1
|
Paverd H, Zormpas-Petridis K, Clayton H, Burge S, Crispin-Ortuzar M. Radiology and multi-scale data integration for precision oncology. NPJ Precis Oncol 2024; 8:158. [PMID: 39060351 PMCID: PMC11282284 DOI: 10.1038/s41698-024-00656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
In this Perspective paper we explore the potential of integrating radiological imaging with other data types, a critical yet underdeveloped area in comparison to the fusion of other multi-omic data. Radiological images provide a comprehensive, three-dimensional view of cancer, capturing features that would be missed by biopsies or other data modalities. This paper explores the complexities and challenges of incorporating medical imaging into data integration models, in the context of precision oncology. We present the different categories of imaging-omics integration and discuss recent progress, highlighting the opportunities that arise from bringing together spatial data on different scales.
Collapse
Affiliation(s)
- Hania Paverd
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | | | - Hannah Clayton
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Sarah Burge
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Mireia Crispin-Ortuzar
- Department of Oncology, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
| |
Collapse
|
2
|
Durant AM, Medero RC, Briggs LG, Choudry MM, Nguyen M, Channar A, Ghaffar U, Banerjee I, Bin Riaz I, Abdul-Muhsin H. The Current Application and Future Potential of Artificial Intelligence in Renal Cancer. Urology 2024:S0090-4295(24)00565-X. [PMID: 39029807 DOI: 10.1016/j.urology.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/12/2024] [Accepted: 07/06/2024] [Indexed: 07/21/2024]
Abstract
Artificial intelligence (AI) is the integration of human tasks into machine processes. The role of AI in kidney cancer evaluation, management, and outcome predictions are constantly evolving. We performed a narrative review utilizing PubMed electronic database to query AI as a method of analysis in kidney cancer research. Key search-words included: Artificial Intelligence, Supervised/Unsupervised Machine Learning, Deep Learning, Natural Language Processing, Neural Networks, radiomics, pathomics, and kidney or renal neoplasms or cancer. 72 clinically relevant and impactful studies related to imaging, histopathology, and outcomes were recognized. We anticipate the incorporation of AI tools into future clinical decision-making for kidney cancer.
Collapse
Affiliation(s)
- Adri M Durant
- Department of Urology, Mayo Clinic Arizona, Phoenix, AZ.
| | - Ramon Correa Medero
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ
| | | | | | - Mimi Nguyen
- Department of Urology, Mayo Clinic Arizona, Phoenix, AZ
| | - Aneeta Channar
- Division of Hematology and Oncology, Department of Internal Medicine, Mayo Clinic Arizona, Phoenix, AZ
| | - Umar Ghaffar
- Department of Urology, Mayo Clinic Rochester, Rochester, MN
| | - Imon Banerjee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ; Department of Radiology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Irbaz Bin Riaz
- Division of Hematology and Oncology, Department of Internal Medicine, Mayo Clinic Arizona, Phoenix, AZ
| | | |
Collapse
|
3
|
Xu J, Miao L, Wang CX, Wang HH, Wang QZ, Li M, Chen HS, Lang N. Preoperative Contrast-Enhanced CT-Based Deep Learning Radiomics Model for Distinguishing Retroperitoneal Lipomas and Well‑Differentiated Liposarcomas. Acad Radiol 2024:S1076-6332(24)00422-7. [PMID: 39003228 DOI: 10.1016/j.acra.2024.06.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/15/2024] [Accepted: 06/22/2024] [Indexed: 07/15/2024]
Abstract
RATIONALE AND OBJECTIVES To assess the efficacy of a preoperative contrast-enhanced CT (CECT)-based deep learning radiomics nomogram (DLRN) for predicting murine double minute 2 (MDM2) gene amplification as a means of distinguishing between retroperitoneal well-differentiated liposarcomas (WDLPS) and lipomas. METHODS This retrospective multi-center study included 167 patients (training/external test cohort, 104/63) with MDM2-positive WDLPS or MDM2-negative lipomas. Clinical data and CECT features were independently measured and analyzed by two radiologists. A clinico-radiological model, radiomics signature (RS), deep learning and radiomics signature (DLRS), and a DLRN incorporating radiomics and deep learning features were developed to differentiate between WDLPS and lipoma. The model utility was evaluated based on the area under the receiver operating characteristic curve (AUC), accuracy, calibration curve, and decision curve analysis (DCA). RESULTS The DLRN showed good performance for distinguishing retroperitoneal lipomas and WDLPS in the training (AUC, 0.981; accuracy, 0.933) and external validation group (AUC, 0.861; accuracy, 0.810). The DeLong test revealed the DLRN was noticeably better than clinico-radiological and RS models (training: 0.981 vs. 0.890 vs. 0.751; validation: 0.861 vs. 0.724 vs. 0.700; both P < 0.05); however, no discernible difference in performance was seen between the DLRN and DLRS (training: 0.981 vs. 0.969; validation: 0.861 vs. 0.837; both P > 0.05). The calibration curve analysis and DCA demonstrated that the nomogram exhibited good calibration and offered substantial clinical advantages. CONCLUSION The DLRN exhibited strong predictive capability in predicting WDLPS and retroperitoneal lipomas preoperatively, making it a promising imaging biomarker that can facilitate personalized management and precision medicine.
Collapse
Affiliation(s)
- Jun Xu
- Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing 100191, China (J.X., C.X.W., H.H.W., Q.Z.W., N.L.)
| | - Lei Miao
- Department of Interventional Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China (L.M.)
| | - Chen-Xi Wang
- Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing 100191, China (J.X., C.X.W., H.H.W., Q.Z.W., N.L.)
| | - Hong-Hao Wang
- Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing 100191, China (J.X., C.X.W., H.H.W., Q.Z.W., N.L.)
| | - Qi-Zheng Wang
- Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing 100191, China (J.X., C.X.W., H.H.W., Q.Z.W., N.L.)
| | - Meng Li
- Department of Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China (M.L.)
| | - Hai-Song Chen
- Department of Radiology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Shinan District, Qingdao, Shandong 266003, China (H.S.C.)
| | - Ning Lang
- Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing 100191, China (J.X., C.X.W., H.H.W., Q.Z.W., N.L.).
| |
Collapse
|
4
|
Greco F, D’Andrea V, Buoso A, Cea L, Bernetti C, Beomonte Zobel B, Mallio CA. Advancements in Radiogenomics for Clear Cell Renal Cell Carcinoma: Understanding the Impact of BAP1 Mutation. J Clin Med 2024; 13:3960. [PMID: 38999524 PMCID: PMC11242378 DOI: 10.3390/jcm13133960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/23/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
Recent advancements in understanding clear cell renal cell carcinoma (ccRCC) have underscored the critical role of the BAP1 gene in its pathogenesis and prognosis. While the von Hippel-Lindau (VHL) mutation has been extensively studied, emerging evidence suggests that mutations in BAP1 and other genes significantly impact patient outcomes. Radiogenomics with and without texture analysis based on CT imaging holds promise in predicting BAP1 mutation status and overall survival outcomes. However, prospective studies with larger cohorts and standardized imaging protocols are needed to validate these findings and translate them into clinical practice effectively, paving the way for personalized treatment strategies in ccRCC. This review aims to summarize the current knowledge on the role of BAP1 mutation in ccRCC pathogenesis and prognosis, as well as the potential of radiogenomics in predicting mutation status and clinical outcomes.
Collapse
Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
| | - Valerio D’Andrea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Andrea Buoso
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Laura Cea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Caterina Bernetti
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (A.B.); (L.C.); (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| |
Collapse
|
5
|
Greco F, D’Andrea V, Beomonte Zobel B, Mallio CA. Radiogenomics and Texture Analysis to Detect von Hippel-Lindau (VHL) Mutation in Clear Cell Renal Cell Carcinoma. Curr Issues Mol Biol 2024; 46:3236-3250. [PMID: 38666933 PMCID: PMC11049152 DOI: 10.3390/cimb46040203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Radiogenomics, a burgeoning field in biomedical research, explores the correlation between imaging features and genomic data, aiming to link macroscopic manifestations with molecular characteristics. In this review, we examine existing radiogenomics literature in clear cell renal cell carcinoma (ccRCC), the predominant renal cancer, and von Hippel-Lindau (VHL) gene mutation, the most frequent genetic mutation in ccRCC. A thorough examination of the literature was conducted through searches on the PubMed, Medline, Cochrane Library, Google Scholar, and Web of Science databases. Inclusion criteria encompassed articles published in English between 2014 and 2022, resulting in 10 articles meeting the criteria out of 39 initially retrieved articles. Most of these studies applied computed tomography (CT) images obtained from open source and institutional databases. This literature review investigates the role of radiogenomics, with and without texture analysis, in predicting VHL gene mutation in ccRCC patients. Radiogenomics leverages imaging modalities such as CT and magnetic resonance imaging (MRI), to analyze macroscopic features and establish connections with molecular elements, providing insights into tumor heterogeneity and biological behavior. The investigations explored diverse mutations, with a specific focus on VHL mutation, and applied CT imaging features for radiogenomic analysis. Moreover, radiomics and machine learning techniques were employed to predict VHL gene mutations based on CT features, demonstrating promising results. Additional studies delved into the relationship between VHL mutation and body composition, revealing significant associations with adipose tissue distribution. The review concludes by highlighting the potential role of radiogenomics in guiding targeted and selective therapies.
Collapse
Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella Della Salute Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
| | - Valerio D’Andrea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| |
Collapse
|
6
|
Wang S, Zhu C, Jin Y, Yu H, Wu L, Zhang A, Wang B, Zhai J. A multi-model based on radiogenomics and deep learning techniques associated with histological grade and survival in clear cell renal cell carcinoma. Insights Imaging 2023; 14:207. [PMID: 38010567 PMCID: PMC10682311 DOI: 10.1186/s13244-023-01557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
OBJECTIVES This study aims to evaluate the efficacy of multi-model incorporated by radiomics, deep learning, and transcriptomics features for predicting pathological grade and survival in patients with clear cell renal cell carcinoma (ccRCC). METHODS In this study, data were collected from 177 ccRCC patients, including radiomics features, deep learning (DL) features, and RNA sequencing data. Diagnostic models were then created using these data through least absolute shrinkage and selection operator (LASSO) analysis. Additionally, a multi-model was developed by combining radiomics, DL, and transcriptomics features. The prognostic performance of the multi-model was evaluated based on progression-free survival (PFS) and overall survival (OS) outcomes, assessed using Harrell's concordance index (C-index). Furthermore, we conducted an analysis to investigate the relationship between the multi-model and immune cell infiltration. RESULTS The multi-model demonstrated favorable performance in discriminating pathological grade, with area under the ROC curve (AUC) values of 0.946 (95% CI: 0.912-0.980) and 0.864 (95% CI: 0.734-0.994) in the training and testing cohorts, respectively. Additionally, it exhibited statistically significant prognostic performance for predicting PFS and OS. Furthermore, the high-grade group displayed a higher abundance of immune cells compared to the low-grade group. CONCLUSIONS The multi-model incorporated radiomics, DL, and transcriptomics features demonstrated promising performance in predicting pathological grade and prognosis in patients with ccRCC. CRITICAL RELEVANCE STATEMENT We developed a multi-model to predict the grade and survival in clear cell renal cell carcinoma and explored the molecular biological significance of the multi-model of different histological grades. KEY POINTS 1. The multi-model achieved an AUC of 0.864 for assessing pathological grade. 2. The multi-model exhibited an association with survival in ccRCC patients. 3. The high-grade group demonstrated a greater abundance of immune cells.
Collapse
Affiliation(s)
- Shihui Wang
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Chao Zhu
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Yidong Jin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - Hongqing Yu
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Lili Wu
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Aijuan Zhang
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Beibei Wang
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Jian Zhai
- Department of Radiology, The First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China.
| |
Collapse
|
7
|
Wei L, Niraula D, Gates EDH, Fu J, Luo Y, Nyflot MJ, Bowen SR, El Naqa IM, Cui S. Artificial intelligence (AI) and machine learning (ML) in precision oncology: a review on enhancing discoverability through multiomics integration. Br J Radiol 2023; 96:20230211. [PMID: 37660402 PMCID: PMC10546458 DOI: 10.1259/bjr.20230211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 06/27/2023] [Indexed: 09/05/2023] Open
Abstract
Multiomics data including imaging radiomics and various types of molecular biomarkers have been increasingly investigated for better diagnosis and therapy in the era of precision oncology. Artificial intelligence (AI) including machine learning (ML) and deep learning (DL) techniques combined with the exponential growth of multiomics data may have great potential to revolutionize cancer subtyping, risk stratification, prognostication, prediction and clinical decision-making. In this article, we first present different categories of multiomics data and their roles in diagnosis and therapy. Second, AI-based data fusion methods and modeling methods as well as different validation schemes are illustrated. Third, the applications and examples of multiomics research in oncology are demonstrated. Finally, the challenges regarding the heterogeneity data set, availability of omics data, and validation of the research are discussed. The transition of multiomics research to real clinics still requires consistent efforts in standardizing omics data collection and analysis, building computational infrastructure for data sharing and storing, developing advanced methods to improve data fusion and interpretability, and ultimately, conducting large-scale prospective clinical trials to fill the gap between study findings and clinical benefits.
Collapse
Affiliation(s)
- Lise Wei
- Department of Radiation Oncology, University of Michigan, Michigan, United States
| | - Dipesh Niraula
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Evan D. H. Gates
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Jie Fu
- Department of Radiation Oncology, Stanford University, Stanford, California, United States
| | - Yi Luo
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Matthew J. Nyflot
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Stephen R. Bowen
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Issam M El Naqa
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Sunan Cui
- Department of Radiation Oncology, University of Washington, Washington, United States
| |
Collapse
|
8
|
Kang W, Qiu X, Luo Y, Luo J, Liu Y, Xi J, Li X, Yang Z. Application of radiomics-based multiomics combinations in the tumor microenvironment and cancer prognosis. J Transl Med 2023; 21:598. [PMID: 37674169 PMCID: PMC10481579 DOI: 10.1186/s12967-023-04437-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023] Open
Abstract
The advent of immunotherapy, a groundbreaking advancement in cancer treatment, has given rise to the prominence of the tumor microenvironment (TME) as a critical area of research. The clinical implications of an improved understanding of the TME are significant and far-reaching. Radiomics has been increasingly utilized in the comprehensive assessment of the TME and cancer prognosis. Similarly, the advancement of pathomics, which is based on pathological images, can offer additional insights into the panoramic view and microscopic information of tumors. The combination of pathomics and radiomics has revolutionized the concept of a "digital biopsy". As genomics and transcriptomics continue to evolve, integrating radiomics with genomic and transcriptomic datasets can offer further insights into tumor and microenvironment heterogeneity and establish correlations with biological significance. Therefore, the synergistic analysis of digital image features (radiomics, pathomics) and genetic phenotypes (genomics) can comprehensively decode and characterize the heterogeneity of the TME as well as predict cancer prognosis. This review presents a comprehensive summary of the research on important radiomics biomarkers for predicting the TME, emphasizing the interplay between radiomics, genomics, transcriptomics, and pathomics, as well as the application of multiomics in decoding the TME and predicting cancer prognosis. Finally, we discuss the challenges and opportunities in multiomics research. In conclusion, this review highlights the crucial role of radiomics and multiomics associations in the assessment of the TME and cancer prognosis. The combined analysis of radiomics, pathomics, genomics, and transcriptomics is a promising research direction with substantial research significance and value for comprehensive TME evaluation and cancer prognosis assessment.
Collapse
Affiliation(s)
- Wendi Kang
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli 17# Chaoyang District, Beijing, 100021, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of, Fudan University, Shanghai, 200011, China
| | - Yingen Luo
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli 17# Chaoyang District, Beijing, 100021, China
| | - Jianwei Luo
- Department of Diagnostic Radiology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, China
| | - Yang Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junqing Xi
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli 17# Chaoyang District, Beijing, 100021, China
| | - Xiao Li
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli 17# Chaoyang District, Beijing, 100021, China
| | - Zhengqiang Yang
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli 17# Chaoyang District, Beijing, 100021, China.
| |
Collapse
|
9
|
Liu Z, Duan T, Zhang Y, Weng S, Xu H, Ren Y, Zhang Z, Han X. Radiogenomics: a key component of precision cancer medicine. Br J Cancer 2023; 129:741-753. [PMID: 37414827 PMCID: PMC10449908 DOI: 10.1038/s41416-023-02317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/02/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Radiogenomics, focusing on the relationship between genomics and imaging phenotypes, has been widely applied to address tumour heterogeneity and predict immune responsiveness and progression. It is an inevitable consequence of current trends in precision medicine, as radiogenomics costs less than traditional genetic sequencing and provides access to whole-tumour information rather than limited biopsy specimens. By providing voxel-by-voxel genetic information, radiogenomics can allow tailored therapy targeting a complete, heterogeneous tumour or set of tumours. In addition to quantifying lesion characteristics, radiogenomics can also be used to distinguish benign from malignant entities, as well as patient characteristics, to better stratify patients according to disease risk, thereby enabling more precise imaging and screening. Here, we have characterised the radiogenomic application in precision medicine using a multi-omic approach. we outline the main applications of radiogenomics in diagnosis, treatment planning and evaluations in the field of oncology with the aim of developing quantitative and personalised medicine. Finally, we discuss the challenges in the field of radiogenomics and the scope and clinical applicability of these methods.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Tian Duan
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
| |
Collapse
|
10
|
Ainiwaer A, Hou WQ, Kadier K, Rehemuding R, Liu PF, Maimaiti H, Qin L, Ma X, Dai JG. A Machine Learning Framework for Diagnosing and Predicting the Severity of Coronary Artery Disease. Rev Cardiovasc Med 2023; 24:168. [PMID: 39077543 PMCID: PMC11264126 DOI: 10.31083/j.rcm2406168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 07/31/2024] Open
Abstract
Background Although machine learning (ML)-based prediction of coronary artery disease (CAD) has gained increasing attention, assessment of the severity of suspected CAD in symptomatic patients remains challenging. Methods The training set for this study consisted of 284 retrospective participants, while the test set included 116 prospectively enrolled participants from whom we collected 53 baseline variables and coronary angiography results. The data was pre-processed with outlier processing and One-Hot coding. In the first stage, we constructed a ML model that used baseline information to predict the presence of CAD with a dichotomous model. In the second stage, baseline information was used to construct ML regression models for predicting the severity of CAD. The non-CAD population was included, and two different scores were used as output variables. Finally, statistical analysis and SHAP plot visualization methods were employed to explore the relationship between baseline information and CAD. Results The study included 269 CAD patients and 131 healthy controls. The eXtreme Gradient Boosting (XGBoost) model exhibited the best performance amongst the different models for predicting CAD, with an area under the receiver operating characteristic curve of 0.728 (95% CI 0.623-0.824). The main correlates were left ventricular ejection fraction, homocysteine, and hemoglobin (p < 0.001). The XGBoost model performed best for predicting the SYNTAX score, with the main correlates being brain natriuretic peptide (BNP), left ventricular ejection fraction, and glycated hemoglobin (p < 0.001). The main relevant features in the model predictive for the GENSINI score were BNP, high density lipoprotein, and homocysteine (p < 0.001). Conclusions This data-driven approach provides a foundation for the risk stratification and severity assessment of CAD. Clinical Trial Registration The study was registered in www.clinicaltrials.gov protocol registration system (number NCT05018715).
Collapse
Affiliation(s)
- Aikeliyaer Ainiwaer
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Wen Qing Hou
- College of Information Science and Technology, Shihezi University, 832003
Shihezi, Xinjiang, China
| | - Kaisaierjiang Kadier
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Rena Rehemuding
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Peng Fei Liu
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Halimulati Maimaiti
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Lian Qin
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Xiang Ma
- Department of Cardiology, The First Affiliated Hospital of Xinjiang
Medical University, 830011 Urumqi, Xinjiang, China
| | - Jian Guo Dai
- College of Information Science and Technology, Shihezi University, 832003
Shihezi, Xinjiang, China
| |
Collapse
|
11
|
Chen W, Lv X, Cao X, Yuan Z, Wang S, Getachew T, Mwacharo JM, Haile A, Quan K, Li Y, Sun W. Integration of the Microbiome, Metabolome and Transcriptome Reveals Escherichia coli F17 Susceptibility of Sheep. Animals (Basel) 2023; 13:ani13061050. [PMID: 36978593 PMCID: PMC10044122 DOI: 10.3390/ani13061050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Escherichia coli (E. coli) F17 is one of the most common pathogens causing diarrhea in farm livestock. In the previous study, we accessed the transcriptomic and microbiomic profile of E. coli F17-antagonism (AN) and -sensitive (SE) lambs; however, the biological mechanism underlying E. coli F17 infection has not been fully elucidated. Therefore, the present study first analyzed the metabolite data obtained with UHPLC-MS/MS. A total of 1957 metabolites were profiled in the present study, and 11 differential metabolites were identified between E. coli F17 AN and SE lambs (i.e., FAHFAs and propionylcarnitine). Functional enrichment analyses showed that most of the identified metabolites were related to the lipid metabolism. Then, we presented a machine-learning approach (Random Forest) to integrate the microbiome, metabolome and transcriptome data, which identified subsets of potential biomarkers for E. coli F17 infection (i.e., GlcADG 18:0-18:2, ethylmalonic acid and FBLIM1); furthermore, the PCCs were calculated and the interaction network was constructed to gain insight into the crosstalk between the genes, metabolites and bacteria in E. coli F17 AN/SE lambs. By combing classic statistical approaches and a machine-learning approach, our results revealed subsets of metabolites, genes and bacteria that could be potentially developed as candidate biomarkers for E. coli F17 infection in lambs.
Collapse
Affiliation(s)
- Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram M. Mwacharo
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economics, Zhengzhou 450046, China
| | - Yutao Li
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-13952750912
| |
Collapse
|
12
|
Radiogenomics in Renal Cancer Management-Current Evidence and Future Prospects. Int J Mol Sci 2023; 24:ijms24054615. [PMID: 36902045 PMCID: PMC10003020 DOI: 10.3390/ijms24054615] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Renal cancer management is challenging from diagnosis to treatment and follow-up. In cases of small renal masses and cystic lesions the differential diagnosis of benign or malignant tissues has potential pitfalls when imaging or even renal biopsy is applied. The recent artificial intelligence, imaging techniques, and genomics advancements have the ability to help clinicians set the stratification risk, treatment selection, follow-up strategy, and prognosis of the disease. The combination of radiomics features and genomics data has achieved good results but is currently limited by the retrospective design and the small number of patients included in clinical trials. The road ahead for radiogenomics is open to new, well-designed prospective studies, with large cohorts of patients required to validate previously obtained results and enter clinical practice.
Collapse
|
13
|
He XM, Zhao JX, He DL, Ren JL, Zhao LP, Huang G. Radiogenomics study to predict the nuclear grade of renal clear cell carcinoma. Eur J Radiol Open 2023; 10:100476. [PMID: 36793772 PMCID: PMC9922923 DOI: 10.1016/j.ejro.2023.100476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/30/2023] Open
Abstract
Purpose To develop models based on radiomics and genomics for predicting the histopathologic nuclear grade with localized clear cell renal cell carcinoma (ccRCC) and to assess whether macro-radiomics models can predict the microscopic pathological changes. Method In this multi-institutional retrospective study, a computerized tomography (CT) radiomic model for nuclear grade prediction was developed. Utilizing a genomics analysis cohort, nuclear grade-associated gene modules were identified, and a gene model was constructed based on top 30 hub mRNA to predict the nuclear grade. Using a radiogenomic development cohort, biological pathways were enriched by hub genes and a radiogenomic map was created. Results The four-features-based SVM model predicted nuclear grade with an area under the curve (AUC) score of 0.94 in validation sets, while a five-gene-based model predicted nuclear grade with an AUC of 0.73 in the genomics analysis cohort. A total of five gene modules were identified to be associated with the nuclear grade. Radiomic features were only associated with 271 out of 603 genes in five gene modules and eight top 30 hub genes. Differences existed in the enrichment pathway between associated and un-associated with radiomic features, which were associated with two genes of five-gene signatures in the mRNA model. Conclusion The CT radiomics models exhibited higher predictive performance than mRNA models. The association between radiomic features and mRNA related to nuclear grade is not universal.
Collapse
Key Words
- Computer Applications
- FDR, False discovery rate
- GLRLM, Gray level run length matrix
- GLSZM, Gray level size matrix
- KEGG, KOBAS-Kyoto Encyclopedia of Genes and Genomes
- Kidney
- NGTDM, Neighborhood gray tone difference matrix
- Neoplasms-Primary
- PPI, Protein-Protein Interaction Networks
- Pathological nuclear grade
- Radiogenomics
- Radiomics
- TCGA, The cancer genome atlas
- TCIA, The cancer imaging archive
- WGCNA, Weighted gene co-expression network
- WHO/ISUP, World Health Organization and International Society of Urological Pathology
- ccRCC, Clear cell renal cell carcinoma
Collapse
Affiliation(s)
- Xuan-ming He
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jian-xin Zhao
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, China
| | - Di-liang He
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, China
| | | | - Lian-ping Zhao
- Department of Radiology, Gansu Provincial Hospital, Lanzhou, China
| | - Gang Huang
- Department of Radiology, Gansu Provincial Hospital, Lanzhou, China,Corresponding author.
| |
Collapse
|
14
|
Li S, Zhou B. A review of radiomics and genomics applications in cancers: the way towards precision medicine. Radiat Oncol 2022; 17:217. [PMID: 36585716 PMCID: PMC9801589 DOI: 10.1186/s13014-022-02192-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
The application of radiogenomics in oncology has great prospects in precision medicine. Radiogenomics combines large volumes of radiomic features from medical digital images, genetic data from high-throughput sequencing, and clinical-epidemiological data into mathematical modelling. The amalgamation of radiomics and genomics provides an approach to better study the molecular mechanism of tumour pathogenesis, as well as new evidence-supporting strategies to identify the characteristics of cancer patients, make clinical decisions by predicting prognosis, and improve the development of individualized treatment guidance. In this review, we summarized recent research on radiogenomics applications in solid cancers and presented the challenges impeding the adoption of radiomics in clinical practice. More standard guidelines are required to normalize radiomics into reproducible and convincible analyses and develop it as a mature field.
Collapse
Affiliation(s)
- Simin Li
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Center of Evidence-Based Medicine, The First Hospital of China Medical University, Shenyang, 110001 Liaoning People’s Republic of China
| | - Baosen Zhou
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Center of Evidence-Based Medicine, The First Hospital of China Medical University, Shenyang, 110001 Liaoning People’s Republic of China
| |
Collapse
|
15
|
Fan G, Qin J, Liu H, Liao X. Commentary: Radiomics in oncology: A 10-year bibliometric analysis. Front Oncol 2022; 12:891056. [PMID: 35936758 PMCID: PMC9355694 DOI: 10.3389/fonc.2022.891056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/28/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Guoxin Fan
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Department of Spine Surgery, Third Affiliated Hospital, Sun Yatsen University, Guangzhou, China
| | - Jiaqi Qin
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, China
| | - Huaqing Liu
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, China
| | - Xiang Liao
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- *Correspondence: Xiang Liao,
| |
Collapse
|
16
|
Fan Y, Kao C, Yang F, Wang F, Yin G, Wang Y, He Y, Ji J, Liu L. Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer. Front Oncol 2022; 12:899900. [PMID: 35761863 PMCID: PMC9232398 DOI: 10.3389/fonc.2022.899900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background With the rapid development and wide application of high-throughput sequencing technology, biomedical research has entered the era of large-scale omics data. We aim to identify genes associated with breast cancer prognosis by integrating multi-omics data. Method Gene-gene interactions were taken into account, and we applied two differential network methods JDINAC and LGCDG to identify differential genes. The patients were divided into case and control groups according to their survival time. The TCGA and METABRIC database were used as the training and validation set respectively. Result In the TCGA dataset, C11orf1, OLA1, RPL31, SPDL1 and IL33 were identified to be associated with prognosis of breast cancer. In the METABRIC database, ZNF273, ZBTB37, TRIM52, TSGA10, ZNF727, TRAF2, TSPAN17, USP28 and ZNF519 were identified as hub genes. In addition, RPL31, TMEM163 and ZNF273 were screened out in both datasets. GO enrichment analysis shows that most of these hub genes were involved in zinc ion binding. Conclusion In this study, a total of 15 hub genes associated with long-term survival of breast cancer were identified, which can promote understanding of the molecular mechanism of breast cancer and provide new insight into clinical research and treatment.
Collapse
Affiliation(s)
- Yeye Fan
- School of Mathematics, Shandong University, Jinan, China
| | - Chunyu Kao
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fu Yang
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fei Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Gengshen Yin
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yongjiu Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yong He
- School of Mathematics, Shandong University, Jinan, China.,Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Jiadong Ji
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Liyuan Liu
- School of Mathematics, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| |
Collapse
|
17
|
What Genetics Can Do for Oncological Imaging: A Systematic Review of the Genetic Validation Data Used in Radiomics Studies. Int J Mol Sci 2022; 23:ijms23126504. [PMID: 35742947 PMCID: PMC9224495 DOI: 10.3390/ijms23126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/04/2023] Open
Abstract
(1) Background: Radiogenomics is motivated by the concept that biomedical images contain information that reflects underlying pathophysiology. This review focused on papers that used genetics to validate their radiomics models and outcomes and assess their contribution to this emerging field. (2) Methods: All original research with the words radiomics and genomics in English and performed in humans up to 31 January 2022, were identified on Medline and Embase. The quality of the studies was assessed with Radiomic Quality Score (RQS) and the Cochrane recommendation for diagnostic accuracy study Quality Assessment 2. (3) Results: 45 studies were included in our systematic review, and more than 50% were published in the last two years. The studies had a mean RQS of 12, and the studied tumors were very diverse. Up to 83% investigated the prognosis as the main outcome, with the rest focusing on response to treatment and risk assessment. Most applied either transcriptomics (54%) and/or genetics (35%) for genetic validation. (4) Conclusions: There is enough evidence to state that new science has emerged, focusing on establishing an association between radiological features and genomic/molecular expression to explain underlying disease mechanisms and enhance prognostic, risk assessment, and treatment response radiomics models in cancer patients.
Collapse
|
18
|
The Next Paradigm Shift in the Management of Clear Cell Renal Cancer: Radiogenomics—Definition, Current Advances, and Future Directions. Cancers (Basel) 2022; 14:cancers14030793. [PMID: 35159060 PMCID: PMC8833879 DOI: 10.3390/cancers14030793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
With improved molecular characterization of clear cell renal cancer and advances in texture analysis as well as machine learning, diagnostic radiology is primed to enter personalized medicine with radiogenomics: the identification of relationships between tumor image features and underlying genomic expression. By developing surrogate image biomarkers, clinicians can augment their ability to non-invasively characterize a tumor and predict clinically relevant outcomes (i.e., overall survival; metastasis-free survival; or complete/partial response to treatment). It is thus important for clinicians to have a basic understanding of this nascent field, which can be difficult due to the technical complexity of many of the studies. We conducted a review of the existing literature for radiogenomics in clear cell kidney cancer, including original full-text articles until September 2021. We provide a basic description of radiogenomics in diagnostic radiology; summarize existing literature on relationships between image features and gene expression patterns, either computationally or by radiologists; and propose future directions to facilitate integration of this field into the clinical setting.
Collapse
|
19
|
The application of radiomics in predicting gene mutations in cancer. Eur Radiol 2022; 32:4014-4024. [DOI: 10.1007/s00330-021-08520-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
|
20
|
Kang CY, Duarte SE, Kim HS, Kim E, Park J, Lee AD, Kim Y, Kim L, Cho S, Oh Y, Gim G, Park I, Lee D, Abazeed M, Velichko YS, Chae YK. OUP accepted manuscript. Oncologist 2022; 27:e471-e483. [PMID: 35348765 PMCID: PMC9177100 DOI: 10.1093/oncolo/oyac036] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
The recent, rapid advances in immuno-oncology have revolutionized cancer treatment and spurred further research into tumor biology. Yet, cancer patients respond variably to immunotherapy despite mounting evidence to support its efficacy. Current methods for predicting immunotherapy response are unreliable, as these tests cannot fully account for tumor heterogeneity and microenvironment. An improved method for predicting response to immunotherapy is needed. Recent studies have proposed radiomics—the process of converting medical images into quantitative data (features) that can be processed using machine learning algorithms to identify complex patterns and trends—for predicting response to immunotherapy. Because patients undergo numerous imaging procedures throughout the course of the disease, there exists a wealth of radiological imaging data available for training radiomics models. And because radiomic features reflect cancer biology, such as tumor heterogeneity and microenvironment, these models have enormous potential to predict immunotherapy response more accurately than current methods. Models trained on preexisting biomarkers and/or clinical outcomes have demonstrated potential to improve patient stratification and treatment outcomes. In this review, we discuss current applications of radiomics in oncology, followed by a discussion on recent studies that use radiomics to predict immunotherapy response and toxicity.
Collapse
Affiliation(s)
| | | | - Hye Sung Kim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eugene Kim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Alice Daeun Lee
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yeseul Kim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Leeseul Kim
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, Evanston, IL, USA
| | - Sukjoo Cho
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Yoojin Oh
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gahyun Gim
- Department of Hematology and Oncology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Inae Park
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dongyup Lee
- Department of Physical Medicine and Rehabilitation, Geisinger Health System, Danville, PA, USA
| | - Mohamed Abazeed
- Department of Radiation Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yury S Velichko
- Department of Radiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Young Kwang Chae
- Corresponding author: Young Kwang Chae, Department of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| |
Collapse
|
21
|
Gulati S, Previtera M, Lara PN. BRCA1-Associated Protein 1 (BAP-1) as a Prognostic and Predictive Biomarker in Clear Cell Renal Cell Carcinoma: A Systematic Review. KIDNEY CANCER 2021. [DOI: 10.3233/kca-210006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: The gene that encodes BRCA1-associated protein 1 (BAP1) has been reported to be dysregulated in several human cancers such as uveal melanoma, malignant pleural mesothelioma, hepatocellular carcinoma, thymic epithelial tumors, and clear-cell renal cell carcinoma (ccRCC). The gene is located on the human chromosome 3p21.3, encoding a deubiquitinase and acts as a classic two-hit tumor suppressor gene. BAP1 predominantly resides in the nucleus, where it interacts with several chromatin-associated factors, as well as regulates calcium signaling in the cytoplasm. As newer therapies continue to evolve for the management of RCC, it is important to understand the role of BAP1 mutation as a prognostic and predictive biomarker. OBJECTIVE: We aimed to systematically evaluate the role of BAP1 mutations in patients with RCC in terms of its impact on prognosis and its role as a predictive biomarker. METHODS: Following PRISMA guidelines, we performed a systematic literature search using PubMed and Embase through March 2021. Titles and abstracts were screened to identify articles for full-text and then a descriptive review was performed. RESULTS: A total of 490 articles were initially identified. Ultimately 71 articles that met our inclusion criteria published between 2012–2021 were included in the analysis. Data were extracted and organized to reflect the role of BAP1 alterations as a marker of prognosis as well as a marker of response to treatments, such as mTOR inhibitors, VEGF tyrosine kinase inhibitors, and immune checkpoint inhibitors. CONCLUSIONS: Alterations in BAP1 appear to be uniformly associated with poor prognosis in patients with RCC. Knowledge gaps remain with regard to the predictive relevance of BAP1 alterations, especially in the context of immunotherapy. Prospective studies are required to more precisely ascertain the predictive value of BAP1 alterations in RCC.
Collapse
Affiliation(s)
- Shuchi Gulati
- Department of Medicine, Division of Hematology and Oncology, University of Cincinnati, Cincinnati, OH, USA
| | - Melissa Previtera
- Academic & Research Services Specialist, Donald C. Harrison Health Sciences Library, University of Cincinnati Libraries, Cincinnati, OH, USA
| | - Primo N. Lara
- Department of Internal Medicine, Division of Hematology and Oncology, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| |
Collapse
|
22
|
Yan L, Yang G, Cui J, Miao W, Wang Y, Zhao Y, Wang N, Gong A, Guo N, Nie P, Wang Z. Radiomics Analysis of Contrast-Enhanced CT Predicts Survival in Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:671420. [PMID: 34249712 PMCID: PMC8268016 DOI: 10.3389/fonc.2021.671420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose To develop and validate the radiomics nomogram that combines clinical factors and radiomics features to estimate overall survival (OS) in patients with clear cell renal cell carcinoma (ccRCC), and assess the incremental value of radiomics for OS estimation. Materials and Methods One hundred ninety-four ccRCC cases were included in the training cohort and 188 ccRCC patients from another hospital as the test cohort. Three-dimensional region-of-interest segmentation was manually segmented on multiphasic contrast-enhanced abdominal CT images. Radiomics score (Rad-score) was calculated from a formula generated via least absolute shrinkage and selection operator (LASSO) Cox regression, after which the association between the Rad-score and OS was explored. The radiomics nomogram (clinical factors + Rad-score) was developed to demonstrate the incremental value of the Rad-score to the clinical nomogram for individualized OS estimation, which was then evaluated in relation to calibration and discrimination. Results Rad-score, calculated using a linear combination of the 11 screened features multiplied by their respective LASSO Cox coefficients, was significantly associated with OS. Calibration curves showed good agreement between the OS predicted by the nomograms and observed outcomes. The radiomics nomogram presented higher discrimination capability compared to clinical nomogram in the training (C-index: 0.884; 95% CI: 0.808–0.940 vs. 0.803; 95% CI: 0.705–0.899, P < 0.05) and test cohorts (C-index: 0.859; 95% CI: 0.800–0.921 vs. 0.846; 95% CI: 0.777–0.915, P < 0.05). Conclusions The radiomics nomogram may be used for predicting OS in patients with ccRCC, and radiomics is useful to assist quantitative and personalized treatment.
Collapse
Affiliation(s)
- Lei Yan
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guangjie Yang
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jingjing Cui
- Scientific Research Department, Huiying Medical Technology Co., Ltd., Beijing, China
| | - Wenjie Miao
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yangyang Wang
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yujun Zhao
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ning Wang
- Department of Radiology, Shandong Provincial Hospital, Jinan, China
| | - Aidi Gong
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Na Guo
- Scientific Research Department, Huiying Medical Technology Co., Ltd., Beijing, China
| | - Pei Nie
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhenguang Wang
- Department of Positron Emission Tomography-Computed Tomography (PET-CT) Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
23
|
Tarazona S, Arzalluz-Luque A, Conesa A. Undisclosed, unmet and neglected challenges in multi-omics studies. NATURE COMPUTATIONAL SCIENCE 2021; 1:395-402. [PMID: 38217236 DOI: 10.1038/s43588-021-00086-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/17/2021] [Indexed: 01/15/2024]
Abstract
Multi-omics approaches have become a reality in both large genomics projects and small laboratories. However, the multi-omics research community still faces a number of issues that have either not been sufficiently discussed or for which current solutions are still limited. In this Perspective, we elaborate on these limitations and suggest points of attention for future research. We finally discuss new opportunities and challenges brought to the field by the rapid development of single-cell high-throughput molecular technologies.
Collapse
Affiliation(s)
- Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Angeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain.
| |
Collapse
|