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Andersson B, Langen B, Liu P, Dávila López M. Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction. Front Oncol 2023; 13:1156009. [PMID: 37256187 PMCID: PMC10225714 DOI: 10.3389/fonc.2023.1156009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Background Molecular radiation biomarkers are an emerging tool in radiation research with applications for cancer radiotherapy, radiation risk assessment, and even human space travel. However, biomarker screening in genome-wide expression datasets using conventional tools is time-consuming and underlies analyst (human) bias. Machine Learning (ML) methods can improve the sensitivity and specificity of biomarker identification, increase analytical speed, and avoid multicollinearity and human bias. Aim To develop a resource-efficient ML framework for radiation biomarker discovery using gene expression data from irradiated normal tissues. Further, to identify biomarker panels predicting radiation dose with tissue specificity. Methods A strategic search in the Gene Expression Omnibus database identified a transcriptomic dataset (GSE44762) for normal tissues radiation responses (murine kidney cortex and medulla) suited for biomarker discovery using an ML approach. The dataset was pre-processed in R and separated into train and test data subsets. High computational cost of Genetic Algorithm/k-Nearest Neighbor (GA/KNN) mandated optimization and 13 ML models were tested using the caret package in R. Biomarker performance was evaluated and visualized via Principal Component Analysis (PCA) and dose regression. The novelty of ML-identified biomarker panels was evaluated by literature search. Results Caret-based feature selection and ML methods vastly improved processing time over the GA approach. The KNN method yielded overall best performance values on train and test data and was implemented into the framework. The top-ranking genes were Cdkn1a, Gria3, Mdm2 and Plk2 in cortex, and Brf2, Ccng1, Cdkn1a, Ddit4l, and Gria3 in medulla. These candidates successfully categorized dose groups and tissues in PCA. Regression analysis showed that correlation between predicted and true dose was high with R2 of 0.97 and 0.99 for cortex and medulla, respectively. Conclusion The caret framework is a powerful tool for radiation biomarker discovery optimizing performance with resource-efficiency for broad implementation in the field. The KNN-based approach identified Brf2, Ddit4l, and Gria3 mRNA as novel candidates that have been uncharacterized as radiation biomarkers to date. The biomarker panel showed good performance in dose and tissue separation and dose regression. Further training with larger cohorts is warranted to improve accuracy, especially for lower doses.
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Affiliation(s)
- Björn Andersson
- Bioinformatics Core Facility, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Britta Langen
- Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas (UT) Southwestern Medical Center, Dallas, TX, United States
| | - Peidi Liu
- Bioinformatics Core Facility, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcela Dávila López
- Bioinformatics Core Facility, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Ferrari M, Mattavelli D, Tomasoni M, Raffetti E, Bossi P, Schreiber A, Orlandi E, Taboni S, Rampinelli V, Gualtieri T, Turri-Zanoni M, Battaglia P, Arosio AD, Bignami M, Tartaro T, Molteni M, Bertazzoni G, Fiaux-Camous D, Jourdaine C, Verillaud B, Eu D, Nair D, Moiyadi A, Shetty P, Ghosh-Laskar S, Budrukkar A, Magrini SM, Guillerm S, Faivre S, Piazza C, Gilbert RW, Irish JC, de Almeida JR, Pai P, Herman P, Castelnuovo P, Nicolai P. The MUSES∗: a prognostic study on 1360 patients with sinonasal cancer undergoing endoscopic surgery-based treatment: ∗MUlti-institutional collaborative Study on Endoscopically treated Sinonasal cancers. Eur J Cancer 2022; 171:161-182. [PMID: 35724468 DOI: 10.1016/j.ejca.2022.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Over the last 2 decades, transnasal endoscopic surgery (TES) has become the most frequently employed surgical technique to treat sinonasal malignancies. The rarity and heterogeneity of sinonasal cancers have hampered large non-population-based analyses. METHODOLOGY All patients receiving TES-including treatment between 1995 and 2021 in 5 referral hospitals were included. A prognostic study was performed, and multivariable models were transformed into nomograms. Training and validation sets were based on results from 3 European and 2 non-European centres, respectively. RESULTS The training and validation set included 940 and 420 patients, respectively. The mean age at surgery, primary-versus-recurrent presentation, histology distribution, type of surgery, T category and type of adjuvant treatment were differently distributed in the training and validation set. In the training set, 5-year overall survival and recurrence-free survival with a 95%-confidence interval were 72.7% (69.5-76.0%) and 66.4% (63.1-69.8%), respectively, significantly varying with histology. At multivariable analyses, age, gender, previous treatment, the extent of resection on the cranial, lateral and posterolateral axes, grade/subtype, T category, nodal status, margin status and adjuvant treatment were all associated with different prognostic outcomes, displaying a heterogeneous significance and effect size according to histology. The internal and external validation of nomograms was satisfactory (optimism-corrected C-index >0.7 and cumulative area under curve >0.7) for all histologies but mucosal melanoma. CONCLUSIONS Outcomes of TES-based treatment of sinonasal cancers vary substantially with histology. This large, non-population-based study provides benchmark data on the prognosis of sinonasal cancers that are deemed suitable for treatment including TES.
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Affiliation(s)
- Marco Ferrari
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Neurosciences, "Azienda Ospedale Università di Padova", University of Padua, Padua, Italy; Guided Therapeutics (GTx) Program International Scholarship, University Health Network (UHN), Toronto, ON, Canada; Technology for Health (PhD Program), Department of Information Engineering, University of Brescia, Brescia, Italy.
| | - Davide Mattavelli
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Michele Tomasoni
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Elena Raffetti
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Bossi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Alberto Schreiber
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Ester Orlandi
- Radiation Oncology Clinical Department, National Center for Oncological Hadrontherapy (CNAO), Pavia, Italy
| | - Stefano Taboni
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Neurosciences, "Azienda Ospedale Università di Padova", University of Padua, Padua, Italy; Guided Therapeutics (GTx) Program International Scholarship, University Health Network (UHN), Toronto, ON, Canada; Artificial Intelligence in Medicine and Innovation in Clinical Research and Methodology (PhD Program), Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Vittorio Rampinelli
- Technology for Health (PhD Program), Department of Information Engineering, University of Brescia, Brescia, Italy; Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Tommaso Gualtieri
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Mario Turri-Zanoni
- Division of Otorhinolaryngology, Department of Surgical Specialties, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy; Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Head and Neck Surgery & Forensic Dissection Research Center (HNS&FDRc), Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Paolo Battaglia
- Division of Otorhinolaryngology, Department of Surgical Specialties, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy; Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Head and Neck Surgery & Forensic Dissection Research Center (HNS&FDRc), Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Alberto D Arosio
- Division of Otorhinolaryngology, Department of Surgical Specialties, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy
| | - Maurizio Bignami
- Division of Otorhinolaryngology, "ASST Lariana", University of Insubria, Como, Italy
| | - Tiziana Tartaro
- Department of Medical Oncology, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy
| | - Marinella Molteni
- Department of Radiotherapy, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy
| | | | | | - Clement Jourdaine
- Hopital Lariboisiere, APHP Nord - Université De Paris, INSERM U 1141, Paris, France
| | - Benjamin Verillaud
- Hopital Lariboisiere, APHP Nord - Université De Paris, INSERM U 1141, Paris, France
| | - Donovan Eu
- Department of Otolaryngology - Head and Neck Surgery/Surgical Oncology, University Health Network, Toronto, Ontario, Canada; Guided Therapeutics (GTx) Program, Techna Institute, University Health Network, Toronto, Ontario, Canada
| | - Deepa Nair
- Department of Head & Neck Surgery, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Sarbani Ghosh-Laskar
- Department of Radiation Oncology, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Ashwini Budrukkar
- Department of Radiation Oncology, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Stefano M Magrini
- Unit of Radiation Oncology, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Sophie Guillerm
- Department of Radiotherapy Assistance Publique - Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | - Sandrine Faivre
- Department of Medical Oncology Assistance Publique - Hôpitaux de Paris, Hôpital Saint Louis, Université de Paris, Paris, France
| | - Cesare Piazza
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiologic Sciences, and Public Health, "ASST Spedali Civili di Brescia", University of Brescia, Brescia, Italy
| | - Ralph W Gilbert
- Department of Otolaryngology - Head and Neck Surgery/Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Jonathan C Irish
- Department of Otolaryngology - Head and Neck Surgery/Surgical Oncology, University Health Network, Toronto, Ontario, Canada; Guided Therapeutics (GTx) Program, Techna Institute, University Health Network, Toronto, Ontario, Canada
| | - John R de Almeida
- Department of Otolaryngology - Head and Neck Surgery/Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Prathamesh Pai
- Department of Head & Neck Surgery, Tata Memorial Hospital and Homi Bhabha National Institute, Mumbai, India
| | - Philippe Herman
- Hopital Lariboisiere, APHP Nord - Université De Paris, INSERM U 1141, Paris, France
| | - Paolo Castelnuovo
- Division of Otorhinolaryngology, Department of Surgical Specialties, "ASST Sette Laghi, Ospedale di Circolo e Fondazione Macchi", Varese, Italy; Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Head and Neck Surgery & Forensic Dissection Research Center (HNS&FDRc), Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Piero Nicolai
- Unit of Otorhinolaryngology - Head and Neck Surgery, Department of Neurosciences, "Azienda Ospedale Università di Padova", University of Padua, Padua, Italy
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Wang J, Jiang YH, Yang PY, Liu F. Increased Collagen Type V α2 (COL5A2) in Colorectal Cancer is Associated with Poor Prognosis and Tumor Progression. Onco Targets Ther 2021; 14:2991-3002. [PMID: 33981148 PMCID: PMC8107053 DOI: 10.2147/ott.s288422] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/16/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is the third most common cancer in males and the second in females worldwide with very poor prognosis. Extracellular matrix proteins like collagens play important roles in cancer progression. Collagen type V α2 (COL5A2) is increased in several cancers but its role in cancer remains unclear. Methods COL5A2 expression was evaluated by interrogation of public Oncomine gene microarray datasets and immunohistochemistry (IHC) analyses of two tissue microarrays containing 180 paired CRC cases. Survival analysis was performed using Kaplan–Meier survival curve and Cox proportional hazards regression methods. COL5A2 was ectopically expressed in CRC cells, and the cell proliferation was measured using the methylthiazolyldiphenyl-tetrazolium bromide (MTT) method. Results COL5A2 gene was significantly upregulated in the most types of CRC comparing with the normal counterparts. The mRNA expression of COL5A2 was associated with cancer stages, gender, recurrence, microsatellite instability and KRAS status of CRC. COL5A2 protein increased in the cancer epithelial cells comparing with the normal counterpart and associated with age and T stage of CRC, whereas stromal expression of COL5A2 has no significant change between cancerous and normal tissues. COL5A2 gene and protein (epithelial expression) are independent risk factors and predict poor prognosis of CRC. Ectopic expression of COL5A2 drives colon cancer cell growth and upregulates WNT/β-catenin and PI3K/mTOR signaling via binding DDR1. Conclusion COL5A2 is a potential prognostic marker of CRC.
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Affiliation(s)
- Jie Wang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Medical Systems Biology of School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ying-Hua Jiang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Medical Systems Biology of School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Peng-Yuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Medical Systems Biology of School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry, Fudan University, Shanghai, 200433, People's Republic of China
| | - Feng Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Medical Systems Biology of School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
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