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Zhuang Z, Lin J, Wan Z, Weng J, Yuan Z, Xie Y, Liu Z, Xie P, Mao S, Wang Z, Wang X, Huang M, Luo Y, Yu H. Radiogenomic profiling of global DNA methylation associated with molecular phenotypes and immune features in glioma. BMC Med 2024; 22:352. [PMID: 39218882 PMCID: PMC11367996 DOI: 10.1186/s12916-024-03573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The radiogenomic analysis has provided valuable imaging biomarkers with biological insights for gliomas. The radiogenomic markers for molecular profile such as DNA methylation remain to be uncovered to assist the molecular diagnosis and tumor treatment. METHODS We apply the machine learning approaches to identify the magnetic resonance imaging (MRI) features that are associated with molecular profiles in 146 patients with gliomas, and the fitting models for each molecular feature (MoRad) are developed and validated. To provide radiological annotations for the molecular profiles, we devise two novel approaches called radiomic oncology (RO) and radiomic set enrichment analysis (RSEA). RESULTS The generated MoRad models perform well for profiling each molecular feature with radiomic features, including mutational, methylation, transcriptional, and protein profiles. Among them, the MoRad models have a remarkable performance in quantitatively mapping global DNA methylation. With RO and RSEA approaches, we find that global DNA methylation could be reflected by the heterogeneity in volumetric and textural features of enhanced regions in T2-weighted MRI. Finally, we demonstrate the associations of global DNA methylation with clinicopathological, molecular, and immunological features, including histological grade, mutations of IDH and ATRX, MGMT methylation, multiple methylation-high subtypes, tumor-infiltrating lymphocytes, and long-term survival outcomes. CONCLUSIONS Global DNA methylation is highly associated with radiological profiles in glioma. Radiogenomic global methylation is an imaging-based quantitative molecular biomarker that is associated with specific consensus molecular subtypes and immune features.
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Affiliation(s)
- Zhuokai Zhuang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Jinxin Lin
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Zixiao Wan
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Jingrong Weng
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
| | - Ze Yuan
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Yumo Xie
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
| | - Zongchao Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Institute, Beijing, 100142, China
| | - Peiyi Xie
- Department of Radiology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
| | - Siyue Mao
- Image and Minimally Invasive Intervention Center, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zongming Wang
- Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaolin Wang
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Meijin Huang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Yanxin Luo
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China
| | - Huichuan Yu
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510655, China.
- Ministry of Education, Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Guangzhou, Guangdong, China.
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Huynh LM, Swanson S, Cima S, Haddadin E, Baine M. Prostate-Specific Membrane Antigen Positron Emission Tomography/Computed Tomography-Derived Radiomic Models in Prostate Cancer Prognostication. Cancers (Basel) 2024; 16:1897. [PMID: 38791977 PMCID: PMC11120365 DOI: 10.3390/cancers16101897] [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: 03/17/2024] [Revised: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The clinical integration of prostate membrane specific antigen (PSMA) positron emission tomography and computed tomography (PET/CT) scans represents potential for advanced data analysis techniques in prostate cancer (PC) prognostication. Among these tools is the use of radiomics, a computer-based method of extracting and quantitatively analyzing subvisual features in medical imaging. Within this context, the present review seeks to summarize the current literature on the use of PSMA PET/CT-derived radiomics in PC risk stratification. A stepwise literature search of publications from 2017 to 2023 was performed. Of 23 articles on PSMA PET/CT-derived prostate radiomics, PC diagnosis, prediction of biopsy Gleason score (GS), prediction of adverse pathology, and treatment outcomes were the primary endpoints of 4 (17.4%), 5 (21.7%), 7 (30.4%), and 7 (30.4%) studies, respectively. In predicting PC diagnosis, PSMA PET/CT-derived models performed well, with receiver operator characteristic curve area under the curve (ROC-AUC) values of 0.85-0.925. Similarly, in the prediction of biopsy and surgical pathology results, ROC-AUC values had ranges of 0.719-0.84 and 0.84-0.95, respectively. Finally, prediction of recurrence, progression, or survival following treatment was explored in nine studies, with ROC-AUC ranging 0.698-0.90. Of the 23 studies included in this review, 2 (8.7%) included external validation. While explorations of PSMA PET/CT-derived radiomic models are immature in follow-up and experience, these results represent great potential for future investigation and exploration. Prior to consideration for clinical use, however, rigorous validation in feature reproducibility and biologic validation of radiomic signatures must be prioritized.
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Affiliation(s)
- Linda My Huynh
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, NE 68105, USA; (L.M.H.); (S.C.)
- Department of Urology, University of California, Irvine, CA 92868, USA;
| | - Shea Swanson
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, NE 68105, USA; (L.M.H.); (S.C.)
| | - Sophia Cima
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, NE 68105, USA; (L.M.H.); (S.C.)
| | - Eliana Haddadin
- Department of Urology, University of California, Irvine, CA 92868, USA;
| | - Michael Baine
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, NE 68105, USA; (L.M.H.); (S.C.)
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Ploypetch S, Wongbandue G, Roytrakul S, Phaonakrop N, Prapaiwan N. Comparative Serum Proteome Profiling of Canine Benign Prostatic Hyperplasia before and after Castration. Animals (Basel) 2023; 13:3853. [PMID: 38136890 PMCID: PMC10740436 DOI: 10.3390/ani13243853] [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: 10/28/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
BPH is the most prevalent prostatic condition in aging dogs. Nevertheless, clinical diagnosis and management remain inconsistent. This study employed in-solution digestion coupled with nano-liquid chromatography tandem mass spectrometry to assess serum proteome profiling of dogs with BPH and those dogs after castration. Male dogs were divided into two groups; control and BPH groups. In the BPH group, each dog was evaluated at two time points: Day 0 (BF subgroup) and Day 30 after castration (AT subgroup). In the BF subgroup, three proteins were significantly upregulated and associated with dihydrotestosterone: solute carrier family 5 member 5, tyrosine-protein kinase, and FRAT regulator of WNT signaling pathway 1. Additionally, the overexpression of polymeric immunoglobulin receptors in the BF subgroup hints at its potential as a novel protein linked to the BPH development process. Conversely, alpha-1-B glycoprotein (A1BG) displayed significant downregulation in the BF subgroup, suggesting A1BG's potential as a predictive protein for canine BPH. Finasteride was associated with increased proteins in the AT subgroup, including apolipoprotein C-I, apolipoprotein E, apolipoprotein A-II, TAO kinase 1, DnaJ homolog subfamily C member 16, PH domain and leucine-rich repeat protein phosphatase 1, neuregulin 1, and pseudopodium enriched atypical kinase 1. In conclusion, this pilot study highlighted alterations in various serum proteins in canine BPH, reflecting different pathological changes occurring in this condition. These proteins could be a source of potential non-invasive biomarkers for diagnosing this disease.
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Affiliation(s)
- Sekkarin Ploypetch
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Grisnarong Wongbandue
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Nawarus Prapaiwan
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
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