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Shanthamallu US, Kilpatrick C, Jones A, Rubin J, Saleh A, Barabási AL, Akmaev VR, Ghiassian SD. A Network-Based Framework to Discover Treatment-Response-Predicting Biomarkers for Complex Diseases. J Mol Diagn 2024:S1525-1578(24)00161-2. [PMID: 39067570 DOI: 10.1016/j.jmoldx.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/10/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Precision medicine's potential to transform complex autoimmune disease treatment is often challenged by limited data availability and inadequate sample size when compared with the number of molecular features found in high-throughput multi-omics data sets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein-protein interaction network to reverse disease states. ProBeNet prioritizes biomarkers by considering the following: i) therapy-targeted proteins, ii) disease-specific molecular signatures, and iii) an underlying network of interactions among cellular components (the human interactome). With ProBeNet, biomarkers were discovered predicting patient responses to both an established autoimmune therapy (infliximab) and an investigational compound (a mitogen-activated protein kinase 3/1 inhibitor). The predictive power of ProBeNet biomarkers was validated with retrospective gene-expression data from patients with ulcerative colitis and rheumatoid arthritis and prospective data from patient-derived tissues from patients with ulcerative colitis and Crohn disease. Machine-learning models using ProBeNet biomarkers significantly outperformed models using either all genes or randomly selected genes, especially when data were limited (<20 samples). These results illustrate the value of ProBeNet for reducing features and for constructing robust machine-learning models when limited data are available. ProBeNet may be used to develop companion and complementary diagnostic assays for complex autoimmune disease therapies, which may help stratify suitable patient subgroups in clinical trials, approve new drugs, and improve patient outcomes.
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Affiliation(s)
| | - Casey Kilpatrick
- Department of Therapeutics, Scipher Medicine, Waltham, Massachusetts
| | - Alex Jones
- Department of Data Science and Network Medicine, Scipher Medicine, Waltham, Massachusetts
| | | | - Alif Saleh
- Department of Data Science and Network Medicine, Scipher Medicine, Waltham, Massachusetts
| | - Albert-László Barabási
- Maret School, Washington, DC; Center for Complex Network Research, Northeastern University, Boston, Massachusetts; (¶)Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts
| | - Viatcheslav R Akmaev
- Department of Data Science and Network Medicine, Scipher Medicine, Waltham, Massachusetts
| | - Susan Dina Ghiassian
- Department of Data Science and Network Medicine, Scipher Medicine, Waltham, Massachusetts.
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2
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Lee G, Moon SH, Kim JH, Jeong DY, Choi J, Choi JY, Lee HY. Multimodal Imaging Approach for Tumor Treatment Response Evaluation in the Era of Immunotherapy. Invest Radiol 2024:00004424-990000000-00234. [PMID: 39018248 DOI: 10.1097/rli.0000000000001096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
ABSTRACT Immunotherapy is likely the most remarkable advancement in lung cancer treatment during the past decade. Although immunotherapy provides substantial benefits, their therapeutic responses differ from those of conventional chemotherapy and targeted therapy, and some patients present unique immunotherapy response patterns that cannot be judged under the current measurement standards. Therefore, the response monitoring of immunotherapy can be challenging, such as the differentiation between real response and pseudo-response. This review outlines the various tumor response patterns to immunotherapy and discusses methods for quantifying computed tomography (CT) and 18F-fluorodeoxyglucose positron emission tomography (PET) in the field of lung cancer. Emerging technologies in magnetic resonance imaging (MRI) and non-FDG PET tracers are also explored. With immunotherapy responses, the role for imaging is essential in both anatomical radiological responses (CT/MRI) and molecular changes (PET imaging). Multiple aspects must be considered when assessing treatment responses using CT and PET. Finally, we introduce multimodal approaches that integrate imaging and nonimaging data, and we discuss future directions for the assessment and prediction of lung cancer responses to immunotherapy.
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Affiliation(s)
- Geewon Lee
- From the Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea (G.L., D.Y.J., J.C., H.Y.L.); Department of Radiology and Medical Research Institute, Pusan National University Hospital, Pusan National University School of Medicine, Busan, South Korea (G.L.); Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea (S.H.M., J.Y.C.); Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea (J.H.K.); Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, South Korea (J.C.); and Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea (H.Y.L.)
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3
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Pettorruso M, Di Lorenzo G, Benatti B, d’Andrea G, Cavallotto C, Carullo R, Mancusi G, Di Marco O, Mammarella G, D’Attilio A, Barlocci E, Rosa I, Cocco A, Padula LP, Bubbico G, Perrucci MG, Guidotti R, D’Andrea A, Marzetti L, Zoratto F, Dell’Osso BM, Martinotti G. Overcoming treatment-resistant depression with machine-learning based tools: a study protocol combining EEG and clinical data to personalize glutamatergic and brain stimulation interventions (SelecTool Project). Front Psychiatry 2024; 15:1436006. [PMID: 39086731 PMCID: PMC11288917 DOI: 10.3389/fpsyt.2024.1436006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Treatment-Resistant Depression (TRD) poses a substantial health and economic challenge, persisting as a major concern despite decades of extensive research into novel treatment modalities. The considerable heterogeneity in TRD's clinical manifestations and neurobiological bases has complicated efforts toward effective interventions. Recognizing the need for precise biomarkers to guide treatment choices in TRD, herein we introduce the SelecTool Project. This initiative focuses on developing (WorkPlane 1/WP1) and conducting preliminary validation (WorkPlane 2/WP2) of a computational tool (SelecTool) that integrates clinical data, neurophysiological (EEG) and peripheral (blood sample) biomarkers through a machine-learning framework designed to optimize TRD treatment protocols. The SelecTool project aims to enhance clinical decision-making by enabling the selection of personalized interventions. It leverages multi-modal data analysis to navigate treatment choices towards two validated therapeutic options for TRD: esketamine nasal spray (ESK-NS) and accelerated repetitive Transcranial Magnetic Stimulation (arTMS). In WP1, 100 subjects with TRD will be randomized to receive either ESK-NS or arTMS, with comprehensive evaluations encompassing neurophysiological (EEG), clinical (psychometric scales), and peripheral (blood samples) assessments both at baseline (T0) and one month post-treatment initiation (T1). WP2 will utilize the data collected in WP1 to train the SelecTool algorithm, followed by its application in a second, out-of-sample cohort of 20 TRD subjects, assigning treatments based on the tool's recommendations. Ultimately, this research seeks to revolutionize the treatment of TRD by employing advanced machine learning strategies and thorough data analysis, aimed at unraveling the complex neurobiological landscape of depression. This effort is expected to provide pivotal insights that will promote the development of more effective and individually tailored treatment strategies, thus addressing a significant void in current TRD management and potentially reducing its profound societal and economic burdens.
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Affiliation(s)
- Mauro Pettorruso
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Department of Mental Health, ASL02 Lanciano-Vasto-Chieti, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Giorgio Di Lorenzo
- Laboratory of Psychophysiology and Cognitive Neuroscience, Chair of Psychiatry, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Institute of Hospitalization and Care With Scientific Character (IRCCS) Fondazione Santa Lucia, Rome, Italy
| | - Beatrice Benatti
- Department of Biomedical and Clinical Sciences Luigi Sacco and Aldo Ravelli Center for Neurotechnology and Brain Therapeutic, University of Milan, Milano, Italy
| | - Giacomo d’Andrea
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Department of Mental Health, ASL02 Lanciano-Vasto-Chieti, Chieti, Italy
| | - Clara Cavallotto
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Rosalba Carullo
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Gianluca Mancusi
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Ornella Di Marco
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Giovanna Mammarella
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Antonio D’Attilio
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Elisabetta Barlocci
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Ilenia Rosa
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Alessio Cocco
- Department of Mental Health, ASL02 Lanciano-Vasto-Chieti, Chieti, Italy
| | - Lorenzo Pio Padula
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Giovanna Bubbico
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Mauro Gianni Perrucci
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Roberto Guidotti
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Department of Mental Health, ASL02 Lanciano-Vasto-Chieti, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Antea D’Andrea
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
| | - Laura Marzetti
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Francesca Zoratto
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Bernardo Maria Dell’Osso
- Department of Biomedical and Clinical Sciences Luigi Sacco and Aldo Ravelli Center for Neurotechnology and Brain Therapeutic, University of Milan, Milano, Italy
| | - Giovanni Martinotti
- Department of Neurosciences, Imaging and Clinical Sciences, Università degli Studi G. D’Annunzio, Chieti, Italy
- Department of Mental Health, ASL02 Lanciano-Vasto-Chieti, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Psychopharmacology, Drug Misuse and Novel Psychoactive Substances Research Unit, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
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4
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Siminea N, Czeizler E, Popescu VB, Petre I, Păun A. Connecting the dots: Computational network analysis for disease insight and drug repurposing. Curr Opin Struct Biol 2024; 88:102881. [PMID: 38991238 DOI: 10.1016/j.sbi.2024.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/22/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024]
Abstract
Network biology is a powerful framework for studying the structure, function, and dynamics of biological systems, offering insights into the balance between health and disease states. The field is seeing rapid progress in all of its aspects: data availability, network synthesis, network analytics, and impactful applications in medicine and drug development. We review the most recent and significant results in network biomedicine, with a focus on the latest data, analytics, software resources, and applications in medicine. We also discuss what in our view are the likely directions of impactful development over the next few years.
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Affiliation(s)
- Nicoleta Siminea
- Faculty of Mathematics and Computer Science, University of Bucharest, Romania; National Institute of Research and Development for Biological Sciences, Romania
| | - Eugen Czeizler
- Faculty of Medicine, University of Helsinki, Finland; National Institute of Research and Development for Biological Sciences, Romania
| | | | - Ion Petre
- Department of Mathematics and Statistics, University of Turku, Finland; National Institute of Research and Development for Biological Sciences, Romania.
| | - Andrei Păun
- Faculty of Mathematics and Computer Science, University of Bucharest, Romania; National Institute of Research and Development for Biological Sciences, Romania.
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5
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Holder AM, Dedeilia A, Sierra-Davidson K, Cohen S, Liu D, Parikh A, Boland GM. Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours. Nat Rev Cancer 2024; 24:498-512. [PMID: 38867074 DOI: 10.1038/s41568-024-00705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Although more than a decade has passed since the approval of immune checkpoint inhibitors (ICIs) for the treatment of melanoma and non-small-cell lung, breast and gastrointestinal cancers, many patients still show limited response. US Food and Drug Administration (FDA)-approved biomarkers include programmed cell death 1 ligand 1 (PDL1) expression, microsatellite status (that is, microsatellite instability-high (MSI-H)) and tumour mutational burden (TMB), but these have limited utility and/or lack standardized testing approaches for pan-cancer applications. Tissue-based analytes (such as tumour gene signatures, tumour antigen presentation or tumour microenvironment profiles) show a correlation with immune response, but equally, these demonstrate limited efficacy, as they represent a single time point and a single spatial assessment. Patient heterogeneity as well as inter- and intra-tumoural differences across different tissue sites and time points represent substantial challenges for static biomarkers. However, dynamic biomarkers such as longitudinal biopsies or novel, less-invasive markers such as blood-based biomarkers, radiomics and the gut microbiome show increasing potential for the dynamic identification of ICI response, and patient-tailored predictors identified through neoadjuvant trials or novel ex vivo tumour models can help to personalize treatment. In this Perspective, we critically assess the multiple new static, dynamic and patient-specific biomarkers, highlight the newest consortia and trial efforts, and provide recommendations for future clinical trials to make meaningful steps forwards in the field.
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Affiliation(s)
- Ashley M Holder
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Aparna Parikh
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
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6
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Premeaux TA, Bowler S, Friday CM, Moser CB, Hoenigl M, Lederman MM, Landay AL, Gianella S, Ndhlovu LC. Machine learning models based on fluid immunoproteins that predict non-AIDS adverse events in people with HIV. iScience 2024; 27:109945. [PMID: 38812553 PMCID: PMC11134891 DOI: 10.1016/j.isci.2024.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/12/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Despite the success of antiretroviral therapy (ART), individuals with HIV remain at risk for experiencing non-AIDS adverse events (NAEs), including cardiovascular complications and malignancy. Several surrogate immune biomarkers in blood have shown predictive value in predicting NAEs; however, composite panels generated using machine learning may provide a more accurate advancement for monitoring and discriminating NAEs. In a nested case-control study, we aimed to develop machine learning models to discriminate cases (experienced an event) and matched controls using demographic and clinical characteristics alongside 49 plasma immunoproteins measured prior to and post-ART initiation. We generated support vector machine (SVM) classifier models for high-accuracy discrimination of individuals aged 30-50 years who experienced non-fatal NAEs at pre-ART and one-year post-ART. Extreme gradient boosting generated a high-accuracy model at pre-ART, while K-nearest neighbors performed poorly all around. SVM modeling may offer guidance to improve disease monitoring and elucidate potential therapeutic interventions.
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Affiliation(s)
- Thomas A. Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Courtney M. Friday
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carlee B. Moser
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Michael M. Lederman
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alan L. Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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7
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Rodler S, Aydogdu C, Brinkmann I, Berg E, Kopliku R, Götz M, Ivanova T, Tamalunas A, Schulz GB, Heinemann V, Stief CG, Casuscelli J. Toxicity-Induced Discontinuation of Immune Checkpoint Inhibitors in Metastatic Urothelial Cancer: 6-Year Experience from a Specialized Uro-Oncology Center. Cancers (Basel) 2024; 16:2246. [PMID: 38927951 PMCID: PMC11201648 DOI: 10.3390/cancers16122246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Immune checkpoint inhibitor (ICI) therapies have been established as the standard-of-care in various uro-oncological cancers. Immune-related adverse events (irAEs) are frequent, but their degree rarely leads to the discontinuation of immunotherapies. Unplanned permanent treatment discontinuation may negatively impact the outcomes of patients, but there are emerging data about a positive correlation between emergence of severe irAEs and therapeutic cancer responses. In this study, a retrospective analysis of patients treated for urothelial carcinoma (UC) with ICI-based immunotherapy was conducted. irAEs were classified according to the Common Terminology Criteria for Adverse Events (CTCAEs) and radiological responses according to the Response Evaluation Criteria In Solid Tumors (RECISTs). Out of 108 patients with metastatic urothelial cancer that underwent immunotherapy, 11 experienced a severe irAE that required permanent discontinuation of ICI therapy. The most frequent irAEs leading to discontinuation were hepatitis (n = 4), pneumonitis (n = 2), and gastritis or colitis (n = 2). Prior to discontinuation (R1), the radiological best response was complete remission (CR) in three patients, partial response (PR) in six, and stable disease (SD) in wo patients. After the discontinuation of ICI therapy (R2), the best responses were CR in six, PR in three, and SD in two patients. Following discontinuation, the majority of these patients showed a sustained treatment response, despite not receiving any cancer-specific treatment. The median time of response after discontinuation of ICI therapy was 26.0 (5.2-55.8) months. We propose accurate counseling and close follow-ups of patients following their discontinuation of ICI therapy due to irAEs, as responses can be durable and deep, and many patients do not require immediate subsequent therapies, even in urothelial cancer. More data are required to find predictors of the length of response to appropriately counsel patients.
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Affiliation(s)
- Severin Rodler
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
- Department of Urology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Can Aydogdu
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Isabel Brinkmann
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Elena Berg
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Rega Kopliku
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
| | - Melanie Götz
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Troya Ivanova
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
| | - Alexander Tamalunas
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Gerald B. Schulz
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
| | - Volker Heinemann
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
- Department of Internal Medicine III, University Hospital of Munich, 81377 Munich, Germany
| | - Christian G. Stief
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
| | - Jozefina Casuscelli
- Department of Urology, University Hospital of Munich, 81377 Munich, Germany
- Comprehensive Cancer Center, University Hospital of Munich, 81377 Munich, Germany
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Li X, Feng X, Zhou J, Luo Y, Chen X, Zhao J, Chen H, Xiong G, Luo G. A muti-modal feature fusion method based on deep learning for predicting immunotherapy response. J Theor Biol 2024; 586:111816. [PMID: 38589007 DOI: 10.1016/j.jtbi.2024.111816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Immune checkpoint therapy (ICT) has greatly improved the survival of cancer patients in the past few years, but only a small number of patients respond to ICT. To predict ICT response, we developed a multi-modal feature fusion model based on deep learning (MFMDL). This model utilizes graph neural networks to map gene-gene relationships in gene networks to low dimensional vector spaces, and then fuses biological pathway features and immune cell infiltration features to make robust predictions of ICT. We used five datasets to validate the predictive performance of the MFMDL. These five datasets span multiple types of cancer, including melanoma, lung cancer, and gastric cancer. We found that the prediction performance of multi-modal feature fusion model based on deep learning is superior to other traditional ICT biomarkers, such as ICT targets or tumor microenvironment-associated markers. In addition, we also conducted ablation experiments to demonstrate the necessity of fusing different modal features, which can improve the prediction accuracy of the model.
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Affiliation(s)
- Xiong Li
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Xuan Feng
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Juan Zhou
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Yuchao Luo
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Xiao Chen
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Jiapeng Zhao
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Haowen Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
| | - Guoming Xiong
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Guoliang Luo
- School of Software, East China Jiaotong University, Nanchang 330013, China
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9
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Wang H, Zhang Y, Zhang H, Cao H, Mao J, Chen X, Wang L, Zhang N, Luo P, Xue J, Qi X, Dong X, Liu G, Cheng Q. Liquid biopsy for human cancer: cancer screening, monitoring, and treatment. MedComm (Beijing) 2024; 5:e564. [PMID: 38807975 PMCID: PMC11130638 DOI: 10.1002/mco2.564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Currently, tumor treatment modalities such as immunotherapy and targeted therapy have more stringent requirements for obtaining tumor growth information and require more accurate and easy-to-operate tumor information detection methods. Compared with traditional tissue biopsy, liquid biopsy is a novel, minimally invasive, real-time detection tool for detecting information directly or indirectly released by tumors in human body fluids, which is more suitable for the requirements of new tumor treatment modalities. Liquid biopsy has not been widely used in clinical practice, and there are fewer reviews of related clinical applications. This review summarizes the clinical applications of liquid biopsy components (e.g., circulating tumor cells, circulating tumor DNA, extracellular vesicles, etc.) in tumorigenesis and progression. This includes the development process and detection techniques of liquid biopsies, early screening of tumors, tumor growth detection, and guiding therapeutic strategies (liquid biopsy-based personalized medicine and prediction of treatment response). Finally, the current challenges and future directions for clinical applications of liquid biopsy are proposed. In sum, this review will inspire more researchers to use liquid biopsy technology to promote the realization of individualized therapy, improve the efficacy of tumor therapy, and provide better therapeutic options for tumor patients.
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Affiliation(s)
- Hao Wang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Yi Zhang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Hao Zhang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Hui Cao
- Department of PsychiatryThe School of Clinical Medicine, Hunan University of Chinese MedicineChangshaChina
- Department of PsychiatryBrain Hospital of Hunan Province (The Second People’s Hospital of Hunan Province)ChangshaChina
| | - Jinning Mao
- Health Management CenterThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xinxin Chen
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Liangchi Wang
- Department of NeurosurgeryFengdu People's Hospital, ChongqingChongqingChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Peng Luo
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Ji Xue
- Department of NeurosurgeryTraditional Chinese Medicine Hospital Dianjiang ChongqingChongqingChina
| | - Xiaoya Qi
- Health Management CenterThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xiancheng Dong
- Department of Cerebrovascular DiseasesDazhou Central HospitalSichuanChina
| | - Guodong Liu
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Quan Cheng
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
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Manitz J, Gerhold‐Ay A, Kieslich P, Shah P, Mrowiec T, Tyroller K. Avelumab first-line maintenance in advanced urothelial carcinoma: Complete screening for prognostic and predictive factors using machine learning in the JAVELIN Bladder 100 phase 3 trial. Cancer Med 2024; 13:e7411. [PMID: 38924353 PMCID: PMC11194683 DOI: 10.1002/cam4.7411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Avelumab first-line (1 L) maintenance is a standard of care for advanced urothelial carcinoma (aUC) based on the JAVELIN Bladder 100 phase 3 trial, which showed that avelumab 1 L maintenance + best supportive care (BSC) significantly prolonged overall survival (OS) and progression-free survival (PFS) vs BSC alone in patients who were progression free after receiving 1 L platinum-containing chemotherapy. Here, we comprehensively screened JAVELIN Bladder 100 trial datasets to identify prognostic factors that define subpopulations of patients with longer or shorter OS irrespective of treatment, and predictive factors that select patients who could obtain a greater OS benefit from avelumab 1 L maintenance treatment. METHODS We performed machine learning analyses to screen a large set of baseline covariates, including patient demographics, disease characteristics, laboratory values, molecular biomarkers, and patient-reported outcomes. Covariates were identified from previously reported analyses and established prognostic and predictive markers. Variables selected from random survival forest models were processed further in univariate Cox models with treatment interaction and visually inspected using correlation analysis and Kaplan-Meier curves. Results were summarized in a multivariable Cox model. RESULTS Prognostic baseline covariates associated with OS included in the final model were assignment to avelumab 1 L maintenance treatment, Eastern Cooperative Oncology Group performance status, site of metastasis, sum of longest target lesion diameters, levels of C-reactive protein and alkaline phosphatase in blood, lymphocyte proportion in intratumoral stroma, tumor mutational burden, and tumor CD8+ T-cell infiltration. Potential predictive factors included site of metastasis, tumor mutation burden, and tumor CD8+ T-cell infiltration. An analysis in patients with PD-L1+ tumors had similar findings to those in the overall population. CONCLUSIONS Machine learning analyses of data from the JAVELIN Bladder 100 trial identified potential prognostic and predictive factors for avelumab 1 L maintenance treatment in patients with aUC, which warrant further evaluation in other clinical datasets.
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11
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Zhang W, Guo J, Lv X, Zhang F. Combined Machine Learning and High-Throughput Calculations Predict Heyd-Scuseria-Ernzerhof Band Gap of 2D Materials and Potential MoSi 2N 4 Heterostructures. J Phys Chem Lett 2024; 15:5413-5419. [PMID: 38743311 DOI: 10.1021/acs.jpclett.4c01013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We present a novel target-driven methodology devised to predict the Heyd-Scuseria-Ernzerhof (HSE) band gap of two-dimensional (2D) materials leveraging the comprehensive C2DB database. This innovative approach integrates machine learning and density functional theory (DFT) calculations to predict the HSE band gap, conduction band minimum (CBM), and valence band maximum (VBM) of 2176 types of 2D materials. Subsequently, we collected a comprehensive data set comprising 3539 types of 2D materials, each characterized by its HSE band gaps, CBM, and VBM. Considering the lattice disparities between MoSi2N4 (MSN) and 2D materials, our analysis predicted 766 potential MSN/2D heterostructures. These heterostructures are further categorized into four distinct types based on the relative positions of their CBM and VBM: Type I encompasses 230 variants, Type II comprises 244 configurations, Type III consists of 284 permutations, and 0 band gap comprises 8 types.
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Affiliation(s)
- Weibin Zhang
- College of Physics and Electronics Information, Yunnan Key Laboratory of Optoelectronic Information Technology, Key Laboratory of Advanced Technique & Preparation for Renewable Energy Materials-Ministry of Education, Yunnan Normal University, Kunming 650500, P.R. China
| | - Jie Guo
- College of Physics and Electronics Information, Yunnan Key Laboratory of Optoelectronic Information Technology, Key Laboratory of Advanced Technique & Preparation for Renewable Energy Materials-Ministry of Education, Yunnan Normal University, Kunming 650500, P.R. China
| | - Xiankui Lv
- College of Physics and Electronics Information, Yunnan Key Laboratory of Optoelectronic Information Technology, Key Laboratory of Advanced Technique & Preparation for Renewable Energy Materials-Ministry of Education, Yunnan Normal University, Kunming 650500, P.R. China
| | - Fuchun Zhang
- College of Physics and Electronic Information, Yan'an University, Yan'an 716000, P. R. China
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Deng D, Xu X, Cui T, Xu M, Luo K, Zhang H, Wang Q, Song C, Li C, Li G, Shang D. PBAC: A pathway-based attention convolution neural network for predicting clinical drug treatment responses. J Cell Mol Med 2024; 28:e18298. [PMID: 38683133 PMCID: PMC11057419 DOI: 10.1111/jcmm.18298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Precise and personalized drug application is crucial in the clinical treatment of complex diseases. Although neural networks offer a new approach to improving drug strategies, their internal structure is difficult to interpret. Here, we propose PBAC (Pathway-Based Attention Convolution neural network), which integrates a deep learning framework and attention mechanism to address the complex biological pathway information, thereby provide a biology function-based robust drug responsiveness prediction model. PBAC has four layers: gene-pathway layer, attention layer, convolution layer and fully connected layer. PBAC improves the performance of predicting drug responsiveness by focusing on important pathways, helping us understand the mechanism of drug action in diseases. We validated the PBAC model using data from four chemotherapy drugs (Bortezomib, Cisplatin, Docetaxel and Paclitaxel) and 11 immunotherapy datasets. In the majority of datasets, PBAC exhibits superior performance compared to traditional machine learning methods and other research approaches (area under curve = 0.81, the area under the precision-recall curve = 0.73). Using PBAC attention layer output, we identified some pathways as potential core cancer regulators, providing good interpretability for drug treatment prediction. In summary, we presented PBAC, a powerful tool to predict drug responsiveness based on the biology pathway information and explore the potential cancer-driving pathways.
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Affiliation(s)
- Dexun Deng
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- School of ComputerUniversity of South ChinaHengyangHunanChina
| | - Xiaoqiang Xu
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cardiology, The First Affiliated Hospital, Hengyang Medical SchoolUniversity of South ChinaHengyangChina
| | - Ting Cui
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
| | - Mingcong Xu
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
| | - Kunpeng Luo
- Department of Gastroenterology and HepatologySecond Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Han Zhang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- School of ComputerUniversity of South ChinaHengyangHunanChina
| | - Qiuyu Wang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- School of ComputerUniversity of South ChinaHengyangHunanChina
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cardiology, The First Affiliated Hospital, Hengyang Medical SchoolUniversity of South ChinaHengyangChina
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
| | - Chao Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- School of ComputerUniversity of South ChinaHengyangHunanChina
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cardiology, The First Affiliated Hospital, Hengyang Medical SchoolUniversity of South ChinaHengyangChina
| | - Chao Li
- Department of AnesthesiologyThe First Affiliated Hospital of University of South ChinaHengyangPR China
| | - Guohua Li
- Department of Pathophysiology, Key Laboratory for Arteriosclerology of Hunan Province, MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical SchoolInstitute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, University of South ChinaHengyangHunanChina
| | - Desi Shang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Hunan Provincial Key Laboratory of Multi‐omics And Artificial Intelligence of Cardiovascular DiseasesUniversity of South ChinaHengyangHunanChina
- School of ComputerUniversity of South ChinaHengyangHunanChina
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cardiology, The First Affiliated Hospital, Hengyang Medical SchoolUniversity of South ChinaHengyangChina
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
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13
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Augustin RC, Luke JJ. Rapidly Evolving Pre- and Post-surgical Systemic Treatment of Melanoma. Am J Clin Dermatol 2024; 25:421-434. [PMID: 38409643 DOI: 10.1007/s40257-024-00852-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
With the development of effective BRAF-targeted and immune-checkpoint immunotherapies for metastatic melanoma, clinical trials are moving these treatments into earlier adjuvant and perioperative settings. BRAF-targeted therapy is a standard of care in resected stage III-IV melanoma, while anti-programmed death-1 (PD1) immunotherapy is now a standard of care option in resected stage IIB through IV disease. With both modalities, recurrence-free survival and distant-metastasis-free survival are improved by a relative 35-50%, yet no improvement in overall survival has been demonstrated. Neoadjuvant anti-PD1 therapy improves event-free survival by approximately an absolute 23%, although improvements in overall survival have yet to be demonstrated. Understanding which patients are most likely to recur and which are most likely to benefit from treatment is now the highest priority question in the field. Biomarker analyses, such as gene expression profiling of the primary lesion and circulating DNA, are preliminarily exciting as potential biomarkers, though each has drawbacks. As in the setting of metastatic disease, markers that inform positive outcomes include interferon-γ gene expression, PD-L1, and high tumor mutational burden, while negative predictors of outcome include circulating factors such as lactate dehydrogenase, interleukin-8, and C-reactive protein. Integrating and validating these markers into clinically relevant models is thus a high priority. Melanoma therapeutics continues to advance with combination adjuvant approaches now investigating anti-PD1 with lymphocyte activation gene 3 (LAG3), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), and individualized neoantigen therapies. How this progress will be integrated into the management of a unique patient to reduce recurrence, limit toxicity, and avoid over-treatment will dominate clinical research and patient care over the next decade.
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Affiliation(s)
- Ryan C Augustin
- UPMC Hillman Cancer Center, 5150 Centre Ave. Room 1.27C, Pittsburgh, PA, 15232, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jason J Luke
- UPMC Hillman Cancer Center, 5150 Centre Ave. Room 1.27C, Pittsburgh, PA, 15232, USA.
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Lu B, Xia Y, Ren Y, Xie M, Zhou L, Vinai G, Morton SA, Wee ATS, van der Wiel WG, Zhang W, Wong PKJ. When Machine Learning Meets 2D Materials: A Review. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305277. [PMID: 38279508 PMCID: PMC10987159 DOI: 10.1002/advs.202305277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/21/2023] [Indexed: 01/28/2024]
Abstract
The availability of an ever-expanding portfolio of 2D materials with rich internal degrees of freedom (spin, excitonic, valley, sublattice, and layer pseudospin) together with the unique ability to tailor heterostructures made layer by layer in a precisely chosen stacking sequence and relative crystallographic alignments, offers an unprecedented platform for realizing materials by design. However, the breadth of multi-dimensional parameter space and massive data sets involved is emblematic of complex, resource-intensive experimentation, which not only challenges the current state of the art but also renders exhaustive sampling untenable. To this end, machine learning, a very powerful data-driven approach and subset of artificial intelligence, is a potential game-changer, enabling a cheaper - yet more efficient - alternative to traditional computational strategies. It is also a new paradigm for autonomous experimentation for accelerated discovery and machine-assisted design of functional 2D materials and heterostructures. Here, the study reviews the recent progress and challenges of such endeavors, and highlight various emerging opportunities in this frontier research area.
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Affiliation(s)
- Bin Lu
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
| | - Yuze Xia
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
| | - Yuqian Ren
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
| | - Miaomiao Xie
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
| | - Liguo Zhou
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
| | - Giovanni Vinai
- Instituto Officina dei Materiali (IOM)‐CNRLaboratorio TASCTriesteI‐34149Italy
| | - Simon A. Morton
- Advanced Light Source (ALS)Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Andrew T. S. Wee
- Department of Physics and Centre for Advanced 2D Materials (CA2DM) and Graphene Research Centre (GRC)National University of SingaporeSingapore117542Singapore
| | - Wilfred G. van der Wiel
- NanoElectronics Group, MESA+ Institute for Nanotechnology and BRAINS Center for Brain‐Inspired Nano SystemsUniversity of TwenteEnschede7500AEThe Netherlands
- Institute of PhysicsUniversity of Münster48149MünsterGermany
| | - Wen Zhang
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
- NanoElectronics Group, MESA+ Institute for Nanotechnology and BRAINS Center for Brain‐Inspired Nano SystemsUniversity of TwenteEnschede7500AEThe Netherlands
| | - Ping Kwan Johnny Wong
- ARTIST Lab for Artificial Electronic Materials and Technologies, School of MicroelectronicsNorthwestern Polytechnical UniversityXi'an710072P. R. China
- Yangtze River Delta Research Institute of Northwestern Polytechnical UniversityTaicang215400P. R. China
- NPU Chongqing Technology Innovation CenterChongqing400000P. R. China
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15
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Sotudian S, Paschalidis IC. ITNR: Inversion Transformer-based Neural Ranking for cancer drug recommendations. Comput Biol Med 2024; 172:108312. [PMID: 38503090 PMCID: PMC10990436 DOI: 10.1016/j.compbiomed.2024.108312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
Personalized drug response prediction is an approach for tailoring effective therapeutic strategies for patients based on their tumors' genomic characterization. While machine learning methods are widely employed in the literature, they often struggle to capture drug-cell line relations across various cell lines. In addressing this challenge, our study introduces a novel listwise Learning-to-Rank (LTR) model named Inversion Transformer-based Neural Ranking (ITNR). ITNR utilizes genomic features and a transformer architecture to decipher functional relationships and construct models that can predict patient-specific drug responses. Our experiments were conducted on three major drug response data sets, showing that ITNR reliably and consistently outperforms state-of-the-art LTR models.
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Affiliation(s)
- Shahabeddin Sotudian
- Department of Electrical and Computer Engineering, Division of Systems Engineering, Boston University, Boston, MA, USA.
| | - Ioannis Ch Paschalidis
- Department of Electrical and Computer Engineering, Division of Systems Engineering, Boston University, Boston, MA, USA; Department of Biomedical Engineering, and Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA.
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16
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Nam DY, Rhee JK. Identifying microRNAs associated with tumor immunotherapy response using an interpretable machine learning model. Sci Rep 2024; 14:6172. [PMID: 38486102 PMCID: PMC10940311 DOI: 10.1038/s41598-024-56843-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
Predicting clinical responses to tumor immunotherapy is essential to reduce side effects and the potential for sustained clinical responses. Nevertheless, preselecting patients who are likely to respond to such treatments remains highly challenging. Here, we explored the potential of microRNAs (miRNAs) as predictors of immune checkpoint blockade responses using a machine learning approach. First, we constructed random forest models to predict the response to tumor ICB therapy using miRNA expression profiles across 19 cancer types. The contribution of individual miRNAs to each prediction process was determined by employing SHapley Additive exPlanations (SHAP) for model interpretation. Remarkably, the predictive performance achieved by using a small number of miRNAs with high feature importance was similar to that achieved by using the entire miRNA set. Additionally, the genes targeted by these miRNAs were closely associated with tumor- and immune-related pathways. In conclusion, this study demonstrates the potential of miRNA expression data for assessing tumor immunotherapy responses. Furthermore, we confirmed the potential of informative miRNAs as biomarkers for the prediction of immunotherapy response, which will advance our understanding of tumor immunotherapy mechanisms.
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Affiliation(s)
- Dong-Yeon Nam
- Department of Bioinformatics & Life Science, Soongsil University, Seoul, Republic of Korea
| | - Je-Keun Rhee
- Department of Bioinformatics & Life Science, Soongsil University, Seoul, Republic of Korea.
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17
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Li Y, Wu X, Fang D, Luo Y. Informing immunotherapy with multi-omics driven machine learning. NPJ Digit Med 2024; 7:67. [PMID: 38486092 PMCID: PMC10940614 DOI: 10.1038/s41746-024-01043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024] Open
Abstract
Progress in sequencing technologies and clinical experiments has revolutionized immunotherapy on solid and hematologic malignancies. However, the benefits of immunotherapy are limited to specific patient subsets, posing challenges for broader application. To improve its effectiveness, identifying biomarkers that can predict patient response is crucial. Machine learning (ML) play a pivotal role in harnessing multi-omic cancer datasets and unlocking new insights into immunotherapy. This review provides an overview of cutting-edge ML models applied in omics data for immunotherapy analysis, including immunotherapy response prediction and immunotherapy-relevant tumor microenvironment identification. We elucidate how ML leverages diverse data types to identify significant biomarkers, enhance our understanding of immunotherapy mechanisms, and optimize decision-making process. Additionally, we discuss current limitations and challenges of ML in this rapidly evolving field. Finally, we outline future directions aimed at overcoming these barriers and improving the efficiency of ML in immunotherapy research.
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Affiliation(s)
- Yawei Li
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Xin Wu
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
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18
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Fan L, Wang J, Zhang Z, Zuo Z, Liu Y, Ye F, Ma B, Sun Z. Identification of RNA methylation-related lncRNAs for prognostic assessment and immunotherapy in bladder cancer-based on single cell/Bulk RNA sequencing data. Funct Integr Genomics 2024; 24:56. [PMID: 38472459 DOI: 10.1007/s10142-024-01283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/10/2023] [Accepted: 01/01/2024] [Indexed: 03/14/2024]
Abstract
Bladder cancer is a malignancy characterized by significant heterogeneity. RNA methylation has received an increasing amount of attention in recent years. RNA data were collected from the GEO database, and cell subsets were classified according to specific cell markers. Epithelial, immunological, and fibroblast cells were clustered individually to explore the tumor heterogeneity. To distinguish between malignant and benign cells, the InferCNV R package was employed. The monocle2 R package was used for pseudotime analysis. The Decouple R package was used for transcription factor analysis of each cell subgroup, and PROGENy was used to predict the activity of pathways related to tumors. The target lncRNA was screened for model construction. In addition, the qPCR experiment was used to detect the transcription level of lncRNA. Epithelial cells, fibroblasts, and T cells significantly differ in tumor and normal tissues. The lncRNAs related to m6A/m5C/m1A were intersected to construct the model. Finally, six model lncRNAs (PSMB8-AS1, THUMPD3-AS1, U47924.27, XXbac-B135H6.15, MIR99AHG, and C14orf132) were screened. High-risk individuals were shown to have a better prognosis. qPCR experiments showed that the model lncRNA was differentially expressed between normal and tumor cells. Immunotherapy will be more effective in treating individuals with lower risk than those with higher risk using 4 candidate drugs. The prognostic m6A/m5C/m1A-related lncRNA model was constructed for evaluating the clinical outcomes of bladder cancer patients and guiding clinical medication.
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Affiliation(s)
- LianMing Fan
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jie Wang
- Department of Urology, The Second People's Hospital of Meishan City, Meishan, 620500, Sichuan, China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China
| | - Zhiya Zhang
- Department of Oncology The Second People's Hospital of Meishan City, Meishan, 620500, Sichuan, China
| | - Zili Zuo
- Department of Urology, The Second People's Hospital of Meishan City, Meishan, 620500, Sichuan, China
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Baoluo Ma
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China.
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China.
| | - Zhou Sun
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China.
- Department of Urology, The First People's Hospital of Jiangxia District, Wuhan, 430200, Hubei, China.
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19
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Guo Y, Remaily BC, Thomas J, Kim K, Kulp SK, Mace TA, Ganesan LP, Owen DH, Coss CC, Phelps MA. Antibody Drug Clearance: An Underexplored Marker of Outcomes with Checkpoint Inhibitors. Clin Cancer Res 2024; 30:942-958. [PMID: 37921739 PMCID: PMC10922515 DOI: 10.1158/1078-0432.ccr-23-1683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Immune-checkpoint inhibitor (ICI) therapy has dramatically changed the clinical landscape for several cancers, and ICI use continues to expand across many cancer types. Low baseline clearance (CL) and/or a large reduction of CL during treatment correlates with better clinical response and longer survival. Similar phenomena have also been reported with other monoclonal antibodies (mAb) in cancer and other diseases, highlighting a characteristic of mAb clinical pharmacology that is potentially shared among various mAbs and diseases. Though tempting to attribute poor outcomes to low drug exposure and arguably low target engagement due to high CL, such speculation is not supported by the relatively flat exposure-response relationship of most ICIs, where a higher dose or exposure is not likely to provide additional benefit. Instead, an elevated and/or increasing CL could be a surrogate marker of the inherent resistant phenotype that cannot be reversed by maximizing drug exposure. The mechanisms connecting ICI clearance, therapeutic efficacy, and resistance are unclear and likely to be multifactorial. Therefore, to explore the potential of ICI CL as an early marker for efficacy, this review highlights the similarities and differences of CL characteristics and CL-response relationships for all FDA-approved ICIs, and we compare and contrast these to selected non-ICI mAbs. We also discuss underlying mechanisms that potentially link mAb CL with efficacy and highlight existing knowledge gaps and future directions where more clinical and preclinical investigations are warranted to clearly understand the value of baseline and/or time-varying CL in predicting response to ICI-based therapeutics.
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Affiliation(s)
- Yizhen Guo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Bryan C. Remaily
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Justin Thomas
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Kyeongmin Kim
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Samuel K. Kulp
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Thomas A. Mace
- Department of Internal Medicine, Division of Rheumatology and Immunology, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Latha P. Ganesan
- Department of Internal Medicine, Division of Rheumatology and Immunology, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Dwight H. Owen
- Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH
| | - Christopher C. Coss
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
| | - Mitch A. Phelps
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH
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20
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Li Q, Yin YH, Liu ZW, Liu LF, Xin GZ. FNICM: A New Methodology To Identify Core Metabolites Based on Significantly Perturbed Metabolic Subnetworks. Anal Chem 2024; 96:3335-3344. [PMID: 38363654 DOI: 10.1021/acs.analchem.3c04131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Metabolomics has emerged as a powerful tool in biomedical research to understand the pathophysiological processes and metabolic biomarkers of diseases. Nevertheless, it is a significant challenge in metabolomics to identify the reliable core metabolites that are closely associated with the occurrence or progression of diseases. Here, we proposed a new research framework by integrating detection-based metabolomics with computational network biology for function-guided and network-based identification of core metabolites, namely, FNICM. The proposed FNICM methodology is successfully utilized to uncover ulcerative colitis (UC)-related core metabolites based on the significantly perturbed metabolic subnetwork. First, seed metabolites were screened out using prior biological knowledge and targeted metabolomics. Second, by leveraging network topology, the perturbations of the detected seed metabolites were propagated to other undetected ones. Ultimately, 35 core metabolites were identified by controllability analysis and were further hierarchized into six levels based on confidence level and their potential significance. The specificity and generalizability of the discovered core metabolites, used as UC's diagnostic markers, were further validated using published data sets of UC patients. More importantly, we demonstrated the broad applicability and practicality of the FNICM framework in different contexts by applying it to multiple clinical data sets, including inflammatory bowel disease, colorectal cancer, and acute coronary syndrome. In addition, FNICM was also demonstrated as a practicality methodology to identify core metabolites correlated with the therapeutic effects of Clematis saponins. Overall, the FNICM methodology is a new framework for identifying reliable core metabolites for disease diagnosis and drug treatment from a systemic and a holistic perspective.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ying-Hao Yin
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Zi-Wei Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Fang Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Gui-Zhong Xin
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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21
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Li G, Li C, Wang C, Wang Z. Suboptimal capability of individual machine learning algorithms in modeling small-scale imbalanced clinical data of local hospital. PLoS One 2024; 19:e0298328. [PMID: 38394317 PMCID: PMC10890755 DOI: 10.1371/journal.pone.0298328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, artificial intelligence (AI) has shown promising applications in various scientific domains, including biochemical analysis research. However, the effectiveness of AI in modeling small-scale, imbalanced datasets remains an open question in such fields. This study explores the capabilities of eight basic AI algorithms, including ridge regression, logistic regression, random forest regression, and others, in modeling a small, imbalanced clinical dataset (total n = 387, class 0 = 27, class 1 = 360) related to the records of the biochemical blood tests from the patients with multiple wasp stings (MWS). Through rigorous evaluation using k-fold cross-validation and comprehensive scoring, we found that none of the models could effectively model the data. Even after fine-tuning the hyperparameters of the best-performing models, the results remained below acceptable thresholds. The study highlights the challenges of applying AI to small-scale datasets with imbalanced groups in biochemical or clinical research and emphasizes the need for novel algorithms tailored to small-scale data. The findings also call for further exploration into techniques such as transfer learning and data augmentation, and they underline the importance of understanding the minimum dataset scale required for effective AI modeling in biochemical contexts.
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Affiliation(s)
- Gang Li
- Department of ICU, 3201 Hospital, Hanzhong, Shaanxi, China
| | - Chenbi Li
- Department of ICU, 3201 Hospital, Hanzhong, Shaanxi, China
| | - Chengli Wang
- Department of ICU, 3201 Hospital, Hanzhong, Shaanxi, China
| | - Zeheng Wang
- Data61, CSIRO, Clayton, VIC, Australia
- Manufacturing, CSIRO, West Lindfield, NSW, Australia
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22
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Lin S, Wang Y, Cai X, Ye Y, Chen Y. Predictive indicators of immune therapy efficacy in hepatocellular carcinoma based on neutrophil-to-lymphocyte ratio. Int Immunopharmacol 2024; 128:111477. [PMID: 38183910 DOI: 10.1016/j.intimp.2023.111477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Hepatocellular carcinoma (HCC) exhibits high incidence and mortality rates in China. Most cases are often diagnosed at late stages and require multi-strategy therapies. In recent years, immune checkpoint inhibitors (ICIs), particularly programmed cell death protein 1 (PD-1) antibodies, have demonstrated effectiveness in comprehensive HCC treatment. However, the efficacy and prognosis vary greatly among patients. Screening suitable patients and predicting outcomes are crucial for improving the efficacy of ICIs. Although PD-L1 expression levels in tumor cells have been used as predictors of PD-1/PD-L1 antibody therapy, they may not consistently correlate with clinical response in some studies; thus, exploring new biomarkers is necessary. The neutrophil-to-lymphocyte ratio (NLR) emerged as a new predictor of ICI immunotherapy efficacy, and its application in HCC is worth exploring. This study utilizes the Cancer Genome Atlas Liver Hepatocellular Carcinoma Collection (TCGA-LIHC) project in the Genomic Data Commons (GDC) database for methylation and transcriptome data analysis. The correlation between NLR and ICI immunotherapy efficacy for HCC was evaluated, identifying differentially expressed genes. Analysis revealed 74 up-regulated and 445 down-regulated genes in the high-NLR group compared to the low-NLR group. NLR-related differential methylation analysis identified 68 hypermethylated and 65 hypomethylated probes in the NLR high group. Furthermore, a machine learning model using 27 intersecting genes predicted PD-1 antibody therapy efficacy, achieving an AUC value of 0.813. In summary, we established a predictive model for HCC immunotherapy based on 27 genes related to differential expressions and NLR-associated methylation, showing significant potential for clinical research potential in this field.
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Affiliation(s)
- Shengzhe Lin
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Yang Wang
- Laboratory of Immuno-Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Xinran Cai
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Yunbin Ye
- Laboratory of Immuno-Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Yanling Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China.
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23
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Lee J, Kim D, Kong J, Ha D, Kim I, Park M, Lee K, Im SH, Kim S. Cell-cell communication network-based interpretable machine learning predicts cancer patient response to immune checkpoint inhibitors. SCIENCE ADVANCES 2024; 10:eadj0785. [PMID: 38295179 PMCID: PMC10830106 DOI: 10.1126/sciadv.adj0785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment. However, only some patients respond to ICIs, and current biomarkers for ICI efficacy have limited performance. Here, we devised an interpretable machine learning (ML) model trained using patient-specific cell-cell communication networks (CCNs) decoded from the patient's bulk tumor transcriptome. The model could (i) predict ICI efficacy for patients across four cancer types (median AUROC: 0.79) and (ii) identify key communication pathways with crucial players responsible for patient response or resistance to ICIs by analyzing more than 700 ICI-treated patient samples from 11 cohorts. The model prioritized chemotaxis communication of immune-related cells and growth factor communication of structural cells as the key biological processes underlying response and resistance to ICIs, respectively. We confirmed the key communication pathways and players at the single-cell level in patients with melanoma. Our network-based ML approach can be used to expand ICIs' clinical benefits in cancer patients.
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Affiliation(s)
- Juhun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang 166-20, Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kwanghwan Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
- ImmunoBiome Inc., Pohang 166-20, Korea
- Institute of Convergence Science, Yonsei University, Seoul 120-749, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
- Institute of Convergence Science, Yonsei University, Seoul 120-749, Korea
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24
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Wang K, Shi J, Tong X, Qu N, Kong X, Ni S, Xing J, Li X, Zheng M. TG468: a text graph convolutional network for predicting clinical response to immune checkpoint inhibitor therapy. Brief Bioinform 2024; 25:bbae017. [PMID: 38390990 PMCID: PMC10886443 DOI: 10.1093/bib/bbae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024] Open
Abstract
Enhancing cancer treatment efficacy remains a significant challenge in human health. Immunotherapy has witnessed considerable success in recent years as a treatment for tumors. However, due to the heterogeneity of diseases, only a fraction of patients exhibit a positive response to immune checkpoint inhibitor (ICI) therapy. Various single-gene-based biomarkers and tumor mutational burden (TMB) have been proposed for predicting clinical responses to ICI; however, their predictive ability is limited. We propose the utilization of the Text Graph Convolutional Network (GCN) method to comprehensively assess the impact of multiple genes, aiming to improve the predictive capability for ICI response. We developed TG468, a Text GCN model framing drug response prediction as a text classification task. By combining natural language processing (NLP) and graph neural network techniques, TG468 effectively handles sparse and high-dimensional exome sequencing data. As a result, TG468 can distinguish survival time for patients who received ICI therapy and outperforms single gene biomarkers, TMB and some classical machine learning models. Additionally, TG468's prediction results facilitate the identification of immune status differences among specific patient types in the Cancer Genome Atlas dataset, providing a rationale for the model's predictions. Our approach represents a pioneering use of a GCN model to analyze exome data in patients undergoing ICI therapy and offers inspiration for future research using NLP technology to analyze exome sequencing data.
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Affiliation(s)
- Kun Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Jiangshan Shi
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences; 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiaochu Tong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences; 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ning Qu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences; 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiangtai Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences; 555 Zuchongzhi Road, Shanghai 201203, China
| | - Shengkun Ni
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences; 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jing Xing
- Lingang Laboratory, Shanghai 200031, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyue Zheng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
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25
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Dakilah I, Harb A, Abu-Gharbieh E, El-Huneidi W, Taneera J, Hamoudi R, Semreen MH, Bustanji Y. Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine. Front Pharmacol 2024; 15:1324001. [PMID: 38313315 PMCID: PMC10834672 DOI: 10.3389/fphar.2024.1324001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
The global burden of cancer continues to rise, underscoring the urgency of developing more effective and precisely targeted therapies. This comprehensive review explores the confluence of precision medicine and CDC25 phosphatases in the context of cancer research. Precision medicine, alternatively referred to as customized medicine, aims to customize medical interventions by taking into account the genetic, genomic, and epigenetic characteristics of individual patients. The identification of particular genetic and molecular drivers driving cancer helps both diagnostic accuracy and treatment selection. Precision medicine utilizes sophisticated technology such as genome sequencing and bioinformatics to elucidate genetic differences that underlie the proliferation of cancer cells, hence facilitating the development of customized therapeutic interventions. CDC25 phosphatases, which play a crucial role in governing the progression of the cell cycle, have garnered significant attention as potential targets for cancer treatment. The dysregulation of CDC25 is a characteristic feature observed in various types of malignancies, hence classifying them as proto-oncogenes. The proteins in question, which operate as phosphatases, play a role in the activation of Cyclin-dependent kinases (CDKs), so promoting the advancement of the cell cycle. CDC25 inhibitors demonstrate potential as therapeutic drugs for cancer treatment by specifically blocking the activity of CDKs and modulating the cell cycle in malignant cells. In brief, precision medicine presents a potentially fruitful option for augmenting cancer research, diagnosis, and treatment, with an emphasis on individualized care predicated upon patients' genetic and molecular profiles. The review highlights the significance of CDC25 phosphatases in the advancement of cancer and identifies them as promising candidates for therapeutic intervention. This statement underscores the significance of doing thorough molecular profiling in order to uncover the complex molecular characteristics of cancer cells.
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Affiliation(s)
- Ibraheem Dakilah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammed H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
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26
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Prelaj A, Miskovic V, Zanitti M, Trovo F, Genova C, Viscardi G, Rebuzzi SE, Mazzeo L, Provenzano L, Kosta S, Favali M, Spagnoletti A, Castelo-Branco L, Dolezal J, Pearson AT, Lo Russo G, Proto C, Ganzinelli M, Giani C, Ambrosini E, Turajlic S, Au L, Koopman M, Delaloge S, Kather JN, de Braud F, Garassino MC, Pentheroudakis G, Spencer C, Pedrocchi ALG. Artificial intelligence for predictive biomarker discovery in immuno-oncology: a systematic review. Ann Oncol 2024; 35:29-65. [PMID: 37879443 DOI: 10.1016/j.annonc.2023.10.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/31/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The widespread use of immune checkpoint inhibitors (ICIs) has revolutionised treatment of multiple cancer types. However, selecting patients who may benefit from ICI remains challenging. Artificial intelligence (AI) approaches allow exploitation of high-dimension oncological data in research and development of precision immuno-oncology. MATERIALS AND METHODS We conducted a systematic literature review of peer-reviewed original articles studying the ICI efficacy prediction in cancer patients across five data modalities: genomics (including genomics, transcriptomics, and epigenomics), radiomics, digital pathology (pathomics), and real-world and multimodality data. RESULTS A total of 90 studies were included in this systematic review, with 80% published in 2021-2022. Among them, 37 studies included genomic, 20 radiomic, 8 pathomic, 20 real-world, and 5 multimodal data. Standard machine learning (ML) methods were used in 72% of studies, deep learning (DL) methods in 22%, and both in 6%. The most frequently studied cancer type was non-small-cell lung cancer (36%), followed by melanoma (16%), while 25% included pan-cancer studies. No prospective study design incorporated AI-based methodologies from the outset; rather, all implemented AI as a post hoc analysis. Novel biomarkers for ICI in radiomics and pathomics were identified using AI approaches, and molecular biomarkers have expanded past genomics into transcriptomics and epigenomics. Finally, complex algorithms and new types of AI-based markers, such as meta-biomarkers, are emerging by integrating multimodal/multi-omics data. CONCLUSION AI-based methods have expanded the horizon for biomarker discovery, demonstrating the power of integrating multimodal data from existing datasets to discover new meta-biomarkers. While most of the included studies showed promise for AI-based prediction of benefit from immunotherapy, none provided high-level evidence for immediate practice change. A priori planned prospective trial designs are needed to cover all lifecycle steps of these software biomarkers, from development and validation to integration into clinical practice.
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Affiliation(s)
- A Prelaj
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan; Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy; ESMO Real World Data and Digital Health Working Group, ESMO, Lugano, Switzerland.
| | - V Miskovic
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan; Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - M Zanitti
- Department of Electronic Systems, Aalborg University Copenhagen, Denmark
| | - F Trovo
- Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - C Genova
- UO Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genoa; Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, Genoa
| | - G Viscardi
- Precision Medicine Department, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - S E Rebuzzi
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, Genoa; Medical Oncology Unit, Ospedale San Paolo, Savona, Italy
| | - L Mazzeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan; Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - L Provenzano
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - S Kosta
- Department of Electronic Systems, Aalborg University Copenhagen, Denmark
| | - M Favali
- Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - A Spagnoletti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - L Castelo-Branco
- ESMO European Society for Medical Oncology, Lugano, Switzerland; NOVA National School of Public Health, Lisboa, Portugal
| | - J Dolezal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, USA
| | - A T Pearson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, USA
| | - G Lo Russo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - C Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - M Ganzinelli
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - C Giani
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - E Ambrosini
- Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - S Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London
| | - L Au
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Medical Oncology, The University of Melbourne, Melbourne, Australia
| | - M Koopman
- Department of Research and Development, Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands; ESMO Real World Data and Digital Health Working Group, ESMO, Lugano, Switzerland
| | - S Delaloge
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; ESMO Real World Data and Digital Health Working Group, ESMO, Lugano, Switzerland
| | - J N Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - F de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan
| | - M C Garassino
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, USA
| | | | - C Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London.
| | - A L G Pedrocchi
- Nearlab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
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27
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Haynes T, Gilbert MR, Breen K, Yang C. Pathways to hypermutation in high-grade gliomas: Mechanisms, syndromes, and opportunities for immunotherapy. Neurooncol Adv 2024; 6:vdae105. [PMID: 39022645 PMCID: PMC11252568 DOI: 10.1093/noajnl/vdae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
Despite rapid advances in the field of immunotherapy, including the success of immune checkpoint inhibition in treating multiple cancer types, clinical response in high-grade gliomas (HGGs) has been disappointing. This has been in part attributed to the low tumor mutational burden (TMB) of the majority of HGGs. Hypermutation is a recently characterized glioma signature that occurs in a small subset of cases, which may open an avenue to immunotherapy. The substantially elevated TMB of these tumors most commonly results from alterations in the DNA mismatch repair pathway in the setting of extensive exposure to temozolomide or, less frequently, from inherited cancer predisposition syndromes. In this review, we discuss the genetics and etiology of hypermutation in HGGs, with an emphasis on the resulting genomic signatures, and the state and future directions of immuno-oncology research in these patient populations.
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Affiliation(s)
- Tuesday Haynes
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Kevin Breen
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
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28
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Grieb N, Schmierer L, Kim HU, Strobel S, Schulz C, Meschke T, Kubasch AS, Brioli A, Platzbecker U, Neumuth T, Merz M, Oeser A. A digital twin model for evidence-based clinical decision support in multiple myeloma treatment. Front Digit Health 2023; 5:1324453. [PMID: 38173909 PMCID: PMC10761485 DOI: 10.3389/fdgth.2023.1324453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
The treatment landscape for multiple myeloma (MM) has experienced substantial progress over the last decade. Despite the efficacy of new substances, patient responses tend to still be highly unpredictable. With increasing cognitive burden that is introduced through a complex and evolving treatment landscape, data-driven assistance tools are becoming more and more popular. Model-based approaches, such as digital twins (DT), enable simulation of probable responses to a set of input parameters based on retrospective observations. In the context of treatment decision-support, those mechanisms serve the goal to predict therapeutic outcomes to distinguish a favorable option from a potential failure. In the present work, we propose a similarity-based multiple myeloma digital twin (MMDT) that emphasizes explainability and interpretability in treatment outcome evaluation. We've conducted a requirement specification process using scientific literature from the medical and methodological domains to derive an architectural blueprint for the design and implementation of the MMDT. In a subsequent stage, we've implemented a four-layer concept where for each layer, we describe the utilized implementation procedure and interfaces to the surrounding DT environment. We further specify our solutions regarding the adoption of multi-line treatment strategies, the integration of external evidence and knowledge, as well as mechanisms to enable transparency in the data processing logic. Furthermore, we define an initial evaluation scenario in the context of patient characterization and treatment outcome simulation as an exemplary use case for our MMDT. Our derived MMDT instance is defined by 475 unique entities connected through 438 edges to form a MM knowledge graph. Using the MMRF CoMMpass real-world evidence database and a sample MM case, we processed a complete outcome assessment. The output shows a valid selection of potential treatment strategies for the integrated medical case and highlights the potential of the MMDT to be used for such applications. DT models face significant challenges in development, including availability of clinical data to algorithmically derive clinical decision support, as well as trustworthiness of the evaluated treatment options. We propose a collaborative approach that mitigates the regulatory and ethical concerns that are broadly discussed when automated decision-making tools are to be included into clinical routine.
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Affiliation(s)
- Nora Grieb
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Lukas Schmierer
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Hyeon Ung Kim
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Sarah Strobel
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Christian Schulz
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Tim Meschke
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Anne Sophie Kubasch
- Department of Hematology, Hemostaseology, Cellular Therapy and Infectiology, University Hospital of Leipzig, Leipzig, Germany
| | - Annamaria Brioli
- Clinic of Internal Medicine C, Hematology and Oncology, Stem Cell Transplantation and Palliative Care, Greifswald University Medicine, Greifswald, Germany
| | - Uwe Platzbecker
- Department of Hematology, Hemostaseology, Cellular Therapy and Infectiology, University Hospital of Leipzig, Leipzig, Germany
| | - Thomas Neumuth
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
| | - Maximilian Merz
- Department of Hematology, Hemostaseology, Cellular Therapy and Infectiology, University Hospital of Leipzig, Leipzig, Germany
| | - Alexander Oeser
- Innovation Center Computer Assisted Surgery (ICCAS), University of Leipzig, Leipzig, Germany
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Yi S, Zhang C, Li M, Qu T, Wang J. Machine learning and experiments identifies SPINK1 as a candidate diagnostic and prognostic biomarker for hepatocellular carcinoma. Discov Oncol 2023; 14:231. [PMID: 38093163 PMCID: PMC10719188 DOI: 10.1007/s12672-023-00849-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Machine learning techniques have been widely used in predicting disease prognosis, including cancer prognosis. One of the major challenges in cancer prognosis is to accurately classify cancer types and stages to optimize early screening and detection, and machine learning techniques have proven to be very useful in this regard. In this study, we aimed at identifying critical genes for diagnosis and outcomes of hepatocellular carcinoma (HCC) patients using machine learning. The HCC expression dataset was downloaded from GSE65372 datasets and TCGA datasets. Differentially expressed genes (DEGs) were identified between 39 HCC and 15 normal samples. For the purpose of locating potential biomarkers, the LASSO and the SVM-RFE assays were performed. The ssGSEA method was used to analyze the TCGA to determine whether there was an association between SPINK1 and tumor immune infiltrates. RT-PCR was applied to examine the expression of SPINK1 in HCC specimens and cells. A series of functional assays were applied to examine the function of SPINK1 knockdown on the proliferation of HCC cells. In this study, 103 DEGs were obtained. Based on LASSO and SVM-RFE analysis, we identified nine critical diagnostic genes, including C10orf113, SPINK1, CNTLN, NRG3, HIST1H2AI, GPRIN3, SCTR, C2orf40 and PITX1. Importantly, we confirmed SPINK1 as a prognostic gene in HCC. Multivariate analysis confirmed that SPINK1 was an independent prognostic factor for overall survivals of HCC patients. We also found that SPINK1 level was positively associated with Macrophages, B cells, TFH, T cells, Th2 cells, iDC, NK CD56bright cells, Th1 cells, aDC, while negatively associated with Tcm and Eosinophils. Finally, we demonstrated that SPINK1 expression was distinctly increased in HCC specimens and cells. Functionally, silence of SPINK1 distinctly suppressed the proliferation of HCC cells via regulating Wnt/β-catenin pathway. The evidence provided suggested that SPINK1 may possess oncogenic properties by inducing dysregulated immune infiltration in HCC. Additionally, SPINK1 was identified as a novel biomarker and therapeutic target for HCC.
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Affiliation(s)
- Shiming Yi
- Department of Hepatobiliary Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Chunlei Zhang
- Department of Colorectal and Anus Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Ming Li
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Tianyi Qu
- Emergency Department, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Jiafeng Wang
- Department of Hepatobiliary Surgery, the Affiliated Taian City Central Hospital of Qingdao University, Taian, China.
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Adeuyan O, Gordon ER, Kenchappa D, Bracero Y, Singh A, Espinoza G, Geskin LJ, Saenger YM. An update on methods for detection of prognostic and predictive biomarkers in melanoma. Front Cell Dev Biol 2023; 11:1290696. [PMID: 37900283 PMCID: PMC10611507 DOI: 10.3389/fcell.2023.1290696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
The approval of immunotherapy for stage II-IV melanoma has underscored the need for improved immune-based predictive and prognostic biomarkers. For resectable stage II-III patients, adjuvant immunotherapy has proven clinical benefit, yet many patients experience significant adverse events and may not require therapy. In the metastatic setting, single agent immunotherapy cures many patients but, in some cases, more intensive combination therapies against specific molecular targets are required. Therefore, the establishment of additional biomarkers to determine a patient's disease outcome (i.e., prognostic) or response to treatment (i.e., predictive) is of utmost importance. Multiple methods ranging from gene expression profiling of bulk tissue, to spatial transcriptomics of single cells and artificial intelligence-based image analysis have been utilized to better characterize the immune microenvironment in melanoma to provide novel predictive and prognostic biomarkers. In this review, we will highlight the different techniques currently under investigation for the detection of prognostic and predictive immune biomarkers in melanoma.
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Affiliation(s)
- Oluwaseyi Adeuyan
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Emily R. Gordon
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Divya Kenchappa
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Yadriel Bracero
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ajay Singh
- Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Larisa J. Geskin
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, United States
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Liu J, Wang H, Wu P, Wang J, Wang J, Hou H, Wang J, Zhang Y. A simplified frailty index and nomogram to predict the postoperative complications and survival in older patients with upper urinary tract urothelial carcinoma. Front Oncol 2023; 13:1187677. [PMID: 37901313 PMCID: PMC10600399 DOI: 10.3389/fonc.2023.1187677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/07/2023] [Indexed: 10/31/2023] Open
Abstract
Purpose This study was designed to investigate the clinical value of a simplified five-item frailty index (sFI) for predicting short- and long-term outcomes in older patients with upper urinary tract urothelial carcinoma (UTUC) patients after radical nephroureterectomy (RNU). Method This retrospective study included 333 patients (aged ≥65 years) with UTUC. Patients were classified into five groups: 0, 1, 2, 3, and 3+, according to sFI score. The variable importance and minimum depth methods were used to screen for significant variables, and univariable and multivariable logistic regression models applied to investigated the relationships between significant variables and postoperative complications. Survival differences between groups were analyzed using Kaplan-Meier plots and log-rank tests. Cox proportional hazards regression was used to evaluate risk factors associated with overall survival (OS) and cancer-specific survival (CSS). Further, we developed a nomogram based on clinicopathological features and the sFI. The area under the curve (AUC), Harrel's concordance index (C-index), calibration curve, and decision curve analysis (DCA) were used to evaluate the nomogram. Result Of 333 cases identified, 31.2% experienced a Clavien-Dindo grade of 2 or greater complication. Random forest-logistic regression modeling showed that sFI significantly influenced the incidence of postoperative complications in older patients (AUC= 0.756). Compared with patients with low sFI score, those with high sFI scores had significantly lower OS and CSS (p < 0.001). Across all patients, the random survival forest-Cox regression model revealed that sFI score was an independent prognostic factor for OS and CSS, with AUC values of 0.815 and 0.823 for predicting 3-year OS and CSS, respectively. The nomogram developed was clinically valuable and had good ability to discriminate abilities for high-risk patients. Further, we developed a survival risk classification system that divided all patients into high-, moderate-, and low-risk groups based on total nomogram points for each patient. Conclusion A simple five-item frailty index may be considered a prognostic factor for the prognosis and postoperative complications of UTUC following RNU. By using this predictive model, clinicians may increase their accuracy in predicting complications and prognosis and improve preoperative decision-making.
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Affiliation(s)
- Jianyong Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Haoran Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Pengjie Wu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Jiawen Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Huimin Hou
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Jianlong Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Yaoguang Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
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Falcone N, Ermis M, Tamay DG, Mecwan M, Monirizad M, Mathes TG, Jucaud V, Choroomi A, de Barros NR, Zhu Y, Vrana NE, Kraatz HB, Kim HJ, Khademhosseini A. Peptide Hydrogels as Immunomaterials and Their Use in Cancer Immunotherapy Delivery. Adv Healthc Mater 2023; 12:e2301096. [PMID: 37256647 PMCID: PMC10615713 DOI: 10.1002/adhm.202301096] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Peptide-based hydrogel biomaterials have emerged as an excellent strategy for immune system modulation. Peptide-based hydrogels are supramolecular materials that self-assemble into various nanostructures through various interactive forces (i.e., hydrogen bonding and hydrophobic interactions) and respond to microenvironmental stimuli (i.e., pH, temperature). While they have been reported in numerous biomedical applications, they have recently been deemed promising candidates to improve the efficacy of cancer immunotherapies and treatments. Immunotherapies seek to harness the body's immune system to preemptively protect against and treat various diseases, such as cancer. However, their low efficacy rates result in limited patient responses to treatment. Here, the immunomaterial's potential to improve these efficacy rates by either functioning as immune stimulators through direct immune system interactions and/or delivering a range of immune agents is highlighted. The chemical and physical properties of these peptide-based materials that lead to immuno modulation and how one may design a system to achieve desired immune responses in a controllable manner are discussed. Works in the literature that reports peptide hydrogels as adjuvant systems and for the delivery of immunotherapies are highlighted. Finally, the future trends and possible developments based on peptide hydrogels for cancer immunotherapy applications are discussed.
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Affiliation(s)
- Natashya Falcone
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Menekse Ermis
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
- BIOMATEN, Center of Excellence in Biomaterials and Tissue Engineering, Middle East Technical University, Ankara, 06800, Turkey
| | - Dilara Goksu Tamay
- BIOMATEN, Center of Excellence in Biomaterials and Tissue Engineering, Middle East Technical University, Ankara, 06800, Turkey
- Department of Biotechnology, Middle East Technical University, Ankara, 06800, Turkey
| | - Marvin Mecwan
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Mahsa Monirizad
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Tess Grett Mathes
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Auveen Choroomi
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Natan Roberto de Barros
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
| | - Nihal Engin Vrana
- SPARTHA Medical, CRBS 1 Rue Eugene Boeckel, Strasbourg, 67000, France
| | - Heinz-Bernhard Kraatz
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Han-Jun Kim
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
- College of Pharmacy, Korea University, Sejong, 30019, Republic of Korea
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation, 1018 Westwood Blvd, Los Angeles, CA, 90034, USA
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Li J, Yao J, Qi L. Identification of TUBB2A as a Cancer-Immunity Cycle-Related Therapeutic Target in Triple-Negative Breast Cancer. Mol Biotechnol 2023:10.1007/s12033-023-00880-2. [PMID: 37742297 DOI: 10.1007/s12033-023-00880-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
OBJECTIVE Triple negative breast cancer (TNBC) is a malignant subtype of breast cancer characterized by the absence of ER, PR, and HER2. We aimed to explore target gene from the perspective of cancer-immunity cycle, providing insights into treatment of TNBC. METHODS We obtained TNBC samples from METABRIC database and downloaded 4 datasets from GEO database, as well as an IMvigor210 dataset. WGCNA was applied to screen genes associated with cancer-immunity cycle in TNBC. GO, KEGG and GSEA analyses were performed to explore the target gene's potential functions and pathways. The binding motifs with transcription factors were predicted with FIMO. Immune infiltration analysis was conducted by CIBERSORT. RESULTS TUBB2A was screened out as our target gene which was negatively correlated with T cell recruitment in cancer-immunity cycle. TUBB2A expressed higher in TNBC samples than in normal samples. High expression of TUBB2A was associated with poor prognosis of TNBC. 12 transcription factors and 5 miRNAs might regulate TUBB2A's expression. The infiltration ratios of 7 types of immune cells such as CD8+ T cells, naive CD4+ T cells and activated memory CD4+ T cells were significantly lower in TUBB2A high expression group. TUBB2A was a potential drug target. CONCLUSION We screened a cancer-immunity cycle-related gene TUBB2A which was negatively correlated with T cell recruiting in TNBC. TUBB2A expressed higher in TNBC samples than in normal samples, associated with poor prognosis.
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Affiliation(s)
- Jia Li
- Department of Breast Surgical Oncology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Xinghualing District, Taiyuan, 030013, Shanxi Province, People's Republic of China
| | - Jingchun Yao
- Department of Head and Neck, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Xinghualing District, Taiyuan, 030013, Shanxi Province, People's Republic of China
| | - Liqiang Qi
- Department of Breast Surgical Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17 Panjiayuan, Huawei South Road, Chaoyang District, Beijing, 100021, People's Republic of China.
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Yang Z, Qi Y, Wang Y, Chen X, Wang Y, Zhang X. Identifying Network Biomarkers in Early Diagnosis of Hepatocellular Carcinoma via miRNA-Gene Interaction Network Analysis. Curr Issues Mol Biol 2023; 45:7374-7387. [PMID: 37754250 PMCID: PMC10529263 DOI: 10.3390/cimb45090466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/26/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer at the histological level. Despite the emergence of new biological technology, advanced-stage HCC remains largely incurable. The prediction of a cancer biomarker is a key problem for targeted therapy in the disease. METHODS We performed a miRNA-gene integrated analysis to identify differentially expressed miRNAs (DEMs) and genes (DEGs) of HCC. The DEM-DEG interaction network was constructed and analyzed. Gene ontology enrichment and survival analyses were also performed in this study. RESULTS By the analysis of healthy and tumor samples, we found that 94 DEGs and 25 DEMs were significantly differentially expressed in different datasets. Gene ontology enrichment analysis showed that these 94 DEGs were significantly enriched in the term "Liver" with a statistical p-value of 1.71 × 10-26. Function enrichment analysis indicated that these genes were significantly overrepresented in the term "monocarboxylic acid metabolic process" with a p-value = 2.94 × 10-18. Two sets (fourteen genes and five miRNAs) were screened by a miRNA-gene integrated analysis of their interaction network. The statistical analysis of these molecules showed that five genes (CLEC4G, GLS2, H2AFZ, STMN1, TUBA1B) and two miRNAs (hsa-miR-326 and has-miR-331-5p) have significant effects on the survival prognosis of patients. CONCLUSION We believe that our study could provide critical clinical biomarkers for the targeted therapy of HCC.
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Affiliation(s)
- Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
| | - Yuanyuan Qi
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
| | - Yijing Wang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
| | - Xiangyun Chen
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
| | - Yuerong Wang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
| | - Xiaoli Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China (X.Z.)
- School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
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Huang Q, Zhou R, Hao X, Zhang W, Chen G, Zhu T. Circulating biomarkers in perioperative management of cancer patients. PRECISION CLINICAL MEDICINE 2023; 6:pbad018. [PMID: 37954451 PMCID: PMC10634636 DOI: 10.1093/pcmedi/pbad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 11/14/2023] Open
Abstract
Owing to the advances in surgical technology, most solid tumours can be controlled by surgical excision. The priority should be tumour control, while some routine perioperative management might influence cancer progression in an unnoticed way. Moreover, it is increasingly recognized that effective perioperative management should include techniques to improve postoperative outcomes. These influences are elucidated by the different functions of circulating biomarkers in cancer patients. Here, circulating biomarkers with two types of clinical functions were reviewed: (i) circulating biomarkers for cancer progression monitoring, for instance, those related to cancer cell malignancy, tumour microenvironment formation, and early metastasis, and (ii) circulating biomarkers with relevance to postoperative outcomes, including systemic inflammation, immunosuppression, cognitive dysfunction, and pain management. This review aimed to provide new perspectives for the perioperative management of patients with cancer and highlight the potential clinical translation value of circulating biomarkers in improving outcomes.
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Affiliation(s)
- Qiyuan Huang
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ruihao Zhou
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuechao Hao
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weiyi Zhang
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guo Chen
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Zhu
- Department of Anaesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu 610041, China
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Chen T, Liu C, Zhang Z, Liang T, Zhu J, Zhou C, Wu S, Yao Y, Huang C, Zhang B, Feng S, Wang Z, Huang S, Sun X, Chen L, Zhan X. Using Machine Learning to Predict Surgical Site Infection After Lumbar Spine Surgery. Infect Drug Resist 2023; 16:5197-5207. [PMID: 37581167 PMCID: PMC10423613 DOI: 10.2147/idr.s417431] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
Objective The objective of this study was to utilize machine learning techniques to analyze perioperative factors and identify blood glucose levels that can predict the occurrence of surgical site infection following posterior lumbar spinal surgery. Methods A total of 4019 patients receiving lumbar internal fixation surgery from an institute were enrolled between June 2012 and February 2021. First, the filtered data were randomized into the test and verification groups. Second, in the test group, specific variables were screened using logistic regression analysis, Lasso regression analysis, support vector machine, and random forest. Specific variables obtained using the four methods were intersected, and a dynamic model was constructed. ROC and calibration curves were constructed to assess model performance. Finally, internal model performance was verified in the verification group using ROC and calibration curves. Results The data from 4019 patients were collected. In total, 1327 eligible cases were selected. By combining logistic regression analysis with three machine learning algorithms, this study identified four predictors associated with SSI, namely Modic changes, sebum thickness, hemoglobin, and glucose. Using this information, a prediction model was developed and visually represented. Then, we constructed ROC and calibration curves using the test group; the area under the ROC curve was 0.988. Further, calibration curve analysis revealed favorable consistency of nomogram-predicted values compared with real measurements. The C-index of our model was 0.986 (95% CI 0.981-0.994). Finally, we used the validation group to validate the model internally; the AUC was 0.987. Calibration curve analysis revealed favorable consistency of nomogram-predicted values compared with real measurements. The C-index was 0.982 (95% CI 0.974-0.999). Conclusion Logistic regression analysis and machine learning were employed to select four risk factors: Modic changes, sebum thickness, hemoglobin, and glucose. Then, a dynamic prediction model was constructed to help clinicians simplify the monitoring and prevention of SSI.
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Affiliation(s)
- Tianyou Chen
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Chong Liu
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Zide Zhang
- Spine Ward, Liuzhou People’s Hospital, Liuzhou, People’s Republic of China
| | - Tuo Liang
- Spine Ward, Liuzhou People’s Hospital, Liuzhou, People’s Republic of China
| | - Jichong Zhu
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Chenxing Zhou
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Shaofeng Wu
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Yuanlin Yao
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Chengqian Huang
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Bin Zhang
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Sitan Feng
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Zequn Wang
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Shengsheng Huang
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Xuhua Sun
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Liyi Chen
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Xinli Zhan
- Department of Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
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Feng Y, McGuire N, Walton A, Fox S, Papa A, Lakhani SR, McCart Reed AE. Predicting breast cancer-specific survival in metaplastic breast cancer patients using machine learning algorithms. J Pathol Inform 2023; 14:100329. [PMID: 37664452 PMCID: PMC10470383 DOI: 10.1016/j.jpi.2023.100329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Metaplastic breast cancer (MpBC) is a rare and aggressive subtype of breast cancer, with data emerging on prognostic factors and survival prediction. This study aimed to develop machine learning models to predict breast cancer-specific survival (BCSS) in MpBC patients, utilizing a dataset of 160 patients with clinical, pathological, and biological variables. An in-depth variable selection process was carried out using gain ratio and correlation-based methods, resulting in 10 variables for model estimation. Five models (decision tree with bagging; logistic regression; multilayer perceptron; naïve Bayes; and, random forest algorithms) were evaluated using 10-fold cross-validation. Despite the constraints posed by the absence of therapeutic information, the random forest model exhibited the highest performance in predicting BCSS, with an ROC area of 0.808. This study emphasizes the potential of machine learning algorithms in predicting prognosis for complex and heterogeneous cancer subtypes using clinical datasets, and their potential to contribute to patient management. Further research that incorporates additional variables, such as treatment response, and more advanced machine learning techniques will likely enhance the predictive power of MpBC prognostic models.
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Affiliation(s)
- Yufan Feng
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane 4029, Australia
| | - Natasha McGuire
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane 4029, Australia
| | - Alexandra Walton
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane 4029, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane 4029, Australia
| | | | - Stephen Fox
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne 3000, Australia
| | - Antonella Papa
- Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane 4029, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane 4029, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane 4029, Australia
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Wang Z, Liu Y, Niu X. Application of artificial intelligence for improving early detection and prediction of therapeutic outcomes for gastric cancer in the era of precision oncology. Semin Cancer Biol 2023; 93:83-96. [PMID: 37116818 DOI: 10.1016/j.semcancer.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023]
Abstract
Gastric cancer is a leading contributor to cancer incidence and mortality globally. Recently, artificial intelligence approaches, particularly machine learning and deep learning, are rapidly reshaping the full spectrum of clinical management for gastric cancer. Machine learning is formed from computers running repeated iterative models for progressively improving performance on a particular task. Deep learning is a subtype of machine learning on the basis of multilayered neural networks inspired by the human brain. This review summarizes the application of artificial intelligence algorithms to multi-dimensional data including clinical and follow-up information, conventional images (endoscope, histopathology, and computed tomography (CT)), molecular biomarkers, etc. to improve the risk surveillance of gastric cancer with established risk factors; the accuracy of diagnosis, and survival prediction among established gastric cancer patients; and the prediction of treatment outcomes for assisting clinical decision making. Therefore, artificial intelligence makes a profound impact on almost all aspects of gastric cancer from improving diagnosis to precision medicine. Despite this, most established artificial intelligence-based models are in a research-based format and often have limited value in real-world clinical practice. With the increasing adoption of artificial intelligence in clinical use, we anticipate the arrival of artificial intelligence-powered gastric cancer care.
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Affiliation(s)
- Zhe Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning, China
| | - Yang Liu
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning, China.
| | - Xing Niu
- China Medical University, Shenyang 110122, Liaoning, China.
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Liu X, Shi J, Li Z, Huang Y, Zhang Z, Zhang C. The Present and Future of Artificial Intelligence in Urological Cancer. J Clin Med 2023; 12:4995. [PMID: 37568397 PMCID: PMC10419644 DOI: 10.3390/jcm12154995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Artificial intelligence has drawn more and more attention for both research and application in the field of medicine. It has considerable potential for urological cancer detection, therapy, and prognosis prediction due to its ability to choose features in data to complete a particular task autonomously. Although the clinical application of AI is still immature and faces drawbacks such as insufficient data and a lack of prospective clinical trials, AI will play an essential role in individualization and the whole management of cancers as research progresses. In this review, we summarize the applications and studies of AI in major urological cancers, including tumor diagnosis, treatment, and prognosis prediction. Moreover, we discuss the current challenges and future applications of AI.
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Affiliation(s)
| | | | | | | | - Zhihong Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China; (X.L.)
| | - Changwen Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China; (X.L.)
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Wei F, Azuma K, Nakahara Y, Saito H, Matsuo N, Tagami T, Kouro T, Igarashi Y, Tokito T, Kato T, Kondo T, Murakami S, Usui R, Himuro H, Horaguchi S, Tsuji K, Murotani K, Ban T, Tamura T, Miyagi Y, Sasada T. Machine learning for prediction of immunotherapeutic outcome in non-small-cell lung cancer based on circulating cytokine signatures. J Immunother Cancer 2023; 11:e006788. [PMID: 37433717 DOI: 10.1136/jitc-2023-006788] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitor (ICI) therapy has substantially improved the overall survival (OS) in patients with non-small-cell lung cancer (NSCLC); however, its response rate is still modest. In this study, we developed a machine learning-based platform, namely the Cytokine-based ICI Response Index (CIRI), to predict the ICI response of patients with NSCLC based on the peripheral blood cytokine profiles. METHODS We enrolled 123 and 99 patients with NSCLC who received anti-PD-1/PD-L1 monotherapy or combined chemotherapy in the training and validation cohorts, respectively. The plasma concentrations of 93 cytokines were examined in the peripheral blood obtained from patients at baseline (pre) and 6 weeks after treatment (early during treatment: edt). Ensemble learning random survival forest classifiers were developed to select feature cytokines and predict the OS of patients undergoing ICI therapy. RESULTS Fourteen and 19 cytokines at baseline and on treatment, respectively, were selected to generate CIRI models (namely preCIRI14 and edtCIRI19), both of which successfully identified patients with worse OS in two completely independent cohorts. At the population level, the prediction accuracies of preCIRI14 and edtCIRI19, as indicated by the concordance indices (C-indices), were 0.700 and 0.751 in the validation cohort, respectively. At the individual level, patients with higher CIRI scores demonstrated worse OS [hazard ratio (HR): 0.274 and 0.163, and p<0.0001 and p=0.0044 in preCIRI14 and edtCIRI19, respectively]. By including other circulating and clinical features, improved prediction efficacy was observed in advanced models (preCIRI21 and edtCIRI27). The C-indices in the validation cohort were 0.764 and 0.757, respectively, whereas the HRs of preCIRI21 and edtCIRI27 were 0.141 (p<0.0001) and 0.158 (p=0.038), respectively. CONCLUSIONS The CIRI model is highly accurate and reproducible in determining the patients with NSCLC who would benefit from anti-PD-1/PD-L1 therapy with prolonged OS and may aid in clinical decision-making before and/or at the early stage of treatment.
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Affiliation(s)
- Feifei Wei
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Koichi Azuma
- Department of Internal Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiro Nakahara
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
- Department of Respiratory Medicine, Kitasato University School of Medicine, Sagamihara, Japan
| | - Haruhiro Saito
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Norikazu Matsuo
- Department of Internal Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tomoyuki Tagami
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co Inc, Kawasaki, Japan
| | - Taku Kouro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Yuka Igarashi
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Takaaki Tokito
- Department of Internal Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Terufumi Kato
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Tetsuro Kondo
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Shuji Murakami
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Ryo Usui
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Hidetomo Himuro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Shun Horaguchi
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Kayoko Tsuji
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Kenta Murotani
- Biostatistics Center, Kurume University School of Medicine, Kurume, Japan
| | - Tatsuma Ban
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Tetsuro Sasada
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
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Abushukair H, Ababneh O, Al-Bzour A, Sahin IH, Saeed A. Next generation immuno-oncology biomarkers in gastrointestinal cancer: what does the future hold? Expert Rev Mol Diagn 2023; 23:863-873. [PMID: 37642360 DOI: 10.1080/14737159.2023.2252739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Gastrointestinal (GI) cancers pose a significant health burden worldwide, necessitating advancements in diagnostic and treatment approaches. One promising avenue is the utilization of next-generation biomarkers, which hold the potential to revolutionize GI cancer management. AREAS COVERED This review explores the latest breakthroughs and expert opinions surrounding the application of next-generation immunotherapy biomarkers. It encompasses various aspects of the currently utilized biomarkers of immunotherapy in the context of GI cancers focusing on microsatellite stable cancers. It explores the promising research on the next generation of biomarkers addressing the challenges associated with integrating them into clinical practice and the need for standardized protocols and regulatory guidelines. EXPERT OPINION Immune profiling, multiplex immunohistochemistry, analysis of immune cell subsets, and novel genomic and epigenomic markers integrated with machine-learning approaches offer new avenues for identifying robust biomarkers. Liquid biopsy-based approaches, such as circulating tumor DNA (ctDNA) and exosome-based analyses, hold promise for real-time monitoring and early detection of treatment response.
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Affiliation(s)
- Hassan Abushukair
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Obada Ababneh
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Ayah Al-Bzour
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Ibrahim Halil Sahin
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anwaar Saeed
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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Pawłowska A, Rekowska A, Kuryło W, Pańczyszyn A, Kotarski J, Wertel I. Current Understanding on Why Ovarian Cancer Is Resistant to Immune Checkpoint Inhibitors. Int J Mol Sci 2023; 24:10859. [PMID: 37446039 DOI: 10.3390/ijms241310859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The standard treatment of ovarian cancer (OC) patients, including debulking surgery and first-line chemotherapy, is unsatisfactory because of recurrent episodes in the majority (~70%) of patients with advanced OC. Clinical trials have shown only a modest (10-15%) response of OC individuals to treatment based on immune checkpoint inhibitors (ICIs). The resistance of OC to therapy is caused by various factors, including OC heterogeneity, low density of tumor-infiltrating lymphocytes (TILs), non-cellular and cellular interactions in the tumor microenvironment (TME), as well as a network of microRNA regulating immune checkpoint pathways. Moreover, ICIs are the most efficient in tumors that are marked by high microsatellite instability and high tumor mutation burden, which is rare among OC patients. The great challenge in ICI implementation is connected with distinguishing hyper-, pseudo-, and real progression of the disease. The understanding of the immunological, molecular, and genetic mechanisms of OC resistance is crucial to selecting the group of OC individuals in whom personalized treatment would be beneficial. In this review, we summarize current knowledge about the selected factors inducing OC resistance and discuss the future directions of ICI-based immunotherapy development for OC patients.
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Affiliation(s)
- Anna Pawłowska
- Independent Laboratory of Cancer Diagnostics and Immunology, Department of Oncological Gynaecology and Gynaecology, Faculty of Medicine, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Anna Rekowska
- Students' Scientific Association, Independent Laboratory of Cancer Diagnostics and Immunology, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Weronika Kuryło
- Students' Scientific Association, Independent Laboratory of Cancer Diagnostics and Immunology, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Anna Pańczyszyn
- Institute of Medical Sciences, Department of Biology and Genetics, Faculty of Medicine, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Jan Kotarski
- Independent Laboratory of Cancer Diagnostics and Immunology, Department of Oncological Gynaecology and Gynaecology, Faculty of Medicine, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Iwona Wertel
- Independent Laboratory of Cancer Diagnostics and Immunology, Department of Oncological Gynaecology and Gynaecology, Faculty of Medicine, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
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Liu J, Wu P, Lai S, Wang J, Hou H, Zhang Y. Prognostic models for upper urinary tract urothelial carcinoma patients after radical nephroureterectomy based on a novel systemic immune-inflammation score with machine learning. BMC Cancer 2023; 23:574. [PMID: 37349696 DOI: 10.1186/s12885-023-11058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/11/2023] [Indexed: 06/24/2023] Open
Abstract
PURPOSE This study aimed to evaluate the clinical significance of a novel systemic immune-inflammation score (SIIS) to predict oncological outcomes in upper urinary tract urothelial carcinoma(UTUC) after radical nephroureterectomy(RNU). METHOD The clinical data of 483 patients with nonmetastatic UTUC underwent surgery in our center were analyzed. Five inflammation-related biomarkers were screened in the Lasso-Cox model and then aggregated to generate the SIIS based on the regression coefficients. Overall survival (OS) was assessed using Kaplan-Meier analyses. The Cox proportional hazards regression and random survival forest model were adopted to build the prognostic model. Then we established an effective nomogram for UTUC after RNU based on SIIS. The discrimination and calibration of the nomogram were evaluated using the concordance index (C-index), area under the time-dependent receiver operating characteristic curve (time-dependent AUC), and calibration curves. Decision curve analysis (DCA) was used to assess the net benefits of the nomogram at different threshold probabilities. RESULT According to the median value SIIS computed by the lasso Cox model, the high-risk group had worse OS (p<0.0001) than low risk-group. Variables with a minimum depth greater than the depth threshold or negative variable importance were excluded, and the remaining six variables were included in the model. The area under the ROC curve (AUROC) of the Cox and random survival forest models were 0.801 and 0.872 for OS at five years, respectively. Multivariate Cox analysis showed that elevated SIIS was significantly associated with poorer OS (p<0.001). In terms of predicting overall survival, a nomogram that considered the SIIS and clinical prognostic factors performed better than the AJCC staging. CONCLUSION The pretreatment levels of SIIS were an independent predictor of prognosis in upper urinary tract urothelial carcinoma after RNU. Therefore, incorporating SIIS into currently available clinical parameters helps predict the long-term survival of UTUC.
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Affiliation(s)
- Jianyong Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Pengjie Wu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Hospital Continence Center, Beijing, China
| | - Shicong Lai
- Department of Urology, Peking University People's Hospital, 100044, Beijing, China
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Hospital Continence Center, Beijing, China.
| | - Huimin Hou
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Hospital Continence Center, Beijing, China.
| | - Yaoguang Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of the Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Hospital Continence Center, Beijing, China.
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Grossarth S, Mosley D, Madden C, Ike J, Smith I, Huo Y, Wheless L. Recent Advances in Melanoma Diagnosis and Prognosis Using Machine Learning Methods. Curr Oncol Rep 2023; 25:635-645. [PMID: 37000340 PMCID: PMC10339689 DOI: 10.1007/s11912-023-01407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 04/01/2023]
Abstract
PURPOSE OF REVIEW The purpose was to summarize the current role and state of artificial intelligence and machine learning in the diagnosis and management of melanoma. RECENT FINDINGS Deep learning algorithms can identify melanoma from clinical, dermoscopic, and whole slide pathology images with increasing accuracy. Efforts to provide more granular annotation to datasets and to identify new predictors are ongoing. There have been many incremental advances in both melanoma diagnostics and prognostic tools using artificial intelligence and machine learning. Higher quality input data will further improve these models' capabilities.
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Affiliation(s)
- Sarah Grossarth
- Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | | | - Christopher Madden
- Department of Dermatology, Vanderbilt University Medicine Center, Nashville, TN, USA
- State University of New York Downstate College of Medicine, Brooklyn, NY, USA
| | - Jacqueline Ike
- Department of Dermatology, Vanderbilt University Medicine Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Isabelle Smith
- Department of Dermatology, Vanderbilt University Medicine Center, Nashville, TN, USA
- Vanderbilt University, Nashville, TN, USA
| | - Yuankai Huo
- Department of Computer Science and Electrical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lee Wheless
- Department of Dermatology, Vanderbilt University Medicine Center, Nashville, TN, USA.
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Tennessee Valley Healthcare System VA Medical Center, Nashville, TN, USA.
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Dora D, Ligeti B, Kovacs T, Revisnyei P, Galffy G, Dulka E, Krizsán D, Kalcsevszki R, Megyesfalvi Z, Dome B, Weiss GJ, Lohinai Z. Non-small cell lung cancer patients treated with Anti-PD1 immunotherapy show distinct microbial signatures and metabolic pathways according to progression-free survival and PD-L1 status. Oncoimmunology 2023; 12:2204746. [PMID: 37197440 PMCID: PMC10184596 DOI: 10.1080/2162402x.2023.2204746] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/13/2023] [Accepted: 04/16/2023] [Indexed: 05/19/2023] Open
Abstract
Due to the high variance in response rates concerning anti-PD1 immunotherapy (IT), there is an unmet need to discover innovative biomarkers to predict immune checkpoint inhibitor (ICI)-efficacy. Our study included 62 Caucasian advanced-stage non-small cell lung cancer (NSCLC) patients treated with anti-PD1 ICI. Gut bacterial signatures were evaluated by metagenomic sequencing and correlated with progression-free survival (PFS), PD-L1 expression and other clinicopathological parameters. We confirmed the predictive role of PFS-related key bacteria with multivariate statistical models (Lasso- and Cox-regression) and validated on an additional patient cohort (n = 60). We find that alpha-diversity showed no significant difference in any comparison. However, there was a significant difference in beta-diversity between patients with long- (>6 months) vs. short (≤6 months) PFS and between chemotherapy (CHT)-treated vs. CHT-naive cases. Short PFS was associated with increased abundance of Firmicutes (F) and Actinobacteria phyla, whereas elevated abundance of Euryarchaeota was specific for low PD-L1 expression. F/Bacteroides (F/B) ratio was significantly increased in patients with short PFS. Multivariate analysis revealed an association between Alistipes shahii, Alistipes finegoldii, Barnesiella visceriola, and long PFS. In contrast, Streptococcus salivarius, Streptococcus vestibularis, and Bifidobacterium breve were associated with short PFS. Using Random Forest machine learning approach, we find that taxonomic profiles performed superiorly in predicting PFS (AUC = 0.74), while metabolic pathways including Amino Acid Synthesis and Fermentation were better predictors of PD-L1 expression (AUC = 0.87). We conclude that specific metagenomic features of the gut microbiome, including bacterial taxonomy and metabolic pathways might be suggestive of ICI efficacy and PD-L1 expression in NSCLC patients.
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Affiliation(s)
- David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Balazs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Tamas Kovacs
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Peter Revisnyei
- Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - Edit Dulka
- County Hospital of Torokbalint, Torokbalint, Hungary
| | - Dániel Krizsán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Regina Kalcsevszki
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Balazs Dome
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Translational Medicine, Lund University, Sweden
| | - Glen J. Weiss
- UMass Chan Medical School, Department of Medicine, Worcester, MA, USA
| | - Zoltan Lohinai
- County Hospital of Torokbalint, Torokbalint, Hungary
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
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Zhang C, Zhang C, Wang H. Immune-checkpoint inhibitor resistance in cancer treatment: Current progress and future directions. Cancer Lett 2023; 562:216182. [PMID: 37076040 DOI: 10.1016/j.canlet.2023.216182] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
Cancer treatment has been advanced with the advent of immune checkpoint inhibitors (ICIs) exemplified by anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), anti-programmed cell death protein 1 (PD-1) and programmed cell death ligand 1 (PD-L1) drugs. Patients have reaped substantial benefit from ICIs in many cancer types. However, few patients benefit from ICIs whereas the vast majority undergoing these treatments do not obtain survival benefit. Even for patients with initial responses, they may encounter drug resistance in their subsequent treatments, which limits the efficacy of ICIs. Therefore, a deepening understanding of drug resistance is critically important for the explorations of approaches to reverse drug resistance and to boost ICI efficacy. In the present review, different mechanisms of ICI resistance have been summarized according to the tumor intrinsic, tumor microenvironment (TME) and host classifications. We further elaborated corresponding strategies to battle against such resistance accordingly, which include targeting defects in antigen presentation, dysregulated interferon-γ (IFN-γ) signaling, neoantigen depletion, upregulation of other T cell checkpoints as well as immunosuppression and exclusion mediated by TME. Moreover, regarding the host, several additional approaches that interfere with diet and gut microbiome have also been described in reversing ICI resistance. Additionally, we provide an overall glimpse into the ongoing clinical trials that utilize these mechanisms to overcome ICI resistance. Finally, we summarize the challenges and opportunities that needs to be addressed in the investigation of ICI resistance mechanisms, with the aim to benefit more patients with cancer.
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Affiliation(s)
- Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Chenxing Zhang
- Department of Nephrology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
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Sharma P, Goswami S, Raychaudhuri D, Siddiqui BA, Singh P, Nagarajan A, Liu J, Subudhi SK, Poon C, Gant KL, Herbrich SM, Anandhan S, Islam S, Amit M, Anandappa G, Allison JP. Immune checkpoint therapy-current perspectives and future directions. Cell 2023; 186:1652-1669. [PMID: 37059068 DOI: 10.1016/j.cell.2023.03.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 04/16/2023]
Abstract
Immune checkpoint therapy (ICT) has dramatically altered clinical outcomes for cancer patients and conferred durable clinical benefits, including cure in a subset of patients. Varying response rates across tumor types and the need for predictive biomarkers to optimize patient selection to maximize efficacy and minimize toxicities prompted efforts to unravel immune and non-immune factors regulating the responses to ICT. This review highlights the biology of anti-tumor immunity underlying response and resistance to ICT, discusses efforts to address the current challenges with ICT, and outlines strategies to guide the development of subsequent clinical trials and combinatorial efforts with ICT.
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Affiliation(s)
- Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Sangeeta Goswami
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deblina Raychaudhuri
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bilal A Siddiqui
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pratishtha Singh
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashwat Nagarajan
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jielin Liu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; MD Anderson UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sumit K Subudhi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Candice Poon
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristal L Gant
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shelley M Herbrich
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swetha Anandhan
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; MD Anderson UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shajedul Islam
- Department of Head & Neck Surgery Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Moran Amit
- Department of Head & Neck Surgery Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gayathri Anandappa
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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48
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Vazquez-Levin MH, Reventos J, Zaki G. Editorial: Artificial intelligence: A step forward in biomarker discovery and integration towards improved cancer diagnosis and treatment. Front Oncol 2023; 13:1161118. [PMID: 37064106 PMCID: PMC10102612 DOI: 10.3389/fonc.2023.1161118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- Mónica Hebe Vazquez-Levin
- Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET) Fundación IBYME (FIBYME), Buenos Aires, Argentina
- *Correspondence: Mónica Hebe Vazquez-Levin, ;
| | - Jaume Reventos
- Institut d’Investigacio Biomedica de Bellvitge (IDIBELL) and Universitat Internacional de Catalunya, Barcelona, Spain
| | - George Zaki
- Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick (NIH), Frederick, MD, United States
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49
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Zhao L, Qi X, Chen Y, Qiao Y, Bu D, Wu Y, Luo Y, Wang S, Zhang R, Zhao Y. Biological knowledge graph-guided investigation of immune therapy response in cancer with graph neural network. Brief Bioinform 2023; 24:6995380. [PMID: 36682018 DOI: 10.1093/bib/bbad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/18/2022] [Accepted: 01/07/2023] [Indexed: 01/23/2023] Open
Abstract
The determination of transcriptome profiles that mediate immune therapy in cancer remains a major clinical and biological challenge. Despite responses induced by immune-check points inhibitors (ICIs) in diverse tumor types and all the big breakthroughs in cancer immunotherapy, most patients with solid tumors do not respond to ICI therapies. It still remains a big challenge to predict the ICI treatment response. Here, we propose a framework with multiple prior knowledge networks guided for immune checkpoints inhibitors prediction-DeepOmix-ICI (or ICInet for short). ICInet can predict the immune therapy response by leveraging geometric deep learning and prior biological knowledge graphs of gene-gene interactions. Here, we demonstrate more than 600 ICI-treated patients with ICI response data and gene expression profile to apply on ICInet. ICInet was used for ICI therapy responses prediciton across different cancer types-melanoma, gastric cancer and bladder cancer, which includes 7 cohorts from different data sources. ICInet is able to robustly generalize into multiple cancer types. Moreover, the performance of ICInet in those cancer types can outperform other ICI biomarkers in the clinic. Our model [area under the curve (AUC = 0.85)] generally outperformed other measures, including tumor mutational burden (AUC = 0.62) and programmed cell death ligand-1 score (AUC = 0.74). Therefore, our study presents a prior-knowledge guided deep learning method to effectively select immunotherapy-response-associated biomarkers, thereby improving the prediction of immunotherapy response for precision oncology.
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Affiliation(s)
- Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoning Qi
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Chen
- The First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, China
| | - Yixuan Qiao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yufan Luo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng Wang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
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50
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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