1
|
Shen D, Lewinger JP. A Regularized Cox Hierarchical Model for Incorporating Annotation Information in Predictive Omic Studies. bioRxiv 2024:2024.03.09.584239. [PMID: 38617211 PMCID: PMC11014500 DOI: 10.1101/2024.03.09.584239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Background Associated with high-dimensional omics data there are often "meta-features" such as biological pathways and functional annotations, summary statistics from similar studies that can be informative for predicting an outcome of interest. We introduce a regularized hierarchical framework for integrating meta-features, with the goal of improving prediction and feature selection performance with time-to-event outcomes. Methods A hierarchical framework is deployed to incorporate meta-features. Regularization is applied to the omic features as well as the meta-features so that high-dimensional data can be handled at both levels. The proposed hierarchical Cox model can be efficiently fitted by a combination of iterative reweighted least squares and cyclic coordinate descent. Results In a simulation study we show that when the external meta-features are informative, the regularized hierarchical model can substantially improve prediction performance over standard regularized Cox regression. We illustrate the proposed model with applications to breast cancer and melanoma survival based on gene expression profiles, which show the improvement in prediction performance by applying meta-features, as well as the discovery of important omic feature sets with sparse regularization at meta-feature level. Conclusions The proposed hierarchical regularized regression model enables integration of external meta-feature information directly into the modeling process for time-to-event outcomes, improves prediction performance when the external meta-feature data is informative. Importantly, when the external meta-features are uninformative, the prediction performance based on the regularized hierarchical model is on par with standard regularized Cox regression, indicating robustness of the framework. In addition to developing predictive signatures, the model can also be deployed in discovery applications where the main goal is to identify important features associated with the outcome rather than developing a predictive model.
Collapse
Affiliation(s)
- Dixin Shen
- Clinical Data Science, Gilead Sciences, Foster City, USA
| | - Juan Pablo Lewinger
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA
| |
Collapse
|
2
|
Quinn TP, Hess JL, Marshe VS, Barnett MM, Hauschild AC, Maciukiewicz M, Elsheikh SSM, Men X, Schwarz E, Trakadis YJ, Breen MS, Barnett EJ, Zhang-James Y, Ahsen ME, Cao H, Chen J, Hou J, Salekin A, Lin PI, Nicodemus KK, Meyer-Lindenberg A, Bichindaritz I, Faraone SV, Cairns MJ, Pandey G, Müller DJ, Glatt SJ. A primer on the use of machine learning to distil knowledge from data in biological psychiatry. Mol Psychiatry 2024:10.1038/s41380-023-02334-2. [PMID: 38177352 DOI: 10.1038/s41380-023-02334-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024]
Abstract
Applications of machine learning in the biomedical sciences are growing rapidly. This growth has been spurred by diverse cross-institutional and interdisciplinary collaborations, public availability of large datasets, an increase in the accessibility of analytic routines, and the availability of powerful computing resources. With this increased access and exposure to machine learning comes a responsibility for education and a deeper understanding of its bases and bounds, borne equally by data scientists seeking to ply their analytic wares in medical research and by biomedical scientists seeking to harness such methods to glean knowledge from data. This article provides an accessible and critical review of machine learning for a biomedically informed audience, as well as its applications in psychiatry. The review covers definitions and expositions of commonly used machine learning methods, and historical trends of their use in psychiatry. We also provide a set of standards, namely Guidelines for REporting Machine Learning Investigations in Neuropsychiatry (GREMLIN), for designing and reporting studies that use machine learning as a primary data-analysis approach. Lastly, we propose the establishment of the Machine Learning in Psychiatry (MLPsych) Consortium, enumerate its objectives, and identify areas of opportunity for future applications of machine learning in biological psychiatry. This review serves as a cautiously optimistic primer on machine learning for those on the precipice as they prepare to dive into the field, either as methodological practitioners or well-informed consumers.
Collapse
Affiliation(s)
- Thomas P Quinn
- Applied Artificial Intelligence Institute (A2I2), Burwood, VIC, 3125, Australia
| | - Jonathan L Hess
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Victoria S Marshe
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada
| | - Michelle M Barnett
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, 2308, Australia
| | - Anne-Christin Hauschild
- Department of Medical Informatics, Medical University Center Göttingen, Göttingen, Lower Saxony, 37075, Germany
| | - Malgorzata Maciukiewicz
- Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
- Department of Rheumatology and Immunology, University Hospital Bern, Bern, 3010, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, 3010, Switzerland
| | - Samar S M Elsheikh
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada
| | - Xiaoyu Men
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Emanuel Schwarz
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany
| | - Yannis J Trakadis
- Department Human Genetics, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Michael S Breen
- Psychiatry, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric J Barnett
- Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Yanli Zhang-James
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mehmet Eren Ahsen
- Department of Business Administration, Gies College of Business, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Biomedical and Translational Sciences, Carle-Illinois School of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
| | - Han Cao
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany
| | - Junfang Chen
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany
| | - Jiahui Hou
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Asif Salekin
- Electrical Engineering and Computer Science, Syracuse University, Syracuse, NY, 13244, USA
| | - Ping-I Lin
- Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW, 2052, Australia
- Mental Health Research Unit, South Western Sydney Local Health District, Liverpool, NSW, 2170, Australia
| | | | - Andreas Meyer-Lindenberg
- Clinical Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany
| | - Isabelle Bichindaritz
- Biomedical and Health Informatics/Computer Science Department, State University of New York at Oswego, Oswego, NY, 13126, USA
- Intelligent Bio Systems Lab, State University of New York at Oswego, Oswego, NY, 13126, USA
| | - Stephen V Faraone
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, 2308, Australia
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel J Müller
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Stephen J Glatt
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Public Health and Preventive Medicine, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| |
Collapse
|
3
|
Chapfuwa P, Tao C, Li C, Khan I, Chandross KJ, Pencina MJ, Carin L, Henao R. Calibration and Uncertainty in Neural Time-to-Event Modeling. IEEE Trans Neural Netw Learn Syst 2023; 34:1666-1680. [PMID: 33119513 PMCID: PMC8439415 DOI: 10.1109/tnnls.2020.3029631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Models for predicting the time of a future event are crucial for risk assessment, across a diverse range of applications. Existing time-to-event (survival) models have focused primarily on preserving pairwise ordering of estimated event times (i.e., relative risk). We propose neural time-to-event models that account for calibration and uncertainty while predicting accurate absolute event times. Specifically, an adversarial nonparametric model is introduced for estimating matched time-to-event distributions for probabilistically concentrated and accurate predictions. We also consider replacing the discriminator of the adversarial nonparametric model with a survival-function matching estimator that accounts for model calibration. The proposed estimator can be used as a means of estimating and comparing conditional survival distributions while accounting for the predictive uncertainty of probabilistic models. Extensive experiments show that the distribution matching methods outperform existing approaches in terms of both calibration and concentration of time-to-event distributions.
Collapse
|
4
|
Yan T, Yan Z, Liu L, Zhang X, Chen G, Xu F, Li Y, Zhang L, Peng M, Wang L, Li D, Zhao D. Survival prediction for patients with glioblastoma multiforme using a Cox proportional hazards denoising autoencoder network. Front Comput Neurosci 2023; 16:916511. [PMID: 36704230 PMCID: PMC9871481 DOI: 10.3389/fncom.2022.916511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Objectives This study aimed to establish and validate a prognostic model based on magnetic resonance imaging and clinical features to predict the survival time of patients with glioblastoma multiforme (GBM). Methods In this study, a convolutional denoising autoencoder (DAE) network combined with the loss function of the Cox proportional hazard regression model was used to extract features for survival prediction. In addition, the Kaplan-Meier curve, the Schoenfeld residual analysis, the time-dependent receiver operating characteristic curve, the nomogram, and the calibration curve were performed to assess the survival prediction ability. Results The concordance index (C-index) of the survival prediction model, which combines the DAE and the Cox proportional hazard regression model, reached 0.78 in the training set, 0.75 in the validation set, and 0.74 in the test set. Patients were divided into high- and low-risk groups based on the median prognostic index (PI). Kaplan-Meier curve was used for survival analysis (p = < 2e-16 in the training set, p = 3e-04 in the validation set, and p = 0.007 in the test set), which showed that the survival probability of different groups was significantly different, and the PI of the network played an influential role in the prediction of survival probability. In the residual verification of the PI, the fitting curve of the scatter plot was roughly parallel to the x-axis, and the p-value of the test was 0.11, proving that the PI and survival time were independent of each other and the survival prediction ability of the PI was less affected than survival time. The areas under the curve of the training set were 0.843, 0.871, 0.903, and 0.941; those of the validation set were 0.687, 0.895, 1.000, and 0.967; and those of the test set were 0.757, 0.852, 0.683, and 0.898. Conclusion The survival prediction model, which combines the DAE and the Cox proportional hazard regression model, can effectively predict the prognosis of patients with GBM.
Collapse
Affiliation(s)
- Ting Yan
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhenpeng Yan
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Lili Liu
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoyu Zhang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Guohui Chen
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Feng Xu
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Ying Li
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Lijuan Zhang
- Shanxi Provincial People's Hospital, Taiyuan, China
| | - Meilan Peng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Lu Wang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dandan Li
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China,*Correspondence: Dandan Li ✉
| | - Dong Zhao
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China,Dong Zhao ✉
| |
Collapse
|
5
|
Bian Z, Chen J, Liu C, Ge Q, Zhang M, Meng J, Liang C. Landscape of the intratumroal microenvironment in bladder cancer: Implications for prognosis and immunotherapy. Comput Struct Biotechnol J 2022; 21:74-85. [PMID: 36514337 PMCID: PMC9730156 DOI: 10.1016/j.csbj.2022.11.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction This study aims to present the landscape of the intratumoral microenvironment and by which establish a classification system that can be used to predict the prognosis of bladder cancer patients and their response to anti-PD-L1 immunotherapy. Methods The expression profiles of 1554 bladder cancer cases were downloaded from seven public datasets. Single-sample gene set enrichment analysis (ssGSEA), univariate Cox regression analysis, and meta-analysis were employed to establish the bladder cancer immune prognostic index (BCIPI). Extensive analyses were executed to investigate the association between BCIPI and overall survival, tumor-infiltrated immunocytes, immunotherapeutic response, mutation load, etc. Results The results obtained from seven independent cohorts and meta-analyses suggested that the BCIPI is an effective classification system for estimating bladder cancer patients' overall survival. Patients in the BCIPI-High subgroup revealed different immunophenotypic outcomes from those in the BCIPI-Low subgroup regarding tumor-infiltrated immunocytes and mutated genes. Subsequent analysis suggested that patients in the BCIPI-High subgroup were more sensitive to anti-PD-L1 immunotherapy than those in the BCIPI-Low subgroup. Conclusions The newly established BCIPI is a valuable tool for predicting overall survival outcomes and immunotherapeutic responses in patients with bladder cancer.
Collapse
Key Words
- AJCC, American Joint Committee on Cancer
- Anti-PD-L1, Antitumor response to atezolizumab
- BCG, Bacillus Calmette-Guerin
- BCIPI, Bladder cancer immune prognostic index
- Bladder cancer
- CNVs, Copy number variations
- FDA, Food and Drug Administration
- FPKM, Fragments per kilobase per million
- Genomic
- ICI, Immune checkpoint inhibitor
- IHC, Immunohistochemistry
- Immunotherapy
- MES, Mesenchymal transition
- NES, Normalized enrichment score
- Overall survival
- RMA, Robust multiarray average
- RMS, Restricted mean survival
- TPM, Transcripts per kilobase million
- ssGSEA, Single-sample GSEA
Collapse
Affiliation(s)
- Zichen Bian
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jia Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Chang Liu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Qintao Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Corresponding authors at: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Corresponding authors at: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, China.
| |
Collapse
|
6
|
Lin B, Tan Z, Mo Y, Yang X, Liu Y, Xu B. Intelligent oncology: The convergence of artificial intelligence and oncology. Journal of the National Cancer Center 2022. [DOI: 10.1016/j.jncc.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
7
|
Ghosh Roy G, Geard N, Verspoor K, He S. MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk. Bioinformatics 2022; 38:5026-5032. [PMID: 36124954 DOI: 10.1093/bioinformatics/btac636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/04/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Survival risk prediction using gene expression data is important in making treatment decisions in cancer. Standard neural network (NN) survival analysis models are black boxes with a lack of interpretability. More interpretable visible neural network architectures are designed using biological pathway knowledge. But they do not model how pathway structures can change for particular cancer types. RESULTS We propose a novel Mutated Pathway Visible Neural Network (MPVNN) architecture, designed using prior signaling pathway knowledge and random replacement of known pathway edges using gene mutation data simulating signal flow disruption. As a case study, we use the PI3K-Akt pathway and demonstrate overall improved cancer-specific survival risk prediction of MPVNN over other similar-sized NN and standard survival analysis methods. We show that trained MPVNN architecture interpretation, which points to smaller sets of genes connected by signal flow within the PI3K-Akt pathway that is important in risk prediction for particular cancer types, is reliable. AVAILABILITY AND IMPLEMENTATION The data and code are available at https://github.com/gourabghoshroy/MPVNN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Gourab Ghosh Roy
- School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK.,School of Computing and Information Systems, University of Melbourne, Melbourne 3052, Australia
| | - Nicholas Geard
- School of Computing and Information Systems, University of Melbourne, Melbourne 3052, Australia
| | - Karin Verspoor
- School of Computing and Information Systems, University of Melbourne, Melbourne 3052, Australia.,School of Computing Technologies, RMIT University, Melbourne 3000, Australia
| | - Shan He
- School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
8
|
Yi Y, Xu T, Tan Y, Lv W, Zhao C, Wu M, Wu Y, Zhang Q. CCDC69 is a prognostic marker of breast cancer and correlates with tumor immune cell infiltration. Front Surg 2022; 9:879921. [PMID: 35910470 PMCID: PMC9334777 DOI: 10.3389/fsurg.2022.879921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Breast cancer (BC) is the most common malignancy and the leading cause of cancer-related death among women worldwide. Early detection, treatment, and metastasis monitoring are very important for the prognosis of BC patients. Therefore, effective biomarkers need to be explored to help monitor the prognosis of BC patients and guide treatment decisions. Methods In this study, the relationship between CCDC69 expression levels and tumor clinical characteristics were analyzed using RNA-seq information in BC samples from the TCGA database. Kaplan-Meier survival analysis was performed to analyze the prognostic value of CCDC69 in BC patients. Besides, gene enrichment analysis in BC samples was used to confirm the main function of CCDC69 in BC. The correlation between the expression of CCDC69 and the number of tumor-infiltrating lymphocytes was confirmed by interaction analysis of TIMER and GEPIA. Results The results showed that CCDC69 expression was significantly lower in cancer samples than in normal tissues, and was significantly lower in highly invasive BC than in carcinoma in situ. Meanwhile, low levels of CCDC69 were associated with a further poor prognosis. CDCC69 expression was positively correlated with the amount of different tumor-infiltrating lymphocytes. Mechanically, it could be presumed that the low expression of CCDC69 in BC might be caused by hypermethylation of the promoter region. Conclusions Summarily, CDCC69 could be used as a potential biomarker to predict the prognosis of BC and the sensitivity to immunotherapy such as PD-1/PD-L1 checkpoint inhibitors.
Collapse
Affiliation(s)
- Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufang Tan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenchang Lv
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chongru Zhao
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Correspondence: Yiping Wu Qi Zhang
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Correspondence: Yiping Wu Qi Zhang
| |
Collapse
|
9
|
Murashova GA, Colbry D. GM FASST: General Method for Labeling Augmented Sub-sampled Images from a Small Data Set for Transfer Learning. Machine Learning with Applications 2021. [DOI: 10.1016/j.mlwa.2021.100168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
10
|
Wu W, Jia L, Zhang Y, Zhao J, Dong Y, Qiang Y. Exploration of the prognostic signature reflecting tumor microenvironment of lung adenocarcinoma based on immunologically relevant genes. Bioengineered 2021; 12:7417-7431. [PMID: 34612148 PMCID: PMC8806418 DOI: 10.1080/21655979.2021.1974779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lung adenocarcinoma (LUAD) represents the major histological type of lung cancer with high mortality globally. Due to the heterogeneous nature, the same treatment strategy to various patients may result in different therapeutic responses. Hence, we aimed to elaborate an effective signature for predicting patient survival outcomes. The TCGA-LUAD cohort from the TCGA portal was used as a training dataset. The GSE26939 and GSE68465 cohorts from the GEO database were taken as validation datasets. All immunologically relevant genes were extracted from the ImmPort. The ESTIMATE algorithm was employed to explore LUAD microenvironment in the training dataset. Further, the DEGs were picked out based on the immune-associated genes reflecting different statuses in the immune context of TME. Univariate/multivariate Cox regression was performed to determine six prognosis- specific genes (PIK3CG, BTK, VEGFD, INHA, INSL4, and PTPRC) and established a risk predictive signature. The time-dependent ROC indicated that AUC values were all greater than 0.70 at 1-, 3-, and 5- year intervals. Corresponding RiskScore of each LUAD patient was calculated from the signature, and they were stratified into the high- and low-risk groups by the median value of RiskScore. K-M curves and Log-rank test demonstrated significant survival differences between the two groups (P < 0.05). Similar results were exhibited in the validation datasets. The RiskScore was incredibly relevant to clinicopathological factors like gender, AJCC stage, and T stage. Also, it can mirror the distribution state of 15 kinds of TIICs and have some predictive value for the sensitivity of therapeutic drugs.
Collapse
Affiliation(s)
- Wei Wu
- Department of Physiology, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, (Shanxi Medical University), Ministry of Education, Taiyuan, China.,Key Laboratory of Cellular Physiology, Shanxi Province, Taiyuan, China
| | - Liye Jia
- College of Information and Computer, Taiyuan University of Technology, Taiyuan,China
| | - Yanan Zhang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan,China
| | - Juanjuan Zhao
- College of Information and Computer, Taiyuan University of Technology, Taiyuan,China
| | - Yunyun Dong
- School of Software, Taiyuan University of Technology, Taiyuan, China
| | - Yan Qiang
- Department of Physiology, Shanxi Medical University, Taiyuan, China
| |
Collapse
|
11
|
Tsopra R, Fernandez X, Luchinat C, Alberghina L, Lehrach H, Vanoni M, Dreher F, Sezerman OU, Cuggia M, de Tayrac M, Miklasevics E, Itu LM, Geanta M, Ogilvie L, Godey F, Boldisor CN, Campillo-Gimenez B, Cioroboiu C, Ciusdel CF, Coman S, Hijano Cubelos O, Itu A, Lange B, Le Gallo M, Lespagnol A, Mauri G, Soykam HO, Rance B, Turano P, Tenori L, Vignoli A, Wierling C, Benhabiles N, Burgun A. A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. BMC Med Inform Decis Mak 2021; 21:274. [PMID: 34600518 PMCID: PMC8487519 DOI: 10.1186/s12911-021-01634-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/22/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Artificial intelligence (AI) has the potential to transform our healthcare systems significantly. New AI technologies based on machine learning approaches should play a key role in clinical decision-making in the future. However, their implementation in health care settings remains limited, mostly due to a lack of robust validation procedures. There is a need to develop reliable assessment frameworks for the clinical validation of AI. We present here an approach for assessing AI for predicting treatment response in triple-negative breast cancer (TNBC), using real-world data and molecular -omics data from clinical data warehouses and biobanks. METHODS The European "ITFoC (Information Technology for the Future Of Cancer)" consortium designed a framework for the clinical validation of AI technologies for predicting treatment response in oncology. RESULTS This framework is based on seven key steps specifying: (1) the intended use of AI, (2) the target population, (3) the timing of AI evaluation, (4) the datasets used for evaluation, (5) the procedures used for ensuring data safety (including data quality, privacy and security), (6) the metrics used for measuring performance, and (7) the procedures used to ensure that the AI is explainable. This framework forms the basis of a validation platform that we are building for the "ITFoC Challenge". This community-wide competition will make it possible to assess and compare AI algorithms for predicting the response to TNBC treatments with external real-world datasets. CONCLUSIONS The predictive performance and safety of AI technologies must be assessed in a robust, unbiased and transparent manner before their implementation in healthcare settings. We believe that the consideration of the ITFoC consortium will contribute to the safe transfer and implementation of AI in clinical settings, in the context of precision oncology and personalized care.
Collapse
Affiliation(s)
- Rosy Tsopra
- Centre de Recherche Des Cordeliers, Inserm, Université de Paris, Sorbonne Université, 75006, Paris, France. .,Inria, HeKA, Inria Paris, France. .,Department of Medical Informatics, Hôpital Européen Georges-Pompidou, AP-HP, Paris, France. .,Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, 35000, Rennes, France.
| | | | - Claudio Luchinat
- Centro Risonanze Magnetiche - CERM/CIRMMP and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino (Florence), Italy
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano Bicocca and ISBE-Italy/SYSBIO - Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano Bicocca and ISBE-Italy/SYSBIO - Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | | | - O Ugur Sezerman
- School of Medicine Biostatistics and Medical Informatics Dept., Acibadem University, Istanbul, Turkey
| | - Marc Cuggia
- Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, 35000, Rennes, France
| | - Marie de Tayrac
- Univ Rennes, Department of Molecular Genetics and Genomics, CHU Rennes, IGDR-UMR6290, CNRS, 35000, Rennes, France
| | | | | | - Marius Geanta
- Centre for Innovation in Medicine, Bucharest, Romania
| | - Lesley Ogilvie
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Florence Godey
- INSERM U1242 « Chemistry, Oncogenesis Stress Signaling », Université de Rennes, 35042, CEDEX, Rennes, France.,Centre de Lutte Contre Le Cancer Eugène Marquis, CRB Santé (BRIF Number: BB-0033-00056), 35042, CEDEX, Rennes, France
| | | | | | | | | | - Simona Coman
- Transilvania University of Brasov, Brasov, Romania
| | | | - Alina Itu
- Transilvania University of Brasov, Brasov, Romania
| | - Bodo Lange
- Alacris Theranostics GmbH, Berlin, Germany
| | - Matthieu Le Gallo
- INSERM U1242 « Chemistry, Oncogenesis Stress Signaling », Université de Rennes, 35042, CEDEX, Rennes, France.,Centre de Lutte Contre Le Cancer Eugène Marquis, CRB Santé (BRIF Number: BB-0033-00056), 35042, CEDEX, Rennes, France
| | - Alexandra Lespagnol
- Department of Molecular Genetics and Genomics, CHU Rennes, 35000, Rennes, France
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communication, University of Milano Bicocca and ISBE-Italy/SYSBIO - Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | | | - Bastien Rance
- Centre de Recherche Des Cordeliers, Inserm, Université de Paris, Sorbonne Université, 75006, Paris, France.,Inria, HeKA, Inria Paris, France.,Department of Medical Informatics, Hôpital Européen Georges-Pompidou, AP-HP, Paris, France
| | - Paola Turano
- Centro Risonanze Magnetiche - CERM/CIRMMP and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino (Florence), Italy
| | - Leonardo Tenori
- Centro Risonanze Magnetiche - CERM/CIRMMP and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino (Florence), Italy
| | - Alessia Vignoli
- Centro Risonanze Magnetiche - CERM/CIRMMP and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino (Florence), Italy
| | | | - Nora Benhabiles
- Direction de La Recherche Fondamentale (DRF), CEA, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Anita Burgun
- Centre de Recherche Des Cordeliers, Inserm, Université de Paris, Sorbonne Université, 75006, Paris, France.,Inria, HeKA, Inria Paris, France.,Department of Medical Informatics, Hôpital Européen Georges-Pompidou, AP-HP, Paris, France.,PaRis Artificial Intelligence Research InstitutE (Prairie), Paris, France
| |
Collapse
|
12
|
Susini T, Saccardin G, Renda I, Giani M, Tartarotti E, Nori J, Vanzi E, Pasqualini E, Bianchi S. Immunohistochemical Evaluation of FGD3 Expression: A New Strong Prognostic Factor in Invasive Breast Cancer. Cancers (Basel) 2021; 13:cancers13153824. [PMID: 34359725 PMCID: PMC8345064 DOI: 10.3390/cancers13153824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/17/2021] [Accepted: 07/25/2021] [Indexed: 12/14/2022] Open
Abstract
Among new prognostic factors for breast cancer, the most promising one seems to be FGD3 (Facio-Genital Dysplasia 3) gene, whose expression improves outcome by inhibiting cell migration. The aim of the study was to evaluate the prognostic role of FGD3 in invasive breast cancer in a series of 401 women, treated at our unit, by evaluating the expression of this gene by immunohistochemistry. Patients with high FGD3 expression showed a significantly better disease-free survival (DFS) (p < 0.001) and overall survival (OS) (p < 0.001). The prognostic value of FGD3 expression was stronger than that of classical pathologic parameters such as histological grade of differentiation, Ki-67 index and molecular subtype. By multivariate Cox analysis, FGD3 expression was confirmed as significant and independent prognostic factor, ranking second after age at diagnosis (≤40 years) for DFS (p = 0.003) and the second strongest predictor of OS, after AJCC Stage (p < 0.001). Our data suggest that inclusion of FGD3 evaluation in the routine workup of breast cancer patients may result in a more accurate stratification of the individual risk. The possibility to assess FGD3 expression by a simple and cheap technique such as immunohistochemistry may enhance the spread of its use in the clinical practice.
Collapse
Affiliation(s)
- Tommaso Susini
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (G.S.); (I.R.); (M.G.); (E.T.)
- Correspondence: ; Tel.: +39-055-275-1752
| | - Giulia Saccardin
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (G.S.); (I.R.); (M.G.); (E.T.)
| | - Irene Renda
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (G.S.); (I.R.); (M.G.); (E.T.)
| | - Milo Giani
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (G.S.); (I.R.); (M.G.); (E.T.)
| | - Enrico Tartarotti
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (G.S.); (I.R.); (M.G.); (E.T.)
| | - Jacopo Nori
- Diagnostic Senology Unit, Azienda Ospedaliero-Universitaria Careggi, 50134 Florence, Italy; (J.N.); (E.V.)
| | - Ermanno Vanzi
- Diagnostic Senology Unit, Azienda Ospedaliero-Universitaria Careggi, 50134 Florence, Italy; (J.N.); (E.V.)
| | - Elisa Pasqualini
- Pathology Unit, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (E.P.); (S.B.)
| | - Simonetta Bianchi
- Pathology Unit, Department of Health Sciences, University of Florence, 50134 Florence, Italy; (E.P.); (S.B.)
| |
Collapse
|
13
|
Zhu K, Cai L, Cui C, de Los Toyos JR, Anastassiou D. Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts. PLoS Comput Biol 2021; 17:e1009228. [PMID: 34283835 DOI: 10.1371/journal.pcbi.1009228] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/30/2021] [Accepted: 06/30/2021] [Indexed: 01/01/2023] Open
Abstract
During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance to therapy in multiple cancer types, characterized by a gene expression signature with prominent presence of genes COL11A1, THBS2 and INHBA. Identifying the underlying biological mechanisms responsible for their creation may facilitate the discovery of targets for potential pan-cancer therapeutics. Using a novel computational approach for single-cell gene expression data analysis identifying the dominant cell populations in a sequence of samples from patients at various stages, we conclude that these fibroblasts are produced by a pan-cancer cellular transition originating from a particular type of adipose-derived stromal cells naturally present in the stromal vascular fraction of normal adipose tissue, having a characteristic gene expression signature. Focusing on a rich pancreatic cancer dataset, we provide a detailed description of the continuous modification of the gene expression profiles of cells as they transition from APOD-expressing adipose-derived stromal cells to COL11A1-expressing cancer-associated fibroblasts, identifying the key genes that participate in this transition. These results also provide an explanation to the well-known fact that the adipose microenvironment contributes to cancer progression.
Collapse
|
14
|
Kwon Y, Kim JR, Park YM, Choi BK, Kim C, Young Kim H, Yoon M. Predicting survival time of Korean hepatocellular carcinoma patients using the Cox proportional hazards model: a retrospective study based on big data analysis. Eur J Gastroenterol Hepatol 2021; 33:1001-1008. [PMID: 33470702 DOI: 10.1097/meg.0000000000002058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIM To predict survival time of Korean hepatocellular carcinoma (HCC) patients by analyzing big data using Cox proportional hazards model. METHODS Big data of the patients who underwent treatment for HCC from 2008 to 2015, provided by Korea Central Cancer Registry, National Cancer Center, and Ministry of Health and Welfare, were analyzed. A total of 10 742 patients with HCC were divided into two groups, with Group I (3021 patients) confirmed on biopsy and Group II (5563 patients) diagnosed as HCC according to HCC diagnostic criteria as outlined in Korean Liver Cancer Association guidelines. Univariate and multivariate Cox regression analyses were performed to identify independent risk factors of recurrence after treatment and survival status. RESULTS A total of 3021 patients in Group I and 5563 patients in Group II were included in the study and the difference in survival time between the two groups was statistically significant (P < 0.05). Recurrence was only included in intrahepatic cases, and the rates were 21.2 and 19.8% while the periods from the first treatment to recurrence were 15.57 and 14.19 months, respectively. Age, diabetes, BMI, platelet, alpha-fetoprotein, histologic tumor maximum size, imaging T stage, presence of recurrence, and duration of recurrence were included in multivariate analysis. CONCLUSION By using nationwide, multicenter big data, it is possible to predict recurrence rate and survival time which can provide the basis for treatment response to develop a predictive program.
Collapse
Affiliation(s)
- Yujin Kwon
- Department of Surgery, Seoul Medical Center, Seoul, Korea
| | - Jae Ri Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Pusan National University College of Medicine, Busan, Korea
| | - Young Mok Park
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Pusan National University College of Medicine, Busan, Korea
| | - Byung Kwan Choi
- Department of Neurosurgery, Pusan National University College of Medicine, Busan, Korea
| | - Choongrak Kim
- Department of Statistics, Pusan National University, Busan, Korea
| | - Hae Young Kim
- Division of Pediatric Surgery, Department of Surgery, Pusan National University College of Medicine, Busan, Korea
| | - Myunghee Yoon
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Pusan National University College of Medicine, Busan, Korea
| |
Collapse
|
15
|
Kalakoti Y, Yadav S, Sundar D. SurvCNN: A Discrete Time-to-Event Cancer Survival Estimation Framework Using Image Representations of Omics Data. Cancers (Basel) 2021; 13:3106. [PMID: 34206288 DOI: 10.3390/cancers13133106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
The utility of multi-omics in personalized therapy and cancer survival analysis has been debated and demonstrated extensively in the recent past. Most of the current methods still suffer from data constraints such as high-dimensionality, unexplained interdependence, and subpar integration methods. Here, we propose SurvCNN, an alternative approach to process multi-omics data with robust computer vision architectures, to predict cancer prognosis for Lung Adenocarcinoma patients. Numerical multi-omics data were transformed into their image representations and fed into a Convolutional Neural network with a discrete-time model to predict survival probabilities. The framework also dichotomized patients into risk subgroups based on their survival probabilities over time. SurvCNN was evaluated on multiple performance metrics and outperformed existing methods with a high degree of confidence. Moreover, comprehensive insights into the relative performance of various combinations of omics datasets were probed. Critical biological processes, pathways and cell types identified from downstream processing of differentially expressed genes suggested that the framework could elucidate elements detrimental to a patient's survival. Such integrative models with high predictive power would have a significant impact and utility in precision oncology.
Collapse
|
16
|
Uzunangelov V, Wong CK, Stuart JM. Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PLoS Comput Biol 2021; 17:e1008878. [PMID: 33861732 PMCID: PMC8081343 DOI: 10.1371/journal.pcbi.1008878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/28/2021] [Accepted: 03/15/2021] [Indexed: 02/03/2023] Open
Abstract
Advancements in sequencing have led to the proliferation of multi-omic profiles of human cells under different conditions and perturbations. In addition, many databases have amassed information about pathways and gene "signatures"-patterns of gene expression associated with specific cellular and phenotypic contexts. An important current challenge in systems biology is to leverage such knowledge about gene coordination to maximize the predictive power and generalization of models applied to high-throughput datasets. However, few such integrative approaches exist that also provide interpretable results quantifying the importance of individual genes and pathways to model accuracy. We introduce AKLIMATE, a first kernel-based stacked learner that seamlessly incorporates multi-omics feature data with prior information in the form of pathways for either regression or classification tasks. AKLIMATE uses a novel multiple-kernel learning framework where individual kernels capture the prediction propensities recorded in random forests, each built from a specific pathway gene set that integrates all omics data for its member genes. AKLIMATE has comparable or improved performance relative to state-of-the-art methods on diverse phenotype learning tasks, including predicting microsatellite instability in endometrial and colorectal cancer, survival in breast cancer, and cell line response to gene knockdowns. We show how AKLIMATE is able to connect feature data across data platforms through their common pathways to identify examples of several known and novel contributors of cancer and synthetic lethality.
Collapse
Affiliation(s)
- Vladislav Uzunangelov
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, United States of America
| | - Christopher K. Wong
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, United States of America
| | - Joshua M. Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, United States of America
- * E-mail:
| |
Collapse
|
17
|
Ferro S, Bottigliengo D, Gregori D, Fabricio ASC, Gion M, Baldi I. Phenomapping of Patients with Primary Breast Cancer Using Machine Learning-Based Unsupervised Cluster Analysis. J Pers Med 2021; 11:272. [PMID: 33916398 DOI: 10.3390/jpm11040272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Primary breast cancer (PBC) is a heterogeneous disease at the clinical, histopathological, and molecular levels. The improved classification of PBC might be important to identify subgroups of the disease, relevant to patient management. Machine learning algorithms may allow a better understanding of the relationships within heterogeneous clinical syndromes. This work aims to show the potential of unsupervised learning techniques for improving classification in PBC. A dataset of 712 women with PBC is used as a motivating example. A set of variables containing biological prognostic parameters is considered to define groups of individuals. Four different clustering methods are used: K-means, self-organising maps, hierarchical agglomerative (HAC), and Gaussian mixture models clustering. HAC outperforms the other clustering methods. With an optimal partitioning parameter, the methods identify two clusters with different clinical profiles. Patients in the first cluster are younger and have lower values of the oestrogen receptor (ER) and progesterone receptor (PgR) than patients in the second cluster. Moreover, cathepsin D values are lower in the first cluster. The three most important variables identified by the HAC are: age, ER, and PgR. Unsupervised learning seems a suitable alternative for the analysis of PBC data, opening up new perspectives in the particularly active domain of dissecting clinical heterogeneity.
Collapse
|
18
|
Sayaman RW, Saad M, Thorsson V, Hu D, Hendrickx W, Roelands J, Porta-Pardo E, Mokrab Y, Farshidfar F, Kirchhoff T, Sweis RF, Bathe OF, Heimann C, Campbell MJ, Stretch C, Huntsman S, Graff RE, Syed N, Radvanyi L, Shelley S, Wolf D, Marincola FM, Ceccarelli M, Galon J, Ziv E, Bedognetti D. Germline genetic contribution to the immune landscape of cancer. Immunity 2021; 54:367-386.e8. [PMID: 33567262 DOI: 10.1016/j.immuni.2021.01.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 10/14/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023]
Abstract
Understanding the contribution of the host's genetic background to cancer immunity may lead to improved stratification for immunotherapy and to the identification of novel therapeutic targets. We investigated the effect of common and rare germline variants on 139 well-defined immune traits in ∼9000 cancer patients enrolled in TCGA. High heritability was observed for estimates of NK cell and T cell subset infiltration and for interferon signaling. Common variants of IFIH1, TMEM173 (STING1), and TMEM108 were associated with differential interferon signaling and variants mapping to RBL1 correlated with T cell subset abundance. Pathogenic or likely pathogenic variants in BRCA1 and in genes involved in telomere stabilization and Wnt-β-catenin also acted as immune modulators. Our findings provide evidence for the impact of germline genetics on the composition and functional orientation of the tumor immune microenvironment. The curated datasets, variants, and genes identified provide a resource toward further understanding of tumor-immune interactions.
Collapse
Affiliation(s)
- Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | | | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wouter Hendrickx
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Jessica Roelands
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Center (BSC); Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08034 Barcelona, Catalonia, Spain
| | - Younes Mokrab
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Weill Cornell Medicine, Doha, Qatar
| | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada; Department of Biomedical Data Science and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Tenaya Therapeutics, South San Francisco, CA 94080, USA
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York University Langone Health, New York, NY 10016, USA
| | - Randy F Sweis
- Department of Medicine, Section of Hematology/Oncology, Committee on Clinical Pharmacology and Pharmacogenomics, Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Oliver F Bathe
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada; Department of Surgery, University of Calgary, Calgary, Alberta AB T2N 4N1, Canada
| | | | - Michael J Campbell
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cynthia Stretch
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada
| | - Scott Huntsman
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Najeeb Syed
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Simon Shelley
- Department of Research and Development, Leukemia Therapeutics, LLC, Hull, MA 02045, USA
| | - Denise Wolf
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II," 80128 Naples, Italy; Istituto di Ricerche Genetiche "G. Salvatore," Biogem s.c.ar.l., 83031 Ariano Irpino, Italy
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre Le Cancer, Centre de Recherche de Cordeliers, Université de Paris, Sorbonne Université, Paris, France
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Davide Bedognetti
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, 16132 Genoa, Italy.
| |
Collapse
|
19
|
Wang G, Anastassiou D. Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis. Sci Rep 2020; 10:17199. [PMID: 33057153 PMCID: PMC7566486 DOI: 10.1038/s41598-020-74276-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
AbstractAnalysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.
Collapse
|
20
|
Jing B, Deng Y, Zhang T, Hou D, Li B, Qiang M, Liu K, Ke L, Li T, Sun Y, Lv X, Li C. Deep learning for risk prediction in patients with nasopharyngeal carcinoma using multi-parametric MRIs. Comput Methods Programs Biomed 2020; 197:105684. [PMID: 32781421 DOI: 10.1016/j.cmpb.2020.105684] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Magnetic resonance images (MRI) is the main diagnostic tool for risk stratification and treatment decision in nasopharyngeal carcinoma (NPC). However, the holistic feature information of multi-parametric MRIs has not been fully exploited by clinicians to accurately evaluate patients. OBJECTIVE To help clinicians fully utilize the missed information to regroup patients, we built an end-to-end deep learning model to extract feature information from multi-parametric MRIs for predicting and stratifying the risk scores of NPC patients. METHODS In this paper, we proposed an end-to-end multi-modality deep survival network (MDSN) to precisely predict the risk of disease progression of NPC patients. Extending from 3D dense net, this proposed MDSN extracted deep representation from multi-parametric MRIs (T1w, T2w, and T1c). Moreover, deep features and clinical stages were integrated through MDSN to more accurately predict the overall risk score (ORS) of individual NPC patient. RESULT A total of 1,417 individuals treated between January 2012 and December 2014 were included for training and validating the end-to-end MDSN. Results were then tested in a retrospective cohort of 429 patients included in the same institution. The C-index of the proposed method with or without clinical stages was 0.672 and 0.651 on the test set, respectively, which was higher than the that of the stage grouping (0.610). CONCLUSIONS The C-index of the model which integrated clinical stages with deep features is 0.062 higher than that of stage grouping alone (0.672 vs 0.610). We conclude that features extracted from multi-parametric MRIs based on MDSN can well assist the clinical stages in regrouping patients.
Collapse
Affiliation(s)
- Bingzhong Jing
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Yishu Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Tao Zhang
- Guangzhou Deepaint intelligence Tenchnology Co.Ltd., Guangzhou 510060, China
| | - Dan Hou
- Guangzhou Deepaint intelligence Tenchnology Co.Ltd., Guangzhou 510060, China
| | - Bin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Mengyun Qiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Kuiyuan Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Liangru Ke
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Radiology, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Taihe Li
- Shenzhen Annet Information System Co.LTD., Guangzhou 510060, China
| | - Ying Sun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Radiotherapy, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Xing Lv
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China.
| | - Chaofeng Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China.
| |
Collapse
|
21
|
Wu M, Hu W, Wang G, Yao Y, Yu XF. Nicotinamide N-Methyltransferase Is a Prognostic Biomarker and Correlated With Immune Infiltrates in Gastric Cancer. Front Genet 2020; 11:580299. [PMID: 33193702 PMCID: PMC7655872 DOI: 10.3389/fgene.2020.580299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is the third most common cause of cancer-related death in the word. Immunotherapy is a promising treatment of cancer. However, it is unclear which GC subpopulation would benefit most from immunotherapy and it is necessary to develop effective biomarkers for predicting immunotherapy response. Nicotinamide N-methyltransferase (NNMT) is a metabolic regulator of cancer-associated fibroblast (CAF) differentiation and cancer progression. In this study, we explored the correlations of NNMT to tumor-infiltrating immune cells (TIICs) and immune marker sets in The Cancer Genome Atlas Stomach Adenocarcinoma STAD (TCGA-STAD). Subsequently, we screened the NNMT correlated genes and performed the enrichment analysis of these genes. We eventually predicted the 19 most potential small-molecule drugs using the connectivity map (CMap) and Comparative Toxicogenomics Database (CTD). Also, nadolol, tranexamic acid, felbinac and dapsone were considered the four most promising drugs for GC. In summary, NNMT can be used as a prognostic biomarker that reflect immune infiltration level and a novel therapeutic target in GC.
Collapse
Affiliation(s)
- Miaowei Wu
- Cancer Institute, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Weilei Hu
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Guosheng Wang
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihan Yao
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Fang Yu
- Cancer Institute, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
22
|
Srijakotre N, Liu HJ, Nobis M, Man J, Yip HYK, Papa A, Abud HE, Anderson KI, Welch HCE, Tiganis T, Timpson P, McLean CA, Ooms LM, Mitchell CA. PtdIns(3,4,5)P 3-dependent Rac exchanger 1 (P-Rex1) promotes mammary tumor initiation and metastasis. Proc Natl Acad Sci U S A 2020; 117:28056-67. [PMID: 33097662 DOI: 10.1073/pnas.2006445117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Rac-GEF, P-Rex1, activates Rac1 signaling downstream of G protein-coupled receptors and PI3K. Increased P-Rex1 expression promotes melanoma progression; however, its role in breast cancer is complex, with differing reports of the effect of its expression on disease outcome. To address this we analyzed human databases, undertook gene array expression analysis, and generated unique murine models of P-Rex1 gain or loss of function. Analysis of PREX1 mRNA expression in breast cancer cDNA arrays and a METABRIC cohort revealed that higher PREX1 mRNA in ER+ve/luminal tumors was associated with poor outcome in luminal B cancers. Prex1 deletion in MMTV-neu or MMTV-PyMT mice reduced Rac1 activation in vivo and improved survival. High level MMTV-driven transgenic PREX1 expression resulted in apicobasal polarity defects and increased mammary epithelial cell proliferation associated with hyperplasia and development of de novo mammary tumors. MMTV-PREX1 expression in MMTV-neu mice increased tumor initiation and enhanced metastasis in vivo, but had no effect on primary tumor growth. Pharmacological inhibition of Rac1 or MEK1/2 reduced P-Rex1-driven tumoroid formation and cell invasion. Therefore, P-Rex1 can act as an oncogene and cooperate with HER2/neu to enhance breast cancer initiation and metastasis, despite having no effect on primary tumor growth.
Collapse
|
23
|
Xu XY, Guo WJ, Pan SH, Zhang Y, Gao FL, Wang JT, Zhang S, Li HY, Wang R, Zhang X. TILRR (FREM1 isoform 2) is a prognostic biomarker correlated with immune infiltration in breast cancer. Aging (Albany NY) 2020; 12:19335-19351. [PMID: 33031059 PMCID: PMC7732299 DOI: 10.18632/aging.103798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
Abstract
In atherosclerosis, upregulated TILRR (FREM1 isoform 2) expression increases immune cell infiltration. We hypothesized that TILRR expression is also correlated with cancer progression. By analyzing data from Oncomine and the Tumor Immune Estimation Resource, we found that TILRR mRNA expression was significantly lower in breast cancer tissue than adjacent normal tissue. Kaplan-Meier survival analysis and immunohistochemical staining revealed shortened overall survival and disease-free survival in patients with low TILRR expression. TILRR transcript expression was positively correlated with immune score, immune cell biomarkers and the expression of CXCL10 and CXCL11. TILRR expression was also positively correlated with CD8+ and CD4+ T-cell infiltration. These correlations were verified using the ESTIMATE algorithm, gene set enrichment analysis and Q-PCR. We concluded that impaired TILRR expression is correlated with breast cancer prognosis and immune cell infiltration.
Collapse
Affiliation(s)
- Xiao-Yi Xu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Wen-Jing Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shi-Hua Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ying Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, China
| | - Feng-Lin Gao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, China
| | - Jiang-Tao Wang
- Department of Pathology, First People Hospital, Changde 415003, Hunan, China
| | - Sheng Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, China
| | - He-Ying Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ren Wang
- Affiliated Cancer Hospital and Institute, Guangzhou Medical University, Guangzhou 511436, Guangdong, China,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Xiao Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, and Guangzhou Medical University, Guangzhou, Guangdong, China,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, Guangdong, China,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, Guangdong, China
| |
Collapse
|
24
|
Xu T, Wang Z, Dong M, Wu D, Liao S, Li X. Chloride intracellular channel protein 2: prognostic marker and correlation with PD-1/PD-L1 in breast cancer. Aging (Albany NY) 2020; 12:17305-17327. [PMID: 32915772 PMCID: PMC7521498 DOI: 10.18632/aging.103712] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
Immune checkpoint inhibition has emerged as an effective treatment for multiple solid tumors, including advanced-stage breast cancer (BC). During the past decade, the US Food and Drug Administration has approved a number of agents for immune checkpoint blockade (ICB). However, the limited data on monotherapy anti-tumor activity in BC underscores the need for robust predictive biomarker development. Here, we used weighted gene coexpression network analysis of genes differentially expressed between BC and normal tissue to identify genes coexpressed with programmed death-1 (PD-1) and its ligand (PD-L1). Tumor Immune Estimation Resource and Gene Expression Profiling Interaction Analysis were used to assess the relationship between gene expression and the abundance of tumor-infiltrating lymphocytes (TILs). We found that chloride intracellular channel protein 2 (CLIC2) was not only coexpressed with PD-1 and PD-L1, but its increased expression was associated with a favorable prognosis and enrichment of multiple TIL types, particularly CD8+ T cells. These results suggest that CLIC2 is a potentially useful biomarker for identifying BC patients who could benefit from ICB.
Collapse
Affiliation(s)
- Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China,Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| | - Zhi Wang
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| | - Menglu Dong
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| | - Di Wu
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| | - Shujie Liao
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan 430030, Hubei, People’s Republic of China
| |
Collapse
|
25
|
Kim JY, Jung HH, Sohn I, Woo SY, Cho H, Cho EY, Lee JE, Kim SW, Nam SJ, Park YH, Ahn JS, Im YH. Prognostication of a 13-immune-related-gene signature in patients with early triple-negative breast cancer. Breast Cancer Res Treat 2020; 184:325-34. [PMID: 32812178 DOI: 10.1007/s10549-020-05874-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022]
Abstract
PURPOSE We investigated the expression profiles of immune genes in patients with triple-negative breast cancer (TNBC) to identify the prognostic value of immune genes and their clinical implications. METHODS NanoString nCounter Analysis of 770 immune-related genes was used to measure immune gene expression in patients with TNBC who underwent curative surgery followed by adjuvant chemotherapy at Samsung Medical Center between 2000 and 2004. Statistical analyses were conducted to identify the associations between gene expression and distant recurrence-free survival (DRFS). RESULTS Of 1189 patients who underwent curative BC surgery, 200 TNBC patients were included and stage was the only clinical factor predictive of DRFS. In terms of immune genes, 155 of 770 genes were associated with DRFS (p < 0.01). Further multivariate analysis revealed that 13 genes, CD1B, CD53, CT45A1, GTF3C1, IL11RA, IL1RN, LRRN3, MAPK1, NEFL, PRKCE, PTPRC, SPACA3 and TNFSF11, were associated with patient prognosis (p < 0.05). The prognostic value of stage and expression levels of 13 immune genes was analyzed and the area under the receiver operating characteristic curve (AUC) was 0.923. Based on the AUC, we divided patients into three genetic risk groups and DRFS rate was significantly different according to genetic risk groups, even in the same stage (p < 0.001). CONCLUSIONS In this study, a 13-gene expression profile in combination with stage precisely predicted distant recurrence of early TNBC. Therefore, this 13-immune-gene signature could help predict TNBC prognosis and provide guidance for treatment as well as the opportunity to develop new targets for immunotherapy in TNBC patients.
Collapse
|
26
|
Hu J, Xu J, Yu M, Gao Y, Liu R, Zhou H, Zhang W. An integrated prognosis model of pharmacogenomic gene signature and clinical information for diffuse large B-cell lymphoma patients following CHOP-like chemotherapy. J Transl Med 2020; 18:144. [PMID: 32228625 PMCID: PMC7106727 DOI: 10.1186/s12967-020-02311-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
Background As the most common form of lymphoma, diffuse large B-cell lymphoma (DLBCL) is a clinical highly heterogeneous disease with variability in therapeutic outcomes and biological features. It is a challenge to identify of clinically meaningful tools for outcome prediction. In this study, we developed a prognosis model fused clinical characteristics with drug resistance pharmacogenomic signature to identify DLBCL prognostic subgroups for CHOP-based treatment. Methods The expression microarray data and clinical characteristics of 791 DLBCL patients from two Gene Expression Omnibus (GEO) databases were used to establish and validate this model. By using univariate Cox regression, eight clinical or genetic signatures were analyzed. The elastic net-regulated Cox regression analysis was used to select the best prognosis related factors into the predictive model. To estimate the prognostic capability of the model, Kaplan–Meier curve and the area under receiver operating characteristic (ROC) curve (AUC) were performed. Results A predictive model comprising 4 clinical factors and 2 pharmacogenomic gene signatures was established after 1000 times cross validation in the training dataset. The AUC of the comprehensive risk model was 0.78, whereas AUC value was lower for the clinical only model (0.68) or the gene only model (0.67). Compared with low-risk patients, the overall survival (OS) of DLBCL patients with high-risk scores was significantly decreased (HR = 4.55, 95% CI 3.14–6.59, log-rank p value = 1.06 × 10−15). The signature also enables to predict prognosis within different molecular subtypes of DLBCL. The reliability of the integrated model was confirmed by independent validation dataset (HR = 3.47, 95% CI 2.42–4.97, log rank p value = 1.53 × 10−11). Conclusions This integrated model has a better predictive capability to ascertain the prognosis of DLBCL patients prior to CHOP-like treatment, which may improve the clinical management of DLBCL patients and provide theoretical basis for individualized treatment.
Collapse
Affiliation(s)
- Jinglei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jing Xu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Muqiao Yu
- Xiangya School of Stomatology, Central South University, Changsha, 410078, Human, People's Republic of China
| | - Yongchao Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
| |
Collapse
|
27
|
Wang S, Zhang Q, Yu C, Cao Y, Zuo Y, Yang L. Immune cell infiltration-based signature for prognosis and immunogenomic analysis in breast cancer. Brief Bioinform 2020; 22:2020-2031. [PMID: 32141494 DOI: 10.1093/bib/bbaa026] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/30/2020] [Accepted: 02/17/2020] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is one of the most human malignant diseases and the leading cause of cancer-related death in the world. However, the prognostic and therapeutic benefits of breast cancer patients cannot be predicted accurately by the current stratifying system. In this study, an immune-related prognostic score was established in 22 breast cancer cohorts with a total of 6415 samples. An extensive immunogenomic analysis was conducted to explore the relationships between immune score, prognostic significance, infiltrating immune cells, cancer genotypes and potential immune escape mechanisms. Our analysis revealed that this immune score was a promising biomarker for estimating overall survival in breast cancer. This immune score was associated with important immunophenotypic factors, such as immune escape and mutation load. Further analysis revealed that patients with high immune scores exhibited therapeutic benefits from chemotherapy and immunotherapy. Based on these results, we can conclude that this immune score may be a useful tool for overall survival prediction and treatment guidance for patients with breast cancer.
Collapse
|
28
|
Abstract
Background Ovarian cancer is a frequently-occurring reproductive system malignancy in females, which leads to an annual of over 100 thousand deaths worldwide. Methods The electronic databases, including GEPIA, ONCOMINE, Metascape, and Kaplan-Meier Plotter, were used to examine both survival and transcriptional data regarding the cell division cycle associated (CDCA) gene family among ovarian cancer patients. Results All CDCA genes expression levels were up-regulated in ovarian cancer tissues relative to those in non-carcinoma ovarian counterparts. Besides, CDCA5/7 expression levels were related to the late tumor stage. In addition, the Kaplan-Meier Plotter database was employed to carry out survival analysis, which suggested that ovarian cancer patients with increased CDCA2/3/5/7 expression levels had poor overall survival (OS) (P<0.05). Moreover, ovarian cancer patients that had up-regulated mRNA expression levels of CDCA2/5/8 had markedly reduced progression-free survival (PFS) (P<0.05); and up-regulated CDCA4 expression showed remarkable association with reduced post-progression survival (PPS) (P<0.05). Additionally, the following processes were affected by CDCA genes alterations, including R-HAS-2500257: resolution of sister chromatid cohesion; GO:0051301: cell division; CORUM: 1118: Chromosomal passenger complex (CPC, including CDCA8, INCENP, AURKB and BIRC5); CORUM: 127: NDC80 kinetochore complex; M129: PID PLK1 pathway; and GO: 0007080: mitotic metaphase plate congression, all of which were subjected to marked regulation since the alterations affected CDCA genes. Conclusions Up-regulated CDCA gene expression in ovarian cancer tissues probably played a crucial part in the occurrence of ovarian cancer. The up-regulated CDCA2/3/5/7 expression levels were used as the potential prognostic markers to improve the poor ovarian cancer survival and prognostic accuracy. Moreover, CDCA genes probably exerted their functions in tumorigenesis through the PLK1 pathway.
Collapse
Affiliation(s)
- Chongxiang Chen
- Guangzhou Institute of Respiratory Diseases, State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China.,Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Siliang Chen
- Department of Hematology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Ma Luo
- Department of Interventional Radiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Honghong Yan
- Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Lanlan Pang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chaoyang Zhu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Weiyan Tan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Qingyu Zhao
- Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jielan Lai
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Huan Li
- Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| |
Collapse
|
29
|
Wang Q, Li M, Yang M, Yang Y, Song F, Zhang W, Li X, Chen K. Analysis of immune-related signatures of lung adenocarcinoma identified two distinct subtypes: implications for immune checkpoint blockade therapy. Aging (Albany NY) 2020; 12:3312-3339. [PMID: 32091408 PMCID: PMC7066911 DOI: 10.18632/aging.102814] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/27/2020] [Indexed: 12/22/2022]
Abstract
Immune checkpoint blockade (ICB) therapies have revolutionized the treatment of human cancers including lung adenocarcinoma (LUAD). However, our understanding of the immune subtyping of LUAD and its association with clinical response of immune checkpoint inhibitor remains incomplete. Here we performed molecular subtyping and association analysis of LUAD from the Cancer Genome Atlas (TCGA) and validated findings from TCGA cohort in 9 independent validation cohorts. We conducted consensus molecular subtyping with nonnegative matrix factorization (NMF). Potential response of ICB therapy was estimated with Tumor Immune Dysfunction and Exclusion (TIDE) algorithm. We identified 2 distinct subtypes of LUAD in TCGA cohort that were characterized by significantly different survival outcomes (i.e., high- and low-risk subtypes). The high-risk subtype was featured by lower TIDE score, upregulation of programmed death-ligand 1 (PD-L1) expression, and higher tumor mutation burden (TMB). The high-risk subtype also harbored significantly elevated cell cycle modulators CDK4/CDK6 and TP53 mutation. These observations were validated in 9 independent LUAD cohorts. Our findings suggest that immune checkpoint blockade therapy may be efficacious for high-risk subtype of LUAD patients.
Collapse
Affiliation(s)
- Qinghua Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Meiling Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Meng Yang
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yichen Yang
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Wei Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| | - Xiangchun Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| |
Collapse
|
30
|
Dong R, Liu J, Sun W, Ping W. Comprehensive Analysis of Aberrantly Expressed Profiles of lncRNAs and miRNAs with Associated ceRNA Network in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. Pathol Oncol Res 2020; 26:1935-1945. [PMID: 31898160 DOI: 10.1007/s12253-019-00780-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/19/2019] [Indexed: 12/24/2022]
Abstract
Lung cancer (LC) continues to be the leading cause of cancer-related deaths worldwide and the prognosis remains poor worldwide. At present, the long non-coding RNAs (lncRNAs) was considered as a part of competing endogenous RNA (ceRNA) network act as natural microRNA (miRNA) sponges to regulate protein-coding gene expression. However, functional roles of lncRNA-mediated ceRNAs in LC are insufficiently understood. To classify the specific mechanism of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), we comprehensively compared the expression profiles of mRNAs, lncRNAs and miRNAs obtained from 509 LUAD, 473 LUSC tissues and 49 adjacent non-cancerous lung tissues, based on The Cancer Genome Atlas (TCGA). After screening for differently expressed (DE) mRNAs, DEmiRNAs, DElncRNAs and weighted gene co-expression network analysis (WGCNA) (|log2FC| > 2.0 and an adjusted p value <0.05), a total of 4478 DEmRNAs, 526 DElncRNAs and 75 DEmiRNAs in LUAD, while 6237 DEmRNAs, 843 DElncRNAs and 117 DEmiRNAs in LUSC were discovered. Interaction (PPI) network analysis was performed to identify 656 nodes and 2987 edges (minimum required interaction score > 0.9), as well as 8 different protein-protein interactions. Gene ontology (GO) analysis mainly associated with cell proliferation. KEGG pathway enrichment analyses most partly associated with metabolism pathway and cytokine-cytokine receptor interaction. Finally, the dysregulated lncRNA-miRNA-ceRNA network was constructed based on correlation analyses and a total of 62 dysregulated lncRNAs, 28 DEmRNAs and 18 DEmiRNAs were involved. The most significant lncRNAs included DElncRNAs, LINC00641 and AC004947.2, miRNAs included miR-6860, miR-1285-3p, miR-767-3p and miR-7974, mRNAs included MAP3K3, FGD3 and ATP1B2. Then we analyzed and described the potential characteristics of biological function and pathological roles of the LUAD and LUSC ceRNA co-regulatory network. Our findings revealed ceRNA network will be beneficial for promoting the understanding of lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of LUAD and LUSC.
Collapse
Affiliation(s)
- Ruolan Dong
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jiawei Liu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Sun
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Ping
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
31
|
Chen B, Lai J, Dai D, Chen R, Li X, Liao N. JAK1 as a prognostic marker and its correlation with immune infiltrates in breast cancer. Aging (Albany NY) 2019; 11:11124-11135. [PMID: 31790361 PMCID: PMC6932910 DOI: 10.18632/aging.102514] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022]
Abstract
Clinical trials testing Janus kinase-1 (JAK1) inhibitors in cancers are under way. Whether the JAK1 mRNA levels in breast tumors correlates with outcome has not been evaluated. JAK1 expression was analyzed via the Oncomine database and Tumor IMmune Estimation Resource site. Tumor tissues from 57 breast cancer patients were used for qRT-PCR and immune infiltration assessment. JAK1 expression was significantly lower in breast invasive carcinoma compared with adjacent normal tissues. Public databases (Kaplan-Meier plotter and PrognoScan) showed that low JAK1 expression was associated with poorer survival. Data from The Cancer Genome Atlas (TCGA) showed that high JAK1 expression was associated with increased survival in both TNM I-II and TNM III-IV patients. JAK1 was inversely correlated with tumor size status, lymph node status, and TNM of breast cancer patients. JAK1 levels were correlated with the T cell transcript-enriched LYM metagene signature and was significantly lower in the low tumor infiltrating lymphocytes (TILs) group. JAK1 expression levels had significant positive correlations with infiltrating levels of CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells in breast cancer and not with other B cells. In conclusion, JAK1 mRNA levels were correlated with prognosis and immune infiltrating levels in breast cancer.
Collapse
Affiliation(s)
- Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Jianguo Lai
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Danian Dai
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Rong Chen
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xuan Li
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| |
Collapse
|
32
|
Kumar L, Greiner R. Gene expression based survival prediction for cancer patients-A topic modeling approach. PLoS One 2019; 14:e0224446. [PMID: 31730620 DOI: 10.1371/journal.pone.0224446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression data, many projects use some dimensionality reduction techniques to overcome this hurdle. We introduce a novel methodology, inspired by topic modeling from the natural language domain, to derive expressive features from the high-dimensional gene expression data. There, a document is represented as a mixture over a relatively small number of topics, where each topic corresponds to a distribution over the words; here, to accommodate the heterogeneity of a patient's cancer, we represent each patient (≈ document) as a mixture over cancer-topics, where each cancer-topic is a mixture over gene expression values (≈ words). This required some extensions to the standard LDA model-e.g., to accommodate the real-valued expression values-leading to our novel discretized Latent Dirichlet Allocation (dLDA) procedure. After using this dLDA to learn these cancer-topics, we can then express each patient as a distribution over a small number of cancer-topics, then use this low-dimensional "distribution vector" as input to a learning algorithm-here, we ran the recent survival prediction algorithm, MTLR, on this representation of the cancer dataset. We initially focus on the METABRIC dataset, which describes each of n = 1,981 breast cancer patients using the r = 49,576 gene expression values, from microarrays. Our results show that our approach (dLDA followed by MTLR) provides survival estimates that are more accurate than standard models, in terms of the standard Concordance measure. We then validate this "dLDA+MTLR" approach by running it on the n = 883 Pan-kidney (KIPAN) dataset, over r = 15,529 gene expression values-here using the mRNAseq modality-and find that it again achieves excellent results. In both cases, we also show that the resulting model is calibrated, using the recent "D-calibrated" measure. These successes, in two different cancer types and expression modalities, demonstrates the generality, and the effectiveness, of this approach. The dLDA+MTLR source code is available at https://github.com/nitsanluke/GE-LDA-Survival.
Collapse
|
33
|
Renda I, Bianchi S, Vezzosi V, Nori J, Vanzi E, Tavella K, Susini T. Expression of FGD3 gene as prognostic factor in young breast cancer patients. Sci Rep 2019; 9:15204. [PMID: 31645624 PMCID: PMC6811624 DOI: 10.1038/s41598-019-51766-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/08/2019] [Indexed: 01/08/2023] Open
Abstract
The FGD3 gene works as a cell migration inhibitor and seems to be a promising indicator of outcome in some human cancers including breast. In this study, we analysed for the first time the prognostic role of FGD3 in young breast cancer patients. We studied the relationship between traditional prognostic factors, FGD3 expression and outcome in ≤40 years breast cancer patients. We found that lower FGD3 expression decreased the probability of disease-free survival (p = 0.042) and overall survival (p = 0.007). In a multivariate analysis for overall survival AJCC stage (p = 0.005) and FGD3 expression (p = 0.03) resulted independent prognostic factors. Low FGD3 expression increased the risk of death from disease (HR 5.73, p = 0.03). Moreover, low FGD3 expression was associated with more widespread lymph node involvement (p = 0.04) and a lower FGD3 staining intensity was found in positive-lymph-node patients vs negative (p = 0.003) and in patients with ≥10 involved lymph nodes vs <10 (p = 0.05). Our results suggest FGD3 to be a significant independent prognostic factor in young breast cancer patients in terms of disease-free survival and overall survival. A lower expression increased the risk of recurrence and death from disease and was associated with widespread lymph node metastases.
Collapse
Affiliation(s)
- Irene Renda
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, Florence, Italy
| | - Simonetta Bianchi
- Pathology Unit, Department of Health Sciences, University of Florence, Florence, Italy
| | - Vania Vezzosi
- Pathology Unit, Department of Health Sciences, University of Florence, Florence, Italy
| | - Jacopo Nori
- Diagnostic Senology Unit, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ermanno Vanzi
- Diagnostic Senology Unit, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ketty Tavella
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Tommaso Susini
- Breast Unit, Gynecology Section, Department of Health Sciences, University of Florence, Florence, Italy.
| |
Collapse
|
34
|
Clements ME, Johnson RW. PREX1 drives spontaneous bone dissemination of ER+ breast cancer cells. Oncogene 2020; 39:1318-34. [PMID: 31636389 DOI: 10.1038/s41388-019-1064-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
A significant proportion of breast cancer patients develop bone metastases, but the mechanisms regulating tumor cell dissemination from the primary site to the skeleton remain largely unknown. Using a novel model of spontaneous bone metastasis derived from human ER+ MCF7 cells, molecular profiling revealed increased PREX1 expression in a cell line established from bone-disseminated MCF7 cells (MCF7b), which were more migratory, invasive, and adhesive in vitro compared to parental MCF7 cells, and this phenotype was mediated by PREX1. MCF7b cells grew poorly in the primary tumor site when re-inoculated in vivo, suggesting these cells are primed to grow in the bone, and were enriched in skeletal sites of metastasis over soft tissue sites. Skeletal dissemination from the primary tumor was reversed with PREX1 knockdown, indicating that PREX1 is a key driver of spontaneous dissemination of tumor cells from the primary site to the bone marrow. In breast cancer patients, PREX1 levels are significantly increased in ER+ tumors and associated with invasive disease and distant metastasis. Together, these findings implicate PREX1 in spontaneous bone dissemination and provide a significant advance to the molecular mechanisms by which breast cancer cells disseminate from the primary tumor site to bone.
Collapse
|
35
|
Abstract
Over the past decade, there has been a paradigm shift in how clinical data are collected, processed and utilized. Machine learning and artificial intelligence, fueled by breakthroughs in high-performance computing, data availability and algorithmic innovations, are paving the way to effective analyses of large, multi-dimensional collections of patient histories, laboratory results, treatments, and outcomes. In the new era of machine learning and predictive analytics, the impact on clinical decision-making in all clinical areas, including rheumatology, will be unprecedented. Here we provide a critical review of the machine-learning methods currently used in the analysis of clinical data, the advantages and limitations of these methods, and how they can be leveraged within the field of rheumatology.
Collapse
Affiliation(s)
- Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Correspondence to Ki-Jo Kim, M.D. Division of Rheumatology, Department of Internal Medicine, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, 93 Jungbu-daero, Paldal-gu, Suwon 16247, Korea Tel: +82-31-249-8805 Fax: +82-31-253-8898 E-mail:
| | - Ilias Tagkopoulos
- Department of Computer Science, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
| |
Collapse
|
36
|
Jing B, Zhang T, Wang Z, Jin Y, Liu K, Qiu W, Ke L, Sun Y, He C, Hou D, Tang L, Lv X, Li C. A deep survival analysis method based on ranking. Artif Intell Med 2019; 98:1-9. [PMID: 31521247 DOI: 10.1016/j.artmed.2019.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 11/27/2022]
Abstract
Survival analyses of populations and the establishment of prognoses for individual patients are important activities in the practice of medicine. Standard survival models, such as the Cox proportional hazards model, require extensive feature engineering or prior knowledge to model at an individual level. Some survival analysis models can avoid these problems by using machine learning extended the CPH model, and higher performance has been reported. In this paper, we propose an innovative loss function that is defined as the sum of an extended mean squared error loss and a pairwise ranking loss based on ranking information on survival data. We apply this loss function to optimize a deep feed-forward neural network (RankDeepSurv), which can be used to model survival data. We demonstrate that the performance of our model, RankDeepSurv, is superior to that of other state-of-the-art survival models based on an analysis of 4 public medical clinical datasets. When modelling the prognosis of nasopharyngeal carcinoma (NPC), RankDeepSurv achieved better prognostic accuracy than the CPH established by clinical experts. The difference between high and low risk groups in the RankDeepSurv model is greater than the difference in the CPH. The results show that our method has considerable potential to model survival data in medical settings.
Collapse
Affiliation(s)
- Bingzhong Jing
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Tao Zhang
- Deepaint Intelligence Technology Co., Ltd., Guangzhou, 510080, China
| | - Zixian Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Medical Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China
| | - Ying Jin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Medical Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China
| | - Kuiyuan Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Wenze Qiu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Liangru Ke
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Radiology, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Radiotherapy, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Caisheng He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China
| | - Dan Hou
- Deepaint Intelligence Technology Co., Ltd., Guangzhou, 510080, China
| | - Linquan Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China.
| | - Xing Lv
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China.
| | - Chaofeng Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou 510060, China; Department of Information, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China; Precision Medicine Centre, Sun Yat-Sen University Cancer Centre, Guangzhou 510060, China.
| |
Collapse
|
37
|
Clarke R, Tyson JJ, Tan M, Baumann WT, Jin L, Xuan J, Wang Y. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers. Endocr Relat Cancer 2019; 26:R345-R368. [PMID: 30965282 PMCID: PMC7045974 DOI: 10.1530/erc-18-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
Drawing on concepts from experimental biology, computer science, informatics, mathematics and statistics, systems biologists integrate data across diverse platforms and scales of time and space to create computational and mathematical models of the integrative, holistic functions of living systems. Endocrine-related cancers are well suited to study from a systems perspective because of the signaling complexities arising from the roles of growth factors, hormones and their receptors as critical regulators of cancer cell biology and from the interactions among cancer cells, normal cells and signaling molecules in the tumor microenvironment. Moreover, growth factors, hormones and their receptors are often effective targets for therapeutic intervention, such as estrogen biosynthesis, estrogen receptors or HER2 in breast cancer and androgen receptors in prostate cancer. Given the complexity underlying the molecular control networks in these cancers, a simple, intuitive understanding of how endocrine-related cancers respond to therapeutic protocols has proved incomplete and unsatisfactory. Systems biology offers an alternative paradigm for understanding these cancers and their treatment. To correctly interpret the results of systems-based studies requires some knowledge of how in silico models are built, and how they are used to describe a system and to predict the effects of perturbations on system function. In this review, we provide a general perspective on the field of cancer systems biology, and we explore some of the advantages, limitations and pitfalls associated with using predictive multiscale modeling to study endocrine-related cancers.
Collapse
Affiliation(s)
- Robert Clarke
- Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Ming Tan
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - William T Baumann
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Lu Jin
- Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Jianhua Xuan
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, USA
| |
Collapse
|
38
|
Economopoulou P, Kotoula V, Koliou GA, Papadopoulou K, Christodoulou C, Pentheroudakis G, Lazaridis G, Arapantoni-Dadioti P, Koutras A, Bafaloukos D, Papakostas P, Patsea H, Pavlakis K, Pectasides D, Kotsakis A, Razis E, Aravantinos G, Samantas E, Kalogeras KT, Economopoulos T, Psyrri A, Fountzilas G. Prognostic Impact of Src, CDKN1B, and JAK2 Expression in Metastatic Breast Cancer Patients Treated with Trastuzumab. Transl Oncol 2019; 12:739-748. [PMID: 30877976 PMCID: PMC6423363 DOI: 10.1016/j.tranon.2019.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND: Src, CDKN1B, and JAK2 play a crucial role in the coordination of cell signaling pathways. In the present study, we aim to investigate the prognostic significance of these biomarkers in HER2-positive metastatic breast cancer (MBC) patients treated with trastuzumab (T). METHODS: Formalin-fixed paraffin-embedded tumor tissue samples from 197 patients with HER2-positive MBC treated with T were retrospectively collected. All tissue samples were centrally assessed for ER, PgR, Ki67, HER2, and PTEN protein expression; EGFR gene amplification; PI3KCA mutational status; and tumor-infiltrating lympocytes density. Src, CDKN1B, and JAK2 mRNA expression was evaluated using quantitative reverse transcription-polymerase chain reaction. RESULTS: Only 133 of the 197 patients (67.5%) were found to be HER2-positive by central assessment. CDKN1B mRNA expression was strongly correlated with Src (rho = 0.71) and JAK2 (rho = 0.54). In HER2-positive patients, low CDKN1B conferred higher risk for progression [hazard ratio (HR) = 1.58, 95% confidence interval (CI) 1.08-2.32, P = .018]. In HER2-negative patients, low Src was associated with longer survival (HR = 0.56, 95% CI 0.32-0.99, P = .045). Upon multivariate analyses, only low CDKN1B and JAK2 mRNA expression remained unfavorable factors for PFS in de novo and relapsed (R)-MBC patients, respectively (HR = 2.36, 95% CI 1.01-5.48, P = .046 and HR = 1.76, 95% CI 1.01-3.06, P = .047, respectively). CONCLUSIONS: Low CDKN1B and JAK2 mRNA expressions were unfavorable prognosticators in a cohort of T-treated MBC patients. Our results suggest that CDKN1B and JAK2, if validated, may serve as prognostic factors potentially implicated in T resistance, which seems to be associated with distinct pathways in de novo and R-MBC.
Collapse
Affiliation(s)
- Panagiota Economopoulou
- Second Department of Internal Medicine, Attikon University Hospital, 1 Rimini St 12462, Haidari, Athens, Greece.
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, Building 17B, 54006, Thessaloniki, Greece; Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, University Campus, Building 17B, 54006, Thessaloniki, Greece.
| | - Georgia-Angeliki Koliou
- Section of Biostatistics, Hellenic Cooperative Oncology Group, 18 Hatzikonstanti St, 11524, Athens, Greece.
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, University Campus, Building 17B, 54006, Thessaloniki, Greece.
| | - Christos Christodoulou
- Second Department of Medical Oncology, Metropolitan Hospital, 9 Ethnarchou Makariou St, 185 47, Piraeus, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, Ioannina University Hospital, Leof. Stavrou Niarchou, 45500, Ioannina, Greece.
| | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Ring Road, Nea Efkarpia, 56450, Thessaloniki, Greece
| | | | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Panepistimioupoli Patron, 26504, Patras, Greece.
| | - Dimitris Bafaloukos
- First department of Medical Oncology, Metropolitan Hospital, 9 Ethnarchou Makariou St, 185 47, Piraeus, Greece.
| | - Pavlos Papakostas
- Oncology Unit, Hippokration Hospital, 114 Vasilissis Sofias Av, 11527, Athens, Greece.
| | - Helen Patsea
- Department of Pathology, IASSO General Hospital, 264 Mesogion Av, 15562, Athens, Greece
| | - Kitty Pavlakis
- Pathology Department, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, 114 Vasilissis Sofias Av, 11527, Athens, Greece.
| | - Athanasios Kotsakis
- Department of Medical Oncology, University General Hospital of Heraklion, Voutes, 71110, Crete, Greece.
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, 4 Erithrou Stavrou St, Marousi, 15123, Athens, Greece.
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Epaminondas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Timiou Stavrou, 14564, Kifisia, Athens, Greece.
| | - Konstantine T Kalogeras
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, University Campus, Building 17B, 54006, Thessaloniki, Greece; Translational Research Section, Hellenic Cooperative Oncology Group, 18 Hatzikonstanti St, 11524, Athens, Greece.
| | - Theofanis Economopoulos
- Second Department of Internal Medicine, Attikon University Hospital, 1 Rimini St 12462, Haidari, Athens, Greece.
| | - Amanta Psyrri
- Second Department of Internal Medicine, Attikon University Hospital, 1 Rimini St 12462, Haidari, Athens, Greece.
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, University Campus, Building 17B, 54006, Thessaloniki, Greece; Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| |
Collapse
|
39
|
Sun C, Cheng X, Wang C, Wang X, Xia B, Zhang Y. Gene expression profiles analysis identifies a novel two-gene signature to predict overall survival in diffuse large B-cell lymphoma. Biosci Rep 2019; 39:BSR20181293. [PMID: 30393234 DOI: 10.1042/BSR20181293] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common hematologic malignancy, however, specific tumor-associated genes and signaling pathways are yet to be deciphered. Differentially expressed genes (DEGs) were computed based on gene expression profiles from GSE32018, GSE56315, and The Cancer Genome Atlas (TCGA) DLBC. Overlapping DEGs were then evaluated for gene ontology (GO), pathways enrichment, DNA methylation, protein–protein interaction (PPI) network analysis as well as survival analysis. Seventy-four up-regulated and 79 down-regulated DEGs were identified. From PPI network analysis, majority of the DEGs were involved in cell cycle, oocyte meiosis, and epithelial-to-mesenchymal transition (EMT) pathways. Six hub genes including CDC20, MELK, PBK, prostaglandin D2 synthase (PTGDS), PCNA, and CDK1 were selected using the Molecular Complex Detection (MCODE). CDC20 and PTGDS were able to predict overall survival (OS) in TCGA DLBC and in an additional independent cohort GSE31312. Furthermore, CDC20 DNA methylation negatively regulated CDC20 expression and was able to predict OS in DLBCL. A two-gene panel consisting of CDC20 and PTGDS had a better prognostic value compared with CDC20 or PTGDS alone in the TCGA cohort (P=0.026 and 0.039). Overall, the present study identified a set of novel genes and pathways that may play a significant role in the initiation and progression of DLBCL. In addition, CDC20 and PTGDS will provide useful guidance for therapeutic applications.
Collapse
|
40
|
Affiliation(s)
- Kitt Shaffer
- From the Department of Radiology, Boston Medical Center, 1 Boston Medical Center Pl, Newton Pavilion, Room 2503, Boston, MA 02118
| |
Collapse
|
41
|
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2018; 48:812-830.e14. [PMID: 29628290 PMCID: PMC5982584 DOI: 10.1016/j.immuni.2018.03.023] [Citation(s) in RCA: 3127] [Impact Index Per Article: 521.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/23/2018] [Accepted: 03/21/2018] [Indexed: 02/08/2023]
Abstract
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.
Collapse
Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| |
Collapse
|
42
|
DuMontier C, Clough-Gorr KM, Silliman RA, Stuck AE, Moser A. Health-Related Quality of Life in a Predictive Model for Mortality in Older Breast Cancer Survivors. J Am Geriatr Soc 2018. [PMID: 29533469 DOI: 10.1111/jgs.15340] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To develop a predictive model and risk score for 10-year mortality using health-related quality of life (HRQOL) in a cohort of older women with early-stage breast cancer. DESIGN Prospective cohort. SETTING Community. PARTICIPANTS U.S. women aged 65 and older diagnosed with Stage I to IIIA primary breast cancer (N=660). MEASUREMENTS We used medical variables (age, comorbidity), HRQOL measures (10-item Physical Function Index and 5-item Mental Health Index from the Medical Outcomes Study (MOS) 36-item Short-Form Survey; 8-item Modified MOS Social Support Survey), and breast cancer variables (stage, surgery, chemotherapy, endocrine therapy) to develop a 10-year mortality risk score using penalized logistic regression models. We assessed model discriminative performance using the area under the receiver operating characteristic curve (AUC), calibration performance using the Hosmer-Lemeshow test, and overall model performance using Nagelkerke R2 (NR). RESULTS Compared to a model including only age, comorbidity, and cancer stage and treatment variables, adding HRQOL variables improved discrimination (AUC 0.742 from 0.715) and overall performance (NR 0.221 from 0.190) with good calibration (p=0.96 from HL test). CONCLUSION In a cohort of older women with early-stage breast cancer, HRQOL measures predict 10-year mortality independently of traditional breast cancer prognostic variables. These findings suggest that interventions aimed at improving physical function, mental health, and social support might improve both HRQOL and survival.
Collapse
Affiliation(s)
- Clark DuMontier
- Division of Gerontology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kerri M Clough-Gorr
- National Cancer Registry Ireland, Cork, Ireland.,University College Cork, Cork, Ireland.,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Rebecca A Silliman
- Section of Geriatrics, Boston Medical Center/Boston University School of Medicine, Boston, Massachusetts
| | - Andreas E Stuck
- Department of Geriatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - André Moser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Department of Geriatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| |
Collapse
|
43
|
Katzman JL, Shaham U, Cloninger A, Bates J, Jiang T, Kluger Y. DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network. BMC Med Res Methodol 2018; 18:24. [PMID: 29482517 PMCID: PMC5828433 DOI: 10.1186/s12874-018-0482-1] [Citation(s) in RCA: 489] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 02/07/2018] [Indexed: 11/18/2022] Open
Abstract
Background Medical practitioners use survival models to explore and understand the relationships between patients’ covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. Methods We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient’s covariates and treatment effectiveness in order to provide personalized treatment recommendations. Results We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient’s covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient’s features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it’s personalized treatment recommendations would increase the survival time of a set of patients. Conclusions The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient’s characteristics on their risk of failure.
Collapse
Affiliation(s)
- Jared L Katzman
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, 06511, CT, USA
| | - Uri Shaham
- Department of Statistics, Yale University, 24 Hillhouse Avenue, New Haven, 06511, CT, USA.,Center of Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, 06511, CT, USA.,Final Research, Herzliya, Israel
| | - Alexander Cloninger
- Applied Mathematics Program, Yale University, 51 Prospect Street, New Haven, 06511, CT, USA.,Department of Mathematics, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Jonathan Bates
- Applied Mathematics Program, Yale University, 51 Prospect Street, New Haven, 06511, CT, USA.,Yale School of Medicine, 333 Cedar Street, New Haven, 06510, CT, USA.,Center of Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, 06511, CT, USA
| | - Tingting Jiang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06511, CT, USA
| | - Yuval Kluger
- Applied Mathematics Program, Yale University, 51 Prospect Street, New Haven, 06511, CT, USA. .,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06511, CT, USA. .,Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, 06511, CT, USA.
| |
Collapse
|
44
|
Peng P, Zhou X, Yi G, Chen P, Wang F, Dong W. Identification of a novel gene pairs signature in the prognosis of gastric cancer. Cancer Med 2018; 7:344-350. [PMID: 29282891 PMCID: PMC5806102 DOI: 10.1002/cam4.1303] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/25/2017] [Accepted: 11/27/2017] [Indexed: 02/06/2023] Open
Abstract
Current prognostic signatures need to be improved in identifying high-risk patients of gastric cancer (GC). Thus, we aimed to develop a reliable prognostic signature that could assess the prognosis risk in GC patients. Two microarray datasets of GSE662254 (n = 300, training set) and GSE15459 (n = 192, test set) were included into analysis. Prognostic genes were screened to construct prognosis-related gene pairs (PRGPs). Then, a penalized Cox proportional hazards regression model identified seven PRGPs, which constructed a prognostic signature and divided patients into high- and low-risk groups according to the signature score. High-risk patients showed a poorer prognosis than low-risk patients in both the training set (hazard ratios [HR]: 6.086, 95% confidence interval [CI]: 4.341-8.533) and test set (1.773 [1.107-2.840]). The PRGPs signature also achieved a higher predictive accuracy (concordance index [C-index]: 0.872, 95% CI: 0.846-0.897) than two existing molecular signatures (0.706 [0.667-0.744] for a 11-gene signature and 0.684 [0.642-0.726] for a 24-lncRNA signature) and TNM stage (0.764 [0.715-0.814]). In conclusion, our study identified a novel gene pairs signature in the prognosis of GC.
Collapse
Affiliation(s)
- Pai‐Lan Peng
- Department of GastroenterologyRenmin Hospital of Wuhan UniversityWuhan430060China
- Department of GastroenterologyThe Central Hospital of Enshi Autonomous PrefectureEnshi445000China
| | - Xiang‐Yu Zhou
- Department of GastroenterologyThe Central Hospital of Enshi Autonomous PrefectureEnshi445000China
| | - Guo‐Dong Yi
- Department of GastroenterologyThe Central Hospital of Enshi Autonomous PrefectureEnshi445000China
| | - Peng‐Fei Chen
- Department of GastroenterologyThe Central Hospital of Enshi Autonomous PrefectureEnshi445000China
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Fan Wang
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Wei‐Guo Dong
- Department of GastroenterologyRenmin Hospital of Wuhan UniversityWuhan430060China
| |
Collapse
|
45
|
Ringnér M, Staaf J. Consensus of gene expression phenotypes and prognostic risk predictors in primary lung adenocarcinoma. Oncotarget 2018; 7:52957-52973. [PMID: 27437773 PMCID: PMC5288161 DOI: 10.18632/oncotarget.10641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022] Open
Abstract
Transcriptional profiling of lung adenocarcinomas has identified numerous gene expression phenotype (GEP) and risk prediction (RP) signatures associated with patient outcome. However, classification agreement between signatures, underlying transcriptional programs, and independent signature validation are less studied. We classified 2395 transcriptional adenocarcinoma profiles, assembled from 17 public cohorts, using 11 GEP and seven RP signatures, finding that 16 signatures were associated with patient survival in the total cohort and in multiple individual cohorts. For significant signatures, total cohort hazard ratios were ~2 in univariate analyses (mean=1.95, range=1.4-2.6). Strong classification agreement between signatures was observed, especially for predicted low-risk patients by adenocarcinoma-derived signatures. Expression of proliferation-related genes correlated strongly with GEP subtype classifications and RP scores, driving the gene signature association with prognosis. A three-group consensus definition of samples across 10 GEP classifiers demonstrated aggregation of samples with specific smoking patterns, gender, and EGFR/KRAS mutations, while survival differences were only significant when patients were divided into low- or high-risk. In summary, our study demonstrates a consensus between GEPs and RPs in lung adenocarcinoma through a common underlying transcriptional program. This consensus generalizes reported problems with current signatures in a clinical context, stressing development of new adenocarcinoma-specific single sample predictors for clinical use.
Collapse
Affiliation(s)
- Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| |
Collapse
|
46
|
Phan NN, Wang CY, Li KL, Chen CF, Chiao CC, Yu HG, Huang PL, Lin YC. Distinct expression of CDCA3, CDCA5, and CDCA8 leads to shorter relapse free survival in breast cancer patient. Oncotarget 2018; 9:6977-6992. [PMID: 29467944 PMCID: PMC5805530 DOI: 10.18632/oncotarget.24059] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/03/2018] [Indexed: 11/25/2022] Open
Abstract
Breast cancer is a dangerous disease that results in high mortality rates for cancer patients. Many methods have been developed for the treatment and prevention of this disease. Determining the expression patterns of certain target genes in specific subtypes of breast cancer is important for developing new therapies for breast cancer. In the present study, we performed a holistic approach to screening the mRNA expression of six members of the cell division cycle-associated gene family (CDCA) with a focus on breast cancer using the Oncomine and The Cancer Cell Line Encyclopedia (CCLE) databases. Furthermore, Gene Expression-Based Outcome for Breast Cancer Online (GOBO) was also used to deeply mine the expression of each CDCA gene in clinical breast cancer tissue and breast cancer cell lines. Finally, the mRNA expression of the CDCA genes as related to breast cancer patient survival were analyzed using a Kaplan-Meier plot. CDCA3, CDCA5, and CDCA8 mRNA expression levels were significantly higher than the control sample in both clinical tumor sample and cancer cell lines. These highly expressed genes in the tumors of breast cancer patients dramatically reduced patient survival. The interaction network of CDCA3, CDCA5, and CDCA8 with their co-expressed genes also revealed that CDCA3 expression was highly correlated with cell cycle related genes such as CCNB2, CDC20, CDKN3, and CCNB1. CDCA5 expression was correlated with BUB1 and TRIP13, while CDCA8 expression was correlated with BUB1 and CCNB1. Altogether, these findings suggested CDCA3, CDCA5, and CDCA8 could have a high potency as targeted breast cancer therapies.
Collapse
Affiliation(s)
- Nam Nhut Phan
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan.,NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Chih-Yang Wang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Lun Li
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Chien-Fu Chen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Chung-Chieh Chiao
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Han-Gang Yu
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA
| | - Pung-Ling Huang
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan.,Department of Horticulture & Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Yen-Chang Lin
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| |
Collapse
|
47
|
Zhu B, Song N, Shen R, Arora A, Machiela MJ, Song L, Landi MT, Ghosh D, Chatterjee N, Baladandayuthapani V, Zhao H. Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers. Sci Rep 2017; 7:16954. [PMID: 29209073 PMCID: PMC5717223 DOI: 10.1038/s41598-017-17031-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types. mRNA and miRNA expression profile frequently performed the best, followed by DNA methylation profile. Germline susceptibility variants displayed low prognostic performance consistently across cancer types. The integration of omic profiles with clinical variables can lead to substantially improved prognostic performance over the use of clinical variables alone in half of cancer types examined. Moreover, we showed that the kernel machine learning method consistently outperformed existing prognostic signatures, suggesting that including a large number of omic biomarkers may provide substantial improvement in prognostic assessment. Our study provides a comprehensive portrait of omic architecture for tumor prognosis across cancers, and highlights the prognostic value of genome-wide omic biomarker aggregation, which may facilitate refined prognostic assessment in the era of precision oncology.
Collapse
Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
| | - Nan Song
- NSABP Foundation, Pittsburgh, PA, 15212, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10021, USA
| | - Arshi Arora
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10021, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Veera Baladandayuthapani
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77230, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| |
Collapse
|
48
|
Li B, Cui Y, Diehn M, Li R. Development and Validation of an Individualized Immune Prognostic Signature in Early-Stage Nonsquamous Non-Small Cell Lung Cancer. JAMA Oncol 2017; 3:1529-1537. [PMID: 28687838 DOI: 10.1001/jamaoncol.2017.1609] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance The prevalence of early-stage non-small cell lung cancer (NSCLC) is expected to increase with recent implementation of annual screening programs. Reliable prognostic biomarkers are needed to identify patients at a high risk for recurrence to guide adjuvant therapy. Objective To develop a robust, individualized immune signature that can estimate prognosis in patients with early-stage nonsquamous NSCLC. Design, Setting, and Participants This retrospective study analyzed the gene expression profiles of frozen tumor tissue samples from 19 public NSCLC cohorts, including 18 microarray data sets and 1 RNA-Seq data set for The Cancer Genome Atlas (TCGA) lung adenocarcinoma cohort. Only patients with nonsquamous NSCLC with clinical annotation were included. Samples were from 2414 patients with nonsquamous NSCLC, divided into a meta-training cohort (729 patients), meta-testing cohort (716 patients), and 3 independent validation cohorts (439, 323, and 207 patients). All patients underwent surgery with a negative surgical margin, received no adjuvant or neoadjuvant therapy, and had publicly available gene expression data and survival information. Data were collected from July 22 through September 8, 2016. Main Outcomes and Measures Overall survival. Results Of 2414 patients (1205 men [50%], 1111 women [46%], and 98 of unknown sex [4%]; median age [range], 64 [15-90] years), a prognostic immune signature of 25 gene pairs consisting of 40 unique genes was constructed using the meta-training data set. In the meta-testing and validation cohorts, the immune signature significantly stratified patients into high- vs low-risk groups in terms of overall survival across and within subpopulations with stage I, IA, IB, or II disease and remained as an independent prognostic factor in multivariate analyses (hazard ratio range, 1.72 [95% CI, 1.26-2.33; P < .001] to 2.36 [95% CI, 1.47-3.79; P < .001]) after adjusting for clinical and pathologic factors. Several biological processes, including chemotaxis, were enriched among genes in the immune signature. The percentage of neutrophil infiltration (5.6% vs 1.8%) and necrosis (4.6% vs 1.5%) was significantly higher in the high-risk immune group compared with the low-risk groups in TCGA data set (P < .003). The immune signature achieved a higher accuracy (mean concordance index [C-index], 0.64) than 2 commercialized multigene signatures (mean C-index, 0.53 and 0.61) for estimation of survival in comparable validation cohorts. When integrated with clinical characteristics such as age and stage, the composite clinical and immune signature showed improved prognostic accuracy in all validation data sets relative to molecular signatures alone (mean C-index, 0.70 vs 0.63) and another commercialized clinical-molecular signature (mean C-index, 0.68 vs 0.65). Conclusions and Relevance The proposed clinical-immune signature is a promising biomarker for estimating overall survival in nonsquamous NSCLC, including early-stage disease. Prospective studies are needed to test the clinical utility of the biomarker in individualized management of nonsquamous NSCLC.
Collapse
Affiliation(s)
- Bailiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Yi Cui
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California.,Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California.,Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, California
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California.,Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, California
| |
Collapse
|
49
|
Cui Y, Li B, Li R. Decentralized Learning Framework of Meta-Survival Analysis for Developing Robust Prognostic Signatures. JCO Clin Cancer Inform 2017; 1:1-13. [PMID: 30657395 PMCID: PMC6873986 DOI: 10.1200/cci.17.00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE A significant hurdle in developing reliable gene expression-based prognostic models has been the limited sample size, which can cause overfitting and false discovery. Combining data from multiple studies can enhance statistical power and reduce spurious findings, but how to address the biologic heterogeneity across different datasets remains a major challenge. Better meta-survival analysis approaches are needed. MATERIAL AND METHODS We presented a decentralized learning framework for meta-survival analysis without the need for data aggregation. Our method consisted of a series of proposals that together alleviated the influence of data heterogeneity and improved the performance of survival prediction. First, we transformed the gene expression profile of every sample into normalized percentile ranks to obtain platform-agnostic features. Second, we used Stouffer's meta-z approach in combination with Harrell's concordance index to prioritize and select genes to be included in the model. Third, we used survival discordance as a scale-independent model loss function. Instead of generating a merged dataset and training the model therein, we avoided comparing patients across datasets and individually evaluated the loss function on each dataset. Finally, we optimized the model by minimizing the joint loss function. RESULTS Through comprehensive evaluation on 31 public microarray datasets containing 6,724 samples of several cancer types, we demonstrated that the proposed method has outperformed (1) single prognostic genes identified using conventional meta-analysis, (2) multigene signatures trained on single datasets, (3) multigene signatures trained on merged datasets as well as by other existing meta-analysis methods, and (4) clinically applicable, established multigene signatures. CONCLUSION The decentralized learning approach can be used to effectively perform meta-analysis of gene expression data and to develop robust multigene prognostic signatures.
Collapse
Affiliation(s)
- Yi Cui
- Yi Cui, Bailiang Li, and Ruijiang Li, Stanford University School of Medicine, Stanford, CA; Yi Cui, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Bailiang Li
- Yi Cui, Bailiang Li, and Ruijiang Li, Stanford University School of Medicine, Stanford, CA; Yi Cui, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Ruijiang Li
- Yi Cui, Bailiang Li, and Ruijiang Li, Stanford University School of Medicine, Stanford, CA; Yi Cui, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| |
Collapse
|
50
|
Willis S, Sun Y, Abramovitz M, Fei T, Young B, Lin X, Ni M, Achua J, Regan MM, Gray KP, Gray R, Wang V, Long B, Kammler R, Sparano JA, Williams C, Goldstein LJ, Salgado R, Loi S, Pruneri G, Viale G, Brown M, Leyland-Jones B. High Expression of FGD3, a Putative Regulator of Cell Morphology and Motility, Is Prognostic of Favorable Outcome in Multiple Cancers. JCO Precis Oncol 2017; 1:1700009. [PMID: 32913979 PMCID: PMC7446538 DOI: 10.1200/po.17.00009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose Identification of single-gene biomarkers that are prognostic of outcome can shed new insights on the molecular mechanisms that drive breast cancer and other cancers. Methods Exploratory analysis of 20,464 single-gene messenger RNAs (mRNAs) in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) discovery cohort indicates that low expression of FGD3 mRNA is prognostic for poor outcome. Prognostic significance of faciogenital dysplasia 3 (FGD3), SUSD3, and other single-gene proliferation markers was evaluated in breast cancer and The Cancer Genome Atlas (TCGA) cohorts. Results A meta-analysis of Cox regression of FGD3 mRNA as a continuous variable for overall survival of estrogen receptor (ER)–positive samples in METABRIC discovery, METABRIC validation, TCGA breast cancer, and Combination Chemotherapy in Treating Women With Breast Cancer (E2197) cohorts resulted in a combined hazard ratio (HR) of 0.69 (95% CI, 0.63 to 0.75), indicating better outcome with high expression. In the ER-negative samples, the combined meta-analysis HR was 0.72 (95% CI, 0.63 to 0.82), suggesting that FGD3 is prognostic regardless of ER status. The potential of FGD3 as a biomarker for freedom from recurrence was evaluated in the Breast International Group 1-98 (BIG 1-98; Letrozole or Tamoxifen in Treating Postmenopausal Women With Breast Cancer) study (HR, 0.85; 95% CI, 0.76 to 0.93) for breast cancer–free interval. In the Hungarian Academy of Science (HAS) breast cancer cohort, splitting on the median had an HR of 0.49 (95% CI, 0.42 to 0.58) for recurrence-free survival. A comparison of the Stouffer P value in five ER-positive cohorts showed that FGD3 (P = 3.8E-14) outperformed MKI67 (P = 1.06E-8) and AURKA (P = 2.61E-5). A comparison of the Stouffer P value in four ER-negative cohorts showed that FGD3 (P = 3.88E-5) outperformed MKI67 (P = .477) and AURKA (P = .820). Conclusion FGD3 was previously shown to inhibit cell migration. FGD3 mRNA is regulated by ESR1 and is associated with favorable outcome in six distinct breast cancer cohorts and four TCGA cancer cohorts. This suggests that FGD3 is an important clinical biomarker.
Collapse
Affiliation(s)
- Scooter Willis
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Yuliang Sun
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Mark Abramovitz
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Teng Fei
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Brandon Young
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Xiaoqian Lin
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Min Ni
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Justin Achua
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Meredith M Regan
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Kathryn P Gray
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Robert Gray
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Victoria Wang
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Bradley Long
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Roswitha Kammler
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Joseph A Sparano
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Casey Williams
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Lori J Goldstein
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Roberto Salgado
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Sherene Loi
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Giancarlo Pruneri
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Giuseppe Viale
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Myles Brown
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| | - Brian Leyland-Jones
- , , , , , , , and , Avera Cancer Institute, Sioux Falls, SD; , , , , , and , Dana-Farber Cancer Institute, Boston, MA; , Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX; , Molecular Core, Scripps Florida, Jupiter, FL; , International Breast Cancer Study Group, Bern, Switzerland; , Montefiore Medical Center, Bronx, NY; , Fox Chase Cancer Center, Philadelphia, PA; , Breast Cancer Translational Research Laboratory/Institut Jules Bordet, Brussels, Belgium; , Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; and and , European Institute of Oncology, University of Milan, Milan, Italy
| |
Collapse
|