1
|
Oliva M, Heirali A, Watson G, Rooney AM, Cochrane K, Jennings S, Taylor R, Xu M, Hosni A, Hope A, Bratman SV, Chepeha D, Weinreb I, Perez-Ordonez B, Nin RM, Waldron J, Xu W, Hansen AR, Siu LL, Coburn B, Spreafico A. Prospective manipulation of the gut microbiome with microbial ecosystem therapeutic 4 (MET4) in HPV-related locoregionally-advanced oropharyngeal cancer squamous cell carcinoma (LA-OPSCC) undergoing primary chemoradiation: ROMA2 study. Br J Cancer 2024:10.1038/s41416-024-02701-y. [PMID: 38714747 DOI: 10.1038/s41416-024-02701-y] [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] [Received: 08/17/2023] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/10/2024] Open
Abstract
BACKGROUND Gut microbiome modulation to boost antitumor immune responses is under investigation. METHODS ROMA-2 evaluated the microbial ecosystem therapeutic (MET)-4 oral consortia, a mixture of cultured human stool-derived immune-responsiveness associated bacteria, given with chemoradiation (CRT) in HPV-related oropharyngeal cancer patients. Co-primary endpoints were safety and changes in stool cumulative MET-4 taxa relative abundance (RA) by 16SRNA sequencing. Stools and plasma were collected pre/post-MET-4 intervention for microbiome and metabolome analysis. RESULTS Twenty-nine patients received ≥1 dose of MET-4 and were evaluable for safety: drug-related adverse events (AEs) occurred in 13/29 patients: all grade 1-2 except one grade 3 (diarrhea). MET-4 was discontinued early in 7/29 patients due to CRT-induced toxicity, and in 1/29 due to MET-4 AEs. Twenty patients were evaluable for ecological endpoints: there was no increase in stool MET-4 RA post-intervention but trended to increase in stage III patients (p = 0.06). MET-4 RA was higher in stage III vs I-II patients at week 4 (p = 0.03) and 2-month follow-up (p = 0.01), which correlated with changes in plasma and stool targeted metabolomics. CONCLUSIONS ROMA-2 did not meet its primary ecologic endpoint, as no engraftment was observed in the overall cohort. Exploratory findings of engraftment in stage III patients warrants further investigation of microbiome interventions in this subgroup.
Collapse
Affiliation(s)
- Marc Oliva
- Department of Medical Oncology, Catalan Institute of Oncology, Barcelona, Spain
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alya Heirali
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Geoffrey Watson
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ashley M Rooney
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Sarah Jennings
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rachel Taylor
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Minge Xu
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ali Hosni
- Department of Radiation Oncology, University of Toronto; Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Andrew Hope
- Department of Radiation Oncology, University of Toronto; Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, University of Toronto; Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Douglas Chepeha
- Department of Otolaryngology- Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ilan Weinreb
- Department of Pathology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Bayardo Perez-Ordonez
- Department of Pathology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ricard Mesia Nin
- Department of Medical Oncology, Catalan Institute of Oncology, Barcelona, Spain
| | - John Waldron
- Department of Radiation Oncology, University of Toronto; Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Wei Xu
- Biostatistics Department, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron R Hansen
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bryan Coburn
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada.
| | - Anna Spreafico
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| |
Collapse
|
2
|
de Almeida JR, Martino R, Hosni A, Goldstein DP, Bratman SV, Chepeha DB, Waldron JN, Weinreb I, Perez-Ordonez B, Yu E, Metser U, Hansen AR, Xu W, Su SJ, Kim J. Transoral Robotic Surgery and Radiation Volume Deintensification in Unknown Primary Squamous Cell Carcinoma of the Neck: The Phase 2 FIND Nonrandomized Controlled Trial. JAMA Otolaryngol Head Neck Surg 2024:2817533. [PMID: 38602692 PMCID: PMC11009865 DOI: 10.1001/jamaoto.2024.0423] [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] [Received: 10/16/2023] [Accepted: 02/17/2024] [Indexed: 04/12/2024]
Abstract
Importance Patients with unknown primary squamous cell carcinoma (CUP) with cervical metastases typically receive comprehensive radiotherapy (RT) of the pharynx and bilateral neck. Typically, these patients receive comprehensive RT of the pharynx and bilateral neck that may produce treatment-related toxic effects. Objective To determine whether localization of occult oropharyngeal cancers with transoral robotic surgery (TORS) combined with reduced pharyngeal and neck RT volumes provides acceptable disease control. Design, Setting, and Participants This phase 2, single-group nonrandomized controlled trial at a single institution accrued 32 prospective participants with p16-positive CUP without a primary squamous cell carcinoma on examination and imaging from 2017 to 2019, and 24-month follow-up. The data analysis was conducted from January 2021 to June 2022. Intervention Diagnostic- (n = 13) or therapeutic-intent (n = 9) TORS, with pharyngeal-sparing radiotherapy (PSRT) prescribed for negative margins or pT0, and unilateral neck RT (UNRT) prescribed for unilateral lymphadenopathy with lateralized primary tumor or pT0. Main Outcomes and Measures Out-of-radiation treatment volume failure (<15% was hypothesized to be acceptable) and reports of local and regional recurrence, overall survival, toxic effects, swallowing outcomes (per the MD Anderson Dysphagia Inventory), and videofluoroscopic swallow (per Dynamic Imaging Grade of Swallowing Toxic Effects [DIGEST]) ratings. Results The study sample comprised 22 patients (mean [SD] age, 59.1 [5.7] years; 3 [14%] females and 19 [86%] male) with CUP. Of these, 19 patients (86%) had tumor stage cN1; 2 (9%), cN2; and 1 (5%), cN3. Five patients (23%), 14 patients (64%), and 3 patients (13%) had 0, 1, or 2 primary tumors, respectively. Twenty patients received RT; of these, 9 patients (45%) underwent PSRT and 10 patients (50%), UNRT. In the diagnostic-intent group, 8 patients (62%) and 5 patients (38%) underwent RT and RT-concurrent chemotherapy, respectively. In the therapeutic-intent group, 6 patients (67%) and 1 patient (11%) received adjuvant RT-concurrent chemotherapy, respectively; 2 patients declined RT. Two-year out-of-radiation treatment volume failure, locoregional control, distant metastasis control, and overall survival were 0%, 100%, 95%, and 100%, respectively. Grade 3 or 4 surgical, acute, and late toxic effects occurred in 2 (9%), 5 (23%), and 1 (5%) patients, respectively. PSRT was associated with lower RT dose to superior constrictors (37 vs 53 Gy; mean difference, 16 Gy; 95% CI, 6.4, 24.9), smaller decline in swallowing scores during treatment (19.3 vs 39.7; mean difference, -20.4; 95% CI, -34.1 to -6.1), and fewer patients with worsening DIGEST grade on findings of videofluoroscopic swallow studies at 2 years (0% vs 60%; difference, 60%; 95% CI, 30% to 90%). Conclusions and Relevance These findings indicate that TORS for p16-positive CUP allows RT volume deintensification with excellent outcomes and support future investigation in randomized clinical trials. Trial Registration ClinicalTrials.gov Identifier: NCT03281499.
Collapse
Affiliation(s)
- John R. de Almeida
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
| | - Rosemary Martino
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
- Rehabilitation Sciences Institute, University of Toronto, Toronto, Canada
- Department of Speech-Language Pathology, University of Toronto, Toronto, Canada
- The Swallowing Lab, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| | - David P. Goldstein
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| | - Douglas B. Chepeha
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| | - John N. Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Canada
| | | | - Eugene Yu
- Department of Medical Imaging, University Health Network, Toronto, Canada
| | - Ur Metser
- Department of Medical Imaging, University Health Network, Toronto, Canada
| | - Aaron R. Hansen
- Department of Medical Oncology, Princess Margaret Cancer Center, Toronto, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Center, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Susie Jie Su
- Department of Biostatistics, Princess Margaret Cancer Center, Toronto, Canada
| | - John Kim
- Department of Radiation Oncology, Princess Margaret Cancer Center/University Health Network, University of Toronto, Toronto, Canada
| |
Collapse
|
3
|
Chepeha DB, Barbon CEA, Esemezie AO, Al Mardini M, Philteos J, Spector ME, Bressmann T, Martino R, Bratman SV, Cho JBC, Hope AJ, Hosni AA, Kim JJH, Ringash JG, Waldron JN, Brown DH, de Almeida JR, Gilbert RW, Goldstein DP, Gullane PJ, Irish JC, Monteiro EA, Yao CMKL. Telemedicine-enabled biofeedback electropalatography rehabilitation (TEBER): A pilot study for patients treated with surgery for oral cavity carcinoma. Head Neck 2024. [PMID: 38561946 DOI: 10.1002/hed.27721] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/22/2024] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To address the rehabilitative barriers to frequency and precision of care, we conducted a pilot study of a biofeedback electropalatography (EPG) device paired with telemedicine for patients who underwent primary surgery +/- adjuvant radiation for oral cavity carcinoma. We hypothesized that lingual optimization followed by telemedicine-enabled biofeedback electropalatography rehabilitation (TEBER) would further improve speech and swallowing outcomes after "standard-of-care" SOC rehabilitation. METHOD Pilot prospective 8-week (TEBER) program following 8 weeks of (SOC) rehabilitation. RESULTS Twenty-seven patients were included and 11 completed the protocol. When examining the benefit of TEBER independent of standard of care, "range-of-liquids" improved by +0.36 [95% CI, 0.02-0.70, p = 0.05] and "range-of-solids" improved by +0.73 [95% CI, 0.12-1.34, p = 0.03]. There was a positive trend toward better oral cavity obliteration; residual volume decreased by -1.2 [95% CI, -2.45 to 0.053, p = 0.06], and "nutritional-mode" increased by +0.55 [95% CI, -0.15 to 1.24, p = 0.08]. CONCLUSION This pilot suggests that TEBER bolsters oral rehabilitation after 8 weeks of SOC lingual range of motion.
Collapse
Affiliation(s)
- Douglas B Chepeha
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Carly E A Barbon
- Department of Head & Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alex O Esemezie
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Majd Al Mardini
- Department of Dentistry, Maxillofacial and Ocular Prosthetics, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Justine Philteos
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Matthew E Spector
- Department of Otolaryngogy-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pensylvania, USA
| | - Tim Bressmann
- Department of Speech-Language Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Rosemary Martino
- Department of Speech-Language Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - John B C Cho
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Andrew J Hope
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Ali Abdalati Hosni
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - John J H Kim
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Jolie G Ringash
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - John N Waldron
- Department of Radiation Oncology, University Health Network-Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Dale H Brown
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - John R de Almeida
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ralph W Gilbert
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Patrick J Gullane
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan C Irish
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric A Monteiro
- Department of Otolaryngology-Head & Neck Surgery, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Christopher M K L Yao
- Department of Otolaryngology-Head & Neck surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
4
|
Sanz-Garcia E, Zou J, Avery L, Spreafico A, Waldron J, Goldstein D, Hansen A, Cho BCJ, de Almeida J, Hope A, Hosni A, Hahn E, Perez-Ordonez B, Zhao Z, Smith C, Zheng Y, Singaravelan N, Bratman SV, Siu LL. Multimodal detection of molecular residual disease in high-risk locally advanced squamous cell carcinoma of the head and neck. Cell Death Differ 2024; 31:460-468. [PMID: 38409276 PMCID: PMC11043441 DOI: 10.1038/s41418-024-01272-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Up to 30% of patients with locally advanced head and neck squamous cell carcinoma (LA-HNSCC) relapse. Molecular residual disease (MRD) detection using multiple assays after definitive therapy has not been reported. In this study, we included patients with LA-HNSCC (stage III Human Papilloma virus (HPV)-positive, III-IVB HPV-negative) treated with curative intent. Plasma was collected pre-treatment, at 4-6 weeks (FU1) and 8-12 weeks (FU2) post-treatment. Circulating tumor DNA (ctDNA) was analyzed using a tumor-informed (RaDaR®) and a tumor-naïve (CAPP-seq) assay. HPV DNA was measured using HPV-sequencing (HPV-seq) and digital PCR (dPCR). A total of 86 plasma samples from 32 patients were analyzed; all patients with at least 1 follow-up sample. Most patients were stage III HPV-positive (50%) and received chemoradiation (78%). No patients had radiological residual disease at FU2. With a median follow-up of 25 months, there were 7 clinical relapses. ctDNA at baseline was detected in 15/17 (88%) by RaDaR and was not associated with recurrence free survival (RFS). Two patients relapsed within a year after definitive therapy and showed MRD at FU2 using RaDaR; detection of ctDNA during follow-up was associated with shorter RFS (p < 0.001). ctDNA detection by CAPP-seq pre-treatment and during follow-up was not associated with RFS (p = 0.09). HPV DNA using HPV-seq or dPCR during follow-up was associated with shorter RFS (p < 0.001). Sensitivity and specificity for MRD at FU2 using RaDaR was 40% and 100% versus 20 and 90.5% using CAPP-seq. Sensitivity and specificity for MRD during follow-up using HPV-seq was 100% and 91.7% versus 50% and 100% using dPCR. In conclusion, HPV DNA and ctDNA can be detected in LA-HNSCC before definitive therapy. The RaDaR assay but not CAPP-seq may detect MRD in patients who relapse within 1 year. HPV-seq may be more sensitive than dPCR for MRD detection.
Collapse
Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Lisa Avery
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Department of Surgical Oncology, Division of ENT, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Aaron Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - B C John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - John de Almeida
- Department of Surgical Oncology, Division of ENT, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ezra Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Bayardo Perez-Ordonez
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Yangqiao Zheng
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Nitthusha Singaravelan
- Cancer Genomics Program, Princess Margaret Cancer Center, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
5
|
Stutheit-Zhao EY, Sanz-Garcia E, Liu ZA, Wong D, Marsh K, Abdul Razak AR, Spreafico A, Bedard PL, Hansen AR, Lheureux S, Torti D, Lam B, Yang SYC, Burgener J, Luo P, Zeng Y, Cheng N, Awadalla P, Bratman SV, Ohashi PS, Pugh TJ, Siu LL. Early changes in tumor-naive cell-free methylomes and fragmentomes predict outcomes in pembrolizumab-treated solid tumors. Cancer Discov 2024:734858. [PMID: 38393391 DOI: 10.1158/2159-8290.cd-23-1060] [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] [Received: 10/01/2023] [Revised: 01/18/2024] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
Early kinetics of circulating tumor DNA (ctDNA) in plasma predict response to pembrolizumab, but typically requires sequencing of matched tumor tissue or fixed gene panels. We analyzed genome-wide methylation and fragment length profiles using cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) in 204 plasma samples from 87 patients before and during treatment with pembrolizumab from a pan-cancer phase II investigator-initiated trial (INSPIRE). We trained a pan-cancer methylation signature using independent methylation array data from The Cancer Genome Atlas to quantify a cancer-specific methylation (CSM) and fragment length score (FLS) for each sample. CSM and FLS are strongly correlated with tumor-informed ctDNA levels. Early kinetics of CSM predict overall survival and progression-free survival, independently of tumor type, PD-L1, and tumor mutation burden. Early kinetics of FLS are associated with overall survival independently of CSM. Our tumor-naïve mutation-agnostic ctDNA approach integrating methylomics and fragmentomics could predict outcomes in patients treated with pembrolizumab.
Collapse
Affiliation(s)
| | | | | | - Derek Wong
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Canada
| | | | | | | | - Aaron R Hansen
- Princess Margaret Hospital, Brisbane, Queensland, Australia
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Canada
| | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Justin Burgener
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, Toronto, Canada
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Han K, Zou J, Zhao Z, Baskurt Z, Zheng Y, Barnes E, Croke J, Ferguson SE, Fyles A, Gien L, Gladwish A, Lecavalier-Barsoum M, Lheureux S, Lukovic J, Mackay H, Marchand EL, Metser U, Milosevic M, Taggar AS, Bratman SV, Leung E. Clinical Validation of Human Papilloma Virus Circulating Tumor DNA for Early Detection of Residual Disease After Chemoradiation in Cervical Cancer. J Clin Oncol 2024; 42:431-440. [PMID: 37972346 PMCID: PMC10824379 DOI: 10.1200/jco.23.00954] [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: 04/29/2023] [Revised: 08/01/2023] [Accepted: 09/15/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE Most cervical cancers are caused by human papilloma virus (HPV), and HPV circulating tumor DNA (ctDNA) may identify patients at highest risk of relapse. Our pilot study using digital polymerase chain reaction (dPCR) showed that detectable HPV ctDNA at the end of chemoradiation (CRT) is associated with inferior progression-free survival (PFS) and that a next-generation sequencing approach (HPV-seq) may outperform dPCR. We aimed to prospectively validate HPV ctDNA as a tool for early detection of residual disease. METHODS This prospective, multicenter validation study accrued patients with stage IB-IVA cervical cancer treated with CRT between 2017 and 2022. Participants underwent phlebotomy at baseline, end of CRT, 4-6 weeks post-CRT, and 3 months post-CRT for HPV ctDNA levels. Plasma HPV genotype-specific DNA levels were quantified using both dPCR and HPV-seq. The primary end point was 2-year PFS. RESULTS With a median follow-up of 2.2 (range, 0.5-5.5) years, there were 24 PFS events among the 70 patients with HPV+ cervical cancer. Patients with detectable HPV ctDNA on dPCR at the end of CRT, 4-6 weeks post-CRT, and 3 months post-CRT had significantly worse 2-year PFS compared with those with undetectable HPV ctDNA (77% v 51%, P = .03; 82% v 15%, P < .001; and 82% v 24%, P < .001, respectively); the median lead time to recurrence was 5.9 months. HPV-seq showed similar results as dPCR. On multivariable analyses, detectable HPV ctDNA on dPCR and HPV-seq remained independently associated with inferior PFS. CONCLUSION Persistent HPV ctDNA after CRT is independently associated with inferior PFS. HPV ctDNA testing can identify, as early as at the end of CRT, patients at high risk of recurrence for future treatment intensification trials.
Collapse
Affiliation(s)
- Kathy Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zeynep Baskurt
- Department of Biostatistics, University Health Network, Toronto, Ontario, Canada
| | - Yangqiao Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elizabeth Barnes
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Jennifer Croke
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Sarah E. Ferguson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Anthony Fyles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Lilian Gien
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Adam Gladwish
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | | | - Stephanie Lheureux
- Division of Medical Oncology, Department of Internal Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jelena Lukovic
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Helen Mackay
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Division of Medical Oncology, Department of Internal Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Ur Metser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Michael Milosevic
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Amandeep S. Taggar
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Eric Leung
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| |
Collapse
|
7
|
Murphy T, Zou J, Arruda A, Wang TT, Zhao Z, Zheng Y, Gupta V, Maze D, McNamara C, Minden MD, Schimmer A, Sibai H, Yee K, Capo-Chichi JM, Stockley T, Schuh A, Bratman SV, Chan SM. Exclusion of persistent mutations in splicing factor genes and isocitrate dehydrogenase 2 improves the prognostic power of molecular measurable residual disease assessment in acute myeloid leukemia. Haematologica 2024; 109:671-675. [PMID: 37345484 PMCID: PMC10828788 DOI: 10.3324/haematol.2023.283510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Tracy Murphy
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Jinfeng Zou
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Andrea Arruda
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Ting Ting Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Zhen Zhao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Yangqiao Zheng
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Vikas Gupta
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Dawn Maze
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | | | - Mark D Minden
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Aaron Schimmer
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Hassan Sibai
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Karen Yee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Jose-Mario Capo-Chichi
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto, ON
| | - Tracy Stockley
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto, ON
| | - Andre Schuh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Steven M Chan
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario.
| |
Collapse
|
8
|
Han K, Zou J, Zhao Z, Baskurt Z, Zheng Y, Barnes T, Croke JM, Fyles A, Gladwish AP, Lecavalier-Barsoum M, Lukovic J, Marchand EL, Milosevic M, Taggar A, Bratman SV, Leung EW. Clinical Validation of HPV ctDNA for Early Detection of Residual Disease Following Chemoradiation in Cervical Cancer. Int J Radiat Oncol Biol Phys 2023; 117:S7-S8. [PMID: 37784556 DOI: 10.1016/j.ijrobp.2023.06.216] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Despite chemoradiation (CRT), 30-40% of patients with locally advanced cervical cancer relapse. Most cases are caused by human papilloma virus (HPV), and HPV circulating tumor DNA (ctDNA) may identify patients at highest risk of relapse. Our previous pilot study showed that detectable HPV ctDNA at the end of CRT is associated with inferior progression-free survival (PFS) using digital polymerase chain reaction (dPCR), and that a next generation sequencing approach (HPV-seq) may outperform dPCR. We hypothesized that HPV ctDNA may identify cervical cancer patients at increased risk of relapse following CRT and aimed to prospectively validate HPV ctDNA as a tool for early detection of residual disease. MATERIALS/METHODS This prospective, multicenter validation study accrued 70 patients with HPV+ stage IB-IVA cervical cancer treated with definitive CRT from 2017-2022. Patients underwent phlebotomy at baseline, end of, 4-6 weeks and 3 months post CRT for HPV ctDNA levels. HPV genotyping was performed on the baseline plasma sample using HPV-seq. HPV genotype-specific DNA levels in plasma were quantified using both dPCR and HPV-seq. PFS was estimated using the Kaplan-Meier method and compared using the log rank test. Multivariable Cox regression analyses incorporating stage and HPV ctDNA detectability assessed independent prognostic factors associated with PFS. RESULTS At the time of abstract, results for 67 patients were available. The majority had squamous histology (84%) and stage IIB (36%) or IIIC1 (25%) disease. HPV genotyping using HPV-seq revealed 54% (36/67) of cases harboring HPV-16, and 46% harboring other HPV types: 15 HPV-18; 5 HPV-59; 2 HPV-31; 2 HPV-33; 2 HPV-52; 1 each HPV-39, HPV-45, HPV-53, HPV-58, and HPV-82. With a median follow up of 2.2 (range 0.4 - 5.2) years, there were 21 PFS events. Most recurrences (14/21) were distant and/or paraaortic; 4 local and nodal/distant; 2 pelvic nodal; and 1 local. Patients with detectable HPV ctDNA on dPCR at the end of, 4-6 weeks and 3 months post CRT had significantly worse 2-year PFS compared to those with undetectable HPV ctDNA (78 vs 52%, p = 0.04; 82 vs 26%, p < 0.001; and 80 vs 23%, p = < 0.001, respectively). HPV-seq showed similar results (87 vs 55%, p = 0.02; 81 vs 45%, p = 0.003; and 84 vs 31%, p = < 0.001, respectively). On multivariable analyses, detectable HPV ctDNA on dPCR and HPV-seq remained independently associated with inferior PFS (see table). CONCLUSION HPV-seq enables HPV genotyping directly from plasma in locally advanced cervical cancer. Persistent HPV ctDNA following CRT is independently associated with inferior PFS in this prospective validation study. HPV ctDNA testing can be used to identify, as early as at the end of CRT, patients at high risk of recurrence in future treatment intensification trials.
Collapse
Affiliation(s)
- K Han
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - J Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Z Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Z Baskurt
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Y Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - T Barnes
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - J M Croke
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - A Fyles
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - A P Gladwish
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Royal Victoria Hospital, Barrie, ON, Canada
| | | | - J Lukovic
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - E L Marchand
- Hopital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - M Milosevic
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - A Taggar
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - S V Bratman
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - E W Leung
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| |
Collapse
|
9
|
Stutheit-Zhao E, King I, Huang SH, Rey-McIntyre K, Cho J, Eng L, Hahn E, Hosni A, Kim J, Tadic T, McNiven AL, McPartlin A, Ringash JG, O'Sullivan B, Siu LL, Spreafico A, Tsai CJ, Waldron J, Hope AJ, Bratman SV. Plasma EBV DNA in Nasopharyngeal Cancer (NPC) Treated with Definitive Radiotherapy (RT). Int J Radiat Oncol Biol Phys 2023; 117:e627-e628. [PMID: 37785875 DOI: 10.1016/j.ijrobp.2023.06.2019] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) EBV DNA has well-studied roles in NPC including early detection and surveillance. There are limited North American data on EBV DNA testing. Our center has used EBV DNA testing since 2010. We hypothesized: (1) higher first post-RT EBV DNA level is associated with worse prognosis, and (2) surveillance EBV DNA is specific for recurrence at a low detection threshold. MATERIALS/METHODS We retrospectively reviewed all patients with non-metastatic (TNM-7 stage I-IVB) NPC treated with definitive RT/chemoRT (CRT) ± adjuvant chemotherapy (AC) between 2010-2017. EBV DNA was assayed by quantitative PCR in a CAP/CLIA-certified laboratory and reported in copies/mL of plasma. Pre-RT is defined as 0-90 days before the first RT fraction and post-RT within one year after RT. We report log odds ratios (LOR) from a linear model of T- and N-category with log-adjusted EBV DNA as the response variable. Survival outcomes were analyzed with log-rank tests and Cox multivariate analyses (MVA) adjusted for age, stage, and treatment, reporting hazard ratios (HR). A total of 95% confidence intervals of LOR and HR are reported. The detection threshold that maximized the F1 accuracy score was considered optimal. RESULTS Of 271 patients in the study window, 179 had pre-RT +/- post-RT EBV DNA testing. Six received RT, 43 CRT, and 130 CRT+AC. With 7-yr median follow-up, 37 recurred and 37 died. Detectable pre-RT EBV DNA was found in 154 (86%) with a median of 928 copies/mL (range: 1-239214). EBV DNA level correlated with higher N category (LOR: 0.28, 0.15-0.42, p<0.001), but not T category (0.04, -0.06-0.13, p = 0.5). Above-median pre-RT EBV DNA was associated with worse recurrence-free survival (RFS) by log-rank test (p = 0.016) and Cox MVA (HR: 2.2, 1.1-4.8, p = 0.03) along with N category, age, and no AC. Post-RT EBV DNA was available in 99 patients at a median of 54 days. RFS, progression-free survival (PFS), and overall survival (OS) were worse in patients with detectable post-RT EBV DNA (Table). RFS and PFS drop further to 20% if EBV DNA was detectable after the full treatment (RT±AC, n = 71). In Cox MVA, post-RT EBV DNA remained independently prognostic (Table). EBV DNA was performed within 30 days of recurrence in 30 patients, and 24 were detectable (80% sensitivity). Conversely, of 152 patients without recurrence and at least 3-yr follow-up, 95 had post-RT EBV DNA testing and 84 were undetectable (88% specificity). An EBV DNA threshold of 31 copies maximized F1 accuracy metric, yielding 74% sensitivity and 97% specificity. CONCLUSION Pre-RT EBV DNA is prognostic and associated with higher N-category. Post-RT EBV DNA is a strong, independent predictor of RFS, PFS, and OS; 31 copies/mL may be a useful threshold to detect recurrence.
Collapse
Affiliation(s)
| | - I King
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - S H Huang
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - J Cho
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - L Eng
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - T Tadic
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - A L McNiven
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - A McPartlin
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - J G Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - B O'Sullivan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - L L Siu
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Spreafico
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C J Tsai
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - S V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
10
|
Barcelona MVN, Huang SH, Su J, Tong L, Bratman SV, Cho J, Hahn E, Hope AJ, Hosni A, Kim J, McPartlin A, O'Sullivan B, Ringash JG, Siu LL, Spreafico A, Eng L, Yao CM, Xu W, Waldron J, Tsai CJ. Outcomes after Contemporary Definitive Radiotherapy Alone in Patients with TNM-7 Stage III/IV Head and Neck Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:e565-e566. [PMID: 37785730 DOI: 10.1016/j.ijrobp.2023.06.1889] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study was undertaken to determine outcomes and prognostic factors of definitive intensity-modulated radiotherapy (IMRT) alone for patients with TNM-7 stage III/IV HNSCC who did not receive concurrent chemotherapy. MATERIALS/METHODS We evaluated TNM-7 stage III/IV HNSCC patients treated with definitive IMRT alone in our institution from 2004-2019. Patients were reclassified according to TNM-8 staging. Stage II HPV+ oropharyngeal cancers (OPC) were subdivided into T1-2N2 and T3N0-2 for analysis. The rationale for chemotherapy omission was obtained retrospectively from clinical documentation. Recurrence-free survival (RFS) and overall survival (OS) were estimated stratified by HPV status (determined by p16 staining, sometimes supplemented by HPV DNA testing). Multivariable analysis (MVA) identified prognostic factors for RFS and OS, taking into account stage and IMRT regimen. Age, performance status, and smoking were also examined for OS. RESULTS A total of 1083 patients were included (460 HPV+ and 623 HPV-). Reasons for omission of chemotherapy were: age >70 years or frailty (n = 551, 51%), cisplatin contraindication (n = 241, 22%), patient refusal (n = 106, 10%), and clinician's decision (n = 185, 17%). Median age was 67 years for HPV+ and 70 years for HPV- cohorts. IMRT mostly utilized altered fractionation regimens (n = 1016, 94%): moderately accelerated (Acc) (70 Gy/35 fractions [f]/6 weeks [w], 55%), hypofractionated (Hypo) (60 Gy/25f/5w, 14%), and hyperfractionated-accelerated (Hyper) (64 Gy/40f/4w, 25%). Median follow-up was 5 years. Five-year RFS and OS for HPV+ TNM-8 stage I/T1-2N2/T3N0-N2/III were 89%/86%/76%/52% and 83%/80%/64%/33% respectively (p<0.01). The same outcomes for HPV- TNM-8 stage III/IVA/IVB were 58%/52%/39% and 47%/27%/13%, respectively (p<0.01). MVA confirmed that HPV+ T3N0-2 subset within stage II and stage III (vs stage I) had lower RFS, and HPV- stage IVA and IVB (vs stage III) carried worse RFS and OS (Table). CONCLUSION Despite the retrospective nature and inherent selection bias, this large single institutional study shows that altered fractionated IMRT alone is an acceptable alternative for elderly, frail or cisplatin ineligible patients with HPV+ stage I/IIA (T1-2N2) OPC. Patients with HPV+ T3N0-2/stage III OPC and HPV- stage III/IV HNSCC have poor outcomes with IMRT alone and may benefit from alternative strategies.
Collapse
Affiliation(s)
- M V N Barcelona
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - S H Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Su
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Tong
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - S V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A McPartlin
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - B O'Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J G Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L L Siu
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Spreafico
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Eng
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C M Yao
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - W Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C J Tsai
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
11
|
Zeng Y, Ye W, Stutheit-Zhao EY, Han M, Bratman SV, Pugh TJ, He HH. MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis. Bioinformatics 2023; 39:btad423. [PMID: 37402621 PMCID: PMC10348834 DOI: 10.1093/bioinformatics/btad423] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023] Open
Abstract
SUMMARY Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising liquid biopsy technology to detect cancers and monitor treatments. While several bioinformatics tools for DNA methylation analysis have been adapted for cfMeDIP-seq data, an end-to-end pipeline and quality control framework specifically for this data type is still lacking. Here, we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation. The major advantages of MEDIPIPE are: (i) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; (ii) flexibility to handle different experimental settings with a single configuration file; and (iii) computationally efficiency for large-scale cfMeDIP-seq profiling data analysis and aggregation. AVAILABILITY AND IMPLEMENTATION This pipeline is an open-source software under the MIT license and it is freely available at https://github.com/pughlab/MEDIPIPE.
Collapse
Affiliation(s)
- Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wenbin Ye
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Eric Y Stutheit-Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
12
|
Taylor K, Zou J, Magalhaes M, Oliva M, Spreafico A, Hansen AR, McDade SS, Coyle VM, Lawler M, Elimova E, Bratman SV, Siu LL. Circulating tumour DNA kinetics in recurrent/metastatic head and neck squamous cell cancer patients. Eur J Cancer 2023; 188:29-38. [PMID: 37182343 DOI: 10.1016/j.ejca.2023.04.014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/16/2023]
Abstract
PURPOSE Immune checkpoint blockade (ICB) has become a standard of care in the treatment of recurrent/metastatic head and neck squamous cell cancer (R/M HNSCC). However, only a subset of patients benefit from treatment. Quantification of plasma circulating tumour DNA (ctDNA) levels and on-treatment kinetics may permit real-time assessment of disease burden under selective pressures of treatment. PATIENTS AND METHODS R/M HNSCC patients treated with systemic therapy, platinum-based chemotherapy (CT) or ICB, underwent serial liquid biopsy sampling. Biomarkers tested included ctDNA measured by CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) and markers of host inflammation measured by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR). RESULTS Among 53 eligible patients, 16 (30%) received CT, 30 (57%) ICB [anti-PD1/L1] monotherapy and 7 (13%) combination immunotherapy (IO). Median progression-free survival (PFS) and overall survival (OS) were 2.8 months (95% CI, 1.3-4.3) and 8.2 months (95% CI, 5.6-10.8), respectively. Seven (13%) patients experienced a partial response and 21 (40%) derived clinical benefit. At baseline, median ctDNA variant allele frequency (VAF) was 4.3%. Baseline ctDNA abundance was not associated with OS (p = 0.56) nor PFS (p = 0.54). However, a change in ctDNA VAF after one cycle of treatment (ΔVAF (T1-2)) was predictive of both PFS (p< 0.01) and OS (p< 0.01). Additionally, decrease in ΔVAF identified patients with longer OS despite early radiological progression, 8.2 vs 4.6 months, hazard ratio 0.44 (95% CI, 0.19-0.87) p = 0.03. After incorporating NLR and PLR into multivariable Cox models, ctDNA ∆VAF retained an association with OS. CONCLUSIONS Early dynamic changes in ctDNA abundance, after one cycle of treatment, compared to baseline predicted both OS and PFS in R/M HNSCC patients on systemic therapy.
Collapse
Affiliation(s)
- Kirsty Taylor
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marcos Magalhaes
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marc Oliva
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron R Hansen
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Simon S McDade
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Vicky M Coyle
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Mark Lawler
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Elena Elimova
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| |
Collapse
|
13
|
Karimzadeh M, Arlidge C, Rostami A, Lupien M, Bratman SV, Hoffman MM. Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome Biol 2023; 24:142. [PMID: 37365652 DOI: 10.1186/s13059-023-02926-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize that changes in chromatin state at the location of integration can result in changes in gene expression that contribute to the tumorigenicity of HPV. RESULTS We find that viral integration events often occur along with changes in chromatin state and expression of genes near the integration site. We investigate whether introduction of new transcription factor binding sites due to HPV integration could invoke these changes. Some regions within the HPV genome, particularly the position of a conserved CTCF binding site, show enriched chromatin accessibility signal. ChIP-seq reveals that the conserved CTCF binding site within the HPV genome binds CTCF in 4 HPV+ cancer cell lines. Significant changes in CTCF binding pattern and increases in chromatin accessibility occur exclusively within 100 kbp of HPV integration sites. The chromatin changes co-occur with out-sized changes in transcription and alternative splicing of local genes. Analysis of The Cancer Genome Atlas (TCGA) HPV+ tumors indicates that HPV integration upregulates genes which have significantly higher essentiality scores compared to randomly selected upregulated genes from the same tumors. CONCLUSIONS Our results suggest that introduction of a new CTCF binding site due to HPV integration reorganizes chromatin state and upregulates genes essential for tumor viability in some HPV+ tumors. These findings emphasize a newly recognized role of HPV integration in oncogenesis.
Collapse
Affiliation(s)
- Mehran Karimzadeh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ariana Rostami
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
14
|
Kazmierski M, Welch M, Kim S, McIntosh C, Rey-McIntyre K, Huang SH, Patel T, Tadic T, Milosevic M, Liu FF, Ryczkowski A, Kazmierska J, Ye Z, Plana D, Aerts HJ, Kann BH, Bratman SV, Hope AJ, Haibe-Kains B. Multi-institutional Prognostic Modeling in Head and Neck Cancer: Evaluating Impact and Generalizability of Deep Learning and Radiomics. Cancer Res Commun 2023; 3:1140-1151. [PMID: 37397861 PMCID: PMC10309070 DOI: 10.1158/2767-9764.crc-22-0152] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 11/14/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023]
Abstract
Artificial intelligence (AI) and machine learning (ML) are becoming critical in developing and deploying personalized medicine and targeted clinical trials. Recent advances in ML have enabled the integration of wider ranges of data including both medical records and imaging (radiomics). However, the development of prognostic models is complex as no modeling strategy is universally superior to others and validation of developed models requires large and diverse datasets to demonstrate that prognostic models developed (regardless of method) from one dataset are applicable to other datasets both internally and externally. Using a retrospective dataset of 2,552 patients from a single institution and a strict evaluation framework that included external validation on three external patient cohorts (873 patients), we crowdsourced the development of ML models to predict overall survival in head and neck cancer (HNC) using electronic medical records (EMR) and pretreatment radiological images. To assess the relative contributions of radiomics in predicting HNC prognosis, we compared 12 different models using imaging and/or EMR data. The model with the highest accuracy used multitask learning on clinical data and tumor volume, achieving high prognostic accuracy for 2-year and lifetime survival prediction, outperforming models relying on clinical data only, engineered radiomics, or complex deep neural network architecture. However, when we attempted to extend the best performing models from this large training dataset to other institutions, we observed significant reductions in the performance of the model in those datasets, highlighting the importance of detailed population-based reporting for AI/ML model utility and stronger validation frameworks. We have developed highly prognostic models for overall survival in HNC using EMRs and pretreatment radiological images based on a large, retrospective dataset of 2,552 patients from our institution.Diverse ML approaches were used by independent investigators. The model with the highest accuracy used multitask learning on clinical data and tumor volume.External validation of the top three performing models on three datasets (873 patients) with significant differences in the distributions of clinical and demographic variables demonstrated significant decreases in model performance. Significance ML combined with simple prognostic factors outperformed multiple advanced CT radiomics and deep learning methods. ML models provided diverse solutions for prognosis of patients with HNC but their prognostic value is affected by differences in patient populations and require extensive validation.
Collapse
Affiliation(s)
- Michal Kazmierski
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mattea Welch
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- TECHNA Institute, Toronto, Ontario, Canada
| | - Sejin Kim
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Chris McIntosh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- TECHNA Institute, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Katrina Rey-McIntyre
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Tirth Patel
- TECHNA Institute, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Tony Tadic
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Michael Milosevic
- TECHNA Institute, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Adam Ryczkowski
- Department of Medical Physics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, University of Medical Sciences, Poznan, Poland
| | - Joanna Kazmierska
- Department of Electroradiology, University of Medical Sciences, Poznan, Poland
- Department of Radiotherapy II, Greater Poland Cancer Centre, Poznan, Poland
| | - Zezhong Ye
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute / Brigham and Women's Hosptial, Boston, Massachusetts
| | - Deborah Plana
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute / Brigham and Women's Hosptial, Boston, Massachusetts
| | - Hugo J.W.L. Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute / Brigham and Women's Hosptial, Boston, Massachusetts
- Radiology and Nuclear Medicine, CARIM and GROW, Maastricht University, Maastricht, the Netherlands
| | - Benjamin H. Kann
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute / Brigham and Women's Hosptial, Boston, Massachusetts
| | - Scott V. Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Andrew J. Hope
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| |
Collapse
|
15
|
Soleimani S, Wang BX, Pedersen S, Eagles J, Brick J, Butler MO, Bratman SV, Siu LL, Ohashi PS, Pugh TJ. Abstract 6667: Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6667] [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: 04/07/2023]
Abstract
Abstract
Introduction: Clinical benefit from Immune Checkpoint Blockade (ICB) is a function of local T-cell specificity for tumor-associated antigens. However, overcoming local T-cell dysfunction necessitates systemic immunity engagement. Therefore, studying the dynamics of both local and peripheral T-cell repertoires in response to ICB is required to identify features of T-cell repertoires associated with pathological response.
Methods: We conducted TCRβ-sequencing on tumor-residing T-cells (n=59), Peripheral Blood Mononuclear Cells (PBMCs) (n=306) and cell-free DNA (cfDNA) (n=73) from pre- and multiple on-ICB timepoints collected from patients enrolled in the pan-cancer INvestigator-initiated Phase II Study of Pembrolizumab Immunological Response Evaluation (INSPIRE; NCT02644369) trial. To assess specificity-agnostic shifts in TCR repertoires, we first compared TCR diversity and clonal expansion in longitudinal tumor and PBMC samples. Then, to temporally track the specificity-associated features of local and systemic TCR repertoires, we leveraged a Graph Neural Network (GNN) model that took in unique TCRβ chains as nodes. The connectivity between the nodes was defined by multi-relational edges that represented VJ-gene usage and GLIPHII-identified (Grouping Lymphocyte Interactions by Paratope Hotspots) specificities derived from a compendium of TCR sequences with empirically confirmed specificities. Results: While absolute diversity and clonal expansion values in baseline tumor (n=33) were not associated with response to ICB, changes in these values were informative between pre- and on-ICB tumors. All patients (n=4) with low baseline tumor TCR diversity and lack of clonotypic re-structuring in tumor TCR repertoire on-ICB had either progressive or short-term stable disease. Furthermore, pairwise comparison of pre- and on-ICB tumors for each patient (n=17) revealed that all the patients, irrespective of their pathological response, experienced emergence of new TCR clonotypes (i.e., clonal replacement) in response to ICB, suggesting only a minority of these TCRs might consist of tumor-associated clonotypes. Patients with clinical benefit also had higher degree of GLIPHII-identified clustering at baseline tumor, highlighting the role of both specificity-agnostic and specificity-centric TCR analysis in determining the response to ICB. Analysis of TCR sequences in blood plasma found cfDNA contains a small number of TCR sequences (median 32, range 12-89) enriched for TCRs found in matched tumor tissues, suggesting that cfDNA TCR repertoire may provide an indirect measurement of tumor-residing T-cells.
Conclusions: TCR diversity and functional clonal annotation are emerging biomarkers of ICB response and cfDNA TCR repertoire can potentially be exploited for clinical diagnostics and monitoring.
Citation Format: Shirin Soleimani, Ben X. Wang, Stephanie Pedersen, Jenna Eagles, Jacob Brick, Marcus O. Butler, Scott V. Bratman, Lillian L. Siu, Pamela S. Ohashi, Trevor J. Pugh. Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6667.
Collapse
Affiliation(s)
| | - Ben X. Wang
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Jenna Eagles
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jacob Brick
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Lillian L. Siu
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Trevor J. Pugh
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| |
Collapse
|
16
|
Brooks PJ, Malkin EZ, De Michino S, Bratman SV. Isolation of salivary cell-free DNA for cancer detection. PLoS One 2023; 18:e0285214. [PMID: 37130100 PMCID: PMC10153704 DOI: 10.1371/journal.pone.0285214] [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] [Received: 01/29/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023] Open
Abstract
Saliva is an emerging source of disease biomarkers, particularly for cancers of the head and neck. Although analysis of cell-free DNA (cfDNA) in saliva holds promise as a liquid biopsy for cancer detection, currently there are no standardized methodologies for the collection and isolation of saliva for the purposes of studying DNA. Here, we evaluated various saliva collection receptacles and DNA purification techniques, comparing DNA quantity, fragment size, source, and stability. Then, using our optimized techniques, we tested the ability to detect human papillomavirus (HPV) DNA- a bona fide cancer biomarker in a subset of head and neck cancers- from patient saliva samples. For saliva collection, we found that the Oragene OG-600 receptacle yielded the highest concentration of total salivary DNA as well as short fragments <300 bp corresponding to mononucleosomal cell-free DNA. Moreover, these short fragments were stabilized beyond 48 hours after collection in contrast to other saliva collection receptacles. For DNA purification from saliva, the QIAamp Circulating Nucleic Acid kit yielded the highest concentration of mononucleosome-sized DNA fragments. Freeze-thaw of saliva samples did not affect DNA yield or fragment size distribution. Salivary DNA isolated from the OG-600 receptacle was found to be composed of both single and double-stranded DNA, including mitochondrial and microbial sources. While levels of nuclear DNA were consistent over time, levels of mitochondrial and microbial DNA were more variable and increased 48 hours after collection. Finally, we found that HPV DNA was stable in OG-600 receptacles, was reliably detected within the saliva of patients with HPV-positive head and neck cancer, and was abundant among mononucleosome-sized cell-free DNA fragments. Our studies have defined optimal techniques for isolating DNA from saliva that will contribute to future applications in liquid biopsy-based cancer detection.
Collapse
Affiliation(s)
- Patricia J Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ethan Z Malkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Steven De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
17
|
Malkin EZ, De Michino S, Lambie M, Gill RG, Zhao Z, Rostami A, Arruda A, Minden MD, Bratman SV. Cell-free DNA topology is unique to its sub-cellular and cellular origins in cancer. JCI Insight 2022; 7:159590. [PMID: 36125881 DOI: 10.1172/jci.insight.159590] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer cells release large quantities of cell-free DNA (cfDNA) into the surrounding tissue and circulation. As cfDNA is a common source of biomarkers for liquid biopsy and has been implicated as a functional mediator for intercellular communication, fundamental characterization of cfDNA topology has widespread biological and clinical ramifications. Whether the topology of cfDNA is such that it exists predominantly in membrane-bound extracellular vesicles (EVs) or in non-vesicular DNA-protein complexes remains poorly understood. Here, we employed a DNA-targeted approach to comprehensively assess total cfDNA topology in cancer. Using preclinical models and patient samples, we demonstrate that nuclear cfDNA is predominantly associated with nucleosomal particles and not EVs, while a substantial subset of mitochondrial cfDNA is membrane-protected and disproportionately derived from non-tumour cells. In addition, discrimination between membrane-protected and accessible mitochondrial cfDNA added diagnostic and prognostic value in a cohort of head and neck cancer patients. Our results support a revised model for cfDNA topology in cancer. Due to its abundance, nuclear cfDNA within nucleosomal particles is the most compelling liquid biopsy substrate, while EV-bound and accessible mitochondrial cfDNA represent distinct reservoirs of potential cancer biomarkers whose structural conformations may also influence their extracellular stability and propensity for uptake by recipient cells.
Collapse
Affiliation(s)
- Ethan Z Malkin
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Steven De Michino
- Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Meghan Lambie
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Rita G Gill
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ariana Rostami
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Mark D Minden
- Princess Margaret Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | |
Collapse
|
18
|
Wilson SL, Shen SY, Harmon L, Burgener JM, Triche T, Bratman SV, De Carvalho DD, Hoffman MM. Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls. Cell Rep Methods 2022; 2:100294. [PMID: 36160046 PMCID: PMC9499995 DOI: 10.1016/j.crmeth.2022.100294] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/17/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) identifies genomic regions with DNA methylation, using a protocol adapted to work with low-input DNA samples and with cell-free DNA (cfDNA). We developed a set of synthetic spike-in DNA controls for cfMeDIP-seq to provide a simple and inexpensive reference for quantitative normalization. We designed 54 DNA fragments with combinations of methylation status (methylated and unmethylated), fragment length (80 bp, 160 bp, 320 bp), G + C content (35%, 50%, 65%), and fraction of CpG dinucleotides within the fragment (1/80 bp, 1/40 bp, 1/20 bp). Using 0.01 ng of spike-in controls enables training a generalized linear model that absolutely quantifies methylated cfDNA in MeDIP-seq experiments. It mitigates batch effects and corrects for biases in enrichment due to known biophysical properties of DNA fragments and other technical biases.
Collapse
Affiliation(s)
- Samantha L. Wilson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Justin M. Burgener
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tim Triche
- Van Andel Institute, Grand Rapids, MI, USA
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael M. Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| |
Collapse
|
19
|
Zhao EY, Bushehri A, Chan B, Wong O, Lee J, Patel T, Kim S, King I, Huang SH, Cho J, Hahn E, Abdalaty AH, Kim J, Ringash J, O’sullivan B, Waldron JN, Bissonnette JP, Giuliani ME, Haibe-Kains B, Tadic T, McNiven A, Hope A, Bratman SV. 125: Daily Assessment of On-Treatment Tumour Regression by Cone Beam CT Reveals Prognostic Dynamic Biomarkers in Nasopharyngeal Cancer. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)04404-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
20
|
Ghatasheh H, Hui Huang S, Su J, Xu W, Bratman SV, Cho J, Giuliani M, Hahn E, Hope A, Kim J, O'Sullivan B, Ringash J, Waldron J, Chepeha DB, Irish JC, Goldstein DP, Spreafico A, Tong L, de Almeida JR, Hosni A. Evaluation of risk-tailored individualized selection of radiation therapy target volume for Head and Neck Carcinoma of Unknown Primary. Radiother Oncol 2022; 175:56-64. [PMID: 35905781 DOI: 10.1016/j.radonc.2022.07.016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Intensity-modulated radiation therapy (IMRT) has enabled risk-tailored approach to elective mucosal and nodal clinical target volumes (CTVs) in treatment of head and neck carcinoma of unknown primary (HNCUP). This study report outcomes following such approach. METHODS HNCUP patients treated with definitive IMRT between 2005 and 2018 were reviewed. Local failure (LF), regional failure (RF), distant metastasis (DM), overall survival (OS) and grade ≥3 late toxicity (LT) were analyzed. Multivariable analysis (MVA) was used to identify OS predictors for entire cohort and cN2-3 subgroup. RESULTS A total of 203 patients were eligible: cN1 (7%), cN2a (14%), cN2b (46%), cN2c (14%) and cN3 (19%). Among 118 patients with known HPV status (by p16 staining), 81 (68%) were positive. IMRT target volume spared contralateral tonsil (55%), bilateral or contralateral sides of hypopharynx (72%), nasopharynx (72%), larynx (87%) and contralateral uninvolved neck (21%). Median follow-up was 5 years. Five-year LF, RF, DM, OS, and LT were 3%, 14%, 10%, 79%, and 7% respectively. Four patients developed mucosal recurrence: 3 within and 1 at the margin of the elective mucosal CTV. None of ipsilateral neck irradiation patients failed in the contralateral uninvolved neck. MVA identified cN2c-N3, HPV-negative status and older age as predictors for inferior OS. Within cN2-3 subgroup (n=189): cN2c-N3, HPV-negative status and older age predicted lower OS, while concurrent chemotherapy was associated with better OS. CONCLUSION Definitive IMRT with risk-adaptive radiation volume de-escalation for HNCUP resulted in high probability of tumor control with acceptable rate of late toxicity.
Collapse
Affiliation(s)
- Hamza Ghatasheh
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada; Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Jie Su
- Biostatistics, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Biostatistics, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Meredith Giuliani
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Ezra Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - John Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada; Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada; Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada; Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Douglas B Chepeha
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Jonathan C Irish
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Anna Spreafico
- Department of Medical Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - Li Tong
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada
| | - John R de Almeida
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre / University of Toronto, Ontario, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre / University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
21
|
Main SC, Cescon DW, Bratman SV. Liquid biopsies to predict CDK4/6 inhibitor efficacy and resistance in breast cancer. Cancer Drug Resist 2022; 5:727-748. [PMID: 36176758 PMCID: PMC9511796 DOI: 10.20517/cdr.2022.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors combined with endocrine therapy have transformed the treatment of estrogen receptor-positive (ER+) and human epidermal growth factor receptor 2 negative (HER2-) metastatic breast cancer. However, some patients do not respond to this treatment, and patients inevitably develop resistance, such that novel biomarkers are needed to predict primary resistance, monitor treatment response for acquired resistance, and personalize treatment strategies. Circumventing the spatial and temporal limitations of tissue biopsy, newly developed liquid biopsy approaches have the potential to uncover biomarkers that can predict CDK4/6 inhibitor efficacy and resistance in breast cancer patients through a simple blood test. Studies on circulating tumor DNA (ctDNA)-based liquid biopsy biomarkers of CDK4/6 inhibitor resistance have focused primarily on genomic alterations and have failed thus far to identify clear and clinically validated predictive biomarkers, but emerging epigenetic ctDNA methodologies hold promise for further discovery. The present review outlines recent advances and future directions in ctDNA-based biomarkers of CDK4/6 inhibitor treatment response.
Collapse
Affiliation(s)
- Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto M5T 1P5, Ontario, Canada
| |
Collapse
|
22
|
Haq SU, Schmid S, Aparnathi MK, Hueniken K, Zhan LJ, Sacdalan D, Li JJ, Patel D, Cheng D, Philip V, Liu G, Bratman SV, Lok BH. Abstract 3396: Identification of small cell lung cancer stage-specific DNA methylation in patients using liquid biopsies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3396] [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
Introduction: Small cell lung cancer (SCLC) is a deadly disease and patients often suffer from recurrent disease. Biologic mechanisms of recurrence are unclear. Epigenetic mechanisms, like DNA methylation, may be operant. SCLC is rarely resected; therefore, the SCLC methylome is understudied due to scarce tumor tissue.
Methods: In this study, we examined the pre-treatment methylome of 72 SCLC patients at our institution through cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) on plasma cell-free DNA (cfDNA) and on sheared genomic DNA from paired peripheral blood leukocytes (PBLs) (n = 72) to increase tumor signal specificity. cfMeDIP-seq was also performed on an independent cohort of healthy non-cancer controls (n = 20) and on tumors from circulating tumor cell-derived xenograft (CDX) models (n = 12 CDXs of 72 patients). cfMeDIP-seq libraries were sequenced at a depth of 100 million reads, paired-end, on the NovaSeq 6000. For all bioinformatic analyses, chromosomes 1-22 were binned into 300-bp windows (n = 9.6e6 genome-wide windows); reads from cfMeDIP-seq were tallied per bin. To filter out noise from non-tumor cells, ENCODE blacklist regions (n = 1e6 windows) were removed and CG-rich (>5 CGs per window), PBL-associated windows with MeDEStrand-converted beta-values < 0.2 were kept (n = 190,769 windows). Subsequent cfDNA analyses were performed using these 190,769 windows.
Results: 33 (45.8%) and 39 (54.2%) of the 72 patients had limited-stage (LS) and extensive-stage (ES) SCLC, respectively. Most were current or former smokers (65/72, 90.3%). Using filtered windows (n = 190,769), methylated cfDNA from SCLC were distinguished from healthy controls: SCLC cfDNA was enriched for hypermethylated CpG islands and shore regions, whereas controls had more methylated open-sea regions. SCLC cohort by consensus clustering of the top 5000 most variant windows revealed two distinct cfDNA methylation patterns. Cluster A (9 ES, 22 LS) and Cluster B (33 ES, 11 LS) were significantly different by stage (X2(1) = 13.79, p < 0.001). There was no significant difference in sex (p = 0.81). Patients in Cluster A had a lower concentration of cfDNA (median = 7.2ng/ml) compared to Cluster B (median = 15.9ng/ml) but not statistically significant (p = 0.33). High concordance between genome-wide methylome profiles was found between paired patient cfDNA and CDX tumor, demonstrating that cfDNA is representative of tumor methylation (Pearson's correlation median r = 0.86).
Conclusion: We identified stage-specific methylation patterns in the plasma of SCLC patients using the cfMeDIP-seq assay that may reveal novel epigenetic and biologic mechanisms of SCLC disease progression. Moreover, CDXs recapitulate the methylome of SCLC cell-free patient samples highlighting their utility in future work as representative models for methylome analysis.
Citation Format: Sami Ul Haq, Sabine Schmid, Mansi K. Aparnathi, Katrina Hueniken, Luna J. Zhan, Danielle Sacdalan, Janice J.N. Li, Devalben Patel, Dangxiao Cheng, Vivek Philip, Geoffrey Liu, Scott V. Bratman, Benjamin H. Lok. Identification of small cell lung cancer stage-specific DNA methylation in patients using liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3396.
Collapse
Affiliation(s)
- Sami Ul Haq
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Mansi K. Aparnathi
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Katrina Hueniken
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Luna J. Zhan
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Danielle Sacdalan
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Janice J.N. Li
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Devalben Patel
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dangxiao Cheng
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vivek Philip
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Geoffrey Liu
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Scott V. Bratman
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Benjamin H. Lok
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
23
|
Huang SH, Jacinto JCK, O'Sullivan B, Su J, Kim J, Ringash J, Spreafico A, Yu E, Perez-Ordonez B, Weinreb I, Cho J, Hope AJ, Bratman SV, Giuliani ME, Hosni A, Hahn E, Goldstein DP, Tong L, Eng L, Xu W, Waldron JN. Clinical presentation and outcome of human papillomavirus-positive nasopharyngeal carcinoma in a North American cohort. Cancer 2022; 128:2908-2921. [PMID: 35588085 DOI: 10.1002/cncr.34266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/10/2022] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The objective of this study was to describe the clinical presentation and outcomes of human papillomavirus (HPV)-positive nasopharyngeal cancer (NPC) versus Epstein-Barr virus (EBV)-positive NPC and HPV-positive oropharyngeal cancer (OPC). METHODS Clinical characteristics and presenting signs/symptoms were compared between patients who had viral-related NPC versus viral-related OPC treated with intensity-modulated radiotherapy from 2005 to 2020 and who were matched 1:1 (by tumor and lymph node categories, smoking, age, sex, histology, and year of diagnosis). Locoregional control (LRC), distant control (DC), and overall survival (OS) were compared using the 2005-2018 cohort to maintain 2 years of minimum follow-up. Multivariable analysis was used to evaluate the cohort effect. RESULTS Similar to HPV-positive OPC (n = 1531), HPV-positive NPC (n = 29) occurred mostly in White patients compared with EBV-positive NPC (n = 422; 86% vs. 15%; p < .001). Primary tumor volumes were larger in HPV-positive NPC versus EBV-positive NPC (median volume, 51 vs. 23 cm3 ; p = .002), with marginally more Level IB nodal involvement. More patients with HPV-positive NPC complained of local pain (38% vs. 3%; p = .002). The median follow-up for the 2005-2018 cohort was 5.3 years. Patients who had HPV-positive NPC (n = 20) had rates of 3-year LRC (95% vs. 90%; p = .360), DC (75% vs. 87%; p = .188), and OS (84% vs. 89%; p = .311) similar to the rates in those who had EBV-positive NPC (n = 374). Patients who had HPV-positive NPC also had rates of LRC (95% vs. 94%; p = .709) and OS (84% vs. 87%; p = .440) similar to the rates in those who had HPV-positive OPC (n = 1287). The DC rate was lower in patients who had HPV-positive disease (75% vs. 90%; p = .046), but the difference became nonsignificant (p = .220) when the analysis was adjusted for tumor and lymph node categories, smoking, and chemotherapy. CONCLUSIONS HPV-positive NPC and EBV-positive NPC seem to be mutually exclusive diseases. Patients who have HPV-positive NPC have greater local symptom burden and larger primary tumors but have similar outcomes compared with patients who have EBV-positive NPC or HPV-positive OPC.
Collapse
Affiliation(s)
- Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery and Surgical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - J C Kennetth Jacinto
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery and Surgical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Jie Su
- Department of Biostatistics, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - John Kim
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery and Surgical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Division of Medical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Eugene Yu
- Department of Neuroradiology and Head and Neck Imaging, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Pathology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Department of Pathology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Andrew J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Meredith E Giuliani
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Ezra Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head and Neck Surgery and Surgical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Li Tong
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Lawson Eng
- Division of Medical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - John N Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery and Surgical Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
24
|
Id Said B, Ailles L, Karamboulas C, Meens J, Huang SH, Xu W, Keshavarzi S, Bratman SV, Cho BCJ, Giuliani M, Hahn E, Kim J, O’Sullivan B, Ringash J, Waldron J, Spreafico A, de Almeida JR, Chepeha DB, Irish JC, Goldstein DP, Hope A, Hosni A. Development and Validation of an Oral Cavity Cancer Outcomes Prediction Score Incorporating Patient-Derived Xenograft Engraftment. JAMA Otolaryngol Head Neck Surg 2022; 148:342-349. [PMID: 35238880 PMCID: PMC8895316 DOI: 10.1001/jamaoto.2022.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE Patient-derived xenografts (PDXs) offer the opportunity to identify patients with oral cavity squamous cell carcinoma (OSCC) who are at risk for recurrence and optimize clinical decision-making. OBJECTIVE To develop and validate a prediction score for locoregional failure (LRF) and distant metastases (DM) in OSCC that incorporates PDX engraftment in addition to known clinicopathological risk factors. DESIGN, SETTING, AND PARTICIPANTS In this retrospective cohort study, PDX models were generated from patients with OSCC treated with curative intent at Princess Margaret Cancer Centre (Toronto, Canada) between 2006 and 2018. The cohort included 288 patients (aged ≥18 years) with a new diagnosis of nonmetastatic (M0) OSCC whose tumor samples were available for engraftment under the skin of xenograft mice. Patients were scored as a nonengrafter if PDX formation did not occur within 6 months. Data analysis was performed between August 2006 and May 2018. INTERVENTIONS All patients received up-front curative-intent surgery followed by either observation or postoperative radiation with or without concurrent chemotherapy based on institutional guidelines. MAIN OUTCOMES AND MEASURES Main outcomes were LRF, DM, and overall survival (OS). Multivariable analysis (MVA) was used to identify predictors of LRF and DM. Factors retained in the final MVA were used to construct a prediction score and classify patients into risk groups. RESULTS Overall, 288 patients (mean [SD] age at diagnosis, 63.3 [12.3] years; 112 [39%] women and 176 [61%] men) with OSCC were analyzed. The MVA identified pT3-4, pathologic extranodal extension, and engraftment as predictors of LRF and DM. Patients whose tumors engrafted (n = 198) were more likely to develop LRF (hazard ratio [HR], 1.98; 95% CI, 1.24-3.18) and DM (HR, 2.64; 95% CI, 1.21-5.75) compared with nonengrafters. A prediction score based on the aforementioned variables identified patients at high risk and low risk for LRF (43.5% vs 26.5%), DM (38.2% vs 8.4%), and inferior OS (34% vs 66%) at 5 years. Additionally, rapid engraftment was shown to be similarly prognostic, with rapid engrafters demonstrating higher rates of relapse and poor OS. CONCLUSIONS In this cohort study, a prediction score using OSCC PDX engraftment, in conjunction with pT3-4 and pathologic extranodal extension, was associated with improved prognostic utility of existing clinical models and predicted patients at risk for LRF, DM, and poor survival.
Collapse
Affiliation(s)
- Badr Id Said
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christina Karamboulas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada,Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sareh Keshavarzi
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada,Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - B. C. John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Meredith Giuliani
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ezra Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - John Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Brian O’Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada,Department of Otolaryngology—Head & Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Department of Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - John R. de Almeida
- Department of Otolaryngology—Head & Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Douglas B. Chepeha
- Department of Otolaryngology—Head & Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan C. Irish
- Department of Otolaryngology—Head & Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - David P. Goldstein
- Department of Otolaryngology—Head & Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
25
|
Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. Sci Adv 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
Collapse
Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
| |
Collapse
|
26
|
Zazuli Z, de Jong C, Xu W, Vijverberg SJH, Masereeuw R, Patel D, Mirshams M, Khan K, Cheng D, Ordonez-Perez B, Huang S, Spreafico A, Hansen AR, Goldstein DP, de Almeida JR, Bratman SV, Hope A, Knox JJ, Wong RKS, Darling GE, Kitchlu A, van Haarlem SWA, van der Meer F, van Lindert ASR, ten Heuvel A, Brouwer J, Ross CJD, Carleton BC, Egberts TCG, Herder GJM, Deneer VHM, Maitland-van der Zee AH, Liu G. Association between Genetic Variants and Cisplatin-Induced Nephrotoxicity: A Genome-Wide Approach and Validation Study. J Pers Med 2021; 11:jpm11111233. [PMID: 34834585 PMCID: PMC8623115 DOI: 10.3390/jpm11111233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
This study aims to evaluate genetic risk factors for cisplatin-induced nephrotoxicity by investigating not previously studied genetic risk variants and further examining previously reported genetic associations. A genome-wide study (GWAS) was conducted in genetically estimated Europeans in a discovery cohort of cisplatin-treated adults from Toronto, Canada, followed by a candidate gene approach in a validation cohort from the Netherlands. In addition, previously reported genetic associations were further examined in both the discovery and validation cohorts. The outcome, nephrotoxicity, was assessed in two ways: (i) decreased estimated glomerular filtration rate (eGFR), calculated using the Chronic Kidney Disease Epidemiology Collaboration formula (CKD-EPI) and (ii) increased serum creatinine according to the Common Terminology Criteria for Adverse Events v4.03 for acute kidney injury (AKI-CTCAE). Four different Illumina arrays were used for genotyping. Standard quality control was applied for pre- and post-genotype imputation data. In the discovery cohort (n = 608), five single-nucleotide polymorphisms (SNPs) reached genome-wide significance. The A allele in rs4388268 (minor allele frequency = 0.23), an intronic variant of the BACH2 gene, was consistently associated with increased risk of cisplatin-induced nephrotoxicity in both definitions, meeting genome-wide significance (β = −8.4, 95% CI −11.4–−5.4, p = 3.9 × 10−8) for decreased eGFR and reaching suggestive association (OR = 3.9, 95% CI 2.3–6.7, p = 7.4 × 10−7) by AKI-CTCAE. In the validation cohort of 149 patients, this variant was identified with the same direction of effect (eGFR: β = −1.5, 95% CI −5.3–2.4, AKI-CTCAE: OR = 1.7, 95% CI 0.8–3.5). Findings of our previously published candidate gene study could not be confirmed after correction for multiple testing. Genetic predisposition of BACH2 (rs4388268) might be important in the development of cisplatin-induced nephrotoxicity, indicating opportunities for mechanistic understanding, tailored therapy and preventive strategies.
Collapse
Affiliation(s)
- Zulfan Zazuli
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
- Department of Pharmacology-Clinical Pharmacy, School of Pharmacy, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Corine de Jong
- Department of Clinical Pharmacy, St. Antonius Hospital, 3430 EM Nieuwegein, The Netherlands;
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
| | - Wei Xu
- Department of Biostatistics, Dalla Lana School of Public Health, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada;
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
| | - Devalben Patel
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Maryam Mirshams
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Khaleeq Khan
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Dangxiao Cheng
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Bayardo Ordonez-Perez
- Department of Laboratory Medicine and Pathology, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Shaohui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Aaron R. Hansen
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - David P. Goldstein
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - John R. de Almeida
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Jennifer J. Knox
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Rebecca K. S. Wong
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Gail E. Darling
- Department of Thoracic Surgery, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Abhijat Kitchlu
- Department of Medicine, Nephrology, University Health Network, University of Toronto, Toronto, ON M5G 2M9, Canada;
| | | | - Femke van der Meer
- Department of Pulmonology, Diakonessenhuis, 3582 KE Utrecht, The Netherlands;
| | - Anne S. R. van Lindert
- Department of Pulmonology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands;
| | - Alexandra ten Heuvel
- Department of Pulmonology, Groene Hart Hospital, 2803 HH Gouda, The Netherlands;
| | - Jan Brouwer
- Department of Pulmonology, Rivierenland Hospital, 4002 WP Tiel, The Netherlands;
| | - Colin J. D. Ross
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; (C.J.D.R.); (B.C.C.)
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Bruce C. Carleton
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; (C.J.D.R.); (B.C.C.)
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, BC V1Y 1T3, Canada
- Pharmaceutical Outcomes Program, British Columbia Children’s Hospital, Vancouver, BC V5Z 4H4, Canada
| | - Toine C. G. Egberts
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Gerarda J. M. Herder
- Meander Medical Center, Department of Pulmonology, 3813 TZ Amersfoort, The Netherlands;
| | - Vera H. M. Deneer
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
- Correspondence: (A.H.M.-v.d.Z.); (G.L.); Tel.: +31-(0)20-566-8137 (A.H.M.-v.d.Z.); +416-946-4501 (ext. 3428) (G.L.)
| | - Geoffrey Liu
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
- Departments of Medical Biophysics, Pharmacology and Toxicology, and Epidemiology, Dalla Lana School of Public Health and University of Toronto, Toronto, ON M5T 3M7, Canada
- Correspondence: (A.H.M.-v.d.Z.); (G.L.); Tel.: +31-(0)20-566-8137 (A.H.M.-v.d.Z.); +416-946-4501 (ext. 3428) (G.L.)
| |
Collapse
|
27
|
Lassen P, Huang SH, Su J, Waldron J, Andersen M, Primdahl H, Johansen J, Kristensen CA, Andersen E, Eriksen JG, Hansen CR, Alsner J, Lilja-Fisher J, Bratman SV, Ringash J, Kim J, Hope A, Spreafico A, de Almeida J, Xu W, O'Sullivan B, Overgaard J. Treatment outcomes and survival following definitive (chemo)radiotherapy in HPV-positive oropharynx cancer: Large-scale comparison of DAHANCA vs PMH cohorts. Int J Cancer 2021; 150:1329-1340. [PMID: 34792199 DOI: 10.1002/ijc.33876] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/17/2021] [Accepted: 11/02/2021] [Indexed: 11/05/2022]
Abstract
We compare outcomes in two large-scale contemporaneously treated HPV-positive (HPV+) oropharynx cancer (OPC) cohorts treated with definitive radiotherapy/chemoradiotherapy (RT/CRT). p16-confirmed HPV+ OPC treated between 2007 and 2015 at PMH and DAHANCA were identified. Locoregional failure (LRF), distant metastasis (DM), and overall survival (OS) were compared. Multivariable analysis (MVA) calculated adjusted-hazard-ratio (aHR) with 95% confidence interval (95% CI), adjusting for cohort, age, gender, performance status, smoking pack-years, T-category and N-category and chemotherapy. Compared to PMH (n = 701), DAHANCA (n = 1174) contained lower TNM-8T-categories (T1-T2: 77% vs 56%), N-categories (N0-N1: 77% vs 67%) and stages (stage I: 63% vs 44% (all P < .001). PMH used standard-fractionation CRT in 69% (481) while 31% (220) received hypofractionated or moderately accelerated RT-alone. All DAHANCA patients were treated with moderately accelerated RT; 96% (1129) received nimorazole (NIM) and 73% (856) concurrent weekly cisplatin. DAHANCA had shorter overall-treatment-time (P < .001), lower gross tumor (66-68 vs 70 Gy) and elective neck (50 vs 56 Gy) doses. Median follow-up was 4.8 years. DAHANCA had higher 5-year LRF (13% vs 7%, aHR = 0.47 [0.34-0.67]), comparable DM (7% vs 12%, aHR = 1.32 [0.95-1.82]), but better OS (85% vs 80%, aHR = 1.30 [1.01-1.68]). CRT patients had a lower risk of LRF (aHR 0.56 [0.39-0.82]), DM (aHR 0.70 [0.50-1.00]) and death (aHR 0.39 [0.29-0.52]) vs RT-alone. We observed exemplary outcomes for two large-scale trans-Atlantic HPV+ OPC cohorts treated in a similar manner. Concurrent chemotherapy was a strong, independent prognostic factor for all endpoints. Our findings underscore the need for a very careful approach to de-intensification of treatment for this disease.
Collapse
Affiliation(s)
- Pernille Lassen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.,Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Jie Su
- Department of Biostatistics, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Maria Andersen
- Department of Oncology, Aalborg Univeristy Hospital, Aalborg, Denmark
| | - Hanne Primdahl
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Johansen
- Department of Oncology, Odense Universitetshospital, Odense, Denmark
| | | | - Elo Andersen
- Department of Oncology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Grau Eriksen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.,Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob Lilja-Fisher
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - John Kim
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Division of Medical Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - John de Almeida
- Department of Otolaryngology - Head & Neck Surgery, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology, Princess Margaret Hospital Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
28
|
Leung E, Han K, Zou J, Zhao Z, Zheng Y, Wang TT, Rostami A, Siu LL, Pugh TJ, Bratman SV. HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA. Clin Cancer Res 2021; 27:5857-5868. [PMID: 34580115 PMCID: PMC9401563 DOI: 10.1158/1078-0432.ccr-19-2384] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 07/22/2019] [Revised: 07/27/2021] [Accepted: 09/02/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Human papillomavirus (HPV) DNA offers a convenient circulating tumor DNA (ctDNA) marker for HPV-associated malignancies, but current methods, such as digital PCR (dPCR), provide insufficient accuracy for clinical applications in patients with low disease burden. We asked whether a next-generation sequencing approach, HPV sequencing (HPV-seq), could provide quantitative and qualitative assessment of HPV ctDNA in low disease burden settings. EXPERIMENTAL DESIGN We conducted preclinical technical validation studies on HPV-seq and applied it retrospectively to a prospective multicenter cohort of patients with locally advanced cervix cancer (NCT02388698) and a cohort of patients with oropharynx cancer. HPV-seq results were compared with dPCR. The primary outcome was progression-free survival (PFS) according to end-of-treatment HPV ctDNA detectability. RESULTS HPV-seq achieved reproducible detection of HPV DNA at levels less than 0.6 copies in cell line data. HPV-seq and dPCR results for patients were highly correlated (R 2 = 0.95, P = 1.9 × 10-29) with HPV-seq detecting ctDNA at levels down to 0.03 copies/mL plasma in dPCR-negative posttreatment samples. Detectable HPV ctDNA at end-of-treatment was associated with inferior PFS with 100% sensitivity and 67% specificity for recurrence. Accurate HPV genotyping was successful from 100% of pretreatment samples. HPV ctDNA fragment sizes were consistently shorter than non-cancer-derived cell-free DNA (cfDNA) fragments, and stereotyped cfDNA fragmentomic patterns were observed across HPV genomes. CONCLUSIONS HPV-seq is a quantitative method for ctDNA detection that outperforms dPCR and reveals qualitative information about ctDNA. Our findings in this proof-of-principle study could have implications for treatment monitoring of disease burden in HPV-related cancers. Future prospective studies are needed to confirm that patients with undetectable HPV ctDNA following chemoradiotherapy have exceptionally high cure rates.
Collapse
Affiliation(s)
- Eric Leung
- Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Kathy Han
- Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yangqiao Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ariana Rostami
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology, Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Corresponding Author: Scott V. Bratman, Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Princess Margaret Cancer Research Tower, 101 College Street, Room 13-305, Toronto, Ontario M5G 1L7, Canada. Phone: 416-634-7077; E-mail:
| |
Collapse
|
29
|
Oliva M, Chepeha D, Araujo DV, Diaz-Mejia JJ, Olson P, Prawira A, Spreafico A, Bratman SV, Shek T, de Almeida J, R Hansen A, Hope A, Goldstein D, Weinreb I, Smith S, Perez-Ordoñez B, Irish J, Torti D, Bruce JP, Wang BX, Fortuna A, Pugh TJ, Der-Torossian H, Shazer R, Attanasio N, Au Q, Tin A, Feeney J, Sethi H, Aleshin A, Chen I, Siu L. Antitumor immune effects of preoperative sitravatinib and nivolumab in oral cavity cancer: SNOW window-of-opportunity study. J Immunother Cancer 2021; 9:jitc-2021-003476. [PMID: 34599023 PMCID: PMC8488751 DOI: 10.1136/jitc-2021-003476] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Sitravatinib, a tyrosine kinase inhibitor that targets TYRO3, AXL, MERTK and the VEGF receptor family, is predicted to increase the M1 to M2-polarized tumor-associated macrophages ratio in the tumor microenvironment and have synergistic antitumor activity in combination with anti-programmed death-1/ligand-1 agents. SNOW is a window-of-opportunity study designed to evaluate the immune and molecular effects of preoperative sitravatinib and nivolumab in patients with oral cavity squamous cell carcinoma. METHODS Patients with newly-diagnosed untreated T2-4a, N0-2 or T1 >1 cm-N2 oral cavity carcinomas were eligible. All patients received sitravatinib 120 mg daily from day 1 up to 48 hours pre-surgery and one dose of nivolumab 240 mg on day 15. Surgery was planned between day 23 and 30. Standard of care adjuvant radiotherapy was given based on clinical stage. Tumor photographs, fresh tumor biopsies and blood samples were collected at baseline, at day 15 after sitravatinib alone, and at surgery after sitravatinib-nivolumab combination. Tumor flow cytometry, multiplex immunofluorescence staining and single-cell RNA sequencing (scRNAseq) were performed on tumor biopsies to study changes in immune-cell populations. Tumor whole-exome sequencing and circulating tumor DNA and cell-free DNA were evaluated at each time point. RESULTS Ten patients were included. Grade 3 toxicity occurred in one patient (hypertension); one patient required sitravatinib dose reduction, and one patient required discontinuation and surgery delay due to G2 thrombocytopenia. Nine patients had clinical-to-pathological downstaging, with one complete response. Independent pathological treatment response (PTR) assessment confirmed a complete PTR and two major PTRs. With a median follow-up of 21 months, all patients are alive with no recurrence. Circulating tumor DNA and cell-free DNA dynamics correlated with clinical and pathological response and distinguished two patient groups with different tumor biological behavior after sitravatinib alone (1A) versus sitravatinib-nivolumab (1B). Tumor immunophenotyping and scRNAseq analyses revealed differential changes in the expression of immune cell populations and sitravatinib-targeted and hypoxia-related genes in group 1A vs 1B patients. CONCLUSIONS The SNOW study shows sitravatinib plus nivolumab is safe and leads to deep clinical and pathological responses in oral cavity carcinomas. Multi-omic biomarker analyses dissect the differential molecular effects of sitravatinib versus the sitravatinib-nivolumab and revealed patients with distinct tumor biology behavior. TRIAL REGISTRATION NUMBER NCT03575598.
Collapse
Affiliation(s)
- Marc Oliva
- Department of Medical Oncology, Institut Catala d' Oncologia, L'Hospitalet de Llobregat, Barcelona, Spain.,Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Douglas Chepeha
- Department of Otolaryngology and Head and Neck Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daniel V Araujo
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology, Hospital de Base São Jose do Rio Preto, Sao Paulo, Brazil
| | - J Javier Diaz-Mejia
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Peter Olson
- Department of Research, Mirati Therapeutics, San Diego, California, USA
| | - Amy Prawira
- Department of Medical Oncology, The Kinghorn Cancer Centre, St Vincent's Hospital, Sidney, New South Wales, Australia
| | - Anna Spreafico
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Scott V Bratman
- Radiation Medicine Program, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Tina Shek
- Radiation Medicine Program, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - John de Almeida
- Department of Otolaryngology and Head and Neck Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron R Hansen
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrew Hope
- Radiation Medicine Program, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - David Goldstein
- Department of Otolaryngology and Head and Neck Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Stephen Smith
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | | | - Jonathan Irish
- Department of Otolaryngology and Head and Neck Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dax Torti
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeffrey P Bruce
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Anthony Fortuna
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ronald Shazer
- Clinical Development, Mirati Therapeutics, San Diego, California, USA
| | | | - Qingyan Au
- Neogenomics Laboratories, Fort Myers, Florida, USA
| | | | | | | | | | - Isan Chen
- Clinical Development, Mirati Therapeutics, San Diego, California, USA
| | - Lillian Siu
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
30
|
Muhanna N, Eu D, Chan HHL, Douglas C, Townson JL, Di Grappa MA, Mohamadi RM, Kelley SO, Bratman SV, Irish JC. Cell-free DNA and circulating tumor cell kinetics in a pre-clinical head and neck Cancer model undergoing radiation therapy. BMC Cancer 2021; 21:1075. [PMID: 34600526 PMCID: PMC8487588 DOI: 10.1186/s12885-021-08791-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Monitoring circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), known as liquid biopsies, continue to be developed as diagnostic and prognostic markers for a wide variety of cancer indications, mainly due to their minimally invasive nature and ability to offer a wide range of phenotypic and genetic information. While liquid biopsies maintain significant promising benefits, there is still limited information regarding the kinetics of ctDNA and CTCs following radiation therapy which remains a vital treatment modality in head and neck cancers. This study aims to describe the kinetics of ctDNA and CTCs following radiation exposure in a preclinical rabbit model with VX2 induced buccal carcinoma. METHODS Seven rabbits were inoculated with VX2 cells in the buccal mucosa and subjected to radiation. At selected time points, blood sampling was performed to monitor differing levels of ctDNA and CTC. Plasma ctDNA was measured with quantitative PCR for papillomavirus E6 while CTCs were quantified using an immunomagnetic nanoparticles within a microfluidic device. Comparisons of CTC detection with EpCAM compared to multiple surface markers (EGFR, HER2 and PSMA) was evaluated and correlated with the tumor size. RESULTS Plasma ctDNA reflects the overall tumor burden within the animal model. Analysis of correlations between ctDNA with tumor and lymph node volumes showed a positive correlation (R = 0.452 and R = 0.433 [p < 0.05]), respectively. Over the course of treatment, ctDNA levels declined and quickly becomes undetectable following tumor eradication. While during the course of treatment, ctDNA levels were noted to rise particularly upon initiation of radiation following scheduled treatment breaks. Levels of CTCs were observed to increase 1 week following inoculation of tumor to the primary site. For CTC detection, the use of multiple surface markers showed a greater sensitivity when compared to detection using only EpCAM. Plasma CTC levels remained elevated following radiation therapy which may account for an increased shedding of CTCs following radiation. CONCLUSION This study demonstrates the utility of ctDNA and CTCs detection in response to radiation treatment in a preclinical head and neck model, allowing for better understanding of liquid biopsy applications in both clinical practice and research development.
Collapse
Affiliation(s)
- Nidal Muhanna
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada. .,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada. .,Department of Otolaryngology-Head and Neck Surgery-Surgical Oncology, University of Toronto, Toronto, Ontario, Canada. .,Department of Otolaryngology-Head and Neck Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
| | - Donovan Eu
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada
| | - Harley H L Chan
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada
| | - Catriona Douglas
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada
| | - Jason L Townson
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada
| | - Marco A Di Grappa
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Reza M Mohamadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Shana O Kelley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Jonathan C Irish
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,TECHNA Institute, Guided Therapeutic (GTx) Program, University Health Network, Toronto, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery-Surgical Oncology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
31
|
Ren J, Pang W, Hueniken K, Haddad G, Hope A, Huang SH, Spreafico A, Hansen AR, Perez-Ordonez B, Goldstein DP, Bratman SV, Zhang W, Zhao Y, Xu W, de Almeida JR, Liu G. Longitudinal health utility and symptom-toxicity trajectories in patients with head and neck cancers. Cancer 2021; 128:497-508. [PMID: 34597435 DOI: 10.1002/cncr.33936] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND This study examined long-term health utility and symptom-toxicity trajectories among patients with head and neck cancer (HNC). METHODS For patients diagnosed with HNC (2014-2019), Health Utility Index 3 (HUI-3), Edmonton Symptom Assessment Scale (ESAS), and MD Anderson Symptom Inventory (MDASI) surveys (including both the core and head and neck cancer modules) were prospectively collected at multiple time points (at the baseline, after surgery, during radiotherapy, and 3, 6, 12, and 24 months after treatment). Locally estimated scatterplot smoothing plots were generated to describe HUI-3, ESAS, and MDASI trajectories over time by clinicodemographic factors, treatment modality, and tumor subsite. Contributions of clinical factors were assessed with univariable and multivariable analyses. RESULTS In 800 patients, the treatment modality and the tumor subsite produced unique HUI-3, ESAS, and MDASI trajectories. Patients treated with surgery alone experienced rapid improvements in HUI-3, ESAS, and MDASI scores postoperatively. Among patients treated with chemoradiotherapy, patients with nasopharyngeal carcinoma had greater declines in HUI-3 during treatment in comparison with patients with oropharyngeal carcinoma, but they had similar ESAS/MDASI scores. Among patients treated with radiotherapy, patients with laryngeal carcinoma had better HUI-3/ESAS/MDASI scores than those with oropharyngeal carcinoma during treatment, but they slowly converged after treatment. Female sex, an age > 75 years, a household income < $40,000, a Charlson comorbidity score > 1, an Eastern Cooperative Oncology Group performance status > 0 (at the baseline), and current smoking were independently associated with worse HUI-3 trajectories. HUI-3 had mild to moderate correlations (ρ = 0.2-0.5) with individual symptom-toxicity trajectories. CONCLUSIONS Long-term HUI-3 trajectories are associated with tumor subsite, clinicodemographic, and treatment factors, and this may be partly explained by relationships with symptoms/toxicities. Separate evaluations by subsite and treatment should occur in health utility and symptom-toxicity studies of HNC. LAY SUMMARY This study indicates that the long-term health utility and symptoms/toxicities of patients with the most common head and neck cancers (ie, squamous cell carcinomas and nasopharyngeal carcinomas) differ over time with a variety of factors, including the tumor anatomic site, treatment volume, clinicodemographic characteristics (eg, age, human papillomavirus status, tumor stage, gender, smoking status, alcohol status, education, and comorbidities), and treatment modalities. Generalizations across all head and neck cancers should be strongly discouraged. Future studies should evaluate health utility, symptoms and toxicities, and patient need assessments separately for each anatomic site and treatment modality.
Collapse
Affiliation(s)
- Jianjun Ren
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,West China Biomedical Big Data Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wendu Pang
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,West China Biomedical Big Data Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Katrina Hueniken
- Department of Biostatistics, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ghazal Haddad
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aaron R Hansen
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Laboratory Medicine and Pathology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Wei Zhang
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,West China Biomedical Big Data Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yu Zhao
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,West China Biomedical Big Data Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Biostatistics, Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - John R de Almeida
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada.,Institute of Health Policy Management and Evaluation, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
32
|
Said BI, Laurie A, Karamboulas C, Meens J, Huang SH, Xu W, Keshavarzi S, Bratman SV, Cho BJ, Giuliani M, Hahn E, Kim J, O’Sullivan B, Ringash J, Waldron J, Spreafico A, de Almeida JR, Chepeha DB, Irish JC, Goldstein DP, Hope A, Hosni A. 45: Patient-Derived Xenograft Engraftment Predicts Oral Cavity Cancer Outcomes. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)08923-4] [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: 12/01/2022]
|
33
|
Cindy Yang SY, Lien SC, Wang BX, Clouthier DL, Hanna Y, Cirlan I, Zhu K, Bruce JP, El Ghamrasni S, Iafolla MAJ, Oliva M, Hansen AR, Spreafico A, Bedard PL, Lheureux S, Razak A, Speers V, Berman HK, Aleshin A, Haibe-Kains B, Brooks DG, McGaha TL, Butler MO, Bratman SV, Ohashi PS, Siu LL, Pugh TJ. Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. Nat Commun 2021; 12:5137. [PMID: 34446728 PMCID: PMC8390680 DOI: 10.1038/s41467-021-25432-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 10/09/2020] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present an in-depth analysis of clinical, whole-exome, transcriptome, and ctDNA profiles of 73 patients with advanced solid tumors, across 30 cancer types, from a phase II basket clinical trial of pembrolizumab (NCT02644369) and report changes in genomic and immune landscapes (primary outcomes). Patients stratified by ctDNA and tumor burden dynamics correspond with survival and clinical benefit. High mutation burden, high expression of immune signatures, and mutations in BRCA2 are associated with pembrolizumab molecular sensitivity, while abundant copy-number alterations and B2M loss-of-heterozygosity corresponded with resistance. Upon treatment, induction of genes expressed by T cell, B cell, and myeloid cell populations are consistent with sensitivity and resistance. We identified the upregulated expression of PLA2G2D, an immune-regulating phospholipase, as a potential biomarker of adaptive resistance to ICB. Together, these findings provide insights into the diversity of immunogenomic mechanisms that underpin pembrolizumab outcomes.
Collapse
Affiliation(s)
- S Y Cindy Yang
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Scott C Lien
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Ben X Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Derek L Clouthier
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kelsey Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marco A J Iafolla
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Marc Oliva
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Aaron R Hansen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Philippe L Bedard
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Stephanie Lheureux
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Albiruni Razak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Vanessa Speers
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hal K Berman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - David G Brooks
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Tracy L McGaha
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marcus O Butler
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Pamela S Ohashi
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University of Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
| |
Collapse
|
34
|
Burgener JM, Zou J, Zhao Z, Zheng Y, Shen SY, Huang SH, Keshavarzi S, Xu W, Liu FF, Liu G, Waldron JN, Weinreb I, Spreafico A, Siu LL, de Almeida JR, Goldstein DP, Hoffman MM, De Carvalho DD, Bratman SV. Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res 2021; 27:4230-4244. [PMID: 34158359 PMCID: PMC9401560 DOI: 10.1158/1078-0432.ccr-21-0110] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 01/10/2021] [Revised: 03/16/2021] [Accepted: 05/28/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Circulating tumor DNA (ctDNA) enables personalized treatment strategies in oncology by providing a noninvasive source of clinical biomarkers. In patients with low ctDNA abundance, tumor-naïve methods are needed to facilitate clinical implementation. Here, using locoregionally confined head and neck squamous cell carcinoma (HNSCC) as an example, we demonstrate tumor-naïve detection of ctDNA by simultaneous profiling of mutations and methylation. EXPERIMENTAL DESIGN We conducted CAncer Personalized Profiling by deep Sequencing (CAPP-seq) and cell-free Methylated DNA ImmunoPrecipitation and high-throughput sequencing (cfMeDIP-seq) for detection of ctDNA-derived somatic mutations and aberrant methylation, respectively. We analyzed 77 plasma samples from 30 patients with stage I-IVA human papillomavirus-negative HNSCC as well as plasma samples from 20 risk-matched healthy controls. In addition, we analyzed leukocytes from patients and controls. RESULTS CAPP-seq identified mutations in 20 of 30 patients at frequencies similar to that of The Tumor Genome Atlas (TCGA). Differential methylation analysis of cfMeDIP-seq profiles identified 941 ctDNA-derived hypermethylated regions enriched for CpG islands and HNSCC-specific methylation patterns. Both methods demonstrated an association between ctDNA abundance and shorter fragment lengths. In addition, mutation- and methylation-based ctDNA abundance was highly correlated (r > 0.85). Patients with detectable pretreatment ctDNA by both methods demonstrated significantly worse overall survival (HR = 7.5; P = 0.025) independent of clinical stage, with lack of ctDNA clearance post-treatment strongly correlating with recurrence. We further leveraged cfMeDIP-seq profiles to validate a prognostic signature identified from TCGA samples. CONCLUSIONS Tumor-naïve detection of ctDNA by multimodal profiling may facilitate biomarker discovery and clinical use in low ctDNA abundance applications.
Collapse
Affiliation(s)
- Justin M. Burgener
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yangqiao Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Sareh Keshavarzi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John N. Waldron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John R. de Almeida
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - David P. Goldstein
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Michael M. Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Vector Institute, Toronto, Ontario, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Scott V. Bratman, Medical Biophysics, Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-946-2121; E-mail: ; and Daniel D. De Carvalho,
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Scott V. Bratman, Medical Biophysics, Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-946-2121; E-mail: ; and Daniel D. De Carvalho,
| |
Collapse
|
35
|
Rostami A, Bratman SV, Han K. Liquid Biopsy Goes Viral: Next-Generation Sequencing to Enhance HPV Detection. Clin Cancer Res 2021; 27:5158-5160. [PMID: 34301747 DOI: 10.1158/1078-0432.ccr-21-2180] [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] [Received: 06/24/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022]
Abstract
Liquid biopsy approaches for the detection of viral DNA can provide important information for the diagnosis and identification of virally-associated cancers. Here we discuss the next-generation sequencing (NGS)-based CaptHPV method for the detection and characterization of plasma human papillomavirus (HPV) DNA in HPV-associated cancers and its potential clinical utility.
Collapse
Affiliation(s)
| | - Scott V Bratman
- Medical Biophysics, Princess Margaret Cancer Centre, University Health Network
| | - Kathy Han
- Radiation Medicine Program, Princess Margaret Cancer Centre
| |
Collapse
|
36
|
Lau SCM, Soleimani S, Zou J, Burgener J, Kuang S, Wong SWY, Ryan M, Wang BX, Pedersen S, Patel D, Bradbury PA, Liu G, Leighl N, Tsao MS, Ohashi PS, Bratman SV, Pugh T, Shepherd FA, Sacher AG. Abstract 563: cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-563] [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
Introduction: Durvalumab immunotherapy has rapidly emerged as standard treatment for stage 3 NSCLC patients following definitive chemoradiotherapy (CRT). Multiple novel immunotherapeutic strategies are in development to enhance the chance of cure in this setting as well. There exists a critical need to identify blood-based biomarkers capable of predicting clinical benefit from adjuvant immunotherapy as well selecting patients at high-risk of relapse for further drug development. Cell-free DNA (cfDNA)-based analysis of both minimal residual disease (MRD) and T-cell receptor (TCR) clonality have immense potential to predict and monitor response to adjuvant immunotherapy. In this study, we have combined innovative cfDNA measures of MRD (CAPPseq), TCR clonality (CapTCR-seq) and methylation (cfMeDIPseq) as potential predictive biomarkers of disease progression in stage 3 NSCLC patients treated with CRT and durvalumab.
Methods: Stage 3 NSCLC patients undergoing CRT and durvalumab were recruited prospectively to undergo serial blood collections at baseline, pre- and post- durvalumab. CAPPseq and cfMeDIPseq were performed as measures of MRD. TCR repertoire analysis (CapTCR-seq) was performed on cfDNA using hybrid-capture TCR sequencing and TCR diversity/clonality was estimated using the Shannon's index. Correlations between MRD, TCR clonality, response and progression-free survival (PFS) were examined using logistic/cox regression.
Results: 79 stage 3 NSCLC patients have been prospectively recruited and undergone serial blood collection. CAPPseq, cfMeDIPseq and capTCR-seq have been completed in 22 patients (5 primary progression on CRT, 17 received durvalumab). Tumor cfDNA was detectable by CAPPseq at baseline in 14 patients. High correlation between tumor cfDNA detected by CAPPseq and cfMeDIPseq was found (R=0.68, p<0.0001). Failure to clear MRD with CRT plus durvalumab was associated with significantly increased risk of recurrence with a median PFS of 5.0 vs 15.0 months (p<0.0001). Lower TCR clonality measured pre-durvalumab trended with lower likelihood of response (OR 0.82, p=0.09) and worse PFS (HR 1.16 P=0.10). Importantly, a decrease in TCR clonality compared to baseline, signaling the lack of clonal expansion on treatment, was significantly associated with a worse PFS (p=0.05). A decrease in TCR clonality of 50% after CRT was associated with a worse PFS (HR 3.5, p=0.14). CAPPseq, cfMeDIPseq and capTCR-seq analyses are ongoing in the full cohort.
Conclusions: Failure to clear MRD and decreasing TCR clonality as assessed by cfDNA was highly correlated with increased risk of recurrence and reduced PFS with consolidation durvalumab. This innovative approach has significant potential to define a new biomarker for the use and development of adjuvant immunotherapy.
Citation Format: Sally CM Lau, Shirin Soleimani, Jinfeng Zou, Justin Burgener, Shelley Kuang, Stephanie WY Wong, Malcolm Ryan, Ben X. Wang, Stephanie Pedersen, Devalben Patel, Penelope A. Bradbury, Geoffrey Liu, Natasha Leighl, Ming S. Tsao, Pamela S. Ohashi, Scott V. Bratman, Trevor Pugh, Frances A. Shepherd, Adrian G. Sacher. cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 563.
Collapse
Affiliation(s)
- Sally CM Lau
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Jinfeng Zou
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Shelley Kuang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Malcolm Ryan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ben X. Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Devalben Patel
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ming S. Tsao
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Trevor Pugh
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | |
Collapse
|
37
|
de Almeida JR, Bratman SV, Hansen AR. Screening for Nasopharyngeal Cancer in High-Risk Populations: A Small Price to Pay for Early Disease Identification? J Natl Cancer Inst 2021; 113:803-804. [PMID: 33351096 PMCID: PMC8491804 DOI: 10.1093/jnci/djaa199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- John R de Almeida
- Department of Otolaryngology Head and Neck Surgery,
Surgical Oncology, Princess Margaret Cancer Center, University of
Toronto, Toronto, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret
Cancer Center, Toronto, Canada
| | - Aaron R Hansen
- Department of Medical Oncology, Princess Margaret
Cancer Center, Toronto, Canada
| |
Collapse
|
38
|
Gudi S, O'Sullivan B, Hosni A, Su J, Hope A, Ringash J, Hueniken K, Liu G, Tong L, Goldstein D, de Almeida J, Hansen AR, Bratman SV, Cho J, Giuliani M, Hahn E, Kim J, Xu W, Waldron J, Huang SH. Outcome and treatment toxicity in east-indian versus white-canadian patients with oral cavity cancer following postoperative (chemo-)radiotherapy delivered under similar multidisciplinary care: A propensity-matched cohort study. Oral Oncol 2021; 120:105419. [PMID: 34175612 DOI: 10.1016/j.oraloncology.2021.105419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE We compare clinical behaviour of East-Indians and White-Canadians with oral cavity squamous cell carcinoma (OSCC) treated at a Western institution within a uniform health care system. MATERIALS/METHODS Newly diagnosed OSCC patients who underwent postoperative (chemo-)radiotherapy (PORT/POCRT) between 2005 and 2017 were included. Data on ethnicity and other variables were extracted from patient-questionnaires, a prospective database and supplemented by chart review. Baseline characteristics were compared between East-Indian versus White-Canadian groups. A propensity-matched (1:1 ratio) of East-Indian versus White-Canadian cohorts was generated to compare locoregional control (LRC), distant control (DC), overall survival (OS), and acute and late toxicities. RESULTS A total of 53 East-Indian and 467 White-Canadian OSCC patients were identified. Compared to White-Canadians, East-Indian patients were younger, had less exposure to smoking and alcohol (p < 0.001), but more chewed betel (areca) nut /tobacco (43% vs 0.2%, p < 0.001). Buccal/retromolar-trigone/lower gingiva primaries were more common in East-Indians (49% vs 25%, p < 0.001). Median follow-up was 5.0 years. Propensity-score paired analysis revealed inferior 3-year LRC (68% vs 81%, p = 0.030), non-significantly lower OS (61% vs 75%, p = 0.257), but similar DC (81% vs 87%, p = 0.428) in East-Indian versus White-Canadian patients. Actuarial rate of toxicities was higher in East-Indians vs White-Canadians: acute toxicity at 6 weeks: 47% vs 30%, p = 0.012; chronic trismus at 5-years: 16% vs 2%, p = 0.013. CONCLUSION East-Indian OSCC patients have a greater betel nut/ chewable tobacco exposure compared to White-Canadians and a different distribution of OSCC sites. Propensity-matched cohort analysis showed lower LRC and higher toxicities in East-Indian OSCC patients, suggesting a complicated interaction between genetic/biological and life-style factors.
Collapse
Affiliation(s)
- Shivakumar Gudi
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Brian O'Sullivan
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Ali Hosni
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Jie Su
- Department of Biostatistics, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Andrew Hope
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Jolie Ringash
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Katrina Hueniken
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
| | - Geoffrey Liu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada; Division of Medical Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Li Tong
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - David Goldstein
- Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John de Almeida
- Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Aaron R Hansen
- Division of Medical Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Scott V Bratman
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John Cho
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Meredith Giuliani
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Ezra Hahn
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John Kim
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Wei Xu
- Department of Biostatistics, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John Waldron
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Shao Hui Huang
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| |
Collapse
|
39
|
Rostami A, Lambie M, Yu CW, Stambolic V, Waldron JN, Bratman SV. Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics. Cell Rep 2021; 31:107830. [PMID: 32610131 DOI: 10.1016/j.celrep.2020.107830] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [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: 06/04/2019] [Revised: 02/22/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
The kinetics of circulating cell-free DNA (cfDNA) release may provide a real-time assessment of induced cell death. However, there is a limited understanding of the underlying biological rationale for cfDNA release following distinct treatments and cell death mechanisms. Here, we uncover a complex interplay between apoptosis, necrosis, and senescence in determining cfDNA release kinetics. Utilizing multiple in vitro and in vivo preclinical models, we show how cfDNA release is modulated through a combination of apoptotic and senescent triggers and inhibitors. Interestingly, we identify treatment-induced senescence as a previously unrecognized determinant of cfDNA kinetics that can counteract its release. Necrosis is the predominant cell death mechanism that consistently contributes to cfDNA release in response to ionizing radiation, and, surprisingly, apoptosis plays a comparatively minor role in some tumors. Based on our results, we propose a model to explain cfDNA release from cells over time, with important implications for future studies.
Collapse
Affiliation(s)
- Ariana Rostami
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Meghan Lambie
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Caberry W Yu
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Vuk Stambolic
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - John N Waldron
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Radiation Oncology, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Radiation Oncology, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada.
| |
Collapse
|
40
|
Reiazi R, Abbas E, Famiyeh P, Rezaie A, Kwan JYY, Patel T, Bratman SV, Tadic T, Liu FF, Haibe-Kains B. The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review. Comput Biol Med 2021; 133:104400. [PMID: 33930766 DOI: 10.1016/j.compbiomed.2021.104400] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 12/15/2020] [Revised: 03/23/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022]
Abstract
The field of radiomics is at the forefront of personalized medicine. However, there is concern that high variation in imaging parameters will impact robustness of radiomic features and subsequently the performance of the predictive models built upon them. Therefore, our review aims to evaluate the impact of imaging parameters on the robustness of radiomic features. We also provide insights into the validity and discrepancy of different methodologies applied to investigate the robustness of radiomic features. We selected 47 papers based on our predefined inclusion criteria and grouped these papers by the imaging parameter under investigation: (i) scanner parameters, (ii) acquisition parameters and (iii) reconstruction parameters. Our review highlighted that most of the imaging parameters are disruptive parameters, and shape along with First order statistics were reported as the most robust radiomic features against variation in imaging parameters. This review identified inconsistencies related to the methodology of the reviewed studies such as the metrics used for robustness, the feature extraction techniques, the reporting style, and their outcome inclusion. We hope this review will aid the scientific community in conducting research in a way that is more reproducible and avoids the pitfalls of previous analyses.
Collapse
Affiliation(s)
- Reza Reiazi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Engy Abbas
- Joint Department of Medical Imaging, University of Toronto, Toronto, Canada
| | - Petra Famiyeh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aria Rezaie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jennifer Y Y Kwan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tirth Patel
- Techna Institute, University Health Network, Toronto, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Tony Tadic
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; Vector Institute, Toronto, Ontario, Canada.
| |
Collapse
|
41
|
Lambie M, Gill R, Ailles L, Bratman SV. Abstract PO-086: Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.radsci21-po-086] [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
Background: Radiotherapy is a mainstay of curative treatment for squamous cell carcinomas (SCC) and is frequently combined with radiosensitizing drugs to improve efficacy. Outcomes for HPV-negative SCCs remain heterogeneous, in part due to variable resistance to ionizing radiation (IR) and modest benefit of existing radiosensitizing drugs. Hypothesis driven testing of novel radiosensitizing drugs has previously been limited due to a lack of robust, efficient, and reproducible methods to assess drug radiation combinations. Aims: To improve the throughput of preclinical studies on radiosensitizers, we have developed an in vitro system for assessing drug/radiation combinations, validated using the known radiosensitizing chemotherapeutic drug cisplatin. We extended the assay to assess the effect of ML-385, a NRF2 inhibitor that increases cellular reactive oxygen species (ROS), and abemaciclib and palbociclib, two CDK4/6 inhibitors predicted to radiosensitize cancer cells by inhibiting entry into more resistant phases of the cell cycle. Experimental Methods: We adapted the 9-day viability assay of Abazeed et al. (Cancer Res., 2013) to enable drug/radiation efficacy assessments. We first validated the assay’s ability to recapitulate clonogenic survival among 19 HPV-negative SCC cell lines. Drug/radiation experiments were performed in the 6 most radioresistant SCC cell lines. ROS levels after 4Gy IR was used to confirm NRF2 suppression. Flow cytometry was used to evaluate cell cycle phase. AKT inhibitor GSK690693 was used in combination with a NRF2 shRNA knockdown cell line to investigate the mechanism of sensitivity. Western blot was used to detect p16. Cellular response to multiple IR doses was summarized using an area-under-the-curve (AUC) metric. The delta AUC across drug doses was used to evaluate radiosensitization. Results: Among the 19 cell lines, AUCs with the clonogenic and 9-day viability assays were strongly correlated (Pearson r=0.74, p=3.00 × 10–4). Six (32%) of the cell lines were reproducibly radioresistant (AUC >3.5) using both assays. All of these cell lines saw sensitization with cisplatin. None of these 6 cell lines harboured mutations in the canonical NRF2 pathway, whereas all 6 harboured either CCND1 amplification, CDKN2A mutation, or both. Only one cell line showed radiosensitization with the NRF2 inhibitor ML-385, an effect that was abrogated by PIK3CA or AKT pathway inhibition. In contrast, 5 of the 6 cell lines showed reproducible radiosensitization following CDK4/6 inhibition; with robust p16 expression detected in the lone unaffected cell line. Conclusion: The 9-day viability assay allows efficient evaluation of putative radiosensitizers. Our tests of putative radiosensitizing drugs in a cohort of radioresistant cell lines have identified CDK4/6 inhibitors to be of interest for further investigation in biomarker-selected populations.
Citation Format: Meghan Lambie, Rita Gill, Laurie Ailles, Scott V. Bratman. Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-086.
Collapse
Affiliation(s)
- Meghan Lambie
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Rita Gill
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Laurie Ailles
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | |
Collapse
|
42
|
Oliva M, Schneeberger PHH, Rey V, Cho M, Taylor R, Hansen AR, Taylor K, Hosni A, Bayley A, Hope AJ, Bratman SV, Ringash J, Singh S, Weinreb I, Perez-Ordoñez B, Chepeha D, Waldron J, Xu W, Guttman D, Siu LL, Coburn B, Spreafico A. Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study). Br J Cancer 2021; 124:1543-1551. [PMID: 33750907 PMCID: PMC8076306 DOI: 10.1038/s41416-020-01253-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.
Collapse
Affiliation(s)
- Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.,Department of Medical Oncology, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Pierre H H Schneeberger
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Victor Rey
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Matthew Cho
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rachel Taylor
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Aaron R Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Kirsty Taylor
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew Bayley
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Simron Singh
- Department of Pathology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ilan Weinreb
- Department of Medical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Bayardo Perez-Ordoñez
- Department of Medical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Douglas Chepeha
- Department of Surgical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - David Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
43
|
Reiazi R, Arrowsmith C, Abbas-Aghababazadeh F, Eles C, Rezaie A, Bratman SV, Hope AJ, Haibe-Kains B. Abstract PO-033: The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.adi21-po-033] [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
Radiomics involves the use of high-dimensional quantitative imaging features for predictive purposes. However, studies showed that these radiomic features are sensitive to the variability of imaging parameters (e.g., scanner model). One of the major challenges in radiomics lies in improving the robustness of quantitative features against the variation in the imaging dataset in multi-center studies. Here, we assess the impact of scanner choice on the computed tomography (CT)-derived radiomic features to predict association of oropharyngeal squamous cell carcinoma with human papillomavirus (HPV), which has a well-established impact on CT-derived radiomic features. This experiment was performed on CT image datasets acquired with two different scanner types. We demonstrate strong scanner dependency by developing a machine learning model to classify HPV status from radiological images. These experiments revealed the effect of scanner type on the robustness of the radiomic features, and the extent of this dependency is reflected on the performance of HPV prediction models. The result of this study highlighted the importance of implementing an appropriate approach to reduce the impact of the imaging domain radiomic features and consequently on the machine learning models.
Citation Format: Reza Reiazi, Collin Arrowsmith, Farnoosh Abbas-Aghababazadeh, Christopher Eles, Aria Rezaie, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains. The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-033.
Collapse
Affiliation(s)
- Reza Reiazi
- 1Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | | | | | | | - Aria Rezaie
- 2Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Scott V. Bratman
- 1Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Andrew J. Hope
- 1Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Benjamin Haibe-Kains
- 1Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| |
Collapse
|
44
|
Reiazi R, Welch M, Bratman SV, Hope AJ, Haibe-Kains B. Abstract PO-034: The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.adi21-po-034] [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
Osteoradionecrosis (ORN), or bone death, is a multifactorial late complication caused by radiotherapy (RT), that diminishes the bone’s ability to withstand trauma and avoid infection. In head and neck cancer (HNC), ORN most commonly manifests in the mandible. It is influenced by RT-induced factors and patient-related parameters. The most effective way to limit RT-induced ORN is to reduce mandibular volumes receiving high RT doses. However, this strategy may also result in a reduced dose to the tumor due to its proximity to the mandible, and therefore must be restricted to only the patients deemed most vulnerable to mandibular ORN. The objective of this study was to design a prognostic model based on RT-planning CT-derived radiomic features extracted from mandible contours along with the patient’s clinical features to predict the probability of mandibular ORN from the end of RT to the onset of ORN in HNC patients. We hypothesized that these features are related to mandibular ORN and that incorporating them into a prediction model will help to identify patients at risk of mandibular ORN after HNC RT. Patient data was retrospectively collected from the Princess Margaret Cancer Centre, University Health Network and based on the following inclusion criteria: patients had (1) had status regarding radiation-induced bone toxicity, (2) the time to the toxicity event was recorded, and (3) head RT-planning CT images in addition to mandible contours. Then, the patient’s history was reviewed by radiation oncologists to collect clinical features. Quantitative image features were then extracted from the segmented mandible for each patient. Finally, multivariable models, a binary classifier, and a regressor were independently trained on three sets of features (radiomic, demo-clinical, and both) to predict the patient’s risk of ORN and the time between the end of RT and the start of ORN respectively. In total, we analyzed CT images from 92 OPC patients with known ORN status (55 positive, 37 negative). We extracted a total of 1877 radiomic features from the manually-segmented Mandible from each patient. Initially, cases were labelled with their status regarding presence and time to radiation toxicity. Top 50, most relevant and least redundant, features were with mRMRe were used for both binary classification and regression models to predict time to the mandibular ORN. Model training upon radiomics and clinical features resulted in the higher accuracy value of 0.93 (AUCROC) compared to the only radiomics features (0.92) and clinical model (0.74). The distribution of AUC values was significantly wider in models trained on clinical features than radiomics or radiomics plus clinical features.
Citation Format: Reza Reiazi, Mattea Welch, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains. The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-034.
Collapse
Affiliation(s)
- Reza Reiazi
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mattea Welch
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V. Bratman
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Andrew J. Hope
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| |
Collapse
|
45
|
de Almeida JR, Seungyeon Kim V, O'Sullivan B, Goldstein DP, Bratman SV, Hui Huang S, Su J, Xu W, Parulekar W, Waldron JN, Hosni A. Comparing unilateral vs. bilateral neck management in lateralized oropharyngeal cancer between surgical and radiation oncologists: An international practice pattern survey. Oral Oncol 2021; 114:105165. [PMID: 33524796 DOI: 10.1016/j.oraloncology.2020.105165] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Management of the neck in oropharyngeal carcinoma varies due to a lack of clarity of patterns of lymphatic drainage and concern of failure in the contralateral neck. With recent advances in transoral surgical techniques, surgical management has become increasingly prevalent as the primary treatment modality. We compare international practice patterns between surgical and radiation oncologists. METHODS A survey of neck management practice patterns was developed and pilot tested by 6 experts. The survey comprised items eliciting the nature of clinical practice, as well as patterns of neck management depending on extent of nodal disease and location and extent of primary site disease. Proportions of surgical and radiation oncologists treating the neck bilaterally were compared using the chi-squared statistic. RESULTS Two-hundred and twenty-two responses were received from 172 surgical oncologists, 44 radiation oncologists, 3 medical oncologists, and 3 non-oncologists from 32 different countries. For tongue base cancers within 1 cm of midline (67% vs. 100%, p < 0.001), and for tonsil cancers with extension to the medial 1/3 of the soft palate (65% vs. 100%, p < 0.001) or tongue base (77% vs. 100%, p < 0.001), surgical oncologists were less likely to treat the neck bilaterally. For isolated tonsil fossa cancers with no nodal disease, both surgical and radiation oncologists were similarly likely to treat unilaterally (99% vs. 97%, p = NS). However, with increasing nodal burden, radiation oncologists were more likely to treat bilaterally for scenarios with a single node < 3 cm (15% vs. 2%, p < 0.001), a single node with extranodal extension (41% vs. 18%, p < 0.001), multiple positive nodes (55% vs. 23% p < 0.001), and node(s) > 6 cm (86% vs. 33%, p < 0.001). For tumors with midline extension, even with a negative PET in the contralateral neck, the majority of surgical and radiation oncologists would still treat the neck bilaterally (53% and 84% respectively). CONCLUSIONS The present study demonstrates significant practice pattern variability for management of the neck in patients with lateralized oropharyngeal carcinoma. Surgical oncologists are less likely to treat the neck bilaterally, regardless of tumor location or nodal burden. Even in the absence of disease in the contralateral neck on imaging, them majority of practitioners are likely to treat bilaterally when the disease approaches midline.
Collapse
Affiliation(s)
- John R de Almeida
- Department of Otolaryngology-Head and Neck Surgery, Department of Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Canada.
| | - Valerie Seungyeon Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head and Neck Surgery, Department of Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - Jie Su
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Canada
| | | | - John N Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Canada
| |
Collapse
|
46
|
Pilar A, Yu E, Su J, O'Sullivan B, Bartlett E, Waldron JN, Ringash J, Spreafico A, Hansen AR, de Almeida J, Bayley A, Bratman SV, Cho J, Giuliani M, Hope A, Hosni A, Kim J, Tong L, Xu W, Huang SH. Prognostic value of clinical and radiologic extranodal extension and their role in the 8th edition TNM cN classification for HPV-negative oropharyngeal carcinoma. Oral Oncol 2021; 114:105167. [PMID: 33508706 DOI: 10.1016/j.oraloncology.2020.105167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/17/2020] [Revised: 11/26/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND/OBJECTIVES We evaluate the performance between the TNM-8 versus TNM-7 cN-classification and explore the relative prognostic contribution of radiologic extranodal extension (rENE) for HPV-negative oropharyngeal cancer (HPV-OPC). MATERIALS/METHODS All HPV- OPC treated with IMRT between 2005 and 2016 were included. cENE was defined as unambiguous "fixation" of a neck mass or "skin involvement" on clinical examination. rENE was recorded by re-reviewing pre-treatment CT/MR. Disease-free survival (DFS) stratified by cENE or rENE were compared. Multivariable analyses (MVA) calculated the adjusted hazard ratio (aHR) for the separate cENE and rENE attributes and their combination. A refined cN-category incorporating both cENE and rENE parameters was proposed. The performance of the revision was compared to TNM-8 and TNM-7. RESULTS Of 361 HPV- OPC, 97 were cN0 and 264 were cN+ with 48 cENE+ and 72 rENE+ respectively. Median follow-up was 5.4 years. The 3-year DFS was lower in cENE+ vs cENE-negative (cENE-) (23% vs 45%; aHR = 1.68, p = 0.008) and rENE+ vs rENE-negative (rENE-) patients (29% vs 45%; aHR = 1.44, p = 0.037). The cENE+/rENE+ subset had the worse DFS vs cENE-/rENE+ or cENE-/rENE- (24%/37%/46%, p = 0.005). We propose a refined cN-category wherein any cENE-/rENE+ case is reclassified one N-stratum higher while any cENE+ case remains cN3b. The stage schema with the refined N-categorization outperformed TNM-8, and both outperformed TNM-7. CONCLUSIONS cENE and rENE are both prognostic but the cENE+/rENE+ subset has the worst outcome. The TNM-8 cN-categories improves outcome prediction compared to the TNM-7. Incorporation of rENE into TNM-8 cN-categories may further augment performance.
Collapse
Affiliation(s)
- Avinash Pilar
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada
| | - Eugene Yu
- Department of Neuroradiology and Head and Neck Imaging, Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Jie Su
- Department of Biostatistics, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Brian O'Sullivan
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Eric Bartlett
- Department of Neuroradiology and Head and Neck Imaging, Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John N Waldron
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Jolie Ringash
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Anna Spreafico
- Division of Medical Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Aaron R Hansen
- Division of Medical Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John de Almeida
- Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Andrew Bayley
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Scott V Bratman
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John Cho
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Meredith Giuliani
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Andrew Hope
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Ali Hosni
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - John Kim
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Li Tong
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Wei Xu
- Department of Biostatistics, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| | - Shao Hui Huang
- Department of Radiation Oncology, The Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery, The Princess Margaret Cancer Centre/University of Toronto, Canada.
| |
Collapse
|
47
|
Rostami A, Yu C, Bratman SV. Serial Cell-free DNA Assessments in Preclinical Models. STAR Protoc 2020; 1:100145. [PMID: 33377039 PMCID: PMC7757313 DOI: 10.1016/j.xpro.2020.100145] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Studying circulating cell-free DNA (cfDNA) release within preclinical model systems provides opportunities to investigate the mechanisms and kinetics underlying this process under various conditions. We present a detailed protocol for longitudinal evaluation of cfDNA release through (1) seeding of cancer cell lines and establishment of xenograft tumors, (2) treatment of cancer cells and xenograft tumors, (3) serial collection of cell line media and xenograft blood, and (4) processing and isolation of cfDNA for (5) quantification of cfDNA by quantitative PCR. For complete details on the use and execution of this protocol please refer to Rostami et al. (2020). Cell line media and xenograft blood can be serially collected after irradiation Small plasma volumes can be simultaneously purified for cell-free DNA (cfDNA) Cell line media can be diluted for quantification of cfDNA using quantitative PCR Human LINE-1 can be used for ultrasensitive detection of cfDNA
Collapse
Affiliation(s)
- Ariana Rostami
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Caberry Yu
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Radiation Oncology, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| |
Collapse
|
48
|
Hosni A, Huang SH, Xu W, Su J, Watson E, Glogauer M, Bayley A, Bratman SV, Cho J, Giuliani M, Hope A, Kim J, O'Sullivan B, Ringash J, Spreafico A, Goldstein DP, Waldron J, de Almeida JR. Healthcare resource utilization following unilateral versus bilateral radiation therapy for oropharyngeal carcinoma. Radiother Oncol 2020; 156:95-101. [PMID: 33264637 DOI: 10.1016/j.radonc.2020.11.028] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE To describe differences in healthcare resource utilization between patients treated with bilateral vs. unilateral neck radiation therapy (RT) for lateralized oropharyngeal cancer. METHODS A propensity score matching strategy was used to identify two otherwise clinically similar cohorts of tonsillar cancer patients treated with either bilateral or unilateral neck RT. Cohorts were matched based on similar propensity scores for age, sex, ECOG performance status, pack-year smoking history, cT-category, cN-category, HPV-status, and use of concurrent chemotherapy. Short term (from start of RT to 3 months following end of RT) resource utilization included: 1) outpatient supportive care visits, 2) hospital admission, and 3) interventions (feeding tube insertion and outpatient intravenous hydration). Long-term resource utilization included feeding tube dependency at 1-year. RESULTS Among 559 patients with tonsillar cancer treated between 2004-2017, propensity score matching identified a unilateral neck RT cohort (n = 81) and bilateral neck RT cohort (n = 81) with similar clinical and treatment characteristics. Bilateral neck RT was associated with a higher likelihood of hospitalization (33% vs 12%, p < 0.01), outpatient IV hydration (33% vs 17%, p = 0.03), and feeding tube insertion (33% vs 10%, p < 0.001); a greater number of total days of hospitalization (110 vs 47 days, p < 0.01) and outpatient IV hydration (135 vs 72 days, p = 0.02); and higher total number of supportive clinic visits (1226 vs 1053 days, p = 0.04). In the long-term, bilateral RT was associated with higher rate of feeding tube dependency at 1-year (7% vs 0%, p < 0.001). CONCLUSION Bilateral RT for tonsillar cancer resulted in significant increase in health resource utilization.
Collapse
Affiliation(s)
- Ali Hosni
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada.
| | - Shao Hui Huang
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre/University of Toronto, Canada
| | - Jie Su
- Department of Biostatistics, Princess Margaret Cancer Centre/University of Toronto, Canada
| | - Erin Watson
- Department of Dental Oncology and Maxillofacial Prosthetics. Princess Margaret Cancer Centre / University of Toronto, Canada
| | - Michael Glogauer
- Department of Dental Oncology and Maxillofacial Prosthetics. Princess Margaret Cancer Centre / University of Toronto, Canada
| | - Andrew Bayley
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Scott V Bratman
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - John Cho
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Meredith Giuliani
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Andrew Hope
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - John Kim
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Brian O'Sullivan
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - Jolie Ringash
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada; Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre/University of Toronto, Canada
| | - Anna Spreafico
- Department of Medical Oncology, Princess Margaret Cancer Centre/University of Toronto, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre/University of Toronto, Canada
| | - John Waldron
- Radiation Medicine Program, Princess Margaret Cancer Centre/University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada
| | - John R de Almeida
- Department of Otolaryngology-Head & Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre/University of Toronto, Canada
| |
Collapse
|
49
|
Abelson S, Zeng AGX, Nofech-Mozes I, Wang TT, Ng SWK, Minden MD, Pugh TJ, Awadalla P, Shlush LI, Murphy T, Chan SM, Dick JE, Bratman SV. Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing. Sci Adv 2020; 6:6/50/eabe3722. [PMID: 33298453 PMCID: PMC7725472 DOI: 10.1126/sciadv.abe3722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
Sensitive mutation detection by next-generation sequencing is critical for early cancer detection, monitoring minimal/measurable residual disease (MRD), and guiding precision oncology. Nevertheless, because of artifacts introduced during library preparation and sequencing, the detection of low-frequency variants at high specificity is problematic. Here, we present Espresso, an error suppression method that considers local sequence features to accurately detect single-nucleotide variants (SNVs). Compared to other advanced error suppression techniques, Espresso consistently demonstrated lower numbers of false-positive mutation calls and greater sensitivity. We demonstrated Espresso's superior performance in detecting MRD in the peripheral blood of patients with acute myeloid leukemia (AML) throughout their treatment course. Furthermore, we showed that accurate mutation calling in a small number of informative genomic loci might provide a cost-efficient strategy for pragmatic risk prediction of AML development in healthy individuals. More broadly, we aim for Espresso to aid with accurate mutation detection in many other research and clinical settings.
Collapse
Affiliation(s)
- Sagi Abelson
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andy G X Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ido Nofech-Mozes
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Stanley W K Ng
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Liran I Shlush
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tracy Murphy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
50
|
Shi W, Misra S, Li M, Su J, Chong LP, McCuske M, Williams J, Xu W, Ghoraie LS, Sutherland DR, Han K, Minden MD, Bratman SV, Yip KW, Liu FF. Inflammatory Biomarkers, Hematopoietic Stem Cells, and Symptoms in Breast Cancer Patients Undergoing Adjuvant Radiation Therapy. JNCI Cancer Spectr 2020; 4:pkaa037. [PMID: 33134822 PMCID: PMC7583146 DOI: 10.1093/jncics/pkaa037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/21/2020] [Revised: 04/06/2020] [Accepted: 04/30/2020] [Indexed: 12/03/2022] Open
Abstract
Background Fatigue and insomnia are common symptoms experienced by breast cancer patients undergoing adjuvant radiation therapy (RT), yet the underlying mechanisms of these symptoms are unclear. In particular, the roles of hematopoietic stem cells (HSCs) and inflammatory cytokines remain to be elucidated. Methods Breast cancer patients (n = 147) completed questionnaires to longitudinally assess symptoms before, during, and after adjuvant RT. Phlebotomies were performed prior to RT, at the second and fifth treatment fractions, end of treatment (EOT), and 1 month after completing RT, assessing for CD34+, CD45+, full hematology, and 17 inflammatory cytokines. The associations between symptoms and all biomarkers were evaluated. All statistical tests were 2-sided. Results General fatigue and insomnia worsened with RT, with peak levels observed at EOT, which remained statistically significant even after controlling for anxiety and depression (P < .05 for all). CD34+, CD45+, white blood cell, and lymphocyte counts decreased, with the lowest levels also observed at EOT (P < .001). Fatigue and insomnia were associated with changes in both interferon γ-induced protein 10 (IP-10) - (P = .03 and P = .01, respectively) and tumor necrosis factor receptor II (TNF-RII) (P = .02 and P = .006, respectively), while mental fatigue was associated with increased matrix metalloproteinases-2 (MMP-2) levels (P = .03). Patients who received prior chemotherapy demonstrated statistically significantly greater severity in all symptoms, with lower baseline HSC levels. Conclusions This is the first longitudinal study to examine linkages between symptoms, HSCs, and cytokines, demonstrating that fatigue and insomnia shared associations with increasing serum levels of IP-10 and TNF-RII, and mental fatigue was associated with increasing serum levels of MMP-2. Our findings highlight opportunities for further research into mechanisms and potential interventions for these symptoms.
Collapse
Affiliation(s)
- Wei Shi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shagun Misra
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Madeline Li
- Department of Supportive Care, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Jie Su
- Division of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisa P Chong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Megan McCuske
- Department of Supportive Care, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Justin Williams
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wei Xu
- Division of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Biostatistics, University of Toronto, Toronto, Ontario, Canada
| | - Laleh S Ghoraie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - D Robert Sutherland
- Department of Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kathy Han
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Department of Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth W Yip
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|