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Bangolo A, Wadhwani N, Nagesh VK, Dey S, Tran HHV, Aguilar IK, Auda A, Sidiqui A, Menon A, Daoud D, Liu J, Pulipaka SP, George B, Furman F, Khan N, Plumptre A, Sekhon I, Lo A, Weissman S. Impact of artificial intelligence in the management of esophageal, gastric and colorectal malignancies. Artif Intell Gastrointest Endosc 2024; 5:90704. [DOI: 10.37126/aige.v5.i2.90704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/28/2024] [Accepted: 03/04/2024] [Indexed: 05/11/2024] Open
Abstract
The incidence of gastrointestinal malignancies has increased over the past decade at an alarming rate. Colorectal and gastric cancers are the third and fifth most commonly diagnosed cancers worldwide but are cited as the second and third leading causes of mortality. Early institution of appropriate therapy from timely diagnosis can optimize patient outcomes. Artificial intelligence (AI)-assisted diagnostic, prognostic, and therapeutic tools can assist in expeditious diagnosis, treatment planning/response prediction, and post-surgical prognostication. AI can intercept neoplastic lesions in their primordial stages, accurately flag suspicious and/or inconspicuous lesions with greater accuracy on radiologic, histopathological, and/or endoscopic analyses, and eliminate over-dependence on clinicians. AI-based models have shown to be on par, and sometimes even outperformed experienced gastroenterologists and radiologists. Convolutional neural networks (state-of-the-art deep learning models) are powerful computational models, invaluable to the field of precision oncology. These models not only reliably classify images, but also accurately predict response to chemotherapy, tumor recurrence, metastasis, and survival rates post-treatment. In this systematic review, we analyze the available evidence about the diagnostic, prognostic, and therapeutic utility of artificial intelligence in gastrointestinal oncology.
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Affiliation(s)
- Ayrton Bangolo
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Nikita Wadhwani
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Vignesh K Nagesh
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Shraboni Dey
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Hadrian Hoang-Vu Tran
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Izage Kianifar Aguilar
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Auda Auda
- Department of Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Aman Sidiqui
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Aiswarya Menon
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Deborah Daoud
- Department of Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - James Liu
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Sai Priyanka Pulipaka
- Department of Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Blessy George
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Flor Furman
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Nareeman Khan
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Adewale Plumptre
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Imranjot Sekhon
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Abraham Lo
- Department of Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
| | - Simcha Weissman
- Department of Internal Medicine, Palisades Medical Center, North Bergen, NJ 07047, United States
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Grupińska J, Budzyń M, Janowski J, Brzeziński J, Gryszczyńska B, Leporowska E, Formanowicz D, Kycler W. Potential of the postoperative lymphocyte-to-monocyte and monocyte-to-red blood cell ratio in predicting locoregional and distant metastases after breast cancer resection - Retrospective study. Adv Med Sci 2024; 69:103-112. [PMID: 38394965 DOI: 10.1016/j.advms.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
PURPOSE Breast cancer is the most common malignancy with high recurrence and mortality rates in women. There are still insufficient biomarkers to predict disease prognosis. Therefore, the present study aimed to investigate the clinical significance of postoperative hematologic parameters and their derivatives in patients with breast cancer who underwent tumor resection. PATIENTS AND METHODS The clinicopathological and laboratory data of 90 female breast cancer patients who underwent surgical treatment in the Greater Poland Cancer Center in Poznan from December 2015 to November 2017 were retrospectively analyzed. Postoperative hematologic parameters, including neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), monocyte-to-red blood cell ratio (MRR), lymphocyte-to-red blood cell ratio (LRR), platelet-to-red blood cell ratio (PRR) were evaluated in recurrence and non-recurrence group. Receiver-operating characteristic (ROC) curve analysis was used to assess the optimal cutoff value of postoperative hematologic parameters for tumor recurrence. The association of postoperative hematologic parameters with disease-free survival (DFS) was investigated by the Kaplan-Meier method and Cox regression analysis. RESULTS Patients with local, regional, or distant metastases accounted for 14% of the total. The postoperative monocyte count and MRR were significantly elevated, whereas postoperative LMR was statistically decreased in the recurrence group. Univariate and multivariate Cox analysis revealed that postoperative LMR ≤3.044 and postoperative MRR >0.1398 were associated with significantly shorter DFS. CONCLUSION Our results revealed that both postoperative LMR and MRR are independent predictors of DFS in breast cancer patients. Large-scale prospective investigations are needed to validate our findings.
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Affiliation(s)
- Joanna Grupińska
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland; Hospital Pharmacy, Greater Poland Cancer Centre, Poznan, Poland.
| | - Magdalena Budzyń
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Jakub Janowski
- Department of Oncological Surgery of Gastrointestinal Diseases, Greater Poland Cancer Centre, Poznan, Poland
| | - Jacek Brzeziński
- Department of Oncological Surgery of Gastrointestinal Diseases, Greater Poland Cancer Centre, Poznan, Poland
| | - Bogna Gryszczyńska
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewa Leporowska
- Department of Laboratory Diagnostics, Greater Poland Cancer Centre, Poznan, Poland
| | - Dorota Formanowicz
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Witold Kycler
- Department of Oncological Surgery of Gastrointestinal Diseases, Greater Poland Cancer Centre, Poznan, Poland
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You Y, Yang Q. Glycosylation-related genes mediated prognostic signature contribute to prognostic prediction and treatment options in ovarian cancer: based on bulk and single‑cell RNA sequencing data. BMC Cancer 2024; 24:207. [PMID: 38355446 PMCID: PMC10865697 DOI: 10.1186/s12885-024-11908-4] [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: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a complex disease with significant tumor heterogeneity with the worst prognosis and highest mortality among all gynecological cancers. Glycosylation is a specific post-translational modification that plays an important role in tumor progression, immune escape and metastatic spread. The aim of this work was to identify the major glycosylation-related genes (GRGs) in OC and construct an effective GRGs signature to predict prognosis and immunotherapy. METHODS AUCell algorithm was used to identify glycosylation-related genes (GRGs) based on the scRNA-seq and bulk RNA-seq data. An effective GRGs signature was conducted using COX and LASSO regression algorithm. The texting dataset and clinical sample data were used to assessed the accuracy of GRGs signature. We evaluated the differences in immune cell infiltration, enrichment of immune checkpoints, immunotherapy response, and gene mutation status among different risk groups. Finally, RT-qPCR, Wound-healing assay, Transwell assay were performed to verify the effect of the CYBRD1 on OC. RESULTS A total of 1187 GRGs were obtained and a GRGs signature including 16 genes was established. The OC patients were divided into high- and low- risk group based on the median riskscore and the patients in high-risk group have poor outcome. We also found that the patients in low-risk group have higher immune cell infiltration, enrichment of immune checkpoints and immunotherapy response. The results of laboratory test showed that CYBRD1 can promote the invasion, and migration of OC and is closely related to the poor prognosis of OC patients. CONCLUSIONS Our study established a GRGs signature consisting of 16 genes based on the scRNA-seq and bulk RNA-seq data, which provides a new perspective on the prognosis prediction and treatment strategy for OC.
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Affiliation(s)
- Yue You
- Department of gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Yang
- Department of gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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Collins GS, Whittle R, Bullock GS, Logullo P, Dhiman P, de Beyer JA, Riley RD, Schlussel MM. Open science practices need substantial improvement in prognostic model studies in oncology using machine learning. J Clin Epidemiol 2024; 165:111199. [PMID: 37898461 DOI: 10.1016/j.jclinepi.2023.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
OBJECTIVE To describe the frequency of open science practices in a contemporary sample of studies developing prognostic models using machine learning methods in the field of oncology. STUDY DESIGN AND SETTING We conducted a systematic review, searching the MEDLINE database between December 1, 2022, and December 31, 2022, for studies developing a multivariable prognostic model using machine learning methods (as defined by the authors) in oncology. Two authors independently screened records and extracted open science practices. RESULTS We identified 46 publications describing the development of a multivariable prognostic model. The adoption of open science principles was poor. Only one study reported availability of a study protocol, and only one study was registered. Funding statements and conflicts of interest statements were common. Thirty-five studies (76%) provided data sharing statements, with 21 (46%) indicating data were available on request to the authors and seven declaring data sharing was not applicable. Two studies (4%) shared data. Only 12 studies (26%) provided code sharing statements, including 2 (4%) that indicated the code was available on request to the authors. Only 11 studies (24%) provided sufficient information to allow their model to be used in practice. The use of reporting guidelines was rare: eight studies (18%) mentioning using a reporting guideline, with 4 (10%) using the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis Or Diagnosis statement, 1 (2%) using Minimum Information About Clinical Artificial Intelligence Modeling and Consolidated Standards Of Reporting Trials-Artificial Intelligence, 1 (2%) using Strengthening The Reporting Of Observational Studies In Epidemiology, 1 (2%) using Standards for Reporting Diagnostic Accuracy Studies, and 1 (2%) using Transparent Reporting of Evaluations with Nonrandomized Designs. CONCLUSION The adoption of open science principles in oncology studies developing prognostic models using machine learning methods is poor. Guidance and an increased awareness of benefits and best practices of open science are needed for prediction research in oncology.
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Affiliation(s)
- Gary S Collins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom.
| | - Rebecca Whittle
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Garrett S Bullock
- Department of Orthopaedic Surgery, Wake Forest School of Medicine, Winston-Salem, NC, USA; Centre for Sport, Exercise and Osteoarthritis Research Versus Arthritis, University of Oxford, Oxford, United Kingdom
| | - Patricia Logullo
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Paula Dhiman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer A de Beyer
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard D Riley
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael M Schlussel
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
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Nopour R. Prediction of five-year survival among esophageal cancer patients using machine learning. Heliyon 2023; 9:e22654. [PMID: 38125437 PMCID: PMC10730993 DOI: 10.1016/j.heliyon.2023.e22654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Background and aim Considering the silent progression of esophageal cancer, the survival prediction of this disease is crucial in enhancing the quality of life of these patients globally. So far, no prediction solution has been introduced for the survival of EC in Iran based on the machine learning approach. So, this study aims to develop a prediction model for the five-year survival of EC based on the ML approach to promote clinical outcomes and various treatment and preventive plans. Material and methods In this retrospective study, we investigated the 1656 cases of survived and non-survived EC patients belonging to Imam Khomeini Hospital in Sari City from 2013 to 2020. The multivariable regression analysis was used to select the best predictors of five-year survival. We leveraged random forest, eXtreme Gradient Boosting, support vector machine, artificial neural networks, Bayesian networks, J-48 decision tree, and K-nearest neighborhood to develop the prediction models. To get the best model for predicting the five-year survival of EC, we compared them using the area under the receiver operator characteristics. Results The age at diagnosis, body mass index, smoking, obstruction, dysphagia, weight loss, lymphadenopathy, chemotherapy, radiotherapy, family history of EC, tumor stage, type of appearance, histological type, grade of differentiation, tumor location, tumor size, lymphatic invasion, vascular invasion, and platelet albumin ratio were considered as the best predictors associated with the five-year survival of EC based on the regression analysis. In this respect, the random forest with the area under the receiver operator characteristics of 0.95 was identified as a superior model. Conclusion The experimental results of the current study showed that the random forest could have a significant role in enhancing the quality of care in EC patients by increasing the effectiveness of follow-up and treatment measures introduced by care providers.
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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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