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Rydzewski NR, Helzer KT, Bootsma M, Shi Y, Bakhtiar H, Sjöström M, Zhao SG. Machine Learning & Molecular Radiation Tumor Biomarkers. Semin Radiat Oncol 2023; 33:243-251. [PMID: 37331779 PMCID: PMC10287033 DOI: 10.1016/j.semradonc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Developing radiation tumor biomarkers that can guide personalized radiotherapy clinical decision making is a critical goal in the effort towards precision cancer medicine. High-throughput molecular assays paired with modern computational techniques have the potential to identify individual tumor-specific signatures and create tools that can help understand heterogenous patient outcomes in response to radiotherapy, allowing clinicians to fully benefit from the technological advances in molecular profiling and computational biology including machine learning. However, the increasingly complex nature of the data generated from high-throughput and "omics" assays require careful selection of analytical strategies. Furthermore, the power of modern machine learning techniques to detect subtle data patterns comes with special considerations to ensure that the results are generalizable. Herein, we review the computational framework of tumor biomarker development and describe commonly used machine learning approaches and how they are applied for radiation biomarker development using molecular data, as well as challenges and emerging research trends.
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Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI; Carbone Cancer Center, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital, Madison, WI.
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Xiang M, Ma TM, Savjani R, Pollom EL, Karnes RJ, Grogan T, Wong JK, Motterle G, Tosoian JJ, Trock BJ, Klein EA, Stish BJ, Dess RT, Spratt DE, Pilar A, Reddy C, Levin-Epstein R, Wedde TB, Lilleby WA, Fiano R, Merrick GS, Stock RG, Demanes DJ, Moran BJ, Huland H, Tran PT, Martin S, Martinez-Monge R, Krauss DJ, Abu-Isa EI, Alam R, Schwen Z, Pisansky TM, Choo CR, Song DY, Greco S, Deville C, McNutt T, DeWeese TL, Ross AE, Ciezki JP, Boutros PC, Nickols NG, Bhat P, Shabsovich D, Juarez JE, Chong N, Kupelian PA, Rettig MB, Zaorsky NG, Berlin A, Tward JD, Davis BJ, Reiter RE, Steinberg ML, Elashoff D, Horwitz EM, Tendulkar RD, Tilki D, Czernin J, Gafita A, Romero T, Calais J, Kishan AU. Performance of a Prostate-Specific Membrane Antigen Positron Emission Tomography/Computed Tomography-Derived Risk-Stratification Tool for High-risk and Very High-risk Prostate Cancer. JAMA Netw Open 2021; 4:e2138550. [PMID: 34902034 PMCID: PMC8669522 DOI: 10.1001/jamanetworkopen.2021.38550] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
IMPORTANCE Prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) can detect low-volume, nonlocalized (ie, regional or metastatic) prostate cancer that was occult on conventional imaging. However, the long-term clinical implications of PSMA PET/CT upstaging remain unclear. OBJECTIVES To evaluate the prognostic significance of a nomogram that models an individual's risk of nonlocalized upstaging on PSMA PET/CT and to compare its performance with existing risk-stratification tools. DESIGN, SETTING, AND PARTICIPANTS This cohort study included patients diagnosed with high-risk or very high-risk prostate cancer (ie, prostate-specific antigen [PSA] level >20 ng/mL, Gleason score 8-10, and/or clinical stage T3-T4, without evidence of nodal or metastatic disease by conventional workup) from April 1995 to August 2018. This multinational study was conducted at 15 centers. Data were analyzed from December 2020 to March 2021. EXPOSURES Curative-intent radical prostatectomy (RP), external beam radiotherapy (EBRT), or EBRT plus brachytherapy (BT), with or without androgen deprivation therapy. MAIN OUTCOMES AND MEASURES PSMA upstage probability was calculated from a nomogram using the biopsy Gleason score, percentage positive systematic biopsy cores, clinical T category, and PSA level. Biochemical recurrence (BCR), distant metastasis (DM), prostate cancer-specific mortality (PCSM), and overall survival (OS) were analyzed using Fine-Gray and Cox regressions. Model performance was quantified with the concordance (C) index. RESULTS Of 5275 patients, the median (IQR) age was 66 (60-72) years; 2883 (55%) were treated with RP, 1669 (32%) with EBRT, and 723 (14%) with EBRT plus BT; median (IQR) PSA level was 10.5 (5.9-23.2) ng/mL; 3987 (76%) had Gleason grade 8 to 10 disease; and 750 (14%) had stage T3 to T4 disease. Median (IQR) follow-up was 5.1 (3.1-7.9) years; 1221 (23%) were followed up for at least 8 years. Overall, 1895 (36%) had BCR, 851 (16%) developed DM, and 242 (5%) died of prostate cancer. PSMA upstage probability was significantly prognostic of all clinical end points, with 8-year C indices of 0.63 (95% CI, 0.61-0.65) for BCR, 0.69 (95% CI, 0.66-0.71) for DM, 0.71 (95% CI, 0.67-0.75) for PCSM, and 0.60 (95% CI, 0.57-0.62) for PCSM (P < .001). The PSMA nomogram outperformed existing risk-stratification tools, except for similar performance to Staging Collaboration for Cancer of the Prostate (STAR-CAP) for PCSM (eg, DM: PSMA, 0.69 [95% CI, 0.66-0.71] vs STAR-CAP, 0.65 [95% CI, 0.62-0.68]; P < .001; Memorial Sloan Kettering Cancer Center nomogram, 0.57 [95% CI, 0.54-0.60]; P < .001; Cancer of the Prostate Risk Assessment groups, 0.53 [95% CI, 0.51-0.56]; P < .001). Results were validated in secondary cohorts from the Surveillance, Epidemiology, and End Results database and the National Cancer Database. CONCLUSIONS AND RELEVANCE These findings suggest that PSMA upstage probability is associated with long-term, clinically meaningful end points. Furthermore, PSMA upstaging had superior risk discrimination compared with existing tools. Formerly occult, PSMA PET/CT-detectable nonlocalized disease may be the main driver of outcomes in high-risk patients.
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Affiliation(s)
- Michael Xiang
- Department of Radiation Oncology, University of California, Los Angeles
| | - Ting Martin Ma
- Department of Radiation Oncology, University of California, Los Angeles
| | - Ricky Savjani
- Department of Radiation Oncology, University of California, Los Angeles
| | - Erqi L. Pollom
- Department of Radiation Oncology, Stanford University, Stanford, California
| | | | - Tristan Grogan
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jessica K. Wong
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | | | - Bruce J. Trock
- Department of Urology, Brady Urological Institute, Johns Hopkins University, Baltimore, Maryland
| | - Eric A. Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Bradley J. Stish
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Robert T. Dess
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Daniel E. Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Avinash Pilar
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Chandana Reddy
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Trude B. Wedde
- Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Wolfgang A. Lilleby
- Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Ryan Fiano
- Schiffler Cancer Center, Wheeling Hospital, Wheeling Jesuit University, Wheeling, West Virginia
| | - Gregory S. Merrick
- Schiffler Cancer Center, Wheeling Hospital, Wheeling Jesuit University, Wheeling, West Virginia
| | - Richard G. Stock
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York City, New York
| | | | - Brian J. Moran
- Prostate Cancer Foundation of Chicago, Westmont, Illinois
| | - Hartwig Huland
- Martini-Klinik Prostate Cancer Center, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Phuoc T. Tran
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Santiago Martin
- Department of Oncology, Clínica Universitaria de Navarra, University of Navarra, Pamplona, Spain
| | - Rafael Martinez-Monge
- Department of Oncology, Clínica Universitaria de Navarra, University of Navarra, Pamplona, Spain
| | - Daniel J. Krauss
- Oakland University William Beaumont School of Medicine, Royal Oak, Michigan
| | - Eyad I. Abu-Isa
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Ridwan Alam
- Department of Urology, Brady Urological Institute, Johns Hopkins University, Baltimore, Maryland
| | - Zeyad Schwen
- Department of Urology, Brady Urological Institute, Johns Hopkins University, Baltimore, Maryland
| | | | - C. Richard Choo
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Daniel Y. Song
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen Greco
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Curtiland Deville
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Todd McNutt
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Theodore L. DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley E. Ross
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jay P. Ciezki
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles
| | - Nicholas G. Nickols
- Department of Radiation Oncology, University of California, Los Angeles
- Department of Radiation Oncology, Veterans Affairs (VA) Greater Los Angeles Healthcare System, Los Angeles, California
| | - Prashant Bhat
- Department of Radiation Oncology, University of California, Los Angeles
| | - David Shabsovich
- Department of Radiation Oncology, University of California, Los Angeles
| | - Jesus E. Juarez
- Department of Radiation Oncology, University of California, Los Angeles
| | - Natalie Chong
- Department of Radiation Oncology, University of California, Los Angeles
| | | | - Matthew B. Rettig
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles
- Department of Hematology and Oncology, Veterans Affairs (VA) Greater Los Angeles Healthcare System, Los Angeles, California
| | - Nicholas G. Zaorsky
- Department of Radiation Oncology, Penn State Cancer Institute, Hershey, Pennsylvania
| | - Alejandro Berlin
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan D. Tward
- Department of Radiation Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Brian J. Davis
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | | | - David Elashoff
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Eric M. Horwitz
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Rahul D. Tendulkar
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center, University Hospital Hamburg Eppendorf, Hamburg, Germany
- Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Czernin
- Ahmanson Translational Theranostics Division, Department of Molecular and Medical Pharmacology, UCLA Medical Center, Los Angeles, California
| | - Andrei Gafita
- Ahmanson Translational Theranostics Division, Department of Molecular and Medical Pharmacology, UCLA Medical Center, Los Angeles, California
| | - Tahmineh Romero
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jeremie Calais
- Ahmanson Translational Theranostics Division, Department of Molecular and Medical Pharmacology, UCLA Medical Center, Los Angeles, California
| | - Amar U. Kishan
- Department of Radiation Oncology, University of California, Los Angeles
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Kasahara T, Ishizaki F, Kazama A, Yuki E, Yamana K, Maruyama R, Oshikane T, Kaidu M, Aoyama H, Bilim V, Nishiyama T, Tomita Y. High-dose-rate brachytherapy and hypofractionated external beam radiotherapy combined with long-term androgen deprivation therapy for very high-risk prostate cancer. Int J Urol 2020; 27:800-806. [PMID: 32633027 DOI: 10.1111/iju.14305] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To estimate the outcomes of high-dose-rate brachytherapy combined with hypofractionated external beam radiotherapy in prostate cancer patients classified as very high risk by the National Comprehensive Cancer Network. METHODS Between June 2009 and September 2015, 66 patients meeting the criteria for very high-risk disease received high-dose-rate brachytherapy (2 fractions of 9 Gy) as a boost of external beam radiotherapy (13 fractions of 3 Gy). Androgen deprivation therapy was administered for approximately 3 years. Biochemical failure was assessed using the Phoenix definition. RESULTS The median follow-up period was 53 months from the completion of radiotherapy. The 5-year biochemical failure-free, distant metastasis-free, prostate cancer-specific and overall survival rates were 88.7, 89.2, 98.5 and 97.0%, respectively. The independent contribution of each component of the very high-risk criteria was assessed in multivariable models. Primary Gleason pattern 5 was associated with increased risks of biochemical failure (P = 0.017) and distant metastasis (P = 0.049), whereas clinical stage ≥T3b or >4 biopsy cores with Gleason score 8-10 had no significant impact on the two outcomes. Grade 3 genitourinary toxicities were observed in two (3.0%) patients, whereas no grade ≥3 gastrointestinal toxicities occurred. CONCLUSIONS The present study shows that this multimodal approach provides potentially excellent cancer control and acceptable associated morbidity for very high-risk disease. Patients with primary Gleason pattern 5 are at a higher risk of poor outcomes, indicating the need for more aggressive approaches in these cases.
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Affiliation(s)
- Takashi Kasahara
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Fumio Ishizaki
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akira Kazama
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Eri Yuki
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazutoshi Yamana
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Maruyama
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomoya Oshikane
- Department of Radiology and Radiation Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Motoki Kaidu
- Department of Radiology and Radiation Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hidefumi Aoyama
- Department of Radiology and Radiation Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Vladimir Bilim
- Department of Urology, Kameda Daiichi Hospital, Niigata, Japan
| | | | - Yoshihiko Tomita
- Division of Molecular Oncology, Department of Urology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Sachpazidis I, Hense J, Mavroidis P, Gainey M, Baltas D. Investigating the role of constrained CVT and CVT in HIPO inverse planning for HDR brachytherapy of prostate cancer. Med Phys 2019; 46:2955-2968. [PMID: 31055834 DOI: 10.1002/mp.13564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
PURPOSE The purpose of this study is to investigate the role of the centroidal Voronoi tessellation (CVT) and constrained CVT (CCVT) in inverse planning in combination with the Hybrid Inverse Planning Optimization (HIPO) algorithm in HDR brachytherapy of prostate cancer. HIPO implemented in Oncentra© Prostate treatment planning system, is used for three-dimensional (3D)-ultrasound-based intraoperative treatment planning in high dose rate brachytherapy. HIPO utilizes a hybrid iterative process to determine the most appropriate placement of a given number of catheters to fulfil predefined dose-volume constraints. The main goals of the current investigation were to identify a way of improving the performance of HIPO inverse planning; accelerating the HIPO, and to evaluate the effect of the two CVT-based initialization methods on the dose distribution in the sub-region of prostate that is not accessible by catheters, when trying to avoid perforation of urethra. METHODS We implemented the CVT algorithm to generate initial catheter configurations before the initialization of the HIPO algorithm. We introduced the CCVT algorithm to improve the dose distribution to the sub-volume of prostate within the bounding box of the urethra contours including its upper vertical extension (U-P). For the evaluation, we considered a total of 15 3D ultrasound-based HDRBT prostate implants. Execution time and treatment plan quality were evaluated based on the dose-volume histograms of prostate (PTV), its sub-volume U-P, and organs at risk (OARs). Furthermore, the conformity index COIN, the homogeneity index HI and the complication-free tumor control probability (P+ ) were used for our treatment plan comparisons. Finally, the plans with the recommended HIPO execution mode were compared to the clinically used intraoperative pre-plans. RESULTS The plan quality achieved with CCVT-based HIPO initialization was superior to the default HIPO initialization method. Focusing on the U-P sub-region of the prostate, the CCVT method resulted in a significant improvement of all dosimetric indices compared to the default HIPO, when both were executed in the adaptive mode. For that recommended HIPO execution mode, and for U-P, CCVT demonstrated in general higher dosimetric indices than CVT. Additionally, the execution time of CCVT initialized HIPO was lower compared to both alternative initialization methods. This is also valid for the values of the aggregate objective function with the differences to the default initialization method being highly significant. Paired non-parametric statistical tests (Wilcoxon signed-rank) showed a significant improvement of dose-volume indices, COIN and P+ for the plans generated by the CCVT-based catheter configuration initialization in HIPO compared to the default HIPO initialization process. Furthermore, in ten out of 15 cases, the CCVT-based HIPO plans fulfilled all the clinical dose-volume constraints in a single trial without any need for further catheter position adaption. CONCLUSION HIPO with CCVT-based initialization demonstrates better performance regarding the aggregate objective function and convergence when compared to the CVT-based and default catheter configuration initialization methods. This improved performance of HIPO inverse planning is clearly not at the cost of the dosimetric and radiobiologically evaluated plan quality. We recommend the use of the CCVT method for HIPO initialization especially in the adaptive planning mode.
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Affiliation(s)
- Ilias Sachpazidis
- Division of Medical Physics, Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Jürgen Hense
- Division of Medical Physics, Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Panayiotis Mavroidis
- Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Mark Gainey
- Division of Medical Physics, Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Dimos Baltas
- Division of Medical Physics, Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
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