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Zeng PYF, Cecchini MJ, Barrett JW, Shammas-Toma M, De Cecco L, Serafini MS, Cavalieri S, Licitra L, Hoebers F, Brakenhoff RH, Leemans CR, Scheckenbach K, Poli T, Wang X, Liu X, Laxague F, Prisman E, Poh C, Bose P, Dort JC, Shaikh MH, Ryan SEB, Dawson A, Khan MI, Howlett CJ, Stecho W, Plantinga P, Daniela da Silva S, Hier M, Khan H, MacNeil D, Mendez A, Yoo J, Fung K, Lang P, Winquist E, Palma DA, Ziai H, Amelio AL, Li SSC, Boutros PC, Mymryk JS, Nichols AC. Immune-based classification of HPV-associated oropharyngeal cancer with implications for biomarker-driven treatment de-intensification. EBioMedicine 2022; 86:104373. [PMID: 36442320 PMCID: PMC9706534 DOI: 10.1016/j.ebiom.2022.104373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND There is significant interest in treatment de-escalation for human papillomavirus-associated (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) patients given the generally favourable prognosis. However, 15-30% of patients recur after primary treatment, reflecting a need for improved risk-stratification tools. We sought to develop a molecular test to risk stratify HPV+ OPSCC patients. METHODS We created an immune score (UWO3) associated with survival outcomes in six independent cohorts comprising 906 patients, including blinded retrospective and prospective external validations. Two aggressive radiation de-escalation cohorts were used to assess the ability of UWO3 to identify patients who recur. Multivariate Cox models were used to assess the associations between the UWO3 immune class and outcomes. FINDINGS A three-gene immune score classified patients into three immune classes (immune rich, mixed, or immune desert) and was strongly associated with disease-free survival in six datasets, including large retrospective and prospective datasets. Pooled analysis demonstrated that the immune rich group had superior disease-free survival compared to the immune desert (HR = 9.0, 95% CI: 3.2-25.5, P = 3.6 × 10-5) and mixed (HR = 6.4, 95% CI: 2.2-18.7, P = 0.006) groups after adjusting for age, sex, smoking status, and AJCC8 clinical stage. Finally, UWO3 was able to identify patients from two small treatment de-escalation cohorts who remain disease-free after aggressive de-escalation to 30 Gy radiation. INTERPRETATION With additional prospective validation, the UWO3 score could enable biomarker-driven clinical decision-making for patients with HPV+ OPSCC based on robust outcome prediction across six independent cohorts. Prospective de-escalation and intensification clinical trials are currently being planned. FUNDING CIHR, European Union, and the NIH.
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Affiliation(s)
- Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Matthew J Cecchini
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Matthew Shammas-Toma
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Loris De Cecco
- Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy
| | - Mara S Serafini
- Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy
| | - Stefano Cavalieri
- Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lisa Licitra
- Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Frank Hoebers
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands
| | - Ruud H Brakenhoff
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - C René Leemans
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - Kathrin Scheckenbach
- Department of Otolaryngology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tito Poli
- Unit of Maxillofacial Surgery, Department of Medicine and Surgery, University of Parma-University Hospital of Parma, Parma, Italy
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Xinyi Liu
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Francisco Laxague
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Eitan Prisman
- Division of Otolaryngology- Head and Neck Surgery, Department of Surgery, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Catherine Poh
- Division of Otolaryngology- Head and Neck Surgery, Department of Surgery, Vancouver General Hospital, Vancouver, British Columbia, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pinaki Bose
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Joseph C Dort
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Mushfiq H Shaikh
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Sarah E B Ryan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Alice Dawson
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Mohammed I Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - William Stecho
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Paul Plantinga
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | | | - Michael Hier
- Department of Otolaryngology Head and Neck Surgery, McGill University, Montreal, Quebec, Canada
| | - Halema Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Pencilla Lang
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Eric Winquist
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - David A Palma
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Hedyeh Ziai
- Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Antonio L Amelio
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shawn S-C Li
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada.
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Patel KB, Cormier N, Fowler J, Partridge A, Theurer J, Black M, Pinto N, Yoo J, Fung K, MacNeil D, Stecho W, Howlett C, Brackstone M, Barrett JW, Nichols A. Detection of Circulating Tumor DNA in Patients with Thyroid Nodules. Int J Endocrinol 2021; 2021:8909224. [PMID: 34475951 PMCID: PMC8407979 DOI: 10.1155/2021/8909224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/17/2021] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Detection of circulating tumor DNA (ctDNA) in cancer patients can potentially serve as a noninvasive, sensitive test of disease status. The purpose of this study was to determine the ability to detect BRAF (V600E) mutations in the plasma of patients with thyroid nodules, with the goal of distinguishing between benign and malignant nodules. METHODS Consecutive patients with thyroid nodules who consented for surgery were recruited. Plasma samples were obtained preoperatively and one month postoperatively. Quantitative PCR was used to determine the levels of the BRAF (V600E) mutation preoperatively and postoperatively. RESULTS A total of 109 patients were recruited. On final pathology, 38 (32.8%) patients had benign thyroid nodules, 45 (38.8%) had classical papillary thyroid cancer (PTC), 23 (19.8%) had nonclassical PTC, and 3 (2.6%) had follicular thyroid cancer. 15/109 patients had detectable BRAF (V600E) ctDNA in their preoperative samples-all of them having classical PTC. Higher T-stage and extrathyroidal extension in PTC were associated with positive BRAF (V600E) ctDNA (p < 0.05). Eighty-eight pairs of preoperative and postoperative plasma samples were collected and analyzed. Of these eighty-eight paired samples, a total of 13/88 (14.8%) patients had detectable BRAF (V600E) ctDNA in their preoperative samples-all of them having classical PTC. 12 of these 13 patients had no detectable BRAF (V600E) postoperatively, while one remaining patient had a significant decline in his levels (p < 0.05). CONCLUSION BRAF (V600E) circulating thyroid tumor DNA can be detected in plasma and is correlated with a final diagnosis of the classical variant of PTC. Given that a postoperative drop in BRAF (V600E) ctDNA levels was observed in all cases suggests its utility as a tumor marker.
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Affiliation(s)
- Krupal B. Patel
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Nicholas Cormier
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - James Fowler
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Allison Partridge
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Julie Theurer
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Morgan Black
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Nicole Pinto
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - William Stecho
- Department of Pathology, Western University, London, Ontario, Canada
| | | | | | - John W. Barrett
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Anthony Nichols
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
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Ruicci KM, Meens J, Plantinga P, Stecho W, Pinto N, Yoo J, Fung K, MacNeil D, Mymryk JS, Barrett JW, Howlett CJ, Boutros PC, Ailles L, Nichols AC. TAM family receptors in conjunction with MAPK signalling are involved in acquired resistance to PI3Kα inhibition in head and neck squamous cell carcinoma. J Exp Clin Cancer Res 2020; 39:217. [PMID: 33059733 PMCID: PMC7559997 DOI: 10.1186/s13046-020-01713-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023]
Abstract
Background Aberrant activation of the phosphatidylinositol 3-kinase (PI3K) pathway is common in many malignancies, including head and neck squamous cell carcinoma (HNSCC). Despite pre-clinical and clinical studies, outcomes from targeting the PI3K pathway have been underwhelming and the development of drug resistance poses a significant barrier to patient treatment. In the present study, we examined mechanisms of acquired resistance to the PI3Kα inhibitor alpelisib (formerly BYL719) in HNSCC cell lines and patient-derived xenografts (PDXs). Methods Five unique PDX mouse models and three HNSCC cell lines were used. All cell lines and xenografts underwent genomic characterization prior to study. Serial drug treatment was conducted in vitro and in vivo to develop multiple, clinically-significant models of resistance to alpelisib. We then used reverse phase protein arrays (RPPAs) to profile the expression of proteins in parental and drug-resistant models. Top hits were validated by immunoblotting and immunohistochemistry. Flow cytometric analysis and RNA interference studies were then used to interrogate the molecular mechanisms underlying acquired drug resistance. Results Prolonged treatment with alpelisib led to upregulation of TAM family receptor tyrosine kinases TYRO3 and AXL. Importantly, a significant shift in expression of both TYRO3 and AXL to the cell surface was detected in drug-resistant cells. Targeted knockdown of TYRO3 and AXL effectively re-sensitized resistant cells to PI3Kα inhibition. In vivo, resistance to alpelisib emerged following 20–35 days of treatment in all five PDX models. Elevated TYRO3 expression was detected in drug-resistant PDX tissues. Downstream of TYRO3 and AXL, we identified activation of intracellular MAPK signalling. Inhibition of MAPK signalling also re-sensitized drug-resistant cells to alpelisib. Conclusions We have identified TYRO3 and AXL receptors to be key mediators of resistance to alpelisib, both in vitro and in vivo. Our findings suggest that pan-TAM inhibition is a promising avenue for combinatorial or second-line therapy alongside PI3Kα inhibition. These findings advance our understanding of the role TAM receptors play in modulating the response of HNSCC to PI3Kα inhibition and suggest a means to prevent, or at least delay, resistance to PI3Kα inhibition in order to improve outcomes for HNSCC patients.
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Affiliation(s)
- Kara M Ruicci
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul Plantinga
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - William Stecho
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Nicole Pinto
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada
| | - Christopher J Howlett
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paul C Boutros
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.,Institute for Precision Health, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, Room B3-431A, 800 Commissioners Road East, London, ON, N6A 5W9, Canada. .,Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada. .,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.
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4
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Black M, Ghasemi F, Sun RX, Stecho W, Datti A, Meens J, Pinto N, Ruicci KM, Khan MI, Han MW, Shaikh M, Yoo J, Fung K, MacNeil D, Palma DA, Winquist E, Howlett CJ, Mymryk JS, Ailles L, Boutros PC, Barrett JW, Nichols AC. Spleen tyrosine kinase expression is correlated with human papillomavirus in head and neck cancer. Oral Oncol 2019; 101:104529. [PMID: 31864959 DOI: 10.1016/j.oraloncology.2019.104529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/25/2019] [Accepted: 12/15/2019] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Spleen tyrosine kinase (SYK) is a promoter of cell survival in a variety of cell types, including normal and cancerous epithelial cells. We hypothesized that SYK would an important therapeutic target to inhibit for the treatment of HNSCC. MATERIALS AND METHODS SYK protein abundance in patient tumours was evaluated. SYK protein and mRNA abundance was used to examine patient survival and human papillomavirus (HPV) status. Small-interfering RNAs and gene editing with CRISPR/Cas9 were used to evaluate SYK expression on proliferation in HNSCC cell lines. The potency of SYK inhibitor ER27319 maleate on cellular proliferation was tested using a panel of 28 HNSCC cell lines and in vivo in HNSCC patient-derived xenograft (PDX) models. RESULTS Moderate to high protein expression of SYK was observed in 24% of patient tumors and high SYK expression was exclusively observed in HPV-positive samples (p < 0.001). SYK inhibition with RNA interference, gene editing or a SYK inhibitor (ER27319) decreased cell proliferation and migration. Treatment of PDXs with ER27319 maleate was observed to reduce tumour burden in vivo in two of three models. CONCLUSIONS HPV-positive HNSCC harbours high SYK protein levels. We demonstrate that proliferation, migration and overall burden of these tumours can be reduced by genetic or pharmacologic inhibition of SYK. Taken together, these data establish SYK as a therapeutic target for HNSCC.
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Affiliation(s)
- Morgan Black
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Farhad Ghasemi
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada
| | - Ren X Sun
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - William Stecho
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Alessandro Datti
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy.
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicole Pinto
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Kara M Ruicci
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - M Imran Khan
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada
| | - Myung Woul Han
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada
| | - Mushfiq Shaikh
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - David A Palma
- Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Eric Winquist
- Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada; Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John W Barrett
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada
| | - Anthony C Nichols
- Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada.
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Ruicci KM, Plantinga P, Pinto N, Khan MI, Stecho W, Dhaliwal SS, Yoo J, Fung K, MacNeil D, Mymryk JS, Barrett JW, Howlett CJ, Nichols AC. Erratum to: Disruption of the RICTOR/mTORC2 complex enhances the response of head and neck squamous cell carcinoma cells to PI3K inhibition. Mol Oncol 2019; 14:230-231. [PMID: 31804024 PMCID: PMC6944101 DOI: 10.1002/1878-0261.12604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Mundi N, Prokopec SD, Ghasemi F, Warner A, Patel K, MacNeil D, Howlett C, Stecho W, Plantinga P, Pinto N, Ruicci KM, Khan MI, Han MW, Yoo J, Fung K, Sahovaler A, Palma DA, Winquist E, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival. Cancers Head Neck 2019; 4:5. [PMID: 31844556 PMCID: PMC6894507 DOI: 10.1186/s41199-019-0045-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
Background The genomic landscape of head and neck cancer has been reported through The Cancer Genome Atlas project. We attempt to determine if high-risk human papillomavirus (HPV) or frequently mutated genes are correlated with survival in an oral cancer cohort. Methods Patient demographic data along with data from final pathology was collected. Tumor DNA was analyzed using a custom Illumina targeted sequencing panel. Five high-risk HPV types were tested by qPCR. Statistical analyses were used to identify associations between patient outcome and mutational status. Results High-risk HPV types were identified in 7% of cases; HPV status was not associated with survival. Mutations were identified in TP53, TERT promoter, & PIK3CA. Mutations in TP53 were significantly associated with poorer overall survival on multi-variate analysis (p = 0.03). Conclusions Mutations in TP53 were associated with poor patient survival. Expanding our sample size may identify further predictors of outcome to direct customized cancer care.
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Affiliation(s)
- Neil Mundi
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,2Victoria Hospital, London Health Science Centre, Room B3-431A, 800 Commissioners Road East, London, ON N6A 5W9 Canada
| | | | - Farhad Ghasemi
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada
| | - Andrew Warner
- 4Department of Oncology, Western University, London, ON Canada
| | - Krupal Patel
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada
| | - Danielle MacNeil
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | | | - William Stecho
- 5Department of Pathology, Western University, London, ON Canada
| | - Paul Plantinga
- 5Department of Pathology, Western University, London, ON Canada
| | - Nicole Pinto
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | - Kara M Ruicci
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | - Mohammed Imran Khan
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada
| | - Myung Woul Han
- 6Department of Otolaryngology, College of Medicine, Ulsan University Hospital, University of Ulsan, Ulsan, South Korea
| | - John Yoo
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | - Kevin Fung
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | - Axel Sahovaler
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada
| | - David A Palma
- 4Department of Oncology, Western University, London, ON Canada
| | - Eric Winquist
- 4Department of Oncology, Western University, London, ON Canada
| | - Joe S Mymryk
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada.,7Department of Microbiology & Immunology, Western University, London, ON Canada
| | - John W Barrett
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
| | - Paul C Boutros
- 3Ontario Institute for Cancer Research, Toronto, ON Canada.,8Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.,9Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada
| | - Anthony C Nichols
- 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.,4Department of Oncology, Western University, London, ON Canada
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7
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Ruicci KM, Plantinga P, Pinto N, Khan MI, Stecho W, Dhaliwal SS, Yoo J, Fung K, MacNeil D, Mymryk JS, Barrett JW, Howlett CJ, Nichols AC. Disruption of the RICTOR/mTORC2 complex enhances the response of head and neck squamous cell carcinoma cells to PI3K inhibition. Mol Oncol 2019; 13:2160-2177. [PMID: 31393061 PMCID: PMC6763779 DOI: 10.1002/1878-0261.12558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 07/28/2019] [Accepted: 08/07/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphoinositide 3-kinase (PI3K) is aberrantly activated in head and neck squamous cell carcinomas (HNSCC) and plays a pivotal role in tumorigenesis by driving Akt signaling, leading to cell survival and proliferation. Phosphorylation of Akt Thr308 by PI3K-PDK1 and Akt Ser473 by mammalian target of rapamycin complex 2 (mTORC2) activates Akt. Targeted inhibition of PI3K is a major area of preclinical and clinical investigation as it reduces Akt Thr308 phosphorylation, suppressing downstream mTORC1 activity. However, inhibition of mTORC1 releases feedback inhibition of mTORC2, resulting in a resurgence of Akt activation mediated by mTORC2. While the role of PI3K-activated Akt signaling is well established in HNSCC, the significance of mTORC2-driven Akt signaling has not been thoroughly examined. Here we explore the expression and function of mTORC2 and its obligate subunit RICTOR in HNSCC primary tumors and cell lines. We find RICTOR to be overexpressed in a subset of HNSCC tumors, including those with PIK3CA or EGFR gene amplifications. Whereas overexpression of RICTOR reduced susceptibility of HNSCC tumor cells to PI3K inhibition, genetic ablation of RICTOR using CRISPR/Cas9 sensitized cells to PI3K inhibition, as well as to EGFR inhibition and cisplatin treatment. Further, mTORC2 disruption led to reduced viability and colony forming abilities of HNSCC cells relative to their parental lines and induced loss of both activating Akt phosphorylation modifications (Thr308 and Ser473). Taken together, our findings establish RICTOR/mTORC2 as a critical oncogenic complex in HNSCC and rationalize the development of an mTORC2-specific inhibitor for use in HNSCC, either combined with agents already under investigation, or as an independent therapy.
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Affiliation(s)
- Kara M. Ruicci
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Paul Plantinga
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Nicole Pinto
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Mohammed I. Khan
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - William Stecho
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Sandeep S. Dhaliwal
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - John Yoo
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Kevin Fung
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Danielle MacNeil
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Joe S. Mymryk
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Microbiology and Immunology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - John W. Barrett
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Christopher J. Howlett
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
| | - Anthony C. Nichols
- Department of Otolaryngology – Head and Neck Surgery, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
- Department of Oncology, Schulich School of Medicine & DentistryWestern UniversityLondonCanada
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8
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Ghasemi F, Prokopec SD, MacNeil D, Mundi N, Gameiro SF, Howlett C, Stecho W, Plantinga P, Pinto N, Ruicci KM, Khan MI, Yoo J, Fung K, Sahovaler A, Palma DA, Winquist E, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Mutational analysis of head and neck squamous cell carcinoma stratified by smoking status. JCI Insight 2019; 4:123443. [PMID: 30626742 DOI: 10.1172/jci.insight.123443] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
Smoking has historically been recognized as a negative prognostic factor in head and neck squamous cell carcinoma (HNSCC). This study aimed to assess the mutational differences between heavy smokers (>20 pack years) and never smokers among the HNSCC patients within The Cancer Genome Atlas (TCGA). Single nucleotide variation and copy number aberration differences between heavy smokers and never smokers were compared within human papillomavirus-positive (HPV-positive) (n = 67) and HPV-negative (n = 431) TCGA cohorts with HNSCC, and the impact of these mutations on survival were assessed. No genes were differentially mutated between smoking and never-smoking patients with HPV-positive tumors. By contrast, in HPV-negative tumors, NSD1 and COL1A11 were found to be more frequently mutated in heavy smokers, while CASP8 was more frequently altered in never smokers. HPV-negative patients with NSD1 mutations experienced significantly improved overall survival compared with NSD1 WT patients. This improved prognosis was validated in an independent cohort of 77 oral cavity cancer patients and a meta-analysis that included 2 additional data sets (688 total patients, hazard ratio for death 0.44, 95% CI, 0.30-0.65). NSD1 mutations are more common in HPV-negative heavy smokers, define a cohort with favorable prognosis, and may represent a clinically useful biomarker to guide treatment deintensification for HPV-negative patients.
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Affiliation(s)
- Farhad Ghasemi
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | | | - Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Neil Mundi
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | | | - Christopher Howlett
- Department of Pathology University of Western Ontario, London, Ontario, Canada
| | - William Stecho
- Department of Pathology University of Western Ontario, London, Ontario, Canada
| | - Paul Plantinga
- Department of Pathology University of Western Ontario, London, Ontario, Canada
| | - Nicole Pinto
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Kara M Ruicci
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Mohammed Imran Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Axel Sahovaler
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | | | | | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology.,Department of Microbiology & Immunology, and
| | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics and.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology
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9
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Lu C, Papillon-Cavanagh S, Gayden T, Mikael LG, Bechet D, Karamboulas C, Ailles L, Karamchandani J, Marchione DM, Garcia BA, Weinreb I, Goldstein D, Lewis PW, Dancu OM, Dhaliwal S, Stecho W, Howlett CJ, Mymryk JS, Barrett JW, Nichols AC, Allis CD, Majewski J, Jabado N. Abstract 08: Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.aacrahns17-08] [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
Human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs) are deadly and common cancers. Recent genomic studies implicate multiple genetic pathways, including cell signaling, cell cycle and immune evasion, in their development. Here we analyze public data sets and uncover a previously unappreciated role of epigenome deregulation in the genesis of 13% of HPV-negative HNSCCs. Specifically, we identify novel recurrent mutations encoding p.Lys36Met (K36M) alterations in multiple H3 histone genes. We further validate the presence of these alterations in multiple independent HNSCC data sets and show that, along with previously described NSD1 mutations, they correspond to a specific DNA methylation cluster. The K36M substitution and NSD1 defects converge on altering methylation of histone H3 at K36 (H3K36), subsequently blocking cellular differentiation and promoting oncogenesis. Our data further indicate limited redundancy for NSD family members in HPV-negative HNSCCs and suggest a potential role for impaired H3K36 methylation in their development. Further investigation of drugs targeting chromatin regulators is warranted in HPV-negative HNSCCs driven by aberrant H3K36 methylation.
Citation Format: Chao Lu, Simon Papillon-Cavanagh, Tenzin Gayden, Leonie G. Mikael, Denise Bechet, Christina Karamboulas, Laurie Ailles, Jason Karamchandani, Dylan M. Marchione, Benjamin A. Garcia, Ilan Weinreb, David Goldstein, Peter W. Lewis, Octavia-Maria Dancu, Sandeep Dhaliwal, William Stecho, Christopher J. Howlett, Joe S. Mymryk, John W. Barrett, Anthony C. Nichols, C David Allis, Jacek Majewski, Nada Jabado. Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 08.
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Affiliation(s)
- Chao Lu
- 1The Rockefeller University, New York, NY,
| | | | | | | | | | | | - Laurie Ailles
- 3Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | | | | | | | - Ilan Weinreb
- 3Princess Margaret Cancer Centre, Toronto, ON, Canada,
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10
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Rahim MN, Selman M, Sauder PJ, Forbes NE, Stecho W, Xu W, Lebar M, Brown EG, Coombs KM. Generation and characterization of a new panel of broadly reactive anti-NS1 mAbs for detection of influenza A virus. J Gen Virol 2012; 94:593-605. [PMID: 23223621 DOI: 10.1099/vir.0.046649-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Influenza A virus (IAV) non-structural protein 1 (NS1) has multiple functions, is essential for virus replication and may be a good target for IAV diagnosis. To generate broadly cross-reactive NS1-specific mAbs, mice were immunized with A/Hong Kong/1/1968 (H3N2) 6×His-tagged NS1 and hybridomas were screened with glutathione S-transferase-conjugated NS1 of A/Puerto Rico/8/1934 (H1N1). mAbs were isotyped and numerous IgG-type clones were characterized further. Most clones specifically recognized NS1 from various H1N1 and H3N2 IAV types by both immunoblot and immunofluorescence microscopy in mouse M1, canine Madin-Darby canine kidney and human A549 cells. mAb epitopes were mapped by overlapping peptides and selective reactivity to the newly described viral NS3 protein. These mAbs detected NS1 in both the cytoplasm and nucleus by immunostaining, and some detected NS1 as early as 5 h post-infection, suggesting their potential diagnostic use for tracking productive IAV replication and characterizing NS1 structure and function. It was also demonstrated that the newly identified NS3 protein is localized in the cytoplasm to high levels.
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Affiliation(s)
- Md Niaz Rahim
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada.,Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J6, Canada
| | - Mohammed Selman
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Patricia J Sauder
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Nicole E Forbes
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - William Stecho
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Wanhong Xu
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada.,Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J6, Canada
| | - Mark Lebar
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada.,Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J6, Canada
| | - Earl G Brown
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kevin M Coombs
- Manitoba Institute of Child Health, Room 513, John Buhler Research Centre, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada.,Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada.,Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J6, Canada
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11
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Ping J, Keleta L, Forbes NE, Dankar S, Stecho W, Tyler S, Zhou Y, Babiuk L, Weingartl H, Halpin RA, Boyne A, Bera J, Hostetler J, Fedorova NB, Proudfoot K, Katzel DA, Stockwell TB, Ghedin E, Spiro DJ, Brown EG. Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse. PLoS One 2011; 6:e21740. [PMID: 21738783 PMCID: PMC3128085 DOI: 10.1371/journal.pone.0021740] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 06/10/2011] [Indexed: 12/11/2022] Open
Abstract
Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20–21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse.
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Affiliation(s)
- Jihui Ping
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Liya Keleta
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicole E. Forbes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Samar Dankar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - William Stecho
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
| | - Shaun Tyler
- National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Lorne Babiuk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Hana Weingartl
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Rebecca A. Halpin
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Alex Boyne
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jayati Bera
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jessicah Hostetler
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Nadia B. Fedorova
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Katie Proudfoot
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Dan A. Katzel
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tim B. Stockwell
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Elodie Ghedin
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - David J. Spiro
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Earl G. Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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