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Abbasi AF, Asim MN, Ahmed S, Vollmer S, Dengel A. Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases. Front Artif Intell 2024; 7:1428501. [PMID: 39021434 PMCID: PMC11252047 DOI: 10.3389/frai.2024.1428501] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Survival prediction integrates patient-specific molecular information and clinical signatures to forecast the anticipated time of an event, such as recurrence, death, or disease progression. Survival prediction proves valuable in guiding treatment decisions, optimizing resource allocation, and interventions of precision medicine. The wide range of diseases, the existence of various variants within the same disease, and the reliance on available data necessitate disease-specific computational survival predictors. The widespread adoption of artificial intelligence (AI) methods in crafting survival predictors has undoubtedly revolutionized this field. However, the ever-increasing demand for more sophisticated and effective prediction models necessitates the continued creation of innovative advancements. To catalyze these advancements, it is crucial to bring existing survival predictors knowledge and insights into a centralized platform. The paper in hand thoroughly examines 23 existing review studies and provides a concise overview of their scope and limitations. Focusing on a comprehensive set of 90 most recent survival predictors across 44 diverse diseases, it delves into insights of diverse types of methods that are used in the development of disease-specific predictors. This exhaustive analysis encompasses the utilized data modalities along with a detailed analysis of subsets of clinical features, feature engineering methods, and the specific statistical, machine or deep learning approaches that have been employed. It also provides insights about survival prediction data sources, open-source predictors, and survival prediction frameworks.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Muhammad Nabeel Asim
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sheraz Ahmed
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sebastian Vollmer
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
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2
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Liao K, Xu Y, Lin B, Xie Y, Yang Q, Zhang W, Zhang B, Wen J, Wang J, Li Z, Cheng Y, Wang X. A prognostic model of patients with pancreatic cancer based on four N 6-methyladenosine-related lncRNAs and analysis of related immune infiltration. Genes Dis 2024; 11:101141. [PMID: 38510478 PMCID: PMC10950808 DOI: 10.1016/j.gendis.2023.101141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/01/2023] [Indexed: 03/22/2024] Open
Affiliation(s)
- Kaili Liao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yuhan Xu
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Bingying Lin
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Yuxuan Xie
- The Second Clinical Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Qijun Yang
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Wenyige Zhang
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Beining Zhang
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Jiarong Wen
- The First Clinical Medical College of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingyi Wang
- School of Public Health, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zimeng Li
- School of Public Health, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yunqi Cheng
- School of Public Health, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xiaozhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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3
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Nopour R. Establishment of prediction model for mortality risk of pancreatic cancer: a retrospective study. BMC Med Inform Decis Mak 2024; 24:181. [PMID: 38937795 PMCID: PMC11210158 DOI: 10.1186/s12911-024-02590-4] [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: 04/17/2024] [Accepted: 06/25/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND AND AIM Pancreatic cancer possesses a high prevalence and mortality rate among other cancers. Despite the low survival rate of this cancer type, the early prediction of this disease has a crucial role in decreasing the mortality rate and improving the prognosis. So, this study. MATERIALS AND METHODS In this retrospective study, we used 654 alive and dead PC cases to establish the prediction model for PC. The six chosen machine learning algorithms and prognostic factors were utilized to build the prediction models. The importance of the predictive factors was assessed using the relative importance of a high-performing algorithm. RESULTS The XG-Boost with AU-ROC of 0.933 (95% CI= [0.906-0.958]) and AU-ROC of 0.836 (95% CI= [0.789-0.865] in internal and external validation modes were considered as the best-performing model for predicting the mortality risk of PC. The factors, including tumor size, smoking, and chemotherapy, were considered the most influential for prediction. CONCLUSION The XG-Boost gained more performance efficiency in predicting the mortality risk of PC patients, so this model can promote the clinical solutions that doctors can achieve in healthcare environments to decrease the mortality risk of these patients.
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Affiliation(s)
- Raoof Nopour
- Department of Health Information Management, Student Research Committee, School of Health Management and Information Sciences Branch, Iran University of Medical Sciences, Tehran, Iran.
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4
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Srivastava P, Yadav VK, Chang TH, Su ECY, Lawal B, Wu ATH, Huang HS. In-silico analysis of TMEM2 as a pancreatic adenocarcinoma and cancer-associated fibroblast biomarker, and functional characterization of NSC777201, for targeted drug development. Am J Cancer Res 2024; 14:3010-3035. [PMID: 39005682 PMCID: PMC11236765 DOI: 10.62347/chxd6134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/13/2024] [Indexed: 07/16/2024] Open
Abstract
Pancreatic adenocarcinoma (PAAD), known as one of the deadliest cancers, is characterized by a complex tumor microenvironment, primarily comprised of cancer-associated fibroblasts (CAFs) in the extracellular matrix. These CAFs significantly alter the matrix by interacting with hyaluronic acid (HA) and the enzyme hyaluronidase, which degrades HA - an essential process for cancer progression and spread. Despite the critical role of this interaction, the specific functions of CAFs and hyaluronidase in PAAD development are not fully understood. Our study investigates this interaction and assesses NSC777201, a new anti-cancer compound targeting hyaluronidase. This research utilized computational methods to analyze gene expression data from the Gene Expression Omnibus (GEO) database, specifically GSE172096, comparing gene expression profiles of cancer-associated and normal fibroblasts. We conducted in-house sequencing of pancreatic cancer cells treated with NSC777201 to identify differentially expressed genes (DEGs) and performed functional enrichment and pathway analysis. The identified DEGs were further validated using the TCGA-PAAD and Human Protein Atlas (HPA) databases for their diagnostic, prognostic, and survival implications, accompanied by Ingenuity Pathway Analysis (IPA) and molecular docking of NSC777201, in-vitro, and preclinical in-vivo validations. The result revealed 416 DEGs associated with CAFs and 570 DEGs related to NSC777201 treatment, with nine overlapping DEGs. A key finding was the transmembrane protein TMEM2, which strongly correlated with FAP, a CAF marker, and was associated with higher-risk groups in PAAD. NSC777201 treatment showed inhibition of TMEM2, validated by rescue assay, indicating the importance of targeting TMEM2. Further analyses, including IPA, demonstrated that NSC777201 regulates CAF cell senescence, enhancing its therapeutic potential. Both in-vitro and in-vivo studies confirmed the inhibitory effect of NSC777201 on TMEM2 expression, reinforcing its role in targeting PAAD. Therefore, TMEM2 has been identified as a theragnostic biomarker in PAAD, influenced by CAF activity and HA accumulation. NSC777201 exhibits significant potential in targeting and potentially reversing critical processes in PAAD progression, demonstrating its efficacy as a promising therapeutic agent.
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Affiliation(s)
- Prateeti Srivastava
- The Program for Translational Medicine, Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
| | - Vijesh Kumar Yadav
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Shuang Ho HospitalNew Taipei 23561, Taiwan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical UniversityTaipei 110, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- Clinical Big Data Research Center, Taipei Medical University HospitalTaipei 110, Taiwan
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
| | - Bashir Lawal
- UPMC Hillman Cancer Center, University of PittsburghPittsburgh, PA 15232, USA
- Department of Pathology, University of PittsburghPittsburgh, PA 15213, USA
| | - Alexander TH Wu
- The Program for Translational Medicine, Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical CenterTaipei 114, Taiwan
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipei 110, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical UniversityTaipei 11031, Taiwan
| | - Hsu-Shan Huang
- Graduate Institute of Medical Sciences, National Defense Medical CenterTaipei 114, Taiwan
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 110, Taiwan
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia SinicaTaipei 11031, Taiwan
- School of Pharmacy, National Defense Medical CenterTaipei 11490, Taiwan
- PhD Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical UniversityTaipei 11031, Taiwan
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D’Antonio DL, Marchetti S, Pignatelli P, Umme S, De Bellis D, Lanuti P, Piattelli A, Curia MC. Effect of 5-Aminolevulinic Acid (5-ALA) in "ALADENT" Gel Formulation and Photodynamic Therapy (PDT) against Human Oral and Pancreatic Cancers. Biomedicines 2024; 12:1316. [PMID: 38927525 PMCID: PMC11201195 DOI: 10.3390/biomedicines12061316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Oral squamous-cell and pancreatic carcinomas are aggressive cancers with a poor outcome. Photodynamic therapy (PDT) consists of the use of photosensitizer-induced cell and tissue damage that is activated by exposure to visible light. PDT selectively acts on cancer cells, which have an accumulation of photosensitizer superior to that of the normal surrounding tissues. 5-aminolevulinic acid (5-ALA) induces the production of protoporphyrin IX (PpIX), an endogenous photosensitizer activated in PDT. This study aimed to test the effect of a new gel containing 5% v/v 5-ALA (ALAD-PDT) on human oral CAL-27 and pancreatic CAPAN-2 cancer cell lines. The cell lines were incubated in low concentrations of ALAD-PDT (0.05%, 0.10%, 0.20%, 0.40%, 0.75%, 1.0%) for 4 h or 8 h, and then irradiated for 7 min with 630 nm RED light. The cytotoxic effects of ALAD-PDT were measured using the MTS assay. Apoptosis, cell cycle, and ROS assays were performed using flow cytometry. PpIX accumulation was measured using a spectrofluorometer after 10 min and 24 and 48 h of treatment. The viability was extremely reduced at all concentrations, at 4 h for CAPAN-2 and at 8 h for CAL-27. ALAD-PDT induced marked apoptosis rates in both oral and pancreatic cancer cells. Elevated ROS production and appreciable levels of PpIX were detected in both cell lines. The use of ALA-PDT as a topical or intralesional therapy would permit the use of very low doses to achieve effective results and minimize side effects. ALAD-PDT has the potential to play a significant role in complex oral and pancreatic anticancer therapies.
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Affiliation(s)
- Domenica Lucia D’Antonio
- Department of Medical, Oral and Biotechnological Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.L.D.); (S.M.); (S.U.)
- Villa Serena Foundation for Research, Via Leonardo Petruzzi 42, 65013 Città Sant’Angelo, Italy
| | - Simona Marchetti
- Department of Medical, Oral and Biotechnological Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.L.D.); (S.M.); (S.U.)
| | - Pamela Pignatelli
- COMDINAV DUE, Nave Cavour, Italian Navy, Stazione Navale Mar Grande, Viale Jonio, 74122 Taranto, Italy;
| | - Samia Umme
- Department of Medical, Oral and Biotechnological Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.L.D.); (S.M.); (S.U.)
| | - Domenico De Bellis
- Center for Advanced Studies and Technology (CAST), “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.D.B.); (P.L.)
- Department of Medicine and Aging Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Paola Lanuti
- Center for Advanced Studies and Technology (CAST), “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.D.B.); (P.L.)
- Department of Medicine and Aging Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Adriano Piattelli
- School of Dentistry, Saint Camillus International University of Health and Medical Sciences, Via di Sant’Alessandro 8, 00131 Rome, Italy;
- Facultad de Medicina, UCAM Universidad Católica San Antonio de Murcia, 30107 Murcia, Spain
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “Gabriele d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (D.L.D.); (S.M.); (S.U.)
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6
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Yao X, Jiang X, Luo H, Liang H, Ye X, Wei Y, Cong S. MOCAT: multi-omics integration with auxiliary classifiers enhanced autoencoder. BioData Min 2024; 17:9. [PMID: 38444019 PMCID: PMC10916109 DOI: 10.1186/s13040-024-00360-6] [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: 12/21/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Integrating multi-omics data is emerging as a critical approach in enhancing our understanding of complex diseases. Innovative computational methods capable of managing high-dimensional and heterogeneous datasets are required to unlock the full potential of such rich and diverse data. METHODS We propose a Multi-Omics integration framework with auxiliary Classifiers-enhanced AuToencoders (MOCAT) to utilize intra- and inter-omics information comprehensively. Additionally, attention mechanisms with confidence learning are incorporated for enhanced feature representation and trustworthy prediction. RESULTS Extensive experiments were conducted on four benchmark datasets to evaluate the effectiveness of our proposed model, including BRCA, ROSMAP, LGG, and KIPAN. Our model significantly improved most evaluation measurements and consistently surpassed the state-of-the-art methods. Ablation studies showed that the auxiliary classifiers significantly boosted classification accuracy in the ROSMAP and LGG datasets. Moreover, the attention mechanisms and confidence evaluation block contributed to improvements in the predictive accuracy and generalizability of our model. CONCLUSIONS The proposed framework exhibits superior performance in disease classification and biomarker discovery, establishing itself as a robust and versatile tool for analyzing multi-layer biological data. This study highlights the significance of elaborated designed deep learning methodologies in dissecting complex disease phenotypes and improving the accuracy of disease predictions.
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Affiliation(s)
- Xiaohui Yao
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Xiaohan Jiang
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
| | - Haoran Luo
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Hong Liang
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Xiufen Ye
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Yanhui Wei
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Shan Cong
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China.
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China.
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Osipov A, Nikolic O, Gertych A, Parker S, Hendifar A, Singh P, Filippova D, Dagliyan G, Ferrone CR, Zheng L, Moore JH, Tourtellotte W, Van Eyk JE, Theodorescu D. The Molecular Twin artificial-intelligence platform integrates multi-omic data to predict outcomes for pancreatic adenocarcinoma patients. NATURE CANCER 2024; 5:299-314. [PMID: 38253803 PMCID: PMC10899109 DOI: 10.1038/s43018-023-00697-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Contemporary analyses focused on a limited number of clinical and molecular biomarkers have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma. Here we describe a precision medicine platform known as the Molecular Twin consisting of advanced machine-learning models and use it to analyze a dataset of 6,363 clinical and multi-omic molecular features from patients with resected pancreatic ductal adenocarcinoma to accurately predict disease survival (DS). We show that a full multi-omic model predicts DS with the highest accuracy and that plasma protein is the top single-omic predictor of DS. A parsimonious model learning only 589 multi-omic features demonstrated similar predictive performance as the full multi-omic model. Our platform enables discovery of parsimonious biomarker panels and performance assessment of outcome prediction models learning from resource-intensive panels. This approach has considerable potential to impact clinical care and democratize precision cancer medicine worldwide.
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Affiliation(s)
- Arsen Osipov
- Department of Medicine (Medical Oncology), Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, Pancreatic Cancer Precision Medicine Center of Excellence, Johns Hopkins University, Baltimore, MD, USA
| | | | - Arkadiusz Gertych
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sarah Parker
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Hendifar
- Department of Medicine (Medical Oncology), Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Grant Dagliyan
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cristina R Ferrone
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lei Zheng
- Department of Oncology, Pancreatic Cancer Precision Medicine Center of Excellence, Johns Hopkins University, Baltimore, MD, USA
| | - Jason H Moore
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Warren Tourtellotte
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer E Van Eyk
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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8
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van Goor IW, Schouten TJ, Verburg DN, Besselink MG, Bonsing BA, Bosscha K, Brosens LA, Busch OR, Cirkel GA, van Dam RM, Festen S, Koerkamp BG, van der Harst E, de Hingh IH, Intven MP, Kazemier G, Los M, Meijer GJ, de Meijer VE, Nieuwenhuijs VB, Roos D, Schreinemakers JM, Stommel MW, Verdonk RC, van Santvoort HC, Daamen LA, Molenaar IQ. Predicting Long-term Disease-free Survival After Resection of Pancreatic Ductal Adenocarcinoma: A Nationwide Cohort Study. Ann Surg 2024; 279:132-137. [PMID: 37450706 PMCID: PMC10727199 DOI: 10.1097/sla.0000000000006004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
OBJECTIVE To develop a prediction model for long-term (≥5 years) disease-free survival (DFS) after the resection of pancreatic ductal adenocarcinoma (PDAC). BACKGROUND Despite high recurrence rates, ~10% of patients have long-term DFS after PDAC resection. A model to predict long-term DFS may aid individualized prognostication and shared decision-making. METHODS This nationwide cohort study included all consecutive patients who underwent PDAC resection in the Netherlands (2014-2016). The best-performing prognostic model was selected by Cox-proportional hazard analysis and Akaike's Information Criterion, presented by hazard ratios (HRs) with 95% confidence intervals (CIs). Internal validation was performed, and discrimination and calibration indices were assessed. RESULTS In all, 836 patients with a median follow-up of 67 months (interquartile range 51-79) were analyzed. Long-term DFS was seen in 118 patients (14%). Factors predictive of long-term DFS were low preoperative carbohydrate antigen 19-9 (logarithmic; HR 1.21; 95% CI 1.10-1.32), no vascular resection (HR 1.33; 95% CI 1.12-1.58), T1 or T2 tumor stage (HR 1.52; 95% CI 1.14-2.04, and HR 1.17; 95% CI 0.98-1.39, respectively), well/moderate tumor differentiation (HR 1.44; 95% CI 1.22-1.68), absence of perineural and lymphovascular invasion (HR 1.42; 95% CI 1.11-1.81 and HR 1.14; 95% CI 0.96-1.36, respectively), N0 or N1 nodal status (HR 1.92; 95% CI 1.54-2.40, and HR 1.33; 95% CI 1.11-1.60, respectively), R0 resection margin status (HR 1.25; 95% CI 1.07-1.46), no major complications (HR 1.14; 95% CI 0.97-1.35) and adjuvant chemotherapy (HR 1.74; 95% CI 1.47-2.06). Moderate performance (concordance index 0.68) with adequate calibration (slope 0.99) was achieved. CONCLUSIONS The developed prediction model, readily available at www.pancreascalculator.com, can be used to estimate the probability of long-term DFS after resection of pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Iris W.J.M. van Goor
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Thijs J. Schouten
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Daphne N. Verburg
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Marc G. Besselink
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, the Netherlands
| | - Bert A. Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Koop Bosscha
- Department of Surgery, Jeroen Bosch Hospital, Den Bosch, the Netherlands
| | - Lodewijk A.A. Brosens
- Department of Pathology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Olivier R. Busch
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, the Netherlands
| | - Geert A. Cirkel
- Department of Medical Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & Meander Medical Center Amersfoort, Utrecht, the Netherlands
| | | | | | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Martijn P.W. Intven
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Geert Kazemier
- Cancer Center Amsterdam, the Netherlands
- Department of Surgery, Amsterdam UMC, location Vrije Universiteit, Amsterdam, the Netherlands
| | - Maartje Los
- Department of Medical Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Gert J. Meijer
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Vincent E. de Meijer
- Department of Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Daphne Roos
- Department of Surgery, Renier de Graaf Gasthuis, Delft, the Netherlands
| | | | - Martijn W.J. Stommel
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert C. Verdonk
- Department of Gastroenterology, Regional Academic Cancer Center Utrecht, Utrecht, the Netherlands
| | - Hjalmar C. van Santvoort
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Lois A. Daamen
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Imaging Division, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - I. Quintus Molenaar
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
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9
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Huang L, Yang H, Chen K, Yuan J, Li J, Dai G, Gu M, Shi Y. The suppressive efficacy of THZ1 depends on KRAS mutation subtype and is associated with super-enhancer activity and the PI3K/AKT/mTOR signalling in pancreatic ductal adenocarcinoma: A hypothesis-generating study. Clin Transl Med 2023; 13:e1500. [PMID: 38037549 PMCID: PMC10689978 DOI: 10.1002/ctm2.1500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 10/24/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Inhibition of CDK7, a potent transcription regulator, may bring new hope for treating pancreatic ductal adenocarcinoma (PDAC), which is featured by large genetic heterogeneity and abundant KRAS mutations. This investigation aimed at exploring the discrepant efficacies of THZ1, a small-molecule covalent CDK7 inhibitor, on PDACs with different KRAS mutations and the underlying mechanisms. METHODS Associations of CDK7 expression with survival by KRAS mutations were first assessed. Effects of THZ1 on PDAC by different KRAS mutations were then investigated in vitro and in vivo. Moreover, the effects of THZ1 on gene transcription and phosphorylation of RNA polymerase II (RNAPOLII) in different KRAS mutant PDACs were assessed, and the effect of THZ1 on super-enhancer activity was evaluated using chromatin immunoprecipitation sequencing. Lastly, the effects of THZ1 on the binding of H3K27ac to PIK3CA and on the PI3K/AKT/mTOR signalling were analysed. RESULTS High CDK7 expression was significantly linked to worse survival within PDAC patients carrying KRAS-G12V mutation but not in those with KRAS-G12D mutation. The apoptosis-inducing effect of THZ1 was markedly stronger in KRAS-G12V PDAC than KRAS-G12D cancer. THZ1 significantly inhibited the growth of xenograft tumour with KRAS-G12V mutation, and the inhibition was markedly stronger than for KRAS-G12D tumour. In mini-cell-derived xenograft (CDX) models, THZ1 significantly suppressed KRAS-G12V PDAC but not KRAS-G12D cancer. THZ1 significantly suppressed the phosphorylation of RNAPOLII, and this effect was stronger in KRAS-G12V PDAC (especially at ser5). KRAS-G12V PDAC had more H3K27ac-binding super-enhancers, and the inhibition of THZ1 on super-enhancer activity was also stronger in KRAS-G12V PDAC. Furthermore, THZ1 significantly weakened the binding of H3K27ac to PIK3CA in KRAS-G12V PDAC. THZ1 significantly suppressed the PI3K/AKT/mTOR pathway and its downstream markers, and this effect was stronger in KRAS-G12V cells. CONCLUSIONS In this hypothesis-generating study, THZ1 might selectively inhibit certain PDACs with KRAS-G12V mutation more potently compared with some other PDACs with KRAS-G12D mutation, which might be associated with its effect on super-enhancer activity and the PI3K/AKT/mTOR signalling. Our findings might offer novel key clues for the precise management of PDAC and important evidence for future targeted trial design. HIGHLIGHTS THZ1 had a stronger effect on PDAC-bearing KRAS-G12V mutation than G12D mutation. Suppressive effect of THZ1 on phosphorylation of RNAPOLII was stronger in KRAS-G12V than KRAS-G12D PDAC. Inhibition of THZ1 on super-enhancer activity and H3K27ac binding to PIK3CA was stronger in KRAS-G12V PDAC. Suppressive effect of THZ1 on PI3K/AKT/mTOR pathway was stronger in KRAS-G12V PDAC.
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Affiliation(s)
- Lei Huang
- Department of OncologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hui Yang
- Department of OncologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kaidi Chen
- School of Pharmaceutical ScienceZhejiang Chinese Medical UniversityHangzhouChina
| | - Jing Yuan
- Department of PathologyChinese PLA General HospitalBeijingChina
| | - Jie Li
- Department of PathologyChinese PLA General HospitalBeijingChina
| | - Guanghai Dai
- Department of Medical OncologyChinese PLA General HospitalBeijingChina
| | - Mancang Gu
- School of Pharmaceutical ScienceZhejiang Chinese Medical UniversityHangzhouChina
- Academy of Chinese Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Yan Shi
- Department of General SurgeryShanghai Seventh People's HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
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10
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Çaparlar MA, Durhan A, Süleymanov M, Binarbaşı C, Koşmaz K. Prognostic Effect of Preoperative Inflammatory Markers on Morbidity and Overall Survival in Pancreatic Adenocarsinoma. Niger J Clin Pract 2023; 26:1902-1909. [PMID: 38158359 DOI: 10.4103/njcp.njcp_426_23] [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: 06/03/2023] [Accepted: 08/14/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND/AIM His study aimed to evaluate the availability of common diagnostic tests and biochemical markers in predicting poor prognosis in patients with pancreatic adenocarcinoma (PAC). The primary outcome measure was to identify predictive prognostic factors. The secondary outcome measure was to compare predictive measures in patients who survived or did not survive in the follow-up period. MATERIALS AND METHODS Medical data of 51 patients were obtained who underwent resection surgery for PAC between January 2016 and May 2022. There were two groups according to the mortality in the follow-up period group general mortality positive (GMP; n = 29) and group general mortality negative (GMN; n = 22). Stage IIb was the most common stage in subgroups. RESULTS Preoperative diagnostic tests revealed that aspartate aminotransferase (AST) level, De Ritis ratio (DRR), carcinoembryonic antigen (CEA), cancer antigen 19-9 (CA 19-9), immature granulocyte (IG) count, and IG ratio (IG%) are higher, and hemoglobin (Hgb) levels are lower in the GMP group (P < 0.05). In univariate analysis, seven variables, including AST ≥20.5 (P = 0.001), DRR ≥1.05 (P ≤ 0.001), CEA ≥3.32 (P = 0.02), IG count ≥0.06 (P < 0.01), Hgb ≤11.75 (P = 0.01), poor differentiation (P < 0.001) and existence of life-threatening complication (P < 0.01) were identified. In multivariate analysis, only DRR (≥1.05;100% specificity and 72% sensitivity) and poor differentiation (P = 0.019) were found to be independent prognostic factors for overall survival. The median overall survival of patients with the DRR ≥1.05 and poor tumor differentiation was lower, and the mortality rate was higher than the patients with DRR and without poor tumor differentiation (10.65 ± 3.11 months vs. 61.86 ± 5.36 months and 100% vs. 26.7%, P < 0.001). CONCLUSION Pretreatment high DRR, high IG counts and IG%, and poor differentiation of the tumor might be used as independent predictors of poor prognosis and mortality in patients with PAC.
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Affiliation(s)
- M A Çaparlar
- Department of General Surgery, Ankara Education and Research Hospital, Ankara, Turkey
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11
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Kumar V, Gaddam M, Moustafa A, Iqbal R, Gala D, Shah M, Gayam VR, Bandaru P, Reddy M, Gadaputi V. The Utility of Artificial Intelligence in the Diagnosis and Management of Pancreatic Cancer. Cureus 2023; 15:e49560. [PMID: 38156176 PMCID: PMC10754023 DOI: 10.7759/cureus.49560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Artificial intelligence (AI) has made significant advancements in the medical domain in recent years. AI, an expansive field comprising Machine Learning (ML) and, within it, Deep Learning (DL), seeks to emulate the intricate operations of the human brain. It examines vast amounts of data and plays a crucial role in decision-making, overcoming limitations related to human evaluation. DL utilizes complex algorithms to analyze data. ML and DL are subsets of AI that utilize hard statistical techniques that help machines consistently improve at tasks with experience. Pancreatic cancer is more common in developed countries and is one of the leading causes of cancer-related mortality worldwide. Managing pancreatic cancer remains a challenge despite significant advancements in diagnosis and treatment. AI has secured an almost ubiquitous presence in the field of oncological workup and management, especially in gastroenterology malignancies. AI is particularly useful for various investigations of pancreatic carcinoma because it has specific radiological features that enable diagnostic procedures without the requirement of a histological study. However, interpreting and evaluating resulting images is not always simple since images vary as the disease progresses. Secondly, a number of factors may impact prognosis and response to the treatment process. Currently, AI models have been created for diagnosing, grading, staging, and predicting prognosis and treatment response. This review presents the most up-to-date knowledge on the use of AI in the diagnosis and treatment of pancreatic carcinoma.
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Affiliation(s)
- Vikash Kumar
- Internal Medicine, The Brooklyn Hospital Center, Brooklyn, USA
| | | | - Amr Moustafa
- Internal Medicine, The Brooklyn Hospital Center, Brooklyn, USA
| | - Rabia Iqbal
- Internal Medicine, The Brooklyn Hospital Center, Brooklyn, USA
| | - Dhir Gala
- Internal Medicine, American University of the Caribbean School of Medicine, Sint Maarten, SXM
| | - Mili Shah
- Internal Medicine, American University of the Caribbean School of Medicine, Sint Maarten, SXM
| | - Vijay Reddy Gayam
- Gastroenterology and Hepatology, The Brooklyn Hospital Center, Brooklyn, USA
| | - Praneeth Bandaru
- Gastroenterology and Hepatology, The Brooklyn Hospital Center, Brooklyn, USA
| | - Madhavi Reddy
- Gastroenterology and Hepatology, The Brooklyn Hospital Center, Brooklyn, USA
| | - Vinaya Gadaputi
- Gastroenterology and Hepatology, Blanchard Valley Health System, Findlay, USA
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12
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Ranjbari S, Arslanturk S. Integration of incomplete multi-omics data using Knowledge Distillation and Supervised Variational Autoencoders for disease progression prediction. J Biomed Inform 2023; 147:104512. [PMID: 37813325 DOI: 10.1016/j.jbi.2023.104512] [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: 06/10/2023] [Revised: 08/31/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVE The rapid advancement of high-throughput technologies in the biomedical field has resulted in the accumulation of diverse omics data types, such as mRNA expression, DNA methylation, and microRNA expression, for studying various diseases. Integrating these multi-omics datasets enables a comprehensive understanding of the molecular basis of cancer and facilitates accurate prediction of disease progression. METHODS However, conventional approaches face challenges due to the dimensionality curse problem. This paper introduces a novel framework called Knowledge Distillation and Supervised Variational AutoEncoders utilizing View Correlation Discovery Network (KD-SVAE-VCDN) to address the integration of high-dimensional multi-omics data with limited common samples. Through our experimental evaluation, we demonstrate that the proposed KD-SVAE-VCDN architecture accurately predicts the progression of breast and kidney carcinoma by effectively classifying patients as long- or short-term survivors. Furthermore, our approach outperforms other state-of-the-art multi-omics integration models. RESULTS Our findings highlight the efficacy of the KD-SVAE-VCDN architecture in predicting the disease progression of breast and kidney carcinoma. By enabling the classification of patients based on survival outcomes, our model contributes to personalized and targeted treatments. The favorable performance of our approach in comparison to several existing models suggests its potential to contribute to the advancement of cancer understanding and management. CONCLUSION The development of a robust predictive model capable of accurately forecasting disease progression at the time of diagnosis holds immense promise for advancing personalized medicine. By leveraging multi-omics data integration, our proposed KD-SVAE-VCDN framework offers an effective solution to this challenge, paving the way for more precise and tailored treatment strategies for patients with different types of cancer.
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Affiliation(s)
- Sima Ranjbari
- Department of Computer Science, Wayne State University, Detroit, 48202, MI, USA.
| | - Suzan Arslanturk
- Department of Computer Science, Wayne State University, Detroit, 48202, MI, USA.
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13
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Shi T, Li M, Yu Y. Machine learning-enhanced insights into sphingolipid-based prognostication: revealing the immunological landscape and predictive proficiency for immunomotherapy and chemotherapy responses in pancreatic carcinoma. Front Mol Biosci 2023; 10:1284623. [PMID: 38028544 PMCID: PMC10643633 DOI: 10.3389/fmolb.2023.1284623] [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: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Background: With a poor prognosis for affected individuals, pancreatic adenocarcinoma (PAAD) is known as a complicated and diverse illness. Immunocytes have become essential elements in the development of PAAD. Notably, sphingolipid metabolism has a dual function in the development of tumors and the invasion of the immune system. Despite these implications, research on the predictive ability of sphingolipid variables for PAAD prognosis is strikingly lacking, and it is yet unclear how they can affect PAAD immunotherapy and targeted pharmacotherapy. Methods: The investigation process included SPG detection while also being pertinent to the prognosis for PAAD. Both the analytical capability of CIBERSORT and the prognostic capability of the pRRophetic R package were used to evaluate the immunological environments of the various HCC subtypes. In addition, CCK-8 experiments on PAAD cell lines were carried out to confirm the accuracy of drug sensitivity estimates. The results of these trials, which also evaluated cell survival and migratory patterns, confirmed the usefulness of sphingolipid-associated genes (SPGs). Results: As a result of this thorough investigation, 32 SPGs were identified, each of which had a measurable influence on the dynamics of overall survival. This collection of genes served as the conceptual framework for the development of a prognostic model, which was carefully assembled from 10 chosen genes. It should be noted that this grouping of patients into cohorts with high and low risk was a sign of different immune profiles and therapy responses. The increased abundance of SPGs was identified as a possible sign of inadequate responses to immune-based treatment approaches. The careful CCK-8 testing carried out on PAAD cell lines was of the highest importance for providing clear confirmation of drug sensitivity estimates. Conclusion: The significance of Sphingolipid metabolism in the complex web of PAAD development is brought home by this study. The novel risk model, built on the complexity of sphingolipid-associated genes, advances our understanding of PAAD and offers doctors a powerful tool for developing personalised treatment plans that are specifically suited to the unique characteristics of each patient.
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Affiliation(s)
| | | | - Yabin Yu
- Department of Hepatobiliary Surgery, The Affiliated Huaian No 1 People’s Hospital of Nanjing Medical University, Huaian, China
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14
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Khadirnaikar S, Shukla S, Prasanna SRM. Integration of pan-cancer multi-omics data for novel mixed subgroup identification using machine learning methods. PLoS One 2023; 18:e0287176. [PMID: 37856446 PMCID: PMC10586677 DOI: 10.1371/journal.pone.0287176] [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: 10/13/2022] [Accepted: 05/30/2023] [Indexed: 10/21/2023] Open
Abstract
Cancer is a heterogeneous disease, and patients with tumors from different organs can share similar epigenetic and genetic alterations. Therefore, it is crucial to identify the novel subgroups of patients with similar molecular characteristics. It is possible to propose a better treatment strategy when the heterogeneity of the patient is accounted for during subgroup identification, irrespective of the tissue of origin. This work proposes a machine learning (ML) based pipeline for subgroup identification in pan-cancer. Here, mRNA, miRNA, DNA methylation, and protein expression features from pan-cancer samples were concatenated and non-linearly projected to a lower dimension using an ML algorithm. This data was then clustered to identify multi-omics-based novel subgroups. The clinical characterization of these ML subgroups indicated significant differences in overall survival (OS) and disease-free survival (DFS) (p-value<0.0001). The subgroups formed by the patients from different tumors shared similar molecular alterations in terms of immune microenvironment, mutation profile, and enriched pathways. Further, decision-level and feature-level fused classification models were built to identify the novel subgroups for unseen samples. Additionally, the classification models were used to obtain the class labels for the validation samples, and the molecular characteristics were verified. To summarize, this work identified novel ML subgroups using multi-omics data and showed that the patients with different tumor types could be similar molecularly. We also proposed and validated the classification models for subgroup identification. The proposed classification models can be used to identify the novel multi-omics subgroups, and the molecular characteristics of each subgroup can be used to design appropriate treatment regimen.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - S. R. M. Prasanna
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
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15
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Viana JN, Pilbeam C, Howard M, Scholz B, Ge Z, Fisser C, Mitchell I, Raman S, Leach J. Maintaining High-Touch in High-Tech Digital Health Monitoring and Multi-Omics Prognostication: Ethical, Equity, and Societal Considerations in Precision Health for Palliative Care. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:461-473. [PMID: 37861713 DOI: 10.1089/omi.2023.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Advances in digital health, systems biology, environmental monitoring, and artificial intelligence (AI) continue to revolutionize health care, ushering a precision health future. More than disease treatment and prevention, precision health aims at maintaining good health throughout the lifespan. However, how can precision health impact care for people with a terminal or life-limiting condition? We examine here the ethical, equity, and societal/relational implications of two precision health modalities, (1) integrated systems biology/multi-omics analysis for disease prognostication and (2) digital health technologies for health status monitoring and communication. We focus on three main ethical and societal considerations: benefits and risks associated with integration of these modalities into the palliative care system; inclusion of underrepresented and marginalized groups in technology development and deployment; and the impact of high-tech modalities on palliative care's highly personalized and "high-touch" practice. We conclude with 10 recommendations for ensuring that precision health technologies, such as multi-omics prognostication and digital health monitoring, for palliative care are developed, tested, and implemented ethically, inclusively, and equitably.
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Affiliation(s)
- John Noel Viana
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- Responsible Innovation Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - Caitlin Pilbeam
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Mark Howard
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Philosophy, School of Philosophical, Historical and International Studies, Monash University, Clayton, Australia
| | - Brett Scholz
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Zongyuan Ge
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Data Science & AI, Monash University, Clayton, Australia
| | - Carys Fisser
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Imogen Mitchell
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
- Intensive Care Unit, Canberra Hospital, Canberra, Australia
| | - Sujatha Raman
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
| | - Joan Leach
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
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16
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [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: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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17
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Huang J, Liang R, Lu C, Lu L, Li S, Tang M, Huang X, Huang S, Mai R, Gao X, Li S, Zeng C, Lin Y, Ye J. A Case of Curative Treatment with Apatinib and Camrelizumab Following Liver Resection for Advanced Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:13486. [PMID: 37686291 PMCID: PMC10487462 DOI: 10.3390/ijms241713486] [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: 06/20/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Hepatocellular carcinoma (HCC), a highly malignant digestive system tumor, poses substantial challenges due to its intricate underlying causes and pronounced post-surgery recurrence. Consequently, the prognosis for HCC remains notably unfavorable. The endorsement of sorafenib and PD-L1 inhibitors for HCC signifies the onset of a new era embracing immunotherapy and targeted treatment approaches for this condition. Hence, comprehending the mechanisms underpinning targeted immune combination therapy has become exceedingly vital for the prospective management of HCC patients. This article initially presents a triumphant instance of curative treatment involving the combination of TKI and PD-1 inhibitor subsequent to liver resection, targeting an advanced stage HCC as classified by the BCLC staging system. The case patient carries a decade-long history of hepatitis B, having undergone a regimen of 20 courses of treatments involving apatinib and camrelizumab. Throughout the treatment period, no occurrences of grade 3 or 4 adverse events (AE) were noted. Subsequently, the patient underwent a left hepatectomy. Following the hepatectomy, their serum AFP levels have consistently remained within normal limits, and CT imaging has indicated the absence of tumor recurrence over a span of 36 months. The patient had been reviewed on time for two years after the operation. The last time a CT was performed for this patient in our hospital was 7 May 2021, and no new tumors were found. Follow-up is still ongoing. When applying combined targeted immune transformation therapy using TKI and ICI for a patient with BCLC advanced stage HCC, apatinib treatment serves a dual purpose. It inhibits the survival and angiogenesis of tumor cells, while also enhancing the efficacy of camrelizumab in obstructing the interaction between PD-1 and PD-L1. This restoration of T cell cytotoxicity subsequently facilitates the elimination of tumor cells, leading to an enhanced anticancer effect.
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Affiliation(s)
- Julu Huang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Rong Liang
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Cheng Lu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Lu Lu
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Shuanghang Li
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Minchao Tang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Xi Huang
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Shilin Huang
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Rongyun Mai
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Xing Gao
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Shizhuo Li
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Can Zeng
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
| | - Yan Lin
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (R.L.); (L.L.); (S.L.); (X.H.); (S.H.); (X.G.)
| | - Jiazhou Ye
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (J.H.); (C.L.); (M.T.); (R.M.); (S.L.); (C.Z.)
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18
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Huang L, Yuan X, Zhao L, Han Q, Yan H, Yuan J, Guan S, Xu X, Dai G, Wang J, Shi Y. Gene signature developed for predicting early relapse and survival in early-stage pancreatic cancer. BJS Open 2023; 7:7169392. [PMID: 37196196 DOI: 10.1093/bjsopen/zrad031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The aim of this study was to construct a predictive signature integrating tumour-mutation- and copy-number-variation-associated features using machine learning to precisely predict early relapse and survival in patients with resected stage I-II pancreatic ductal adenocarcinoma. METHODS Patients with microscopically confirmed stage I-II pancreatic ductal adenocarcinoma undergoing R0 resection at the Chinese PLA General Hospital between March 2015 and December 2016 were enrolled. Whole exosome sequencing was performed, and genes with different mutation or copy number variation statuses between patients with and without relapse within 1 year were identified using bioinformatics analysis. A support vector machine was used to evaluate the importance of the differential gene features and to develop a signature. Signature validation was performed in an independent cohort. The associations of the support vector machine signature and single gene features with disease-free survival and overall survival were assessed. Biological functions of integrated genes were further analysed. RESULTS Overall, 30 and 40 patients were included in the training and validation cohorts, respectively. Some 11 genes with differential patterns were first identified; using a support vector machine, four features (mutations of DNAH9, TP53, and TUBGCP6, and copy number variation of TMEM132E) were further selected and integrated to construct a predictive signature (the support vector machine classifier). In the training cohort, the 1-year disease-free survival rates were 88 per cent (95 per cent c.i. 73 to 100) and 7 per cent (95 per cent c.i. 1 to 47) in the low-support vector machine subgroup and the high-support vector machine subgroup respectively (P < 0.001). Multivariable analyses showed that high support vector machine was significantly and independently associated with both worse overall survival (HR 29.20 (95 per cent c.i. 4.48 to 190.21); P < 0.001) and disease-free survival (HR 72.04 (95 per cent c.i. 6.74 to 769.96); P < 0.001). The area under the curve of the support vector machine signature for 1-year disease-free survival (0.900) was significantly larger than the area under the curve values of the mutations of DNAH9 (0.733; P = 0.039), TP53 (0.767; P = 0.024), and TUBGCP6 (0.733; P = 0.023), the copy number variation of TMEM132E (0.700; P = 0.014), TNM stage (0.567; P = 0.002), and differentiation grade (0.633; P = 0.005), suggesting higher predictive accuracy for prognosis. The value of the signature was further validated in the validation cohort. The four genes included in the support vector machine signature (DNAH9, TUBGCP6, and TMEM132E were novel in pancreatic ductal adenocarcinoma) were significantly associated with the tumour immune microenvironment, G protein-coupled receptor binding and signalling, cell-cell adhesion, etc. CONCLUSION The newly constructed support vector machine signature precisely and powerfully predicted relapse and survival in patients with stage I-II pancreatic ductal adenocarcinoma after R0 resection.
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Affiliation(s)
- Lei Huang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medical Centre on Ageing of Ruijin Hospital, MCARJH, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaodong Yuan
- Organ Transplant Center, Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Liangchao Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quanli Han
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Huan Yan
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Jing Yuan
- Department of Pathology, Chinese PLA General Hospital, Beijing, China
| | - Shasha Guan
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Xiaofeng Xu
- Shanghai Chief Technician Studio (Information & Technology), Shanghai, China
| | - Guanghai Dai
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Junqing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Shi
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Kim J, Kim H, Lee MS, Lee H, Kim YJ, Lee WY, Yun SH, Kim HC, Hong HK, Hannenhalli S, Cho YB, Park D, Choi SS. Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients. J Transl Med 2023; 21:209. [PMID: 36941605 PMCID: PMC10029176 DOI: 10.1186/s12967-023-04053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Previous investigations of transcriptomic signatures of cancer patient survival and post-therapy relapse have focused on tumor tissue. In contrast, here we show that in colorectal cancer (CRC) transcriptomes derived from normal tissues adjacent to tumors (NATs) are better predictors of relapse. RESULTS Using the transcriptomes of paired tumor and NAT specimens from 80 Korean CRC patients retrospectively determined to be in recurrence or nonrecurrence states, we found that, when comparing recurrent with nonrecurrent samples, NATs exhibit a greater number of differentially expressed genes (DEGs) than tumors. Training two prognostic elastic net-based machine learning models-NAT-based and tumor-based in our Samsung Medical Center (SMC) cohort, we found that NAT-based model performed better in predicting the survival when the model was applied to the tumor-derived transcriptomes of an independent cohort of 450 COAD patients in TCGA. Furthermore, compositions of tumor-infiltrating immune cells in NATs were found to have better prognostic capability than in tumors. We also confirmed through Cox regression analysis that in both SMC-CRC as well as in TCGA-COAD cohorts, a greater proportion of genes exhibited significant hazard ratio when NAT-derived transcriptome was used compared to when tumor-derived transcriptome was used. CONCLUSIONS Taken together, our results strongly suggest that NAT-derived transcriptomes and immune cell composition of CRC are better predictors of patient survival and tumor recurrence than the primary tumor.
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Affiliation(s)
- Jinho Kim
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, 24341, Korea
| | - Hyunjung Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, 13620, Korea
| | - Min-Seok Lee
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, 24341, Korea
| | - Heetak Lee
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, 13620, Korea
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseng-gu, Daejeon, 34126, Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea
| | - Hye Kyung Hong
- Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, Korea
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, Bethesda, 20814, MD, USA
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, Korea.
| | | | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, 24341, Korea.
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Khadirnaikar S, Shukla S, Prasanna SRM. Machine learning based combination of multi-omics data for subgroup identification in non-small cell lung cancer. Sci Rep 2023; 13:4636. [PMID: 36944673 PMCID: PMC10030850 DOI: 10.1038/s41598-023-31426-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023] Open
Abstract
Non-small Cell Lung Cancer (NSCLC) is a heterogeneous disease with a poor prognosis. Identifying novel subtypes in cancer can help classify patients with similar molecular and clinical phenotypes. This work proposes an end-to-end pipeline for subgroup identification in NSCLC. Here, we used a machine learning (ML) based approach to compress the multi-omics NSCLC data to a lower dimensional space. This data is subjected to consensus K-means clustering to identify the five novel clusters (C1-C5). Survival analysis of the resulting clusters revealed a significant difference in the overall survival of clusters (p-value: 0.019). Each cluster was then molecularly characterized to identify specific molecular characteristics. We found that cluster C3 showed minimal genetic aberration with a high prognosis. Next, classification models were developed using data from each omic level to predict the subgroup of unseen patients. Decision‑level fused classification models were then built using these classifiers, which were used to classify unseen patients into five novel clusters. We also showed that the multi-omics-based classification model outperformed single-omic-based models, and the combination of classifiers proved to be a more accurate prediction model than the individual classifiers. In summary, we have used ML models to develop a classification method and identified five novel NSCLC clusters with different genetic and clinical characteristics.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India.
| | - S R M Prasanna
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
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21
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Yang D, Wu Y, Wan Z, Xu Z, Li W, Yuan P, Shang Q, Peng J, Tao L, Chen Q, Dan H, Xu H. HISMD: A Novel Immune Subtyping System for HNSCC. J Dent Res 2023; 102:270-279. [PMID: 36333876 DOI: 10.1177/00220345221134605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Immune subtyping is an important way to reveal immune heterogeneity, which may contribute to the diversity of the progression and treatment in head and neck squamous cell carcinoma (HNSCC). However, reported immune subtypes mainly focus on levels of immune infiltration and are mostly based on a mono-omics profile. This study aimed to identify a comprehensive immune subtype for HNSCC via multi-omics clustering and build a novel subtype prediction system for clinical application. Data were obtained from The Cancer Genome Atlas database and our independent multicenter cohort. Multi-omics clustering was performed to identify 3 clusters of 499 patients in The Cancer Genome Atlas based on immune-related gene expression and somatic mutations. The immune characteristics and biological features of the obtained clusters were revealed by bioinformatics, and 3 immune subtypes were identified: 1) adaptive immune activation subtype predominantly enriched in T cells, 2) innate immune activation subtype predominantly enriched in macrophages, and 3) immune desert subtype. Subsequently, the clinical implications of each subtype were analyzed per clinical epidemiology. We found that adaptive immune activation showed better survival outcomes and had a similar response to chemotherapy with innate immune activation, whereas immune desert might be relatively resistant to chemotherapy. Moreover, a subtype prediction system was developed by deep learning with whole slide images and named HISMD: HNSCC Immune Subtypes via Multi-omics and Deep Learning. We endowed HISMD with interpretability through image-based key feature extraction. The clinical implications, biological significances, and predictive stability of HISMD were successfully verified by using our independent multicenter cohort data set. In summary, this study revealed the immune heterogeneity of HNSCC and obtained a novel, highly accurate, and interpretable immune subtyping prediction system. For clinical implementation in the future, additional validation and utility studies are warranted.
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Affiliation(s)
- D Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z Wan
- Department of Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - W Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - P Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Q Shang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - L Tao
- College of Mathematics, Sichuan University, Chengdu, China
| | - Q Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Affiliated Stomatology Hospital, Zhejiang University School of Stomatology, Hangzhou, China
| | - H Dan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - H Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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22
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Chen Y, Meng J, Lu X, Li X, Wang C. Clustering analysis revealed the autophagy classification and potential autophagy regulators' sensitivity of pancreatic cancer based on multi-omics data. Cancer Med 2023; 12:733-746. [PMID: 35684936 PMCID: PMC9844610 DOI: 10.1002/cam4.4932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy and is unresponsive to conventional therapeutic modalities due to its high heterogeneity, expounding the necessity, and priority of searching for effective biomarkers and drugs. Autophagy, as an evolutionarily conserved biological process, is upregulated in PDAC and its regulation is linked to a poor prognosis. Increased autophagy sequestered MHC-I on PDAC cells and weaken the antigen presentation and antitumor immune response, indicating the potential therapeutic strategies of autophagy inhibitors. METHODS By performing 10 state-of-the-art multi-omics clustering algorithms, we constructed a robust PDAC classification model to reveal the autophagy-related genes among different subgroups. OUTCOMES After building a more comprehensive regulating network for potential autophagy regulators exploration, we concluded the top 20 autophagy-related hub genes (GAPDH, MAPK3, RHEB, SQSTM1, EIF2S1, RAB5A, CTSD, MAP1LC3B, RAB7A, RAB11A, FADD, CFKN2A, HSP90AB1, VEGFA, RELA, DDIT3, HSPA5, BCL2L1, BAG3, and ERBB2), six miRNAs, five transcription factors, and five immune infiltrated cells as biomarkers. The drug sensitivity database was screened based on the biomarkers to predict possible drug-targeting signal pathways, hoping to yield novel insights, and promote the progress of the anticancer therapeutic strategy. CONCLUSION We succefully constructed an autophagy-related mRNA/miRNA/TF/Immune cells network based on a 10 state-of art algorithm multi-omics analysis, and screened the drug sensitivity dataset for detecting potential signal pathway which might be possible autophagy modulators' targets.
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Affiliation(s)
- Yonghao Chen
- Department of GastroenterologyWest China Hospital of Sichuan UniversityChengduSichuanP.R. China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical UniversityHefeiP.R. China
- Institute of UrologyAnhui Medical UniversityHefeiP.R. China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical UniversityHefeiP.R. China
| | - Xiaofan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational PharmacyChina Pharmaceutical UniversityNanjingP.R. China
| | - Xiao Li
- Department of GastroenterologyWest China Hospital of Sichuan UniversityChengduSichuanP.R. China
| | - Chunhui Wang
- Department of GastroenterologyWest China Hospital of Sichuan UniversityChengduSichuanP.R. China
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23
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Sminia P, Guipaud O, Viktorsson K, Ahire V, Baatout S, Boterberg T, Cizkova J, Dostál M, Fernandez-Palomo C, Filipova A, François A, Geiger M, Hunter A, Jassim H, Edin NFJ, Jordan K, Koniarová I, Selvaraj VK, Meade AD, Milliat F, Montoro A, Politis C, Savu D, Sémont A, Tichy A, Válek V, Vogin G. Clinical Radiobiology for Radiation Oncology. RADIOBIOLOGY TEXTBOOK 2023:237-309. [DOI: 10.1007/978-3-031-18810-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
AbstractThis chapter is focused on radiobiological aspects at the molecular, cellular, and tissue level which are relevant for the clinical use of ionizing radiation (IR) in cancer therapy. For radiation oncology, it is critical to find a balance, i.e., the therapeutic window, between the probability of tumor control and the probability of side effects caused by radiation injury to the healthy tissues and organs. An overview is given about modern precision radiotherapy (RT) techniques, which allow optimal sparing of healthy tissues. Biological factors determining the width of the therapeutic window are explained. The role of the six typical radiobiological phenomena determining the response of both malignant and normal tissues in the clinic, the 6R’s, which are Reoxygenation, Redistribution, Repopulation, Repair, Radiosensitivity, and Reactivation of the immune system, is discussed. Information is provided on tumor characteristics, for example, tumor type, growth kinetics, hypoxia, aberrant molecular signaling pathways, cancer stem cells and their impact on the response to RT. The role of the tumor microenvironment and microbiota is described and the effects of radiation on the immune system including the abscopal effect phenomenon are outlined. A summary is given on tumor diagnosis, response prediction via biomarkers, genetics, and radiomics, and ways to selectively enhance the RT response in tumors. Furthermore, we describe acute and late normal tissue reactions following exposure to radiation: cellular aspects, tissue kinetics, latency periods, permanent or transient injury, and histopathology. Details are also given on the differential effect on tumor and late responding healthy tissues following fractionated and low dose rate irradiation as well as the effect of whole-body exposure.
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Lee C, Baek B, Cho SH, Jang T, Jeon S, Lee S, Lee H, Nam J. Machine learning with in silico analysis markedly improves survival prediction modeling in colon cancer patients. Cancer Med 2022; 12:7603-7615. [PMID: 36345155 PMCID: PMC10067044 DOI: 10.1002/cam4.5420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Predicting the survival of cancer patients provides prognostic information and therapeutic guidance. However, improved prediction models are needed for use in diagnosis and treatment. OBJECTIVE This study aimed to identify genomic prognostic biomarkers related to colon cancer (CC) based on computational data and to develop survival prediction models. METHODS We performed machine-learning (ML) analysis to screen pathogenic survival-related driver genes related to patient prognosis by integrating copy number variation and gene expression data. Moreover, in silico system analysis was performed to clinically assess data from ML analysis, and we identified RABGAP1L, MYH9, and DRD4 as candidate genes. These three genes and tumor stages were used to generate survival prediction models. Moreover, the genes were validated by experimental and clinical analyses, and the theranostic application of the survival prediction models was assessed. RESULTS RABGAP1L, MYH9, and DRD4 were identified as survival-related candidate genes by ML and in silico system analysis. The survival prediction model using the expression of the three genes showed higher predictive performance when applied to predict the prognosis of CC patients. A series of functional analyses revealed that each knockdown of three genes reduced the protumor activity of CC cells. In particular, validation with an independent cohort of CC patients confirmed that the coexpression of MYH9 and DRD4 gene expression reflected poorer clinical outcomes in terms of overall survival and disease-free survival. CONCLUSIONS Our survival prediction approach will contribute to providing information on patients and developing a therapeutic strategy for CC patients.
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Affiliation(s)
- Choong‐Jae Lee
- School of Life Sciences Gwangju Institute of Science and Technology Gwangju Korea
| | - Bin Baek
- School of Electrical Engineering and Computer Science Gwangju Institute of Science and Technology Gwangju Korea
| | - Sang Hee Cho
- Department of Hemato‐Oncology Chonnam National University Medical School Gwangju Korea
| | - Tae‐Young Jang
- School of Life Sciences Gwangju Institute of Science and Technology Gwangju Korea
| | - So‐El Jeon
- School of Life Sciences Gwangju Institute of Science and Technology Gwangju Korea
| | - Sunjae Lee
- School of Life Sciences Gwangju Institute of Science and Technology Gwangju Korea
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science Gwangju Institute of Science and Technology Gwangju Korea
| | - Jeong‐Seok Nam
- School of Life Sciences Gwangju Institute of Science and Technology Gwangju Korea
- Cell Logistics Research Center Gwangju Institute of Science and Technology Gwangju South Korea
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Systematic review, meta-analysis and single-centre experience of the diagnostic accuracy of intraoperative near-infrared indocyanine green-fluorescence in detecting pancreatic tumours. HPB (Oxford) 2022; 24:1823-1831. [PMID: 35654671 DOI: 10.1016/j.hpb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/20/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND During pancreatic resections assessing tumour boundaries and identifying the ideal resection margins can be challenging due to the associated pancreatic gland inflammation and texture. This is particularly true in the context of minimally invasive surgery, where there is a very limited or absent tactile feedback. Indocyanine green (ICG) fluorescence imaging can assist surgeons by simply providing valuable real-time intraoperative information at low cost with minimal side effects. This meta-analysis summarises the available evidence on the use of near-infrared fluorescence imaging with ICG for the intraoperative visualization of pancreatic tumours (PROSPERO ID: CRD42021247203). METHODS MEDLINE, Embase, and Web Of Science electronic databases were searched to identify manuscripts where ICG was intravenously administered prior to or during pancreatic surgery and reporting the prevalence of pancreatic lesions visualised through fluorescence imaging. RESULTS Six studies with 7 series' reporting data on 64 pancreatic lesions were included in the analysis. MINOR scores ranged from 6 to 10, with a median of 8. The most frequent indications were pancreatic adenocarcinoma and neuroendocrine tumours. In most cases (67.2%) ICG was administered during surgery. ICG fluorescence identified 48/64 lesions (75%) with 81.3% accuracy, 0.788 (95%CI 0.361-0.961) sensitivity, 1 (95%CI 0.072-1) specificity and positive predictive value of 0.982 (95%CI 0.532-1). In line with the literature, ICG fluorescence identified 5/6 (83.3%) of pancreatic lesions during robotic pancreatic resections performed at our Institution. CONCLUSION This meta-analysis is the first summarising the results of ICG immunofluorescence in detecting pancreatic tumours during surgery, showing good accuracy. Additional research is needed to define optimal ICG administration strategies and fluorescence intensity cut-offs.
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Chen S, Zang Y, Xu B, Lu B, Ma R, Miao P, Chen B. An Unsupervised Deep Learning-Based Model Using Multiomics Data to Predict Prognosis of Patients with Stomach Adenocarcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5844846. [PMID: 36339684 PMCID: PMC9633210 DOI: 10.1155/2022/5844846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/25/2022] [Accepted: 10/08/2022] [Indexed: 09/08/2023]
Abstract
METHODS Patients (363 in total) with stomach adenocarcinoma from The Cancer Genome Atlas (TCGA) cohort were included. An autoencoder was constructed to integrate the RNA sequencing, miRNA sequencing, and methylation data. The features of the bottleneck layer were used to perform the k-means clustering algorithm to obtain different subgroups for evaluating the prognosis-related risk of stomach adenocarcinoma. The model's robustness was verified using a 10-fold cross-validation (CV). Survival was analyzed by the Kaplan-Meier method. Univariate and multivariate Cox regression was used to estimate hazard risk. The model was validated in three independent cohorts with different endpoints. RESULTS The patients were divided into low-risk and high-risk groups according to the k-means clustering algorithm. The high-risk group had a significantly higher risk of poor survival (log-rank P value = 2.80e - 06; adjusted hazard ratio = 2.386, 95% confidence interval: 1.607~3.543), a concordance index (C-index) of 0.714, and a Brier score of 0.184. The model performed well both in the 10-fold CV procedure and three independent cohorts from the Gene Expression Omnibus (GEO) repository. CONCLUSIONS A robust and generalizable model based on the autoencoder was proposed to integrate multiomics data and predict the prognosis of patients with stomach adenocarcinoma. The model demonstrates better performance than two alternative approaches on prognosis prediction. The results might provide the grounds for further exploring the potential biomarkers to predict the prognosis of patients with stomach adenocarcinoma.
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Affiliation(s)
- Sizhen Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yiteng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Biyun Xu
- Department of Biostatistics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Beier Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Rongji Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Pengcheng Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Bingwei Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
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Huang B, Huang H, Zhang S, Zhang D, Shi Q, Liu J, Guo J. Artificial intelligence in pancreatic cancer. Am J Cancer Res 2022; 12:6931-6954. [PMID: 36276650 PMCID: PMC9576619 DOI: 10.7150/thno.77949] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/24/2022] [Indexed: 11/30/2022] Open
Abstract
Pancreatic cancer is the deadliest disease, with a five-year overall survival rate of just 11%. The pancreatic cancer patients diagnosed with early screening have a median overall survival of nearly ten years, compared with 1.5 years for those not diagnosed with early screening. Therefore, early diagnosis and early treatment of pancreatic cancer are particularly critical. However, as a rare disease, the general screening cost of pancreatic cancer is high, the accuracy of existing tumor markers is not enough, and the efficacy of treatment methods is not exact. In terms of early diagnosis, artificial intelligence technology can quickly locate high-risk groups through medical images, pathological examination, biomarkers, and other aspects, then screening pancreatic cancer lesions early. At the same time, the artificial intelligence algorithm can also be used to predict the survival time, recurrence risk, metastasis, and therapy response which could affect the prognosis. In addition, artificial intelligence is widely used in pancreatic cancer health records, estimating medical imaging parameters, developing computer-aided diagnosis systems, etc. Advances in AI applications for pancreatic cancer will require a concerted effort among clinicians, basic scientists, statisticians, and engineers. Although it has some limitations, it will play an essential role in overcoming pancreatic cancer in the foreseeable future due to its mighty computing power.
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Affiliation(s)
- Bowen Huang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Haoran Huang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shuting Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Dingyue Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qingya Shi
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jianzhou Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Junchao Guo
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
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Looi CK, Gan LL, Sim W, Hii LW, Chung FFL, Leong CO, Lim WM, Mai CW. Histone Deacetylase Inhibitors Restore Cancer Cell Sensitivity towards T Lymphocytes Mediated Cytotoxicity in Pancreatic Cancer. Cancers (Basel) 2022; 14:3709. [PMID: 35954379 PMCID: PMC9367398 DOI: 10.3390/cancers14153709] [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: 06/16/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/04/2023] Open
Abstract
Despite medical advancements, the prognosis of pancreatic ductal adenocarcinoma (PDAC) has not improved significantly over the past 50 years. By utilising the large-scale genomic datasets available from the Australia Pancreatic Cancer Project (PACA-AU) and The Cancer Genomic Atlas Project (TCGA-PAAD), we studied the immunophenotype of PDAC in silico and identified that tumours with high cytotoxic T lymphocytes (CTL) killing activity were associated with favourable clinical outcomes. Using the STRING protein-protein interaction network analysis, the identified differentially expressed genes with low CTL killing activity were associated with TWIST/IL-6R, HDAC5, and EOMES signalling. Following Connectivity Map analysis, we identified 44 small molecules that could restore CTL sensitivity in the PDAC cells. Further high-throughput chemical library screening identified 133 inhibitors that effectively target both parental and CTL-resistant PDAC cells in vitro. Since CTL-resistant PDAC had a higher expression of histone proteins and its acetylated proteins compared to its parental cells, we further investigated the impact of histone deacetylase inhibitors (HDACi) on CTL-mediated cytotoxicity in PDAC cells in vitro, namely SW1990 and BxPC3. Further analyses revealed that givinostat and dacinostat were the two most potent HDAC inhibitors that restored CTL sensitivity in SW1990 and BxPC3 CTL-resistant cells. Through our in silico and in vitro studies, we demonstrate the novel role of HDAC inhibition in restoring CTL resistance and that combinations of HDACi with CTL may represent a promising therapeutic strategy, warranting its further detailed molecular mechanistic studies and animal studies before embarking on the clinical evaluation of these novel combined PDAC treatments.
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Affiliation(s)
- Chin-King Looi
- School of Postgraduate Studies, International Medical University, Kuala Lumpur 57000, Malaysia; (C.-K.L.); (L.-L.G.)
| | - Li-Lian Gan
- School of Postgraduate Studies, International Medical University, Kuala Lumpur 57000, Malaysia; (C.-K.L.); (L.-L.G.)
- Clinical Research Centre, Hospital Tuanku Ja’afar Seremban, Ministry of Health Malaysia, Seremban 70300, Malaysia
| | - Wynne Sim
- School of Medicine, International Medical University, Kuala Lumpur 57000, Malaysia;
| | - Ling-Wei Hii
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Kuala Lumpur 57000, Malaysia; (L.-W.H.); (C.-O.L.); (W.-M.L.)
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia
| | - Felicia Fei-Lei Chung
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya 47500, Malaysia;
| | - Chee-Onn Leong
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Kuala Lumpur 57000, Malaysia; (L.-W.H.); (C.-O.L.); (W.-M.L.)
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia
- AGTC Genomics, Kuala Lumpur 57000, Malaysia
| | - Wei-Meng Lim
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Kuala Lumpur 57000, Malaysia; (L.-W.H.); (C.-O.L.); (W.-M.L.)
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia
- School of Pharmacy, Monash University Malaysia, Subang Jaya 47500, Malaysia
| | - Chun-Wai Mai
- Center for Cancer and Stem Cell Research, Development and Innovation (IRDI), Institute for Research, International Medical University, Kuala Lumpur 57000, Malaysia; (L.-W.H.); (C.-O.L.); (W.-M.L.)
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Pudong New District, Shanghai 200127, China
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Combining Molecular, Imaging, and Clinical Data Analysis for Predicting Cancer Prognosis. Cancers (Basel) 2022; 14:cancers14133215. [PMID: 35804988 PMCID: PMC9265023 DOI: 10.3390/cancers14133215] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The rise of Big Data, the widespread use of Machine Learning, and the cheapening of omics techniques have allowed for the creation of more sophisticated and accurate models in biomedical research. This article presents the state-of-the-art predictive models of cancer prognosis that use multimodal data, considering clinical, molecular (omics and non-omics), and image data. The subject of study, the data modalities used, the data processing and modelling methods applied, the validation strategies involved, the integration strategies encompassed, and the evolution of prognostic predictive models are discussed. Finally, we discuss challenges and opportunities in this field of cancer research, with great potential impact on the clinical management of patients and, by extension, on the implementation of personalised and precision medicine. Abstract Cancer is one of the most detrimental diseases globally. Accordingly, the prognosis prediction of cancer patients has become a field of interest. In this review, we have gathered 43 state-of-the-art scientific papers published in the last 6 years that built cancer prognosis predictive models using multimodal data. We have defined the multimodality of data as four main types: clinical, anatomopathological, molecular, and medical imaging; and we have expanded on the information that each modality provides. The 43 studies were divided into three categories based on the modelling approach taken, and their characteristics were further discussed together with current issues and future trends. Research in this area has evolved from survival analysis through statistical modelling using mainly clinical and anatomopathological data to the prediction of cancer prognosis through a multi-faceted data-driven approach by the integration of complex, multimodal, and high-dimensional data containing multi-omics and medical imaging information and by applying Machine Learning and, more recently, Deep Learning techniques. This review concludes that cancer prognosis predictive multimodal models are capable of better stratifying patients, which can improve clinical management and contribute to the implementation of personalised medicine as well as provide new and valuable knowledge on cancer biology and its progression.
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Wei Z, Han D, Zhang C, Wang S, Liu J, Chao F, Song Z, Chen G. Deep Learning-Based Multi-Omics Integration Robustly Predicts Relapse in Prostate Cancer. Front Oncol 2022; 12:893424. [PMID: 35814412 PMCID: PMC9259796 DOI: 10.3389/fonc.2022.893424] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivePost-operative biochemical relapse (BCR) continues to occur in a significant percentage of patients with localized prostate cancer (PCa). Current stratification methods are not adequate to identify high-risk patients. The present study exploits the ability of deep learning (DL) algorithms using the H2O package to combine multi-omics data to resolve this problem.MethodsFive-omics data from 417 PCa patients from The Cancer Genome Atlas (TCGA) were used to construct the DL-based, relapse-sensitive model. Among them, 265 (63.5%) individuals experienced BCR. Five additional independent validation sets were applied to assess its predictive robustness. Bioinformatics analyses of two relapse-associated subgroups were then performed for identification of differentially expressed genes (DEGs), enriched pathway analysis, copy number analysis and immune cell infiltration analysis.ResultsThe DL-based model, with a significant difference (P = 6e-9) between two subgroups and good concordance index (C-index = 0.767), were proven to be robust by external validation. 1530 DEGs including 678 up- and 852 down-regulated genes were identified in the high-risk subgroup S2 compared with the low-risk subgroup S1. Enrichment analyses found five hallmark gene sets were up-regulated while 13 were down-regulated. Then, we found that DNA damage repair pathways were significantly enriched in the S2 subgroup. CNV analysis showed that 30.18% of genes were significantly up-regulated and gene amplification on chromosomes 7 and 8 was significantly elevated in the S2 subgroup. Moreover, enrichment analysis revealed that some DEGs and pathways were associated with immunity. Three tumor-infiltrating immune cell (TIIC) groups with a higher proportion in the S2 subgroup (p = 1e-05, p = 8.7e-06, p = 0.00014) and one TIIC group with a higher proportion in the S1 subgroup (P = 1.3e-06) were identified.ConclusionWe developed a novel, robust classification for understanding PCa relapse. This study validated the effectiveness of deep learning technique in prognosis prediction, and the method may benefit patients and prevent relapse by improving early detection and advancing early intervention.
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Affiliation(s)
- Ziwei Wei
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Shiyu Wang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jinke Liu
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Fan Chao
- Department of Urology, Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, China
| | - Zhenyu Song
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Gang Chen, ; Zhenyu Song,
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Gang Chen, ; Zhenyu Song,
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Rangwani S, Ardeshna DR, Rodgers B, Melnychuk J, Turner R, Culp S, Chao WL, Krishna SG. Application of Artificial Intelligence in the Management of Pancreatic Cystic Lesions. Biomimetics (Basel) 2022; 7:biomimetics7020079. [PMID: 35735595 PMCID: PMC9221027 DOI: 10.3390/biomimetics7020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
The rate of incidentally detected pancreatic cystic lesions (PCLs) has increased over the past decade and was recently reported at 8%. These lesions pose a unique challenge, as each subtype of PCL carries a different risk of malignant transformation, ranging from 0% (pancreatic pseudocyst) to 34–68% (main duct intraductal papillary mucinous neoplasm). It is imperative to correctly risk-stratify the malignant potential of these lesions in order to provide the correct care course for the patient, ranging from monitoring to surgical intervention. Even with the multiplicity of guidelines (i.e., the American Gastroenterology Association guidelines and Fukuoka/International Consensus guidelines) and multitude of diagnostic information, risk stratification of PCLs falls short. Studies have reported that 25–64% of patients undergoing PCL resection have pancreatic cysts with no malignant potential, and up to 78% of mucin-producing cysts resected harbor no malignant potential on pathological evaluation. Clinicians are now incorporating artificial intelligence technology to aid in the management of these difficult lesions. This review article focuses on advancements in artificial intelligence within digital pathomics, radiomics, and genomics as they apply to the diagnosis and risk stratification of PCLs.
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Affiliation(s)
- Shiva Rangwani
- Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (S.R.); (D.R.A.)
| | - Devarshi R. Ardeshna
- Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (S.R.); (D.R.A.)
| | - Brandon Rodgers
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA; (B.R.); (J.M.); (R.T.)
| | - Jared Melnychuk
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA; (B.R.); (J.M.); (R.T.)
| | - Ronald Turner
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA; (B.R.); (J.M.); (R.T.)
| | - Stacey Culp
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43210, USA;
| | - Wei-Lun Chao
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA;
| | - Somashekar G. Krishna
- Department of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +614-293-6255
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Wang JH, Li CR, Hou PL. Feature screening for survival trait with application to TCGA high-dimensional genomic data. PeerJ 2022; 10:e13098. [PMID: 35291482 PMCID: PMC8918142 DOI: 10.7717/peerj.13098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/21/2022] [Indexed: 01/12/2023] Open
Abstract
Background In high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA). Results Simulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas. Conclusions These applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible.
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Rumer KK, Hedou J, Tsai A, Einhaus J, Verdonk F, Stanley N, Choisy B, Ganio E, Bonham A, Jacobsen D, Warrington B, Gao X, Tingle M, McAllister TN, Fallahzadeh R, Feyaerts D, Stelzer I, Gaudilliere D, Ando K, Shelton A, Morris A, Kebebew E, Aghaeepour N, Kin C, Angst MS, Gaudilliere B. Integrated Single-cell and Plasma Proteomic Modeling to Predict Surgical Site Complications: A Prospective Cohort Study. Ann Surg 2022; 275:582-590. [PMID: 34954754 PMCID: PMC8816871 DOI: 10.1097/sla.0000000000005348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The aim of this study was to determine whether single-cell and plasma proteomic elements of the host's immune response to surgery accurately identify patients who develop a surgical site complication (SSC) after major abdominal surgery. SUMMARY BACKGROUND DATA SSCs may occur in up to 25% of patients undergoing bowel resection, resulting in significant morbidity and economic burden. However, the accurate prediction of SSCs remains clinically challenging. Leveraging high-content proteomic technologies to comprehensively profile patients' immune response to surgery is a promising approach to identify predictive biological factors of SSCs. METHODS Forty-one patients undergoing non-cancer bowel resection were prospectively enrolled. Blood samples collected before surgery and on postoperative day one (POD1) were analyzed using a combination of single-cell mass cytometry and plasma proteomics. The primary outcome was the occurrence of an SSC, including surgical site infection, anastomotic leak, or wound dehiscence within 30 days of surgery. RESULTS A multiomic model integrating the single-cell and plasma proteomic data collected on POD1 accurately differentiated patients with (n = 11) and without (n = 30) an SSC [area under the curve (AUC) = 0.86]. Model features included coregulated proinflammatory (eg, IL-6- and MyD88- signaling responses in myeloid cells) and immunosuppressive (eg, JAK/STAT signaling responses in M-MDSCs and Tregs) events preceding an SSC. Importantly, analysis of the immunological data obtained before surgery also yielded a model accurately predicting SSCs (AUC = 0.82). CONCLUSIONS The multiomic analysis of patients' immune response after surgery and immune state before surgery revealed systemic immune signatures preceding the development of SSCs. Our results suggest that integrating immunological data in perioperative risk assessment paradigms is a plausible strategy to guide individualized clinical care.
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Affiliation(s)
- Kristen K. Rumer
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Julien Hedou
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Amy Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
| | - Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Sorbonne University, GRC 29, DMU DREAM, Assistance Publique-Hôpitaux de Paris, France
| | - Natalie Stanley
- Department of Computer Science and Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Benjamin Choisy
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Adam Bonham
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Danielle Jacobsen
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Beata Warrington
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Xiaoxiao Gao
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Tiffany N. McAllister
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Ina Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Dyani Gaudilliere
- Division of Plastic and Reconstructive Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Andrew Shelton
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Arden Morris
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Electron Kebebew
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Cindy Kin
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
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Identification of the robust predictor for sepsis based on clustering analysis. Sci Rep 2022; 12:2336. [PMID: 35149759 PMCID: PMC8837750 DOI: 10.1038/s41598-022-06310-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Sepsis is a life-threatening disorder with high incidence and mortality rate. However, the early detection of sepsis is challenging due to lack of specific marker and various etiology. This study aimed to identify robust risk factors for sepsis via cluster analysis. The integrative task of the automatic platform (i.e., electronic medical record) and the expert domain was performed to compile clinical and medical information for 2,490 sepsis patients and 16,916 health check-up participants. The subjects were categorized into 3 and 4 groups based on seven clinical and laboratory markers (Age, WBC, NLR, Hb, PLT, DNI, and MPXI) by K-means clustering. Logistic regression model was performed for all subjects including healthy control and sepsis patients, and cluster-specific cases, separately, to identify sepsis-related features. White blood cell (WBC), well-known parameter for sepsis, exhibited the insignificant association with the sepsis status in old age clusters (K3C3 and K4C3). Besides, NLR and DNI were the robust predictors in all subjects as well as three or four cluster-specific subjects including K3C3 or K4C3. We implemented the cluster-analysis for real-world hospital data to identify the robust predictors for sepsis, which could contribute to screen likely overlooked and potential sepsis patients (e.g., sepsis patients without WBC count elevation).
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Liu X, Wang W, Liu X, Zhang Z, Yu L, Li R, Guo D, Cai W, Quan X, Wu H, Dai M, Liang Z. Multi-omics analysis of intra-tumoural and inter-tumoural heterogeneity in pancreatic ductal adenocarcinoma. Clin Transl Med 2022; 12:e670. [PMID: 35061935 PMCID: PMC8782496 DOI: 10.1002/ctm2.670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
The poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is associated with the tumour heterogeneity. To explore intra- and inter-tumoural heterogeneity in PDAC, we analysed the multi-omics profiles of 61 PDAC lesion samples, along with the matched pancreatic normal tissue samples, from 19 PDAC patients. Haematoxylin and Eosin (H&E) staining revealed that diversely differentiated lesions coexisted both within and across individual tumours. Whole exome sequencing (WES) of samples from multi-region revealed diverse types of mutations in diverse genes between cancer cells within a tumour and between tumours from different individuals. The copy number variation (CNV) analysis also showed that PDAC exhibited intra- and inter-tumoural heterogeneity in CNV and that high average CNV burden was associated poor prognosis of the patients. Phylogenetic tree analysis and clonality/timing analysis of mutations displayed diverse evolutionary pathways and spatiotemporal characteristics of genomic alterations between different lesions from the same or different tumours. Hierarchical clustering analysis illustrated higher inter-tumoural heterogeneity than intra-tumoural heterogeneity of PDAC at the transcriptional levels as lesions from the same patients are grouped into a single cluster. Immune marker genes are differentially expressed in different regions and tumour samples as shown by tumour microenvironment (TME) analysis. TME appeared to be more heterogeneous than tumour cells in the same patient. Lesion-specific differentially methylated regions (DMRs) were identified by methylated DNA immunoprecipitation sequencing (MeDIP-seq). Furthermore, the integration analysis of multi-omics data showed that the mRNA levels of some genes, such as PLCB4, were significantly correlated with the gene copy numbers. The mRNA expressions of potential PDAC biomarkers ZNF521 and KDM6A were correlated with copy number alteration and methylation, respectively. Taken together, our results provide a comprehensive view of molecular heterogeneity and evolutionary trajectories of PDAC and may guide personalised treatment strategies in PDAC therapy.
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Affiliation(s)
- Xiaoqian Liu
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of PathologyQilu Hospital (Qingdao)Cheeloo College of MedicineShandong UniversityQingdaoShandongChina
| | - Wenqian Wang
- Department of General SurgeryPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiaoding Liu
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhiwen Zhang
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lianyuan Yu
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ruiyu Li
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Dan Guo
- Clinical BiobankMedical Research CentrePeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weijing Cai
- Shanghai Tongshu Biotechnology Co., LtdShanghaiChina
| | - Xueping Quan
- Shanghai Tongshu Biotechnology Co., LtdShanghaiChina
| | - Huanwen Wu
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Menghua Dai
- Department of General SurgeryPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhiyong Liang
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Verdonk F, Einhaus J, Tsai AS, Hedou J, Choisy B, Gaudilliere D, Kin C, Aghaeepour N, Angst MS, Gaudilliere B. Measuring the human immune response to surgery: multiomics for the prediction of postoperative outcomes. Curr Opin Crit Care 2021; 27:717-725. [PMID: 34545029 PMCID: PMC8585713 DOI: 10.1097/mcc.0000000000000883] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW Postoperative complications including infections, cognitive impairment, and protracted recovery occur in one-third of the 300 million surgeries performed annually worldwide. Complications cause personal suffering along with a significant economic burden on our healthcare system. However, the accurate prediction of postoperative complications and patient-targeted interventions for their prevention remain as major clinical challenges. RECENT FINDINGS Although multifactorial in origin, the dysregulation of immunological mechanisms that occur in response to surgical trauma is a key determinant of postoperative complications. Prior research, primarily focusing on inflammatory plasma markers, has provided important clues regarding their pathogenesis. However, the recent advent of high-content, single-cell transcriptomic, and proteomic technologies has considerably improved our ability to characterize the immune response to surgery, thereby providing new means to understand the immunological basis of postoperative complications and to identify prognostic biological signatures. SUMMARY The comprehensive and single-cell characterization of the human immune response to surgery has significantly advanced our ability to predict the risk of postoperative complications. Multiomic modeling of patients' immune states holds promise for the discovery of preoperative predictive biomarkers, ultimately providing patients and surgeons with actionable information to improve surgical outcomes. Although recent studies have generated a wealth of knowledge, laying the foundation for a single-cell atlas of the human immune response to surgery, larger-scale multiomic studies are required to derive robust, scalable, and sufficiently powerful models to accurately predict the risk of postoperative complications in individual patients.
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Affiliation(s)
- Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Julien Hedou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Benjamin Choisy
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | | | - Cindy Kin
- Department of Surgery, Stanford University School of Medicine
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
- Department of Biomedical Data Science, Stanford University
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
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Deep Learning for Human Disease Detection, Subtype Classification, and Treatment Response Prediction Using Epigenomic Data. Biomedicines 2021; 9:biomedicines9111733. [PMID: 34829962 PMCID: PMC8615388 DOI: 10.3390/biomedicines9111733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 11/17/2021] [Indexed: 12/25/2022] Open
Abstract
Deep learning (DL) is a distinct class of machine learning that has achieved first-class performance in many fields of study. For epigenomics, the application of DL to assist physicians and scientists in human disease-relevant prediction tasks has been relatively unexplored until very recently. In this article, we critically review published studies that employed DL models to predict disease detection, subtype classification, and treatment responses, using epigenomic data. A comprehensive search on PubMed, Scopus, Web of Science, Google Scholar, and arXiv.org was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Among 1140 initially identified publications, we included 22 articles in our review. DNA methylation and RNA-sequencing data are most frequently used to train the predictive models. The reviewed models achieved a high accuracy ranged from 88.3% to 100.0% for disease detection tasks, from 69.5% to 97.8% for subtype classification tasks, and from 80.0% to 93.0% for treatment response prediction tasks. We generated a workflow to develop a predictive model that encompasses all steps from first defining human disease-related tasks to finally evaluating model performance. DL holds promise for transforming epigenomic big data into valuable knowledge that will enhance the development of translational epigenomics.
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Ward RA, Aghaeepour N, Bhattacharyya RP, Clish CB, Gaudillière B, Hacohen N, Mansour MK, Mudd PA, Pasupneti S, Presti RM, Rhee EP, Sen P, Spec A, Tam JM, Villani AC, Woolley AE, Hsu JL, Vyas JM. Harnessing the Potential of Multiomics Studies for Precision Medicine in Infectious Disease. Open Forum Infect Dis 2021; 8:ofab483. [PMID: 34805429 PMCID: PMC8598922 DOI: 10.1093/ofid/ofab483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
The field of infectious diseases currently takes a reactive approach and treats infections as they present in patients. Although certain populations are known to be at greater risk of developing infection (eg, immunocompromised), we lack a systems approach to define the true risk of future infection for a patient. Guided by impressive gains in "omics" technologies, future strategies to infectious diseases should take a precision approach to infection through identification of patients at intermediate and high-risk of infection and deploy targeted preventative measures (ie, prophylaxis). The advances of high-throughput immune profiling by multiomics approaches (ie, transcriptomics, epigenomics, metabolomics, proteomics) hold the promise to identify patients at increased risk of infection and enable risk-stratifying approaches to be applied in the clinic. Integration of patient-specific data using machine learning improves the effectiveness of prediction, providing the necessary technologies needed to propel the field of infectious diseases medicine into the era of personalized medicine.
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Affiliation(s)
- Rebecca A Ward
- Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, California, USA
| | - Roby P Bhattacharyya
- Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cancer for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael K Mansour
- Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Philip A Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shravani Pasupneti
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Veterans Affairs Palo Alto Health Care System, Medical Service, Palo Alto, California, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of lnternal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eugene P Rhee
- The Nephrology Division and Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pritha Sen
- Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Andrej Spec
- Division of Infectious Diseases, Department of lnternal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jenny M Tam
- Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ann E Woolley
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joe L Hsu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Veterans Affairs Palo Alto Health Care System, Medical Service, Palo Alto, California, USA
| | - Jatin M Vyas
- Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Park S, Soh J, Lee H. Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data. BMC Bioinformatics 2021; 22:269. [PMID: 34034645 PMCID: PMC8152321 DOI: 10.1186/s12859-021-04146-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Predicting the drug response of a patient is important for precision oncology. In recent studies, multi-omics data have been used to improve the prediction accuracy of drug response. Although multi-omics data are good resources for drug response prediction, the large dimension of data tends to hinder performance improvement. In this study, we aimed to develop a new method, which can effectively reduce the large dimension of data, based on the supervised deep learning model for predicting drug response. RESULTS We proposed a novel method called Supervised Feature Extraction Learning using Triplet loss (Super.FELT) for drug response prediction. Super.FELT consists of three stages, namely, feature selection, feature encoding using a supervised method, and binary classification of drug response (sensitive or resistant). We used multi-omics data including mutation, copy number aberration, and gene expression, and these were obtained from cell lines [Genomics of Drug Sensitivity in Cancer (GDSC), Cancer Cell Line Encyclopedia (CCLE), and Cancer Therapeutics Response Portal (CTRP)], patient-derived tumor xenografts (PDX), and The Cancer Genome Atlas (TCGA). GDSC was used for training and cross-validation tests, and CCLE, CTRP, PDX, and TCGA were used for external validation. We performed ablation studies for the three stages and verified that the use of multi-omics data guarantees better performance of drug response prediction. Our results verified that Super.FELT outperformed the other methods at external validation on PDX and TCGA and was good at cross-validation on GDSC and external validation on CCLE and CTRP. In addition, through our experiments, we confirmed that using multi-omics data is useful for external non-cell line data. CONCLUSION By separating the three stages, Super.FELT achieved better performance than the other methods. Through our results, we found that it is important to train encoders and a classifier independently, especially for external test on PDX and TCGA. Moreover, although gene expression is the most powerful data on cell line data, multi-omics promises better performance for external validation on non-cell line data than gene expression data. Source codes of Super.FELT are available at https://github.com/DMCB-GIST/Super.FELT .
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Affiliation(s)
- Sejin Park
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Jihee Soh
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea.
- Graduate School of Artificial Intelligence, Gwangju Institute of Science and Technology, Gwangju, South Korea.
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Giulietti M, Cecati M, Sabanovic B, Scirè A, Cimadamore A, Santoni M, Montironi R, Piva F. The Role of Artificial Intelligence in the Diagnosis and Prognosis of Renal Cell Tumors. Diagnostics (Basel) 2021; 11:206. [PMID: 33573278 PMCID: PMC7912267 DOI: 10.3390/diagnostics11020206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
The increasing availability of molecular data provided by next-generation sequencing (NGS) techniques is allowing improvement in the possibilities of diagnosis and prognosis in renal cancer. Reliable and accurate predictors based on selected gene panels are urgently needed for better stratification of renal cell carcinoma (RCC) patients in order to define a personalized treatment plan. Artificial intelligence (AI) algorithms are currently in development for this purpose. Here, we reviewed studies that developed predictors based on AI algorithms for diagnosis and prognosis in renal cancer and we compared them with non-AI-based predictors. Comparing study results, it emerges that the AI prediction performance is good and slightly better than non-AI-based ones. However, there have been only minor improvements in AI predictors in terms of accuracy and the area under the receiver operating curve (AUC) over the last decade and the number of genes used had little influence on these indices. Furthermore, we highlight that different studies having the same goal obtain similar performance despite the fact they use different discriminating genes. This is surprising because genes related to the diagnosis or prognosis are expected to be tumor-specific and independent of selection methods and algorithms. The performance of these predictors will be better with the improvement in the learning methods, as the number of cases increases and by using different types of input data (e.g., non-coding RNAs, proteomic and metabolic). This will allow for more precise identification, classification and staging of cancerous lesions which will be less affected by interpathologist variability.
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Affiliation(s)
- Matteo Giulietti
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Monia Cecati
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Berina Sabanovic
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Andrea Scirè
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60126 Ancona, Italy;
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of Marche, United Hospitals, 60126 Ancona, Italy; (A.C.); (R.M.)
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62012 Macerata, Italy;
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of Marche, United Hospitals, 60126 Ancona, Italy; (A.C.); (R.M.)
| | - Francesco Piva
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
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41
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Veenstra TD. Omics in Systems Biology: Current Progress and Future Outlook. Proteomics 2021; 21:e2000235. [PMID: 33320441 DOI: 10.1002/pmic.202000235] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.
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