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Amrane K, Meur CL, Thuillier P, Berthou C, Uguen A, Deandreis D, Bourhis D, Bourbonne V, Abgral R. Review on radiomic analysis in 18F-fluorodeoxyglucose positron emission tomography for prediction of melanoma outcomes. Cancer Imaging 2024; 24:87. [PMID: 38970050 PMCID: PMC11225300 DOI: 10.1186/s40644-024-00732-5] [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: 11/02/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
Over the past decade, several strategies have revolutionized the clinical management of patients with cutaneous melanoma (CM), including immunotherapy and targeted tyrosine kinase inhibitor (TKI)-based therapies. Indeed, immune checkpoint inhibitors (ICIs), alone or in combination, represent the standard of care for patients with advanced disease without an actionable mutation. Notably BRAF combined with MEK inhibitors represent the therapeutic standard for disease disclosing BRAF mutation. At the same time, FDG PET/CT has become part of the routine staging and evaluation of patients with cutaneous melanoma. There is growing interest in using FDG PET/CT measurements to predict response to ICI therapy and/or target therapy. While semiquantitative values such as standardized uptake value (SUV) are limited for predicting outcome, new measures including tumor metabolic volume, total lesion glycolysis and radiomics seem promising as potential imaging biomarkers for nuclear medicine. The aim of this review, prepared by an interdisciplinary group of experts, is to take stock of the current literature on radiomics approaches that could improve outcomes in CM.
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Affiliation(s)
- Karim Amrane
- Department of Oncology, Regional Hospital of Morlaix, Morlaix, 29600, France.
- Lymphocytes B et Autoimmunité, Inserm, UMR1227, Univ Brest, Inserm, LabEx IGO, Brest, France.
| | - Coline Le Meur
- Department of Radiotherapy, University Hospital of Brest, Brest, France
| | - Philippe Thuillier
- Department of Endocrinology, University Hospital of Brest, Brest, France
- UMR Inserm 1304 GETBO, University of Western Brittany, Brest, IFR 148, France
| | - Christian Berthou
- Lymphocytes B et Autoimmunité, Inserm, UMR1227, Univ Brest, Inserm, LabEx IGO, Brest, France
- Department of Hematology, University Hospital of Brest, Brest, France
| | - Arnaud Uguen
- Lymphocytes B et Autoimmunité, Inserm, UMR1227, Univ Brest, Inserm, LabEx IGO, Brest, France
- Department of Pathology, University Hospital of Brest, Brest, France
| | - Désirée Deandreis
- Department of Nuclear Medicine, Gustave Roussy Institute, University of Paris Saclay, Paris, France
| | - David Bourhis
- UMR Inserm 1304 GETBO, University of Western Brittany, Brest, IFR 148, France
- Department of Nuclear Medicine, University Hospital of Brest, Brest, France
| | - Vincent Bourbonne
- Department of Radiotherapy, University Hospital of Brest, Brest, France
- Inserm, UMR1101, LaTIM, University of Western Brittany, Brest, France
| | - Ronan Abgral
- UMR Inserm 1304 GETBO, University of Western Brittany, Brest, IFR 148, France
- Department of Nuclear Medicine, University Hospital of Brest, Brest, France
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Chen J, Zeng H, Cheng Y, Yang B. Identifying radiogenomic associations of breast cancer based on DCE-MRI by using Siamese Neural Network with manufacturer bias normalization. Med Phys 2024. [PMID: 38922986 DOI: 10.1002/mp.17266] [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: 01/17/2024] [Revised: 06/08/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND AND PURPOSE The immunohistochemical test (IHC) for Human Epidermal Growth Factor Receptor 2 (HER2) and hormone receptors (HR) provides prognostic information and guides treatment for patients with invasive breast cancer. The objective of this paper is to establish a non-invasive system for identifying HER2 and HR in breast cancer using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). METHODS In light of the absence of high-performance algorithms and external validation in previously published methods, this study utilizes 3D deep features and radiomics features to represent the information of the Region of Interest (ROI). A Siamese Neural Network was employed as the classifier, with 3D deep features and radiomics features serving as the network input. To neutralize manufacturer bias, a batch effect normalization method, ComBat, was introduced. To enhance the reliability of the study, two datasets, Predict Your Therapeutic Response with Imaging and moLecular Analysis (I-SPY 1) and I-SPY 2, were incorporated. I-SPY 2 was utilized for model training and validation, while I-SPY 1 was exclusively employed for external validation. Additionally, a breast tumor segmentation network was trained to improve radiomic feature extraction. RESULTS The results indicate that our approach achieved an average Area Under the Curve (AUC) of 0.632, with a Standard Error of the Mean (SEM) of 0.042 for HER2 prediction in the I-SPY 2 dataset. For HR prediction, our method attained an AUC of 0.635 (SEM 0.041), surpassing other published methods in the AUC metric. Moreover, the proposed method yielded competitive results in other metrics. In external validation using the I-SPY 1 dataset, our approach achieved an AUC of 0.567 (SEM 0.032) for HR prediction and 0.563 (SEM 0.033) for HER2 prediction. CONCLUSION This study proposes a non-invasive system for identifying HER2 and HR in breast cancer. Although the results do not conclusively demonstrate superiority in both tasks, they indicate that the proposed method achieved good performance and is a competitive classifier compared to other reference methods. Ablation studies demonstrate that both radiomics features and deep features for the Siamese Neural Network are beneficial for the model. The introduced manufacturer bias normalization method has been shown to enhance the method's performance. Furthermore, the external validation of the method enhances the reliability of this research. Source code, pre-trained segmentation network, Radiomics and deep features, data for statistical analysis, and Supporting Information of this article are online at: https://github.com/FORRESTHUACHEN/Siamese_Neural_Network_based_Brest_cancer_Radiogenomic.
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Affiliation(s)
- Junhua Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Haiyan Zeng
- Department of Radiation Oncology, Division of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanyan Cheng
- Medical Engineering Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong, China
| | - Banghua Yang
- School of Medicine, Shanghai University, Shanghai, China
- School of Mechatronic Engineering and Automation, Research Center of Brain Computer Engineering, Shanghai University, Shanghai, China
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Chang H, Liu Y, Wang Y, Li L, Mu Y, Zheng M, Liu J, Zhang J, Bai R, Li Y, Zuo X. Unveiling the Links Between Microbial Alteration and Host Gene Disarray in Crohn's Disease via TAHMC. Adv Biol (Weinh) 2024:e2400064. [PMID: 38837746 DOI: 10.1002/adbi.202400064] [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: 02/03/2024] [Revised: 03/03/2024] [Indexed: 06/07/2024]
Abstract
A compelling correlation method linking microbial communities and host gene expression in tissues is currently absent. A novel pipeline is proposed, dubbed Transcriptome Analysis of Host-Microbiome Crosstalk (TAHMC), designed to concurrently restore both host gene expression and microbial quantification from bulk RNA-seq data. Employing this approach, it discerned associations between the tissue microbiome and host immunity in the context of Crohn's disease (CD). Further, machine learning is utilized to separately construct networks of associations among host mRNA, long non-coding RNA, and tissue microbes. Unique host genes and tissue microbes are extracted from these networks for potential utility in CD diagnosis. Experimental validation of the predicted host gene regulation by microbes from the association network is achieved through the co-culturing of Faecalibacterium prausnitzii with Caco-2 cells. Collectively, the TAHMC pipeline accurately recovers both host gene expression and microbial quantification from CD RNA-seq data, thereby illuminating potential causal links between shifts in microbial composition as well as diversity within CD mucosal tissues and aberrant host gene expression.
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Affiliation(s)
- Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yongshuai Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yijun Mu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Junfei Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jinghui Zhang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Runze Bai
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
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Li Y, Xie G, Zha Y, Ning K. GAN-GMHI: a generative adversarial network with high discriminative power for microbiome-based disease prediction. J Genet Genomics 2023; 50:1026-1028. [PMID: 36972797 DOI: 10.1016/j.jgg.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Affiliation(s)
- Yuxue Li
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Gang Xie
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yuguo Zha
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Kang Ning
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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Wu H, Liu X, Peng L, Yang Y, Zhou Z, Du D, Xu H, Lv W, Lu L. Optimal batch determination for improved harmonization and prognostication of multi-center PET/CT radiomics feature in head and neck cancer. Phys Med Biol 2023; 68:225014. [PMID: 37844604 DOI: 10.1088/1361-6560/ad03d1] [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: 05/06/2023] [Accepted: 10/16/2023] [Indexed: 10/18/2023]
Abstract
Objective. To determine the optimal approach for identifying and mitigating batch effects in PET/CT radiomics features, and further improve the prognosis of patients with head and neck cancer (HNC), this study investigated the performance of three batch harmonization methods.Approach. Unsupervised harmonization identified the batch labels by K-means clustering. Supervised harmonization regarding the image acquisition factors (center, manufacturer, scanner, filter kernel) as known/given batch labels, and Combat harmonization was then implemented separately and sequentially based on the batch labels, i.e. harmonizing features among batches determined by each factor individually or harmonizing features among batches determined by multiple factors successively. Extensive experiments were conducted to predict overall survival (OS) on public PET/CT datasets that contain 800 patients from 9 centers.Main results. In the external validation cohort, results show that compared to original models without harmonization, Combat harmonization would be beneficial in OS prediction with C-index of 0.687-0.740 versus 0.684-0.767. Supervised harmonization slightly outperformed unsupervised harmonization in all models (C-index: 0.692-0.767 versus 0.684-0.750). Separate harmonization outperformed sequential harmonization in CT_m+clinic and CT_cm+clinic models with C-index of 0.752 and 0.722, respectively, while sequential harmonization involved clinical features in PET_rs+clinic model further improving the performance and achieving the highest C-index of 0.767.Significance. Optimal batch determination especially sequential harmonization for Combat holds the potential to improve the prognostic power of radiomics model in multi-center HNC dataset with PET/CT imaging.
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Affiliation(s)
- Huiqin Wu
- Department of Medical Imaging, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, 518037, People's Republic of China
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Xiaohui Liu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Lihong Peng
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Yuling Yang
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Zidong Zhou
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Dongyang Du
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Hui Xu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Wenbing Lv
- School of Information and Yunnan Key Laboratory of Intelligent Systems and Computing, Yunnan University, Kunming, Yunnan, 650504, People's Republic of China
| | - Lijun Lu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
- Pazhou Lab, Guangzhou 510330, People's Republic of China
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Lim CH, Choi JY, Choi JH, Lee JH, Lee J, Lim CW, Kim Z, Woo SK, Park SB, Park JM. Development and External Validation of 18F-FDG PET-Based Radiomic Model for Predicting Pathologic Complete Response after Neoadjuvant Chemotherapy in Breast Cancer. Cancers (Basel) 2023; 15:3842. [PMID: 37568658 PMCID: PMC10417050 DOI: 10.3390/cancers15153842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The aim of our retrospective study is to develop and externally validate an 18F-FDG PET-derived radiomics model for predicting pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC) in breast cancer patients. A total of 87 breast cancer patients underwent curative surgery after NAC at Soonchunhyang University Seoul Hospital and were randomly assigned to a training cohort and an internal validation cohort. Radiomic features were extracted from pretreatment PET images. A radiomic-score model was generated using the LASSO method. A combination model incorporating significant clinical variables was constructed. These models were externally validated in a separate cohort of 28 patients from Soonchunhyang University Buscheon Hospital. The model performances were assessed using area under the receiver operating characteristic (AUC). Seven radiomic features were selected to calculate the radiomic-score. Among clinical variables, human epidermal growth factor receptor 2 status was an independent predictor of pCR. The radiomic-score model achieved good discriminability, with AUCs of 0.963, 0.731, and 0.729 for the training, internal validation, and external validation cohorts, respectively. The combination model showed improved predictive performance compared to the radiomic-score model alone, with AUCs of 0.993, 0.772, and 0.906 in three cohorts, respectively. The 18F-FDG PET-derived radiomic-based model is useful for predicting pCR after NAC in breast cancer.
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Affiliation(s)
- Chae Hong Lim
- Department of Nuclear Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea;
| | - Joon Young Choi
- Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea;
| | - Joon Ho Choi
- Department of Nuclear Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea
| | - Jun-Hee Lee
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Jihyoun Lee
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Cheol Wan Lim
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea
| | - Zisun Kim
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea
| | - Sang-Keun Woo
- Division of Applied RI, Korea Institutes of Radiological and Medical Sciences, Seoul 01812, Republic of Korea
| | - Soo Bin Park
- Department of Nuclear Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea;
| | - Jung Mi Park
- Department of Nuclear Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea
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Xu H, Hao Y, Zhang Y, Zhou D, Kärkkäinen T, Nickerson LD, Li H, Cong F. Harmonization of multi-site functional MRI data with dual-projection based ICA model. Front Neurosci 2023; 17:1225606. [PMID: 37547146 PMCID: PMC10401882 DOI: 10.3389/fnins.2023.1225606] [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: 05/19/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Modern neuroimaging studies frequently merge magnetic resonance imaging (MRI) data from multiple sites. A larger and more diverse group of participants can increase the statistical power, enhance the reliability and reproducibility of neuroimaging research, and obtain findings more representative of the general population. However, measurement biases caused by site differences in scanners represent a barrier when pooling data collected from different sites. The existence of site effects can mask biological effects and lead to spurious findings. We recently proposed a powerful denoising strategy that implements dual-projection (DP) theory based on ICA to remove site-related effects from pooled data, demonstrating the method for simulated and in vivo structural MRI data. This study investigates the use of our DP-based ICA denoising method for harmonizing functional MRI (fMRI) data collected from the Autism Brain Imaging Data Exchange II. After frequency-domain and regional homogeneity analyses, two modalities, including amplitude of low frequency fluctuation (ALFF) and regional homogeneity (ReHo), were used to validate our method. The results indicate that DP-based ICA denoising method removes unwanted site effects for both two fMRI modalities, with increases in the significance of the associations between non-imaging variables (age, sex, etc.) and fMRI measures. In conclusion, our DP method can be applied to fMRI data in multi-site studies, enabling more accurate and reliable neuroimaging research findings.
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Affiliation(s)
- Huashuai Xu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
- Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
| | - Yuxing Hao
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Yunge Zhang
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Dongyue Zhou
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Tommi Kärkkäinen
- Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
| | - Lisa D. Nickerson
- McLean Imaging Center, McLean Hospital, Belmont, MA, United States
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Huanjie Li
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Fengyu Cong
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
- Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
- School of Artificial Intelligence, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
- Key Laboratory of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, China
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Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023; 19:346-362. [PMID: 37198436 PMCID: PMC10191412 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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9
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Zhao G, Wu M, Yan Q. Comprehensive Analysis to Reveal Amino Acid Metabolism-Associated Genes as a Prognostic Index in Gastric Cancer. Mediators Inflamm 2023; 2023:3276319. [PMID: 37214189 PMCID: PMC10195167 DOI: 10.1155/2023/3276319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
Background Amino acid metabolism (AAM) is related to tumor growth, prognosis, and therapeutic response. Tumor cells use more amino acids with less synthetic energy than normal cells for rapid proliferation. However, the possible significance of AAM-related genes in the tumor microenvironment (TME) is poorly understood. Methods Gastric cancer (GC) patients were classified into molecular subtypes by consensus clustering analysis using AAMs genes. AAM pattern, transcriptional patterns, prognosis, and TME in distinct molecular subtypes were systematically investigated. AAM gene score was built by least absolute shrinkage and selection operator (Lasso) regression. Results The study revealed that copy number variation (CNV) changes were prevalent in selected AAM-related genes, and most of these genes exhibited a high frequency of CNV deletion. Three molecular subtypes (clusters A, B, and C) were developed based on 99 AAM genes, which cluster B had better prognosis outcome. We developed a scoring system (AAM score) based on 4 AAM gene expressions to measure the AAM patterns of each patient. Importantly, we constructed a survival probability prediction nomogram. The AAM score was substantially associated with the index of cancer stem cells and sensitivity to chemotherapy intervention. Conclusion Overall, we detected prognostic AAM features in GC patients, which may help define TME characteristics and explore more effective treatment approaches.
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Affiliation(s)
- Gangjun Zhao
- Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Mi Wu
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Qiuwen Yan
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Medical School of Ningbo University, Ningbo, China
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Gebre RK, Senjem ML, Raghavan S, Schwarz CG, Gunter JL, Hofrenning EI, Reid RI, Kantarci K, Graff-Radford J, Knopman DS, Petersen RC, Jack CR, Vemuri P. Cross-scanner harmonization methods for structural MRI may need further work: A comparison study. Neuroimage 2023; 269:119912. [PMID: 36731814 PMCID: PMC10170652 DOI: 10.1016/j.neuroimage.2023.119912] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/01/2023] Open
Abstract
The clinical usefulness MRI biomarkers for aging and dementia studies relies on precise brain morphological measurements; however, scanner and/or protocol variations may introduce noise or bias. One approach to address this is post-acquisition scan harmonization. In this work, we evaluate deep learning (neural style transfer, CycleGAN and CGAN), histogram matching, and statistical (ComBat and LongComBat) methods. Participants who had been scanned on both GE and Siemens scanners (cross-sectional participants, known as Crossover (n = 113), and longitudinally scanned participants on both scanners (n = 454)) were used. The goal was to match GE MPRAGE (T1-weighted) scans to Siemens improved resolution MPRAGE scans. Harmonization was performed on raw native and preprocessed (resampled, affine transformed to template space) scans. Cortical thicknesses were measured using FreeSurfer (v.7.1.1). Distributions were checked using Kolmogorov-Smirnov tests. Intra-class correlation (ICC) was used to assess the degree of agreement in the Crossover datasets and annualized percent change in cortical thickness was calculated to evaluate the Longitudinal datasets. Prior to harmonization, the least agreement was found at the frontal pole (ICC = 0.72) for the raw native scans, and at caudal anterior cingulate (0.76) and frontal pole (0.54) for the preprocessed scans. Harmonization with NST, CycleGAN, and HM improved the ICCs of the preprocessed scans at the caudal anterior cingulate (>0.81) and frontal poles (>0.67). In the Longitudinal raw native scans, over- and under-estimations of cortical thickness were observed due to the changing of the scanners. ComBat matched the cortical thickness distributions throughout but was not able to increase the ICCs or remove the effects of scanner changeover in the Longitudinal datasets. CycleGAN and NST performed slightly better to address the cortical thickness variations between scanner change. However, none of the methods succeeded in harmonizing the Longitudinal dataset. CGAN was the worst performer for both datasets. In conclusion, the performance of the methods was overall similar and region dependent. Future research is needed to improve the existing approaches since none of them outperformed each other in terms of harmonizing the datasets at all ROIs. The findings of this study establish framework for future research into the scan harmonization problem.
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Affiliation(s)
- Robel K Gebre
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Matthew L Senjem
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; Department of Information Technology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | - Robert I Reid
- Department of Information Technology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kejal Kantarci
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - David S Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Clifford R Jack
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA
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11
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Yosef A, Shnaider E, Schneider M, Gurevich M. Heuristic normalization procedure for batch effect correction. Soft comput 2023. [DOI: 10.1007/s00500-023-08049-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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12
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Massimino L, Barchi A, Mandarino FV, Spanò S, Lamparelli LA, Vespa E, Passaretti S, Peyrin-Biroulet L, Savarino EV, Jairath V, Ungaro F, Danese S. A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis. J Transl Med 2023; 21:46. [PMID: 36698146 PMCID: PMC9875471 DOI: 10.1186/s12967-023-03898-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is a chronic immune-mediated rare disease, characterized by esophageal dysfunctions. It is likely to be primarily activated by food antigens and is classified as a chronic disease for most patients. Therefore, a deeper understanding of the pathogenetic mechanisms underlying EoE is needed to implement and improve therapeutic lines of intervention and ameliorate overall patient wellness. METHODS RNA-seq data of 18 different studies on EoE, downloaded from NCBI GEO with faster-qdump ( https://github.com/ncbi/sra-tools ), were batch-corrected and analyzed for transcriptomics and metatranscriptomics profiling as well as biological process functional enrichment. The EoE TaMMA web app was designed with plotly and dash. Tabula Sapiens raw data were downloaded from the UCSC Cell Browser. Esophageal single-cell raw data analysis was performed within the Automated Single-cell Analysis Pipeline. Single-cell data-driven bulk RNA-seq data deconvolution was performed with MuSiC and CIBERSORTx. Multi-omics integration was performed with MOFA. RESULTS The EoE TaMMA framework pointed out disease-specific molecular signatures, confirming its reliability in reanalyzing transcriptomic data, and providing new EoE-specific molecular markers including CXCL14, distinguishing EoE from gastroesophageal reflux disorder. EoE TaMMA also revealed microbiota dysbiosis as a predominant characteristic of EoE pathogenesis. Finally, the multi-omics analysis highlighted the presence of defined classes of microbial entities in subsets of patients that may participate in inducing the antigen-mediated response typical of EoE pathogenesis. CONCLUSIONS Our study showed that the complex EoE molecular network may be unraveled through advanced bioinformatics, integrating different components of the disease process into an omics-based network approach. This may implement EoE management and treatment in the coming years.
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Affiliation(s)
- Luca Massimino
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alberto Barchi
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesco Vito Mandarino
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Salvatore Spanò
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Edoardo Vespa
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Sandro Passaretti
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Laurent Peyrin-Biroulet
- Inserm NGERE, University of Lorraine, Vandoeuvre-les-Nancy, France
- Nancy University Hospital, Vandoeuvre-les-Nancy, France
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology, and Gastroenterology, University of Padua, Padua, Italy
- Gastroenterology Unit, Azienda Ospedale Università di Padova, Padua, Italy
| | - Vipul Jairath
- Department of Medicine, Division of Gastroenterology, Western University, London, ON, Canada
| | - Federica Ungaro
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy.
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy.
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy.
| | - Silvio Danese
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy.
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy.
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy.
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13
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Akiyoshi T, Wang Z, Kaneyasu T, Gotoh O, Tanaka N, Amino S, Yamamoto N, Kawachi H, Mukai T, Hiyoshi Y, Nagasaki T, Yamaguchi T, Konishi T, Fukunaga Y, Noda T, Mori S. Transcriptomic Analyses of Pretreatment Tumor Biopsy Samples, Response to Neoadjuvant Chemoradiotherapy, and Survival in Patients With Advanced Rectal Cancer. JAMA Netw Open 2023; 6:e2252140. [PMID: 36662520 PMCID: PMC9860531 DOI: 10.1001/jamanetworkopen.2022.52140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/03/2022] [Indexed: 01/21/2023] Open
Abstract
Importance Neoadjuvant chemoradiotherapy (CRT) is the standard of care for advanced rectal cancer. Yet, estimating response to CRT remains an unmet clinical challenge. Objective To investigate and better understand the transcriptomic factors associated with response to neoadjuvant CRT and survival in patients with advanced rectal cancer. Design, Setting, and Participants A single-center, retrospective, case series was conducted at a comprehensive cancer center. Pretreatment biopsies from 298 patients with rectal cancer who were later treated with neoadjuvant CRT between April 1, 2004, and September 30, 2020, were analyzed by RNA sequencing. Data analysis was performed from July 1, 2021, to May 31, 2022. Exposures Chemoradiotherapy followed by total mesorectal excision or watch-and-wait management. Main Outcomes and Measures Transcriptional subtyping was performed by consensus molecular subtype (CMS) classification. Immune cell infiltration was assessed using microenvironment cell populations-counter (MCP-counter) scores and single-sample gene set enrichment analysis (ssGSEA). Patients with surgical specimens of tumor regression grade 3 to 4 or whose care was managed by the watch-and-wait approach for more than 3 years were defined as good responders. Results Of the 298 patients in the study, 205 patients (68.8%) were men, and the median age was 61 (IQR, 52-67) years. Patients classified as CMS1 (6.4%) had a significantly higher rate of good response, albeit survival was comparable among the 4 subtypes. Good responders exhibited an enrichment in various immune-related pathways, as determined by ssGSEA. Microenvironment cell populations-counter scores for cytotoxic lymphocytes were significantly higher for good responders than nonresponders (median, 0.76 [IQR, 0.53-1.01] vs 0.58 [IQR, 0.43-0.83]; P < .001). Cytotoxic lymphocyte MCP-counter score was independently associated with response to CRT, as determined in the multivariable analysis (odds ratio, 3.81; 95% CI, 1.82-7.97; P < .001). Multivariable Cox proportional hazards regression analysis, including postoperative pathologic factors, revealed the cytotoxic lymphocyte MCP-counter score to be independently associated with recurrence-free survival (hazard ratio [HR], 0.38; 95% CI, 0.16-0.92; P = .03) and overall survival (HR, 0.16; 95% CI, 0.03-0.83; P = .03). Conclusions and Relevance In this case series of patients with rectal cancer treated with neoadjuvant CRT, the cytotoxic lymphocyte score in pretreatment biopsy samples, as computed by RNA sequencing, was associated with response to CRT and survival. This finding suggests that the cytotoxic lymphocyte score might serve as a biomarker in personalized multimodal rectal cancer treatment.
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Affiliation(s)
- Takashi Akiyoshi
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Zhe Wang
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomoko Kaneyasu
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Osamu Gotoh
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Norio Tanaka
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sayuri Amino
- Project for Development of Genomics-Based Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Noriko Yamamoto
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Toshiki Mukai
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yukiharu Hiyoshi
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Toshiya Nagasaki
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomohiro Yamaguchi
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tsuyoshi Konishi
- Department of Colon and Rectal Surgery, The University of Texas MD Anderson Cancer Center, Houston
| | - Yosuke Fukunaga
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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14
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Yosef A, Shnaider E, Schneider M, Gurevich M. Normalization of Large-Scale Transcriptome Data Using Heuristic Methods. Bioinform Biol Insights 2023; 17:11779322231160397. [PMID: 37020503 PMCID: PMC10068970 DOI: 10.1177/11779322231160397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/09/2023] [Indexed: 04/03/2023] Open
Abstract
In this study, we introduce an artificial intelligent method for addressing the batch effect of a transcriptome data. The method has several clear advantages in comparison with the alternative methods presently in use. Batch effect refers to the discrepancy in gene expression data series, measured under different conditions. While the data from the same batch (measurements performed under the same conditions) are compatible, combining various batches into 1 data set is problematic because of incompatible measurements. Therefore, it is necessary to perform correction of the combined data (normalization), before performing biological analysis. There are numerous methods attempting to correct data set for batch effect. These methods rely on various assumptions regarding the distribution of the measurements. Forcing the data elements into pre-supposed distribution can severely distort biological signals, thus leading to incorrect results and conclusions. As the discrepancy between the assumptions regarding the data distribution and the actual distribution is wider, the biases introduced by such “correction methods” are greater. We introduce a heuristic method to reduce batch effect. The method does not rely on any assumptions regarding the distribution and the behavior of data elements. Hence, it does not introduce any new biases in the process of correcting the batch effect. It strictly maintains the integrity of measurements within the original batches.
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15
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Berger T, Noble DJ, Yang Z, Shelley LEA, McMullan T, Bates A, Thomas S, Carruthers LJ, Beckett G, Duffton A, Paterson C, Jena R, McLaren DB, Burnet NG, Nailon WH. Assessing the generalisability of radiomics features previously identified as predictive of radiation-induced sticky saliva and xerostomia. Phys Imaging Radiat Oncol 2023; 25:100404. [PMID: 36660107 PMCID: PMC9843480 DOI: 10.1016/j.phro.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Background and purpose While core to the scientific approach, reproducibility of experimental results is challenging in radiomics studies. A recent publication identified radiomics features that are predictive of late irradiation-induced toxicity in head and neck cancer (HNC) patients. In this study, we assessed the generalisability of these findings. Materials and Methods The procedure described in the publication in question was applied to a cohort of 109 HNC patients treated with 50-70 Gy in 20-35 fractions using helical radiotherapy although there were inherent differences between the two patient populations and methodologies. On each slice of the planning CT with delineated parotid and submandibular glands, the imaging features that were previously identified as predictive of moderate-to-severe xerostomia and sticky saliva 12 months post radiotherapy (Xer12m and SS12m) were calculated. Specifically, Short Run Emphasis (SRE) and maximum CT intensity (maxHU) were evaluated for improvement in prediction of Xer12m and SS12m respectively, compared to models solely using baseline toxicity and mean dose to the salivary glands. Results None of the associations previously identified as statistically significant and involving radiomics features in univariate or multivariate models could be reproduced on our cohort. Conclusion The discrepancies observed between the results of the two studies delineate limits to the generalisability of the previously reported findings. This may be explained by the differences in the approaches, in particular the imaging characteristics and subsequent methodological implementation. This highlights the importance of external validation, high quality reporting guidelines and standardisation protocols to ensure generalisability, replication and ultimately clinical implementation.
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Affiliation(s)
- Thomas Berger
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK.,Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - David J Noble
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.,The University of Cambridge, Department of Oncology, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK.,Department of Clinical Oncology, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Zhuolin Yang
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK.,School of Engineering, the University of Edinburgh, the King's Buildings, Mayfield Road, Edinburgh EH9 3JL, UK
| | - Leila E A Shelley
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Thomas McMullan
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Amy Bates
- The University of Cambridge, Department of Oncology, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Simon Thomas
- Department of Medical Physics and Clinical Engineering, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Linda J Carruthers
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - George Beckett
- Edinburgh Parallel Computing Centre, Bayes Centre, 47 Potterrow, Edinburgh EH8 9BT, UK
| | - Aileen Duffton
- Beatson West of Scotland Cancer Centre, Great Western Road, Glasgow G12 0YN, UK
| | - Claire Paterson
- Beatson West of Scotland Cancer Centre, Great Western Road, Glasgow G12 0YN, UK
| | - Raj Jena
- The University of Cambridge, Department of Oncology, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Duncan B McLaren
- Department of Clinical Oncology, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Neil G Burnet
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - William H Nailon
- Department of Oncology Physics, Edinburgh Cancer Centre, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK.,School of Engineering, the University of Edinburgh, the King's Buildings, Mayfield Road, Edinburgh EH9 3JL, UK
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16
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Bayer JMM, Thompson PM, Ching CRK, Liu M, Chen A, Panzenhagen AC, Jahanshad N, Marquand A, Schmaal L, Sämann PG. Site effects how-to and when: An overview of retrospective techniques to accommodate site effects in multi-site neuroimaging analyses. Front Neurol 2022; 13:923988. [PMID: 36388214 PMCID: PMC9661923 DOI: 10.3389/fneur.2022.923988] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/12/2022] [Indexed: 09/12/2023] Open
Abstract
Site differences, or systematic differences in feature distributions across multiple data-acquisition sites, are a known source of heterogeneity that may adversely affect large-scale meta- and mega-analyses of independently collected neuroimaging data. They influence nearly all multi-site imaging modalities and biomarkers, and methods to compensate for them can improve reliability and generalizability in the analysis of genetics, omics, and clinical data. The origins of statistical site effects are complex and involve both technical differences (scanner vendor, head coil, acquisition parameters, imaging processing) and differences in sample characteristics (inclusion/exclusion criteria, sample size, ancestry) between sites. In an age of expanding international consortium research, there is a growing need to disentangle technical site effects from sample characteristics of interest. Numerous statistical and machine learning methods have been developed to control for, model, or attenuate site effects - yet to date, no comprehensive review has discussed the benefits and drawbacks of each for different use cases. Here, we provide an overview of the different existing statistical and machine learning methods developed to remove unwanted site effects from independently collected neuroimaging samples. We focus on linear mixed effect models, the ComBat technique and its variants, adjustments based on image quality metrics, normative modeling, and deep learning approaches such as generative adversarial networks. For each method, we outline the statistical foundation and summarize strengths and weaknesses, including their assumptions and conditions of use. We provide information on software availability and comment on the ease of use and the applicability of these methods to different types of data. We discuss validation and comparative reports, mention caveats and provide guidance on when to use each method, depending on context and specific research questions.
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Affiliation(s)
- Johanna M. M. Bayer
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Orygen, Parkville, VIC, Australia
| | - Paul M. Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, United States
| | - Christopher R. K. Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, United States
| | - Mengting Liu
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, China
| | - Andrew Chen
- Department of Biostatistics, Epidemiology, and Informatics, Penn Statistics in Imaging and Visualization Center, University of Pennsylvania, Philadelphia, PA, United States
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, United States
| | - Alana C. Panzenhagen
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Neda Jahanshad
- Laboratory of Brain eScience, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, CA, United States
| | - Andre Marquand
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, Netherlands
| | - Lianne Schmaal
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Orygen, Parkville, VIC, Australia
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17
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Rasche L, Schinke C, Maura F, Bauer MA, Ashby C, Deshpande S, Poos AM, Zangari M, Thanendrarajan S, Davies FE, Walker BA, Barlogie B, Landgren O, Morgan GJ, van Rhee F, Weinhold N. The spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states. Nat Commun 2022; 13:4517. [PMID: 35922426 PMCID: PMC9349320 DOI: 10.1038/s41467-022-32145-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Deciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multiple Myeloma patients during up to 14 years. Applying imaging-guided sampling we observe three evolutionary patterns, including relapse driven by a single-cell expansion, competing/co-existing sub-clones, and unique sub-clones at distinct locations. While we do not find the unique relapse sub-clone in the baseline focal lesion(s), we show a close phylogenetic relationship between baseline focal lesions and relapse disease, highlighting focal lesions as hotspots of tumor evolution. In patients with ≥3 focal lesions on positron-emission-tomography at diagnosis, relapse is driven by multiple distinct sub-clones, whereas in other patients, a single-cell expansion is typically seen (p < 0.01). Notably, we observe resistant sub-clones that can be hidden over years, suggesting that a prerequisite for curative therapies would be to overcome not only tumor heterogeneity but also dormancy.
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Affiliation(s)
- Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Francesco Maura
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alexandra M Poos
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Faith E Davies
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany.
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18
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AutoComBat: a generic method for harmonizing MRI-based radiomic features. Sci Rep 2022; 12:12762. [PMID: 35882891 PMCID: PMC9325761 DOI: 10.1038/s41598-022-16609-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The use of multicentric data is becoming essential for developing generalizable radiomic signatures. In particular, Magnetic Resonance Imaging (MRI) data used in brain oncology are often heterogeneous in terms of scanners and acquisitions, which significantly impact quantitative radiomic features. Various methods have been proposed to decrease dependency, including methods acting directly on MR images, i.e., based on the application of several preprocessing steps before feature extraction or the ComBat method, which harmonizes radiomic features themselves. The ComBat method used for radiomics may be misleading and presents some limitations, such as the need to know the labels associated with the "batch effect". In addition, a statistically representative sample is required and the applicability of a signature whose batch label is not present in the train set is not possible. This work aimed to compare a priori and a posteriori radiomic harmonization methods and propose a code adaptation to be machine learning compatible. Furthermore, we have developed AutoComBat, which aims to automatically determine the batch labels, using either MRI metadata or quality metrics as inputs of the proposed constrained clustering. A heterogeneous dataset consisting of high and low-grade gliomas coming from eight different centers was considered. The different methods were compared based on their ability to decrease relative standard deviation of radiomic features extracted from white matter and on their performance on a classification task using different machine learning models. ComBat and AutoComBat using image-derived quality metrics as inputs for batch assignment and preprocessing methods presented promising results on white matter harmonization, but with no clear consensus for all MR images. Preprocessing showed the best results on the T1w-gd images for the grading task. For T2w-flair, AutoComBat, using either metadata plus quality metrics or metadata alone as inputs, performs better than the conventional ComBat, highlighting its potential for data harmonization. Our results are MRI weighting, feature class and task dependent and require further investigations on other datasets.
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Xu H, Zhang L, Xia X, Shao W. Identification of a Five-mRNA Signature as a Novel Potential Prognostic Biomarker for Glioblastoma by Integrative Analysis. Front Genet 2022; 13:931938. [PMID: 35873480 PMCID: PMC9305328 DOI: 10.3389/fgene.2022.931938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the availability of advanced multimodal therapy, the prognosis of patients suffering from glioblastoma (GBM) remains poor. We conducted a genome-wide integrative analysis of mRNA expression profiles in 302 GBM tissues and 209 normal brain tissues from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project to examine the prognostic and predictive value of specific mRNAs in GBM. A total of 26 mRNAs were identified to be closely related to GBM patients’ OS (p < 0.05). Utilizing survival analysis and the Cox regression model, we discovered a set of five mRNAs (PTPRN, ABCC3, MDK, NMB, and RALYL) from these 26 mRNAs that displayed the capacity to stratify patients into high- and low-risk groups with statistically different overall survival in the training set. The model of the five-mRNA biomarker signature was successfully verified on a testing set and independent sets. Moreover, multivariate Cox regression analysis revealed that the five-mRNA biomarker signature was a prognostic factor for the survival of patients with GBM independent of clinical characteristics and molecular features (p < 0.05). Gene set enrichment analysis indicated that the five-mRNA biomarker signature might be implicated in the incidence and development of GBM through its roles in known cancer-related pathways, signaling molecules, and the immune system. Moreover, consistent with the bioinformatics analysis, NMB, ABCC3, and MDK mRNA expression was considerably higher in four human GBM cells, and the expression of PTPRN and RALYL was decreased in GBM cells (p < 0.05). Our study developed a novel candidate model that provides new prospective prognostic biomarkers for GBM.
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Affiliation(s)
- Huifang Xu
- Department of Neurology, Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Linfang Zhang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiujuan Xia
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wei Shao
- Department of Neurology, Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Wei Shao,
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20
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Nan Y, Ser JD, Walsh S, Schönlieb C, Roberts M, Selby I, Howard K, Owen J, Neville J, Guiot J, Ernst B, Pastor A, Alberich-Bayarri A, Menzel MI, Walsh S, Vos W, Flerin N, Charbonnier JP, van Rikxoort E, Chatterjee A, Woodruff H, Lambin P, Cerdá-Alberich L, Martí-Bonmatí L, Herrera F, Yang G. Data harmonisation for information fusion in digital healthcare: A state-of-the-art systematic review, meta-analysis and future research directions. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2022; 82:99-122. [PMID: 35664012 PMCID: PMC8878813 DOI: 10.1016/j.inffus.2022.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 05/13/2023]
Abstract
Removing the bias and variance of multicentre data has always been a challenge in large scale digital healthcare studies, which requires the ability to integrate clinical features extracted from data acquired by different scanners and protocols to improve stability and robustness. Previous studies have described various computational approaches to fuse single modality multicentre datasets. However, these surveys rarely focused on evaluation metrics and lacked a checklist for computational data harmonisation studies. In this systematic review, we summarise the computational data harmonisation approaches for multi-modality data in the digital healthcare field, including harmonisation strategies and evaluation metrics based on different theories. In addition, a comprehensive checklist that summarises common practices for data harmonisation studies is proposed to guide researchers to report their research findings more effectively. Last but not least, flowcharts presenting possible ways for methodology and metric selection are proposed and the limitations of different methods have been surveyed for future research.
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Affiliation(s)
- Yang Nan
- National Heart and Lung Institute, Imperial College London, London, Northern Ireland UK
| | - Javier Del Ser
- Department of Communications Engineering, University of the Basque Country UPV/EHU, Bilbao 48013, Spain
- TECNALIA, Basque Research and Technology Alliance (BRTA), Derio 48160, Spain
| | - Simon Walsh
- National Heart and Lung Institute, Imperial College London, London, Northern Ireland UK
| | - Carola Schönlieb
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, Northern Ireland UK
| | - Michael Roberts
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, Northern Ireland UK
- Oncology R&D, AstraZeneca, Cambridge, Northern Ireland UK
| | - Ian Selby
- Department of Radiology, University of Cambridge, Cambridge, Northern Ireland UK
| | - Kit Howard
- Clinical Data Interchange Standards Consortium, Austin, TX, United States of America
| | - John Owen
- Clinical Data Interchange Standards Consortium, Austin, TX, United States of America
| | - Jon Neville
- Clinical Data Interchange Standards Consortium, Austin, TX, United States of America
| | - Julien Guiot
- University Hospital of Liège (CHU Liège), Respiratory medicine department, Liège, Belgium
- University of Liege, Department of clinical sciences, Pneumology-Allergology, Liège, Belgium
| | - Benoit Ernst
- University Hospital of Liège (CHU Liège), Respiratory medicine department, Liège, Belgium
- University of Liege, Department of clinical sciences, Pneumology-Allergology, Liège, Belgium
| | | | | | - Marion I. Menzel
- Technische Hochschule Ingolstadt, Ingolstadt, Germany
- GE Healthcare GmbH, Munich, Germany
| | - Sean Walsh
- Radiomics (Oncoradiomics SA), Liège, Belgium
| | - Wim Vos
- Radiomics (Oncoradiomics SA), Liège, Belgium
| | - Nina Flerin
- Radiomics (Oncoradiomics SA), Liège, Belgium
| | | | | | - Avishek Chatterjee
- Department of Precision Medicine, Maastricht University, Maastricht, The Netherlands
| | - Henry Woodruff
- Department of Precision Medicine, Maastricht University, Maastricht, The Netherlands
| | - Philippe Lambin
- Department of Precision Medicine, Maastricht University, Maastricht, The Netherlands
| | - Leonor Cerdá-Alberich
- Medical Imaging Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Luis Martí-Bonmatí
- Medical Imaging Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Francisco Herrera
- Department of Computer Sciences and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI) University of Granada, Granada, Spain
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Guang Yang
- National Heart and Lung Institute, Imperial College London, London, Northern Ireland UK
- Cardiovascular Research Centre, Royal Brompton Hospital, London, Northern Ireland UK
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, Northern Ireland UK
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21
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Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages. Int J Mol Sci 2022; 23:ijms23052469. [PMID: 35269612 PMCID: PMC8910154 DOI: 10.3390/ijms23052469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Piwi interacting RNAs (piRNAs) are small non-coding single-stranded RNA species 20–31 nucleotides in size generated from distinct loci. In germline tissues, piRNAs are amplified via a “ping-pong cycle” to produce secondary piRNAs, which act in transposon silencing. In contrast, the role of somatic-derived piRNAs remains obscure. Here, we investigated the identity and distribution of piRNAs in human somatic tissues to determine their function and potential role in Parkinson’s disease (PD). Human datasets were curated from the Gene Expression Omnibus (GEO) database and a workflow was developed to identify piRNAs, which revealed 902 somatic piRNAs of which 527 were expressed in the brain. These were mainly derived from chromosomes 1, 11, and 19 compared to the germline tissues, which were from 15 and 19. Approximately 20% of somatic piRNAs mapped to transposon 3′ untranslated regions (UTRs), but a large proportion were sensed to the transcript in contrast to germline piRNAs. Gene set enrichment analysis suggested that somatic piRNAs function in neurodegenerative disease. piRNAs undergo dysregulation in different PD subtypes (PD and Parkinson’s disease dementia (PDD)) and stages (premotor and motor). piR-has-92056, piR-hsa-150797, piR-hsa-347751, piR-hsa-1909905, piR-hsa-2476630, and piR-hsa-2834636 from blood small extracellular vesicles were identified as novel biomarkers for PD diagnosis using a sparse partial least square discriminant analysis (sPLS-DA) (accuracy: 92%, AUC = 0.89). This study highlights a role for piRNAs in PD and provides tools for novel biomarker development.
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22
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Zaragori T, Oster J, Roch V, Hossu G, Chawki MB, Grignon R, Pouget C, Gauchotte G, Rech F, Blonski M, Taillandier L, Imbert L, Verger A. 18F-FDOPA PET for the Noninvasive Prediction of Glioma Molecular Parameters: A Radiomics Study. J Nucl Med 2022; 63:147-157. [PMID: 34016731 PMCID: PMC8717204 DOI: 10.2967/jnumed.120.261545] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
The assessment of gliomas by 18F-FDOPA PET imaging as an adjunct to MRI showed high performance by combining static and dynamic features to noninvasively predict the isocitrate dehydrogenase (IDH) mutations and the 1p/19q codeletion, which the World Health Organization classified as significant parameters in 2016. The current study evaluated whether other 18F-FDOPA PET radiomics features further improve performance and the contributions of each of these features to performance. Methods: Our study included 72 retrospectively selected, newly diagnosed glioma patients with 18F-FDOPA PET dynamic acquisitions. A set of 114 features, including conventional static features and dynamic features, as well as other radiomics features, were extracted and machine-learning models trained to predict IDH mutations and the 1p/19q codeletion. Models were based on a machine-learning algorithm built from stable, relevant, and uncorrelated features selected by hierarchic clustering followed by a bootstrapped feature selection process. Models were assessed by comparing area under the curve using a nested cross-validation approach. Feature importance was assessed using Shapley additive explanations values. Results: The best models were able to predict IDH mutations (logistic regression with L2 regularization) and the 1p/19q codeletion (support vector machine with radial basis function kernel) with an area under the curve of 0.831 (95% CI, 0.790-0.873) and 0.724 (95% CI, 0.669-0.782), respectively. For the prediction of IDH mutations, dynamic features were the most important features in the model (time to peak, 35.5%). In contrast, other radiomics features were the most useful for predicting the 1p/19q codeletion (up to 14.5% of importance for the small-zone low-gray-level emphasis). Conclusion:18F-FDOPA PET is an effective tool for the noninvasive prediction of glioma molecular parameters using a full set of amino-acid PET radiomics features. The contribution of each feature set shows the importance of systematically integrating dynamic acquisition for prediction of the IDH mutations as well as developing the use of radiomics features in routine practice for prediction of the 1p/19q codeletion.
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Affiliation(s)
- Timothée Zaragori
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France
- IADI UMR 1254, INSERM, Université de Lorraine, Nancy, France
| | - Julien Oster
- IADI UMR 1254, INSERM, Université de Lorraine, Nancy, France
| | - Véronique Roch
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Gabriela Hossu
- IADI UMR 1254, INSERM, Université de Lorraine, Nancy, France
- CIC 1433 Innovation Technologique, INSERM, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Mohammad B Chawki
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Rachel Grignon
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Celso Pouget
- Department of Pathology, CHRU-Nancy, Université de Lorraine, Nancy, France
- INSERM U1256, Université de Lorraine, Nancy, France
| | - Guillaume Gauchotte
- Department of Pathology, CHRU-Nancy, Université de Lorraine, Nancy, France
- INSERM U1256, Université de Lorraine, Nancy, France
| | - Fabien Rech
- Department of Neurosurgery, CHRU-Nancy, Université de Lorraine, Nancy, France
- Centre de Recherche en Automatique de Nancy CRAN UMR 7039, CNRS, Université de Lorraine, Nancy, France; and
| | - Marie Blonski
- Centre de Recherche en Automatique de Nancy CRAN UMR 7039, CNRS, Université de Lorraine, Nancy, France; and
- Department of Neuro-Oncology, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Luc Taillandier
- Centre de Recherche en Automatique de Nancy CRAN UMR 7039, CNRS, Université de Lorraine, Nancy, France; and
- Department of Neuro-Oncology, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Laëtitia Imbert
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France
- IADI UMR 1254, INSERM, Université de Lorraine, Nancy, France
| | - Antoine Verger
- Department of Nuclear Medicine and Nancyclotep Imaging Platform, CHRU-Nancy, Université de Lorraine, Nancy, France;
- IADI UMR 1254, INSERM, Université de Lorraine, Nancy, France
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23
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Whitney HM, Li H, Ji Y, Liu P, Giger ML. Multi-Stage Harmonization for Robust AI across Breast MR Databases. Cancers (Basel) 2021; 13:cancers13194809. [PMID: 34638294 PMCID: PMC8508003 DOI: 10.3390/cancers13194809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Batch harmonization of radiomic features extracted from magnetic resonance images of breast lesions from two databases was applied to an artificial intelligence/machine learning classification workflow. Training and independent test sets from the two databases, as well as the combination of them, were used in pre-harmonization and post-harmonization forms to investigate the generalizability of performance in the task of distinguishing between malignant and benign lesions. Most training and independent test scenarios were statistically equivalent, demonstrating that batch harmonization with feature selection harmonization can potentially develop generalizable classification models. Abstract Radiomic features extracted from medical images may demonstrate a batch effect when cases come from different sources. We investigated classification performance using training and independent test sets drawn from two sources using both pre-harmonization and post-harmonization features. In this retrospective study, a database of thirty-two radiomic features, extracted from DCE-MR images of breast lesions after fuzzy c-means segmentation, was collected. There were 944 unique lesions in Database A (208 benign lesions, 736 cancers) and 1986 unique lesions in Database B (481 benign lesions, 1505 cancers). The lesions from each database were divided by year of image acquisition into training and independent test sets, separately by database and in combination. ComBat batch harmonization was conducted on the combined training set to minimize the batch effect on eligible features by database. The empirical Bayes estimates from the feature harmonization were applied to the eligible features of the combined independent test set. The training sets (A, B, and combined) were then used in training linear discriminant analysis classifiers after stepwise feature selection. The classifiers were then run on the A, B, and combined independent test sets. Classification performance was compared using pre-harmonization features to post-harmonization features, including their corresponding feature selection, evaluated using the area under the receiver operating characteristic curve (AUC) as the figure of merit. Four out of five training and independent test scenarios demonstrated statistically equivalent classification performance when compared pre- and post-harmonization. These results demonstrate that translation of machine learning techniques with batch data harmonization can potentially yield generalizable models that maintain classification performance.
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Affiliation(s)
- Heather M. Whitney
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; (H.L.); (Y.J.)
- Department of Physics, Wheaton College, Wheaton, IL 60187, USA
- Correspondence: (H.M.W.); (M.L.G.)
| | - Hui Li
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; (H.L.); (Y.J.)
| | - Yu Ji
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; (H.L.); (Y.J.)
- Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China;
| | - Peifang Liu
- Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China;
| | - Maryellen L. Giger
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; (H.L.); (Y.J.)
- Correspondence: (H.M.W.); (M.L.G.)
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24
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Orlhac F, Eertink JJ, Cottereau AS, Zijlstra JM, Thieblemont C, Meignan MA, Boellaard R, Buvat I. A guide to ComBat harmonization of imaging biomarkers in multicenter studies. J Nucl Med 2021; 63:172-179. [PMID: 34531263 DOI: 10.2967/jnumed.121.262464] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of PET image acquisition and reconstruction parameters on SUV measurements or radiomic feature values is widely documented. This "scanner" effect is detrimental to the design and validation of predictive or prognostic models and limits the use of large multicenter cohorts. To reduce the impact of this scanner effect, the ComBat method has been proposed and is now used in various contexts. The purpose of this article is to explain and illustrate the use of ComBat based on practical examples. We also give examples in which the ComBat assumptions are not met; thus, ComBat should not be used.
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Affiliation(s)
- Fanny Orlhac
- Institut Curie, Universite PSL, Inserm, U1288 LITO, Universite Paris Saclay, France
| | - Jakoba J Eertink
- Amsterdam UMC, Vrije Universiteit Amsterdam, department of Hematology, Cancer Center, Netherlands
| | | | - Josee M Zijlstra
- Amsterdam UMC, Vrije Universiteit Amsterdam, department of Hematology, Cancer Center, Netherlands
| | - Catherine Thieblemont
- APHP, Hopital Saint-Louis, Service d'hemato-oncologie, DMU DHI, Universite de Paris, France
| | - Michel A Meignan
- AP-HP, Universite Paris-Est, Hopital Henri Mondor, Lysa Imaging, France
| | - Ronald Boellaard
- Amsterdam UMC, Vrije Universiteit Amsterdam, department of Radiology and Nuclear Medicine, Cancer Center, Netherlands
| | - Irene Buvat
- Institut Curie, Universite PSL, Inserm, U1288 LITO, Universite Paris Saclay, France
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25
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Modos D, Thomas JP, Korcsmaros T. A handy meta-analysis tool for IBD research. NATURE COMPUTATIONAL SCIENCE 2021; 1:571-572. [PMID: 38217126 DOI: 10.1038/s43588-021-00124-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Affiliation(s)
- Dezso Modos
- Earlham Institute, Norwich, UK
- Quadram Institute Bioscience, Norwich, UK
| | - John P Thomas
- Earlham Institute, Norwich, UK
- Quadram Institute Bioscience, Norwich, UK
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, UK.
- Quadram Institute Bioscience, Norwich, UK.
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26
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Massimino L, Lamparelli LA, Houshyar Y, D'Alessio S, Peyrin-Biroulet L, Vetrano S, Danese S, Ungaro F. The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework. NATURE COMPUTATIONAL SCIENCE 2021; 1:511-515. [PMID: 38217242 PMCID: PMC10766544 DOI: 10.1038/s43588-021-00114-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 01/15/2024]
Abstract
Inflammatory bowel disease (IBD) is a class of chronic disorders whose etiogenesis is still unknown. Despite the high number of IBD-related omics studies, the RNA-sequencing data produced results that are hard to compare because of the experimental variability and different data analysis approaches. We here introduce the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-sequencing datasets. IBD TaMMA is an open-source platform where scientists can explore simultaneously the freely available IBD-associated transcriptomics and microbial profiles thanks to its interactive interface, resulting in a useful tool to the IBD community.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.
| | | | - Yashar Houshyar
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Laurent Peyrin-Biroulet
- Inserm NGERE, University of Lorraine, Vandoeuvre-les-Nancy, France
- Nancy University Hospital, Vandoeuvre-les-Nancy, France
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.
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27
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Cadow J, Manica M, Mathis R, Guo T, Aebersold R, Rodríguez Martínez M. On the feasibility of deep learning applications using raw mass spectrometry data. Bioinformatics 2021; 37:i245-i253. [PMID: 34252933 PMCID: PMC8275322 DOI: 10.1093/bioinformatics/btab311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
SUMMARY In recent years, SWATH-MS has become the proteomic method of choice for data-independent-acquisition, as it enables high proteome coverage, accuracy and reproducibility. However, data analysis is convoluted and requires prior information and expert curation. Furthermore, as quantification is limited to a small set of peptides, potentially important biological information may be discarded. Here we demonstrate that deep learning can be used to learn discriminative features directly from raw MS data, eliminating hence the need of elaborate data processing pipelines. Using transfer learning to overcome sample sparsity, we exploit a collection of publicly available deep learning models already trained for the task of natural image classification. These models are used to produce feature vectors from each mass spectrometry (MS) raw image, which are later used as input for a classifier trained to distinguish tumor from normal prostate biopsies. Although the deep learning models were originally trained for a completely different classification task and no additional fine-tuning is performed on them, we achieve a highly remarkable classification performance of 0.876 AUC. We investigate different types of image preprocessing and encoding. We also investigate whether the inclusion of the secondary MS2 spectra improves the classification performance. Throughout all tested models, we use standard protein expression vectors as gold standards. Even with our naïve implementation, our results suggest that the application of deep learning and transfer learning techniques might pave the way to the broader usage of raw mass spectrometry data in real-time diagnosis. AVAILABILITY AND IMPLEMENTATION The open source code used to generate the results from MS images is available on GitHub: https://ibm.biz/mstransc. The raw MS data underlying this article cannot be shared publicly for the privacy of individuals that participated in the study. Processed data including the MS images, their encodings, classification labels and results can be accessed at the following link: https://ibm.box.com/v/mstc-supplementary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joris Cadow
- Cognitive Computing & Industry Solutions, IBM Research Europe - Zurich, Rueschlikon 8803, Switzerland
| | - Matteo Manica
- Cognitive Computing & Industry Solutions, IBM Research Europe - Zurich, Rueschlikon 8803, Switzerland
| | - Roland Mathis
- Cognitive Computing & Industry Solutions, IBM Research Europe - Zurich, Rueschlikon 8803, Switzerland
| | - Tiannan Guo
- Institute of Basic Medical Sciences, School of Life Science, Westlake University, Hangzhou 310024, China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich 8093, Switzerland
| | - María Rodríguez Martínez
- Cognitive Computing & Industry Solutions, IBM Research Europe - Zurich, Rueschlikon 8803, Switzerland
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28
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Da-ano R, Lucia F, Masson I, Abgral R, Alfieri J, Rousseau C, Mervoyer A, Reinhold C, Pradier O, Schick U, Visvikis D, Hatt M. A transfer learning approach to facilitate ComBat-based harmonization of multicentre radiomic features in new datasets. PLoS One 2021; 16:e0253653. [PMID: 34197503 PMCID: PMC8248970 DOI: 10.1371/journal.pone.0253653] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To facilitate the demonstration of the prognostic value of radiomics, multicenter radiomics studies are needed. Pooling radiomic features of such data in a statistical analysis is however challenging, as they are sensitive to the variability in scanner models, acquisition protocols and reconstruction settings, which is often unavoidable in a multicentre retrospective analysis. A statistical harmonization strategy called ComBat was utilized in radiomics studies to deal with the "center-effect". The goal of the present work was to integrate a transfer learning (TL) technique within ComBat-and recently developed alternate versions of ComBat with improved flexibility (M-ComBat) and robustness (B-ComBat)-to allow the use of a previously determined harmonization transform to the radiomic feature values of new patients from an already known center. MATERIAL AND METHODS The proposed TL approach were incorporated in the four versions of ComBat (standard, B, M, and B-M ComBat). The proposed approach was evaluated using a dataset of 189 locally advanced cervical cancer patients from 3 centers, with magnetic resonance imaging (MRI) and positron emission tomography (PET) images, with the clinical endpoint of predicting local failure. The impact performance of the TL approach was evaluated by comparing the harmonization achieved using only parts of the data to the reference (harmonization achieved using all the available data). It was performed through three different machine learning pipelines. RESULTS The proposed TL technique was successful in harmonizing features of new patients from a known center in all versions of ComBat, leading to predictive models reaching similar performance as the ones developed using the features harmonized with all the data available. CONCLUSION The proposed TL approach enables applying a previously determined ComBat transform to new, previously unseen data.
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Affiliation(s)
- Ronrick Da-ano
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- * E-mail:
| | - François Lucia
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | - Ingrid Masson
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Department of Radiation Oncology, Institut de cancérologie de l’Ouest René-Gauducheau, Saint-Herblain, France
| | - Ronan Abgral
- Department of Nuclear Medicine, University of Brest, Brest, France
| | - Joanne Alfieri
- Department of Radiation Oncology, McGill University Health Centre, Montreal, Quebec
| | - Caroline Rousseau
- Department of Nuclear Medicine, Institut de cancérologie de l’Ouest René-Gauducheau, Saint-Herblain, France
| | - Augustin Mervoyer
- Department of Radiation Oncology, Institut de cancérologie de l’Ouest René-Gauducheau, Saint-Herblain, France
| | - Caroline Reinhold
- Department of Radiology, McGill University Health Centre, Montreal, Canada
- Augmented Intelligence & Precision Health Laboratory of the Research Institute of McGill University Health Centre, Montreal, Canada
| | - Olivier Pradier
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | - Ulrike Schick
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | | | - Mathieu Hatt
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
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Zheng W, Zhang S, Jiang S, Huang Z, Chen X, Guo H, Li M, Zheng S. Evaluation of immune status in testis and macrophage polarization associated with testicular damage in patients with nonobstructive azoospermia. Am J Reprod Immunol 2021; 86:e13481. [PMID: 34192390 DOI: 10.1111/aji.13481] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Immune cells residing in the testicular interstitial space form the immunological microenvironment of the testis. They are assumed to play a role in maintaining testicular homeostasis and immune privilege. However, the immune status and related cell polarization in patients with nonobstructive azoospermia (NOA) remains poorly characterized. System evaluation of the testis immunological microenvironment in NOA patients may help to reveal the mechanisms of idiopathic azoospermia. STUDY DESIGN The gene expression patterns of immune cells in normal human testes were systematically analyzed by single-cell RNA sequencing (scRNA-seq) and preliminarily verification by the human protein atlas (HPA) online database. The immune cell infiltration profiles and immune status of patients with NOA was analyzed by single-sample gene set enrichment analysis (ssGSEA) and gene set variation analysis (GSVA) based on four independent public microarray datasets (GSE45885, GSE45887, GSE9210, and GSE145467), obtained from Gene Expression Omnibus (GEO) online database. The relationship between immune cells and spermatogenesis score was further analyzed by Spearman correlation analysis. Finally, immunohistochemistry (IHC) staining was performed to identify the main immune cell types and their polarization status in patients with NOA. RESULTS Both scRNA-seq and HPA analysis showed that testicular macrophages represent the largest pool of immune cells in the normal testis, and also exhibit an attenuated inflammatory response by expressing high levels of tolerance proteins (CD163, IL-10, TGF-β, and VEGF) and reduced expression of TLR signaling pathway-related genes. Correlation analysis revealed that the testicular immune score and macrophages including M1 and M2 macrophages were significantly negatively correlated with spermatogenesis score in patients with NOA (GSE45885 and GSE45887). In addition, the number of M1 and M2 macrophages was significantly higher in patients with NOA (GSE9210 and GSE145467) than in normal testis. GSVA analysis indicated that the immunological microenvironment in NOA tissues was manifested by activated immune system and pro-inflammatory status. IHC staining results showed that the number of M1 and M2 macrophages was significantly higher in NOA tissues than in normal testis and negatively correlated with the Johnson score. CONCLUSION Testicular macrophage polarization may play a vital role in NOA development and is a promising potential therapeutic target.
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Affiliation(s)
- Wenzhong Zheng
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shiqiang Zhang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shaoqin Jiang
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhangcheng Huang
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xiaobao Chen
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Huan Guo
- Department of Urology, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Center, Shenzhen University, Shenzhen, China
| | - Mengqiang Li
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Song Zheng
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
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Wong J, George RB, Hanley CM, Saliba C, Yee DA, Jerath A. Tranexamic acid: current use in obstetrics, major orthopedic, and trauma surgery. Can J Anaesth 2021; 68:894-917. [PMID: 33993459 DOI: 10.1007/s12630-021-01967-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
PURPOSE In this Continuing Professional Development module, we review the practical pharmacology of tranexamic acid and its clinical use in trauma, obstetrics, and major orthopedic surgery. PRINCIPAL FINDINGS Tranexamic acid is a synthetic drug that inhibits fibrinolysis. Multiple clinical trials in various clinical settings have shown that it can reduce blood loss, transfusion rates, and bleeding-associated mortality. In trauma and obstetrical bleeding, early tranexamic acid administration (< three hours) may have greater clinical benefits. Overall, tranexamic acid use appears safe with no significant increase of thromboembolic or seizure events. Nevertheless, current evidence has limitations related to wide heterogeneity in dose, route, and timing of drug administration, as well as generalizability of the large-scale trial findings to higher income nations. CONCLUSIONS Tranexamic acid is an efficacious and safe pharmacological-based blood conservation technique in the management of clinically significant hemorrhage. All anesthesiologists should have a good understanding of the pharmacotherapeutic properties and perioperative role of tranexamic acid therapy both inside and outside of the operating room. The use of tranexamic acid is likely to continue to rise with endorsement by various clinical guidelines and healthcare organizations. Further quantitative research is needed to evaluate optimal dosing and drug efficacy in these clinical scenarios.
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Affiliation(s)
- Jean Wong
- Department of Anesthesia and Pain Management, Toronto Western Hospital, University Health Network and Women's College Hospital, Toronto, ON, Canada
- Department of Anesthesia and Pain Medicine, University of Toronto, Toronto, ON, Canada
| | - Ronald B George
- Department of Anesthesia and Perioperative Care, UCSF, San Francisco, CA, USA
| | - Ciara M Hanley
- Department of Anesthesia, Sunnybrook Health Science Centre, Toronto, ON, Canada
- Department of Anesthesia and Pain Medicine, University of Toronto, Toronto, ON, Canada
| | - Chadi Saliba
- Department of Anesthesia, Sunnybrook Health Science Centre, Toronto, ON, Canada
- Department of Anesthesia and Pain Medicine, University of Toronto, Toronto, ON, Canada
| | - Doreen A Yee
- Department of Anesthesia, Sunnybrook Health Science Centre, Toronto, ON, Canada
- Department of Anesthesia and Pain Medicine, University of Toronto, Toronto, ON, Canada
| | - Angela Jerath
- Department of Anesthesia, Sunnybrook Health Science Centre, Toronto, ON, Canada.
- Department of Anesthesia and Pain Medicine, University of Toronto, Toronto, ON, Canada.
- Sunnybrook Research Institute, Sunnybrook Health Science Centre, Toronto, ON, Canada.
- Toronto General Hospital Research Institute, Toronto, ON, Canada.
- Institute of Clinical Evaluative Sciences, Toronto, ON, Canada.
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DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies. Sci Rep 2021; 11:5657. [PMID: 33707505 PMCID: PMC7952378 DOI: 10.1038/s41598-021-84824-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
As a powerful phenotyping technology, metabolomics provides new opportunities in biomarker discovery through metabolome-wide association studies (MWAS) and the identification of metabolites having a regulatory effect in various biological processes. While mass spectrometry-based (MS) metabolomics assays are endowed with high throughput and sensitivity, MWAS are doomed to long-term data acquisition generating an overtime-analytical signal drift that can hinder the uncovering of real biologically relevant changes. We developed “dbnorm”, a package in the R environment, which allows for an easy comparison of the model performance of advanced statistical tools commonly used in metabolomics to remove batch effects from large metabolomics datasets. “dbnorm” integrates advanced statistical tools to inspect the dataset structure not only at the macroscopic (sample batches) scale, but also at the microscopic (metabolic features) level. To compare the model performance on data correction, “dbnorm” assigns a score that help users identify the best fitting model for each dataset. In this study, we applied “dbnorm” to two large-scale metabolomics datasets as a proof of concept. We demonstrate that “dbnorm” allows for the accurate selection of the most appropriate statistical tool to efficiently remove the overtime signal drift and to focus on the relevant biological components of complex datasets.
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Liu Y, Xue M, Cao D, Qin L, Wang Y, Miao Z, Wang P, Hu X, Shen J, Xiong B. Multi-omics characterization of WNT pathway reactivation to ameliorate BET inhibitor resistance in liver cancer cells. Genomics 2021; 113:1057-1069. [PMID: 33667649 DOI: 10.1016/j.ygeno.2021.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/17/2021] [Accepted: 02/28/2021] [Indexed: 01/10/2023]
Abstract
The Bromodomain and Extra-terminal domain (BET) proteins are promising targets in treating cancers. Although BET inhibitors have been in clinical trials, they are limited by lacking of suitable biomarkers to indicate drug responses in different cancers. Here we identify DHRS2, ETV4 and NOTUM as potential biomarkers to indicate drug resistance in liver cancer cells of a recently discovered BET inhibitor, Hjp-6-171. Furthermore, we confirm that reactivation of WNT pathway, the target of NOTUM, contributes to the drug sensitivity restoration in Hjp-6-171 resistant cells. Specially, combinations of Hjp-6-171 and a GSK3β inhibitor CHIR-98014 show remarkable therapeutic effects in vitro and in vivo. Integrating RNA-seq and ChIP-seq data, we reveal the expression signature of β-catenin regulated genes is contrary in sensitive cells to that in resistant cells. We propose WNT signaling molecules such as β-catenin and ETV4 to be candidate biomarkers to indicate BET inhibitor responses in liver cancer patients.
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Affiliation(s)
- Yuwei Liu
- SARI center for stem cell and nanomedicine, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mengzhu Xue
- SARI center for stem cell and nanomedicine, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Danyan Cao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lihuai Qin
- Center for chemical biology and drug discovery, department of pharmacological sciences, Tisch cancer institute, Icahn School of medicine at Mount Sinai, New York 10029, USA
| | - Ying Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zehong Miao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peng Wang
- Bio-Med Big Data Center, Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xin Hu
- Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Jingkang Shen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bing Xiong
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc 2020; 16:1-9. [PMID: 33288955 DOI: 10.1038/s41596-020-00409-w] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/08/2020] [Indexed: 01/01/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( https://scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.
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Affiliation(s)
| | | | - Davis McCarthy
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Melbourne Integrative Genomics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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Shi YR, Xiong K, Ye X, Yang P, Wu Z, Zu XB. Development of a prognostic signature for bladder cancer based on immune-related genes. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1380. [PMID: 33313125 PMCID: PMC7723522 DOI: 10.21037/atm-20-1102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Although the prognosis of patients with bladder cancer (BC) has improved significantly with the use of multimodal therapy, reliable prognostic biomarkers are still urgently needed due to the heterogeneity of tumors. Our aim was to develop an individualized immune-related gene pair (IRGP) signature that could precisely predict prognosis in BC patients. Methods Gene expression profiles and corresponding clinical information were collected from eight microarray data sets and one RNA-Seq data set. Results Among 1,811 immune genes, a 30-IRGP signature consisting of 52 unique genes was generated in the training cohort, which significantly stratified patients into low- and high-risk groups in terms of overall survival. In the testing and validation cohorts, the IRGP signature was also associated with patient prognosis in the univariate and multivariate Cox regression analyses. Several biological processes, including the immune response, chemotaxis, and the inflammatory response, were enriched among genes in the IRGP signature. When the signature was integrated with the TNM stage, an IRGP nomogram was developed and showed improved prognostic accuracy relative to the IRGP signature alone. Conclusions In short, we identified a robust IRGP signature for estimating overall survival in BC patients that could also be used as a promising biomarker for identifying high-risk patients for individualized therapy.
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Affiliation(s)
- Ying-Rui Shi
- Department of Radiation Oncology, Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Kun Xiong
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xu Ye
- Department of Radiation Oncology, Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Pei Yang
- Department of Radiation Oncology, Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Zheng Wu
- Department of Radiation Oncology, Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiong-Bing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
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Random survival forest to predict transplant-eligible newly diagnosed multiple myeloma outcome including FDG-PET radiomics: a combined analysis of two independent prospective European trials. Eur J Nucl Med Mol Imaging 2020; 48:1005-1015. [PMID: 33006656 DOI: 10.1007/s00259-020-05049-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/20/2020] [Indexed: 01/15/2023]
Abstract
PURPOSE Fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) is included in the International Myeloma Working Group (IMWG) imaging guidelines for the work-up at diagnosis and the follow-up of multiple myeloma (MM) notably because it is a reliable tool as a predictor of prognosis. Nevertheless, none of the published studies focusing on the prognostic value of PET-derived features at baseline consider tumor heterogeneity, which could be of high importance in MM. The aim of this study was to evaluate the prognostic value of baseline PET-derived features in transplant-eligible newly diagnosed (TEND) MM patients enrolled in two prospective independent European randomized phase III trials using an innovative statistical random survival forest (RSF) approach. METHODS Imaging ancillary studies of IFM/DFCI2009 and EMN02/HO95 trials formed part of the present analysis (IMAJEM and EMN02/HO95, respectively). Among all patients initially enrolled in these studies, those with a positive baseline FDG-PET/CT imaging and focal bone lesions (FLs) and/or extramedullary disease (EMD) were included in the present analysis. A total of 17 image features (visual and quantitative, reflecting whole imaging characteristics) and 5 clinical/histopathological parameters were collected. The statistical analysis was conducted using two RSF approaches (train/validation + test and additional nested cross-validation) to predict progression-free survival (PFS). RESULTS One hundred thirty-nine patients were considered for this study. The final model based on the first RSF (train/validation + test) approach selected 3 features (treatment arm, hemoglobin, and SUVmaxBone Marrow (BM)) among the 22 involved initially, and two risk groups of patients (good and poor prognosis) could be defined with a mean hazard ratio of 4.3 ± 1.5 and a mean log-rank p value of 0.01 ± 0.01. The additional RSF (nested cross-validation) analysis highlighted the robustness of the proposed model across different splits of the dataset. Indeed, the first features selected using the train/validation + test approach remained the first ones over the folds with the nested approach. CONCLUSION We proposed a new prognosis model for TEND MM patients at diagnosis based on two RSF approaches. TRIAL REGISTRATION IMAJEM: NCT01309334 and EMN02/HO95: NCT01134484.
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36
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Glucose Metabolism Quantified by SUVmax on Baseline FDG-PET/CT Predicts Survival in Newly Diagnosed Multiple Myeloma Patients: Combined Harmonized Analysis of Two Prospective Phase III Trials. Cancers (Basel) 2020; 12:cancers12092532. [PMID: 32899991 PMCID: PMC7564454 DOI: 10.3390/cancers12092532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Multiple myeloma (MM) is associated with high morbidity and mortality and variable survival that requires early identification of high-risk patients in order to quickly adapt treatment. FDG-PET/CT is a promising technique for initial staging of symptomatic MM. The aim of our retrospective study was to asses the prognostic value of this technique at baseline in symptomatic MM patients included in two large European prospective studies. After harmonization of data by and ad-hoc approach called M-Combat, we confirmed the prognostic value of FDG-PET/CT in a population of 227 MM patients, by integrating a new prognostic biomarker named “bone SUVmax” (including the maximum intensity of fixation of focal lesions and bone marrow) which is strongly correlated with a poorer prognosis of MM patients. Prognostic patient stratification is currently based on laboratory tests and genomic abnormalities, but FDG-PET/CT is likely to be an important method of defining high-risk patients, and thus, to potentially better adapt future therapeutic management. Abstract Background: Multiple myeloma is a hematological neoplasm characterized by a clonal proliferation of malignant plasma cells in the bone marrow, and is associated with high morbidity and mortality and variable survival. Positron emission tomography combined with computed tomography using 18F-deoxyfluoroglucose (FDG-PET/CT) is a promising technique for initial staging of symptomatic multiple myeloma patients. The objective of this study was to assess the prognostic value of this technique at baseline in symptomatic multiple myeloma patients included in two large European prospective studies (French and Italian). Methods: We retrospectively performed a combined harmonized analysis of 227 newly diagnosed transplant eligible multiple myeloma patients from two separate phase III trials. All images were centrally reviewed and analyzed using visual criteria and maximal standardized uptake value. An ad-hoc approach (called modified Combat) was applied to harmonize the data and then remove the “country effect” in order to strengthen the reliability of the final conclusions. Results: Using a multivariate analysis including treatment arm, R-ISS score, presence of extra-medullary disease and bone SUVmax, only bone SUVmax (p = 0.016) was an independent prognosis factor with an OS threshold of 7.1. For PFS, treatment arm and presence of extra-medullary disease were both independent prognosis biomarkers (p = 0.022 and 0.006 respectively). Conclusions: Our results show that bone SUVmax is a simple and reliable biomarker to analyze FDG-PET/CT at baseline that strongly correlates with a poorer prognosis for MM patients.
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Ai D, Wang Y, Li X, Pan H. Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder. Biomolecules 2020; 10:biom10091207. [PMID: 32825264 PMCID: PMC7563725 DOI: 10.3390/biom10091207] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023] Open
Abstract
An effective feature extraction method is key to improving the accuracy of a prediction model. From the Gene Expression Omnibus (GEO) database, which includes 13,487 genes, we obtained microarray gene expression data for 238 samples from colorectal cancer (CRC) samples and normal samples. Twelve gene modules were obtained by weighted gene co-expression network analysis (WGCNA) on 173 samples. By calculating the Pearson correlation coefficient (PCC) between the characteristic genes of each module and colorectal cancer, we obtained a key module that was highly correlated with CRC. We screened hub genes from the key module by considering module membership, gene significance, and intramodular connectivity. We selected 10 hub genes as a type of feature for the classifier. We used the variational autoencoder (VAE) for 1159 genes with significantly different expressions and mapped the data into a 10-dimensional representation, as another type of feature for the cancer classifier. The two types of features were applied to the support vector machines (SVM) classifier for CRC. The accuracy was 0.9692 with an AUC of 0.9981. The result shows a high accuracy of the two-step feature extraction method, which includes obtaining hub genes by WGCNA and a 10-dimensional representation by variational autoencoder (VAE).
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Affiliation(s)
- Dongmei Ai
- Basic Experimental Center of Natural Science, University of Science and Technology Beijing, Beijing 100083, China
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.L.); (H.P.)
- Correspondence: ; Tel.: +86-136-2105-2939
| | - Yuduo Wang
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.L.); (H.P.)
| | - Xiaoxin Li
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.L.); (H.P.)
| | - Hongfei Pan
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.L.); (H.P.)
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Wang X, Yi H, Wang J, Liu Z, Yin Y, Zhang H. GDASC: a GPU parallel-based web server for detecting hidden batch factors. Bioinformatics 2020; 36:4211-4213. [PMID: 32386292 DOI: 10.1093/bioinformatics/btaa427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/13/2020] [Accepted: 05/01/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY We developed GDASC, a web version of our former DASC algorithm implemented with GPU. It provides a user-friendly web interface for detecting batch factors. Based on the good performance of DASC algorithm, it is able to give the most accurate results. For two steps of DASC, data-adaptive shrinkage and semi-non-negative matrix factorization, we designed parallelization strategies facing convex clustering solution and decomposition process. It runs more than 50 times faster than the original version on the representative RNA sequencing quality control dataset. With its accuracy and high speed, this server will be a useful tool for batch effects analysis. AVAILABILITY AND IMPLEMENTATION http://bioinfo.nankai.edu.cn/gdasc.php. CONTACT zhanghan@nankai.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiao Wang
- Department of Computer Science and Technology, College of Computer Science
| | - Haidong Yi
- Department of Computer Science and Technology, College of Computer Science.,Department of Automation and Intelligence Science, College of Artificial Intelligence, Nankai University, 300350 Tianjin, China
| | - Jia Wang
- Department of Computer Science and Technology, College of Computer Science
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston 77030, USA
| | - Yanbin Yin
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Han Zhang
- Department of Automation and Intelligence Science, College of Artificial Intelligence, Nankai University, 300350 Tianjin, China
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Abstract
Along with the progress of global aging, the prognosis of severe ischemic heart disease (IHD) remains poor, and thus the development of effective angiogenic therapy remains an important clinical unmet need. We have developed low-energy extracorporeal cardiac shock wave therapy as an innovative minimally invasive angiogenic therapy and confirmed its efficacy in a porcine chronic myocardial ischemia model in animal experiments as well as in patients with refractory angina. Since ultrasound is more advantageous for clinical application than shock waves, we then aimed to develop ultrasound therapy for IHD. We demonstrated that specific conditions of low-intensity pulsed ultrasound (LIPUS) therapy improve myocardial ischemia in animal models through the enhancement of angiogenesis mediated by endothelial mechanotransduction. To examine the effectiveness of our LIPUS therapy in patients with severe angina pectoris, we are now conducting a prospective multicenter clinical trial in Japan. Furthermore, to overcome the current serious situation of dementia pandemic but with no effective treatments worldwide, we have recently demonstrated that our LIPUS therapy also improves cognitive impairment in mouse models of Alzheimer's disease and vascular dementia. Here, we summarize the progress in our studies to develop angiogenic therapies with sound waves.
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Affiliation(s)
- Tomohiko Shindo
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiroaki Shimokawa
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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Da-Ano R, Masson I, Lucia F, Doré M, Robin P, Alfieri J, Rousseau C, Mervoyer A, Reinhold C, Castelli J, De Crevoisier R, Rameé JF, Pradier O, Schick U, Visvikis D, Hatt M. Performance comparison of modified ComBat for harmonization of radiomic features for multicenter studies. Sci Rep 2020; 10:10248. [PMID: 32581221 PMCID: PMC7314795 DOI: 10.1038/s41598-020-66110-w] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/04/2020] [Indexed: 11/08/2022] Open
Abstract
Multicenter studies are needed to demonstrate the clinical potential value of radiomics as a prognostic tool. However, variability in scanner models, acquisition protocols and reconstruction settings are unavoidable and radiomic features are notoriously sensitive to these factors, which hinders pooling them in a statistical analysis. A statistical harmonization method called ComBat was developed to deal with the "batch effect" in gene expression microarray data and was used in radiomics studies to deal with the "center-effect". Our goal was to evaluate modifications in ComBat allowing for more flexibility in choosing a reference and improving robustness of the estimation. Two modified ComBat versions were evaluated: M-ComBat allows to transform all features distributions to a chosen reference, instead of the overall mean, providing more flexibility. B-ComBat adds bootstrap and Monte Carlo for improved robustness in the estimation. BM-ComBat combines both modifications. The four versions were compared regarding their ability to harmonize features in a multicenter context in two different clinical datasets. The first contains 119 locally advanced cervical cancer patients from 3 centers, with magnetic resonance imaging and positron emission tomography imaging. In that case ComBat was applied with 3 labels corresponding to each center. The second one contains 98 locally advanced laryngeal cancer patients from 5 centers with contrast-enhanced computed tomography. In that specific case, because imaging settings were highly heterogeneous even within each of the five centers, unsupervised clustering was used to determine two labels for applying ComBat. The impact of each harmonization was evaluated through three different machine learning pipelines for the modelling step in predicting the clinical outcomes, across two performance metrics (balanced accuracy and Matthews correlation coefficient). Before harmonization, almost all radiomic features had significantly different distributions between labels. These differences were successfully removed with all ComBat versions. The predictive ability of the radiomic models was always improved with harmonization and the improved ComBat provided the best results. This was observed consistently in both datasets, through all machine learning pipelines and performance metrics. The proposed modifications allow for more flexibility and robustness in the estimation. They also slightly but consistently improve the predictive power of resulting radiomic models.
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Affiliation(s)
- R Da-Ano
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France.
| | - I Masson
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Department of Radiation Oncology, Institut de cancérologie de l'Ouest René-Gauducheau, Saint-Herblain, France
| | - F Lucia
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | - M Doré
- Department of Radiation Oncology, Institut de cancérologie de l'Ouest René-Gauducheau, Saint-Herblain, France
| | - P Robin
- Department of Nuclear Medicine, University of Brest, Brest, France
| | - J Alfieri
- Department of Radiation Oncology, McGill University Health Centre, Montreal, Quebec, Canada
| | - C Rousseau
- Department of Nuclear Medicine, Institut de cancerologie de l'Ouest René-Gauducheau, Saint-Herblain, France
- CRCINA, University of Nantes, INSERM UMR1232, CNRS-ERL6001, Nantes, France
| | - A Mervoyer
- Department of Radiation Oncology, Institut de cancérologie de l'Ouest René-Gauducheau, Saint-Herblain, France
| | - C Reinhold
- Department of Radiology, McGill University Health Centre, Montreal, Canada
| | - J Castelli
- Radiotherapy Department Cancer, Institute Eugene Marquis, Rennes, France
- University of Rennes 1, LTSI, Rennes, France
| | - R De Crevoisier
- Radiotherapy Department Cancer, Institute Eugene Marquis, Rennes, France
- University of Rennes 1, LTSI, Rennes, France
| | - J F Rameé
- Department of Medical Oncology, Centre Hospitalier de Vendee, La Roche sur Yon, France
| | - O Pradier
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | - U Schick
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
- Radiation Oncology Department, University Hospital, Brest, France
| | - D Visvikis
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
| | - M Hatt
- INSERM, UMR 1101, LaTIM, University of Brest, Brest, France
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Samaras P, Schmidt T, Frejno M, Gessulat S, Reinecke M, Jarzab A, Zecha J, Mergner J, Giansanti P, Ehrlich HC, Aiche S, Rank J, Kienegger H, Krcmar H, Kuster B, Wilhelm M. ProteomicsDB: a multi-omics and multi-organism resource for life science research. Nucleic Acids Res 2020; 48:D1153-D1163. [PMID: 31665479 PMCID: PMC7145565 DOI: 10.1093/nar/gkz974] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 11/22/2022] Open
Abstract
ProteomicsDB (https://www.ProteomicsDB.org) started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data. In this manuscript, we summarize new developments since the previous update that was published in Nucleic Acids Research in 2017. Over the past two years, we have enriched the data content by additional datasets and extended the platform to support protein turnover data. Another important new addition is that ProteomicsDB now supports the storage and visualization of data collected from other organisms, exemplified by Arabidopsis thaliana. Due to the generic design of ProteomicsDB, all analytical features available for the original human resource seamlessly transfer to other organisms. Furthermore, we introduce a new service in ProteomicsDB which allows users to upload their own expression datasets and analyze them alongside with data stored in ProteomicsDB. Initially, users will be able to make use of this feature in the interactive heat map functionality as well as the drug sensitivity prediction, but ultimately will be able to use all analytical features of ProteomicsDB in this way.
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Affiliation(s)
- Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,Innovation Center Network, SAP SE, Potsdam, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | | | | | - Johannes Rank
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Harald Kienegger
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Helmut Krcmar
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
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42
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Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, van der Kloet F, Harms AC, Balzano-Nogueira L, Lagani V, Tsamardinos I, Lappe M, Maier D, Westerhuis JA, Hankemeier T, Imhof A, Ballestar E, Mortazavi A, Merkenschlager M, Tegner J, Conesa A. STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse. Sci Data 2019; 6:256. [PMID: 31672995 PMCID: PMC6823427 DOI: 10.1038/s41597-019-0202-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/02/2019] [Indexed: 12/30/2022] Open
Abstract
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
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Affiliation(s)
- David Gomez-Cabrero
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Isabel Ferreirós-Vidal
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ricardo N Ramirez
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Carlos Company
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Andreas Schmidt
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Theo Reijmers
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Francesco Marabita
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Garcia-Gomez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Thomas Carroll
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Lee Cooper
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ziwei Liang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Frans van der Kloet
- Centre for Human Metabolomics, Faculty of Natural Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Leandro Balzano-Nogueira
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Vincenzo Lagani
- Computer Science Department, University of Crete, Heraklion, Greece
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia, United States
| | - Ioannis Tsamardinos
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia, United States
- Gnosis Data Analysis PC, Heraklion, Greece
| | - Michael Lappe
- QIAGEN Aarhus A/S, Silkeborgvej 2, 8000, Aarhus, Denmark
| | | | - Johan A Westerhuis
- Centre for Human Metabolomics, Faculty of Natural Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ali Mortazavi
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, Genetics Institute, University of Florida, Gainesville, Florida, USA.
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43
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Huang X, Gao J, Zhao Y, He M, Ke S, Wu J, Zhou Y, Fu H, Yang H, Chen C, Huang L. Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows. Front Microbiol 2019; 10:2123. [PMID: 31572329 PMCID: PMC6751307 DOI: 10.3389/fmicb.2019.02123] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Perinatal care is important in mammals due to its contribution to fetal growth, maternal health, and lactation. Substantial changes in host hormones, metabolism, and immunity around the parturition period may be accompanied by alterations in the gut microbiome. However, to our knowledge, changes in the gut microbiome and their contribution to the shifts in host metabolism around parturition have not been investigated in pigs. Furthermore, pigs are an ideal biomedical model for studying the interactions of the gut microbiota with host metabolism, due to the ease of controlling feeding conditions. Here we report dramatic remodeling of the gut microbiota and the potential functional capacity during the late stages of pregnancy (5 days before parturition, LP) to postpartum (within 6 h after delivery, PO) in both experimental and validated populations of sows (n = 107). The richness of bacteria in the gut of both pregnant and delivery sows significantly decreased, whilst the β-diversity dramatically expanded. The ratio of Bacteroidetes to Firmicutes, and the relative abundance of Prevotella significantly decreased, whilst the relative abundance of the predominant genus Lactobacillus significantly increased from LP to PO state. The predicted functional capacities of the gut microbiome related to amino acid metabolism, the metabolism of cofactors and vitamins, and glycan biosynthesis were significantly decreased from LP to PO state. However, the abundance of the functional capacities associated with carbohydrate and lipid metabolism were increased. Consistent with these changes, serum metabolites enriched at the LP stage were associated with the metabolism of amino acids and vitamins. In contrast, metabolites enriched at the PO stage were related to lipid metabolism. We further identified that the richness and β-diversity of the gut microbiota and the abundance of Lactobacillus accounted for shifts in the levels of bile acid metabolites associated with lipid metabolism. The results suggest that host-microbiota interactions during the perinatal period impact host metabolism. These benefit the lactation of sows by providing energy from lipid metabolism for milk production.
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Affiliation(s)
- Xiaochang Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jun Gao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuanzhang Zhao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shanlin Ke
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jinyuan Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yunyan Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hao Fu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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44
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Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TGP. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun 2019; 10:4128. [PMID: 31511524 PMCID: PMC6739408 DOI: 10.1038/s41467-019-12071-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/16/2019] [Indexed: 12/02/2022] Open
Abstract
Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.
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Affiliation(s)
- Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marie-Ming Aynaud
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Olivier Mirabeau
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Gal Mazor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mor Varon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Moritz Gartlgruber
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marlene Dallmayer
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Michaela C Baldauf
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefanie Stein
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital of Essen, Essen, Germany
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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45
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Sannino G, Marchetto A, Ranft A, Jabar S, Zacherl C, Alba-Rubio R, Stein S, Wehweck FS, Kiran MM, Hölting TLB, Musa J, Romero-Pérez L, Cidre-Aranaz F, Knott MML, Li J, Jürgens H, Sastre A, Alonso J, Da Silveira W, Hardiman G, Gerke JS, Orth MF, Hartmann W, Kirchner T, Ohmura S, Dirksen U, Grünewald TGP. Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients. EBioMedicine 2019; 47:156-162. [PMID: 31427232 PMCID: PMC6796576 DOI: 10.1016/j.ebiom.2019.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Up to 30-40% of Ewing sarcoma (EwS) patients with non-metastatic disease develop local or metastatic relapse within a time span of 2-10 years. This is in part caused by the absence of prognostic biomarkers that can identify high-risk patients and thus assign them to risk-adapted monitoring and treatment regimens. Since cancer stemness has been associated with tumour relapse and poor patient outcomes, we investigated in the current study the prognostic potential SOX2 (sex determining region Y box 2) - a major transcription factor involved in development and stemness - which was previously described to contribute to the undifferentiated phenotype of EwS. METHODS Two independent patient cohorts, one consisting of 189 retrospectively collected EwS tumours with corresponding mRNA expression data (test-cohort) and the other consisting of 141 prospectively collected formalin-fixed and paraffin-embedded resected tumours (validation and cohort), were employed to analyse SOX2 expression levels through DNA microarrays or immunohistochemistry, respectively, and to compare them with clinical parameters and patient outcomes. Two methods were employed to test the validity of the results at both the mRNA and protein levels. FINDINGS Both cohorts showed that only a subset of EwS patients (16-20%) expressed high SOX2 mRNA or protein levels, which significantly correlated with poor overall survival. Multivariate analyses of our validation-cohort revealed that high SOX2 expression represents a major risk-factor for poor survival (HR = 3·19; 95%CI 1·74-5·84; p < 0·01) that is independent from metastasis and other known clinical risk-factors at the time of diagnosis. Univariate analyses demonstrated that SOX2-high expression was correlated with tumour relapse (p = 0·002). The median first relapse was at 14·7 months (range: 3·5-180·7). INTERPRETATION High SOX2 expression constitutes an independent prognostic biomarker for EwS patients with poor outcomes. This may help to identify patients with localised disease who are at high risk for tumour relapse within the first two years after diagnosis. FUNDING The laboratory of T. G. P. Grünewald is supported by grants from the 'Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München (WiFoMed)', by LMU Munich's Institutional Strategy LMUexcellent within the framework of the German Excellence Initiative, the 'Mehr LEBEN für krebskranke Kinder - Bettina-Bräu-Stiftung', the Walter Schulz Foundation, the Wilhelm Sander-Foundation (2016.167.1), the Friedrich-Baur foundation, the Matthias-Lackas foundation, the Barbara & Hubertus Trettner foundation, the Dr. Leopold & Carmen Ellinger foundation, the Gert & Susanna Mayer foundation, the Deutsche Forschungsgemeinschaft (DFG 391665916), and by the German Cancer Aid (DKH-111886 and DKH-70112257). J. Li was supported by a scholarship of the China Scholarship Council (CSC), J. Musa was supported by a scholarship of the Kind-Philipp foundation, and T. L. B. Hölting by a scholarship of the German Cancer Aid. M. F. Orth and M. M. L. Knott were supported by scholarships of the German National Academic Foundation. G. Sannino was supported by a scholarship from the Fritz-Thyssen Foundation (FTF-40.15.0.030MN). The work of U. Dirksen is supported by grants from the German Cancer Aid (DKH-108128, DKH-70112018, and DKH-70113419), the ERA-Net-TRANSCAN consortium (project number 01KT1310), and Euro Ewing Consortium (EEC, project number EU-FP7 602,856), both funded under the European Commission Seventh Framework Program FP7-HEALTH (http://cordis.europa.eu/), the Barbara & Hubertus Trettner foundation, and the Gert & Susanna Mayer foundation. G. Hardiman was supported by grants from the National Science Foundation (SC EPSCoR) and National Institutes of Health (U01-DA045300). The laboratory of J. Alonso was supported by Instituto de Salud Carlos III (PI12/00816; PI16CIII/00026); Asociación Pablo Ugarte (TPY-M 1149/13; TRPV 205/18), ASION (TVP 141/17), Fundación Sonrisa de Alex & Todos somos Iván (TVP 1324/15).
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Affiliation(s)
- Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Andreas Ranft
- Department of Pediatrics III, West German Cancer Centre, University Hospital Essen, Essen, Germany
| | - Susanne Jabar
- Department of Pediatrics III, West German Cancer Centre, University Hospital Essen, Essen, Germany
| | - Constanze Zacherl
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rebeca Alba-Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefanie Stein
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Fabienne S Wehweck
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Merve M Kiran
- Department of Pathology, Medical Faculty, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Heribert Jürgens
- Department of Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Ana Sastre
- Unidad hemato-oncología pediátrica, Hospital Infantil Universitario La Paz, Madrid, Spain
| | - Javier Alonso
- Pediatric Solid Tumour Laboratory, Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), Spain
| | - Willian Da Silveira
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Gary Hardiman
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA; School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Wolfgang Hartmann
- Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Uta Dirksen
- Department of Pediatrics III, West German Cancer Centre, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), partner site Essen, Germany.
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Magee R, Londin E, Rigoutsos I. TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease. Parkinsonism Relat Disord 2019; 65:203-209. [PMID: 31402278 DOI: 10.1016/j.parkreldis.2019.05.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Parkinson's Disease (PD) is diagnosed clinically. Reliable non-invasive PD biomarkers are actively sought. Transfer RNAs produce short non-coding RNAs, the tRNA-derived fragments (tRF). tRF have been shown to play diverse roles, including in amyotrophic lateral sclerosis, and the response to ischemic stroke. Rich tRF populations are being reported in biofluids. We explored the possibility that tRF can serve as non-invasive biomarkers for PD. METHODS We collected existing RNA-seq samples and re-analyzed a total of 254 legacy datasets from 3 previous studies, from male and female PD patients and controls that belong to three categories: prefrontal cortex samples from 29 patients and 33 controls; cerebrospinal fluid (CSF) samples from 63 patients and 64 controls; and, serum samples from 34 patients and 31 controls. First, we identified tRF exhaustively and deterministically in every dataset. Second, we determined tRF that are differentially abundant (DA) between PD and control samples, using uncorrected t-tests. Lastly, we assessed all the DA tRF from the previous step with Partial Least Squares - Discriminant Analysis (PLS-DA) to stringently sub-select tRF that can distinguish PD patients from controls. RESULTS We show that PLS-DA identified tRF from prefrontal cortex, CSF, and serum that can distinguish PD patients from controls. A handful of identified tRF were previously investigated in neurological contexts. Signatures built from relatively few tRF suffice to distinguish PD from control in each category of samples with high sensitivity (89-100%) and specificity (79-98%). CONCLUSION tRF-based signatures are promising candidates that warrant further evaluation as non-invasive PD biomarkers.
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Affiliation(s)
- Rogan Magee
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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47
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Martinez-Romero J, Bueno-Fortes S, Martín-Merino M, Ramirez de Molina A, De Las Rivas J. Survival marker genes of colorectal cancer derived from consistent transcriptomic profiling. BMC Genomics 2018; 19:857. [PMID: 30537927 PMCID: PMC6288855 DOI: 10.1186/s12864-018-5193-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Identification of biomarkers associated with the prognosis of different cancer subtypes is critical to achieve better therapeutic assistance. In colorectal cancer (CRC) the discovery of stable and consistent survival markers remains a challenge due to the high heterogeneity of this class of tumors. In this work, we identified a new set of gene markers for CRC associated to prognosis and risk using a large unified cohort of patients with transcriptomic profiles and survival information. Results We built an integrated dataset with 1273 human colorectal samples, which provides a homogeneous robust framework to analyse genome-wide expression and survival data. Using this dataset we identified two sets of genes that are candidate prognostic markers for CRC in stages III and IV, showing either up-regulation correlated with poor prognosis or up-regulation correlated with good prognosis. The top 10 up-regulated genes found as survival markers of poor prognosis (i.e. low survival) were: DCBLD2, PTPN14, LAMP5, TM4SF1, NPR3, LEMD1, LCA5, CSGALNACT2, SLC2A3 and GADD45B. The stability and robustness of the gene survival markers was assessed by cross-validation, and the best-ranked genes were also validated with two external independent cohorts: one of microarrays with 482 samples; another of RNA-seq with 269 samples. Up-regulation of the top genes was also proved in a comparison with normal colorectal tissue samples. Finally, the set of top 100 genes that showed overexpression correlated with low survival was used to build a CRC risk predictor applying a multivariate Cox proportional hazards regression analysis. This risk predictor yielded an optimal separation of the individual patients of the cohort according to their survival, with a p-value of 8.25e-14 and Hazard Ratio 2.14 (95% CI: 1.75–2.61). Conclusions The results presented in this work provide a solid rationale for the prognostic utility of a new set of genes in CRC, demonstrating their potential to predict colorectal tumor progression and evolution towards poor survival stages. Our study does not provide a fixed gene signature for prognosis and risk prediction, but instead proposes a robust set of genes ranked according to their predictive power that can be selected for additional tests with other CRC clinical cohorts. Electronic supplementary material The online version of this article (10.1186/s12864-018-5193-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge Martinez-Romero
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.,Molecular Oncology and Nutritional Genomics of Cancer Group, Precision Nutrition and Cancer Program, IMDEA Food Institute (CEI, UAM/CSIC), Madrid, Spain
| | - Santiago Bueno-Fortes
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC) and University of Salamanca (USAL), Salamanca, Spain
| | - Manuel Martín-Merino
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.,Department of Computer Science, Universidad Pontificia de Salamanca (UPSA), Salamanca, Spain
| | - Ana Ramirez de Molina
- Molecular Oncology and Nutritional Genomics of Cancer Group, Precision Nutrition and Cancer Program, IMDEA Food Institute (CEI, UAM/CSIC), Madrid, Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.
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Rusilowicz MJ, Dickinson M, Charlton AJ, O’Keefe S, Wilson J. MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways. PLoS One 2018; 13:e0205968. [PMID: 30372459 PMCID: PMC6205582 DOI: 10.1371/journal.pone.0205968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 10/04/2018] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION Modern analytical techniques such as LC-MS, GC-MS and NMR are increasingly being used to study the underlying dynamics of biological systems by tracking changes in metabolite levels over time. Such techniques are capable of providing information on large numbers of metabolites simultaneously, a feature that is exploited in non-targeted studies. However, since the dynamics of specific metabolites are unlikely to be known a priori this presents an initial subjective challenge as to where the focus of the investigation should be. Whilst a number of feed-forward software tools are available for manipulation of metabolomic data, no tool centralizes on clustering and focus is typically directed by a workflow that is chosen in advance. RESULTS We present an interactive approach to time-course analyses and a complementary implementation in a software package, MetaboClust. This is presented through the analysis of two LC-MS time-course case studies on plants (Medicago truncatula and Alopecurus myosuroides). We demonstrate a dynamic, user-centric workflow to clustering with intrinsic visual feedback at all stages of analysis. The software is used to apply data correction, generate the time-profiles, perform exploratory statistical analysis and assign tentative metabolite identifications. Clustering is used to group metabolites in an unbiased manner, allowing pathway analysis to score metabolic pathways, based on their overlap with clusters showing interesting trends.
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Affiliation(s)
- Martin J. Rusilowicz
- Department of Computer Science, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | | | | | - Simon O’Keefe
- Department of Computer Science, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Mathematics, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
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49
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Zheng W, Zou Z, Lin S, Chen X, Wang F, Li X, Dai J. Identification and functional analysis of spermatogenesis‐associated gene modules in azoospermia by weighted gene coexpression network analysis. J Cell Biochem 2018; 120:3934-3944. [PMID: 30269365 DOI: 10.1002/jcb.27677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/21/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Wenzhong Zheng
- Department of Urology Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Zihao Zou
- Department of Urology The Third Affiliated Hospital of Guanzhou Medical University, Guanzhou Medical University Guanzhou China
| | - Shouren Lin
- Department of Reproductive Medicine Peking University Shenzhen Hospital Shenzhen China
| | - Xiang Chen
- Department of Urology Zhongshan Hospital, Fudan University Shanghai China
| | - Feixiang Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice Shanghai China
| | - Xianxin Li
- Department of Surgery Shenzhen Sun Yat‐Sen Cardiovascular Hospital Shenzhen China
| | - Jican Dai
- Department of Urology Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
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50
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Komor MA, Bosch LJ, Bounova G, Bolijn AS, Delis-van Diemen PM, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, van Grieken NC, Carvalho B, Wessels LF, Jimenez CR, Fijneman RJ, Meijer GA. Consensus molecular subtype classification of colorectal adenomas. J Pathol 2018; 246:266-276. [PMID: 29968252 PMCID: PMC6221003 DOI: 10.1002/path.5129] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/08/2018] [Accepted: 06/20/2018] [Indexed: 01/15/2023]
Abstract
Consensus molecular subtyping is an RNA expression‐based classification system for colorectal cancer (CRC). Genomic alterations accumulate during CRC pathogenesis, including the premalignant adenoma stage, leading to changes in RNA expression. Only a minority of adenomas progress to malignancies, a transition that is associated with specific DNA copy number aberrations or microsatellite instability (MSI). We aimed to investigate whether colorectal adenomas can already be stratified into consensus molecular subtype (CMS) classes, and whether specific CMS classes are related to the presence of specific DNA copy number aberrations associated with progression to malignancy. RNA sequencing was performed on 62 adenomas and 59 CRCs. MSI status was determined with polymerase chain reaction‐based methodology. DNA copy number was assessed by low‐coverage DNA sequencing (n = 30) or array‐comparative genomic hybridisation (n = 32). Adenomas were classified into CMS classes together with CRCs from the study cohort and from The Cancer Genome Atlas (n = 556), by use of the established CMS classifier. As a result, 54 of 62 (87%) adenomas were classified according to the CMS. The CMS3 ‘metabolic subtype’, which was least common among CRCs, was most prevalent among adenomas (n = 45; 73%). One of the two adenomas showing MSI was classified as CMS1 (2%), the ‘MSI immune’ subtype. Eight adenomas (13%) were classified as the ‘canonical’ CMS2. No adenomas were classified as the ‘mesenchymal’ CMS4, consistent with the fact that adenomas lack invasion‐associated stroma. The distribution of the CMS classes among adenomas was confirmed in an independent series. CMS3 was enriched with adenomas at low risk of progressing to CRC, whereas relatively more high‐risk adenomas were observed in CMS2. We conclude that adenomas can be stratified into the CMS classes. Considering that CMS1 and CMS2 expression signatures may mark adenomas at increased risk of progression, the distribution of the CMS classes among adenomas is consistent with the proportion of adenomas expected to progress to CRC. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Malgorzata A Komor
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Linda Jw Bosch
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gergana Bounova
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne S Bolijn
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pien M Delis-van Diemen
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian Rausch
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Youri Hoogstrate
- Department of Urology, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Guido Jenster
- Department of Urology, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Beatriz Carvalho
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk Fa Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Connie R Jimenez
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Remond Ja Fijneman
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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