increasing birth weight. The age of the first oral feedings was later for the infants of the lower birth weights but enteral feeding became the major nutrition for all weight categories by the second week of life. During the first 50 days the infants accumulated a deficit of 3780 to 5460 kJ relative to their estimated need of 504 kJ/kg per day, with the smaller infants accumulating a significantly larger deficit. The growth of infants appropriate for gestational age and of infants small for gestational age differed from each other and from the commonly used graph of Dancis et al (J Pediatr. 1948;33:570-572).
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Affiliation(s)
- T R Fenton
- Foothills Hospital, Calgary, Alberta, Canada
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Abstract
Aldosterone is important in the regulation of sodium conservation by both kidney and colon. In the very preterm neonate marked urinary salt wasting occurs because of immature renal tubular function, but little is known of the ontogeny of colonic transport processes. Using an in vivo rectal dialysis technique, we have shown that in the human infant the colon has well developed salt conserving mechanisms from early in the last trimester of gestation and that aldosterone is an important regulatory hormone. Sodium transport mechanisms in the colon appear to develop before those in the kidney and it is possible that the colon is the major organ of sodium conservation in the preterm neonate.
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Abstract
Four Asian babies were investigated because they failed to thrive. In all four cases the failure to thrive was a result of the mother's social isolation and inability to communicate, and to the father's refusal to accept that there was a problem in the family.
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Affiliation(s)
- T R Fenton
- Department of Paediatrics, St George's Hospital Medical School, London
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Abstract
Five cases of air embolism in ventilated very low birthweight infants are reported. In all cases the outcome was fatal with the babies dying at about 15 hours of age.
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Affiliation(s)
- T R Fenton
- Department of Child Health, St George's Hospital Medical School, London
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Abstract
The object of the research was to estimate wall stresses caused by vasoconstriction at arterial branches. The basic procedure was a combination of experimental strain measurement and analytical stress analysis. Segments of canine renal arteries were perfused and stimulated to constrict with dopamine hydrochloride and norepinephrine. Surface wall deformation was measured with a stereo-photographic technique. A plane stress finite element analysis was used to calculate wall stresses based on the experimentally derived deformations. The major result of the study was to demonstrate tensile stresses, and in some cases biaxial tension, in contracting vessels. Peak stresses in the apex of the acute angle of the branches were approximately three times unpenetrated hoop stress in the parent vessels. The results imply that constriction at a branch site may be capable of generating sufficient wall tension to tear arterial tissue, and that smooth muscle reactivity is important with respect to the etiology of cerebral aneurysms and the clinical management of acute branch site pathology.
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Abstract
In a child with congenital secretory diarrhoea, jejunal perfusion studies showed net water and electrolyte secretion and suggested a defect in sodium/proton exchange. A technique was developed for investigation of such exchange in brush-border membrane vesicles from jejunal biopsy specimens. Vesicles from control specimens displayed proton-gradient-dependent sodium uptake, whereas those from the patient did not. These findings, as well as pointing to a cause of congenital secretory diarrhoea, confirm the existence and importance of jejunal sodium/proton exchange in man.
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Fenton TR, Taylor JR. Simulation of endothelial response to injury. IEEE Trans Biomed Eng 1984; 31:252-5. [PMID: 6706354 DOI: 10.1109/tbme.1984.325335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Abstract
A laboratory study of the hydrostatic collapse of diseased tibial arteries demonstrated hysteresis in the pressure-flow behaviour which resembled that seen in the stress-strain relations of the arterial tissue. The pressures at which the vessels collapsed were found to be considerably lower than expected on the basis of theoretical elastic models. Also, the pressures at which the vessels reopened were consistently lower than the pressures at which they collapsed. These findings were explained on the basis of viscoelasticity. The difference between collapse and opening pressure may provide insight into the mechanical properties of vessels, and a clue to errors in non-invasive measurements of blood pressure which depend upon collapse of arteries.
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