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Rowley SD, Gunning TS, Pelliccia M, Della Pia A, Lee A, Behrmann J, Bangolo A, Jandir P, Zhang H, Kaur S, Suh HC, Donato M, Albitar M, Ip A. Using Targeted Transcriptome and Machine Learning of Pre- and Post-Transplant Bone Marrow Samples to Predict Acute Graft-versus-Host Disease and Overall Survival after Allogeneic Stem Cell Transplantation. Cancers (Basel) 2024; 16:1357. [PMID: 38611035 PMCID: PMC11011125 DOI: 10.3390/cancers16071357] [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: 02/21/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Acute graft-versus-host disease (aGvHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). We performed RNA analysis of 1408 candidate genes in bone marrow samples obtained from 167 patients undergoing HSCT. RNA expression data were used in a machine learning algorithm to predict the presence or absence of aGvHD using either random forest or extreme gradient boosting algorithms. Patients were randomly divided into training (2/3 of patients) and validation (1/3 of patients) sets. Using post-HSCT RNA data, the machine learning algorithm selected 92 genes for predicting aGvHD that appear to play a role in PI3/AKT, MAPK, and FOXO signaling, as well as microRNA. The algorithm selected 20 genes for predicting survival included genes involved in MAPK and chemokine signaling. Using pre-HSCT RNA data, the machine learning algorithm selected 400 genes and 700 genes predicting aGvHD and overall survival, but candidate signaling pathways could not be specified in this analysis. These data show that NGS analyses of RNA expression using machine learning algorithms may be useful biomarkers of aGvHD and overall survival for patients undergoing HSCT, allowing for the identification of major signaling pathways associated with HSCT outcomes and helping to dissect the complex steps involved in the development of aGvHD. The analysis of pre-HSCT bone marrow samples may lead to pre-HSCT interventions including choice of remission induction regimens and modifications in patient health before HSCT.
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Affiliation(s)
- Scott D. Rowley
- Georgetown University School of Medicine, Washington, DC 20007, USA
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Thomas S. Gunning
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michael Pelliccia
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Alexandra Della Pia
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Albert Lee
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - James Behrmann
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Ayrton Bangolo
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Parul Jandir
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hong Zhang
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Sukhdeep Kaur
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hyung C. Suh
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michele Donato
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Maher Albitar
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Andrew Ip
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
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Bernardi S, Vallati M, Gatta R. Artificial Intelligence-Based Management of Adult Chronic Myeloid Leukemia: Where Are We and Where Are We Going? Cancers (Basel) 2024; 16:848. [PMID: 38473210 DOI: 10.3390/cancers16050848] [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: 01/18/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Artificial intelligence (AI) is emerging as a discipline capable of providing significant added value in Medicine, in particular in radiomic, imaging analysis, big dataset analysis, and also for generating virtual cohort of patients. However, in coping with chronic myeloid leukemia (CML), considered an easily managed malignancy after the introduction of TKIs which strongly improved the life expectancy of patients, AI is still in its infancy. Noteworthy, the findings of initial trials are intriguing and encouraging, both in terms of performance and adaptability to different contexts in which AI can be applied. Indeed, the improvement of diagnosis and prognosis by leveraging biochemical, biomolecular, imaging, and clinical data can be crucial for the implementation of the personalized medicine paradigm or the streamlining of procedures and services. In this review, we present the state of the art of AI applications in the field of CML, describing the techniques and objectives, and with a general focus that goes beyond Machine Learning (ML), but instead embraces the wider AI field. The present scooping review spans on publications reported in Pubmed from 2003 to 2023, and resulting by searching "chronic myeloid leukemia" and "artificial intelligence". The time frame reflects the real literature production and was not restricted. We also take the opportunity for discussing the main pitfalls and key points to which AI must respond, especially considering the critical role of the 'human' factor, which remains key in this domain.
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Affiliation(s)
- Simona Bernardi
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy
- CREA-Centro di Ricerca Emato-Oncologica AIL, ASST Spedali Civili of Brescia, 25123 Brescia, Italy
| | - Mauro Vallati
- School of Computing and Engineering, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Roberto Gatta
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy
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Ahmadieh-Yazdi A, Mahdavinezhad A, Tapak L, Nouri F, Taherkhani A, Afshar S. Using machine learning approach for screening metastatic biomarkers in colorectal cancer and predictive modeling with experimental validation. Sci Rep 2023; 13:19426. [PMID: 37940644 PMCID: PMC10632378 DOI: 10.1038/s41598-023-46633-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Colorectal cancer (CRC) liver metastasis accounts for the majority of fatalities associated with CRC. Early detection of metastasis is crucial for improving patient outcomes but can be delayed due to a lack of symptoms. In this research, we aimed to investigate CRC metastasis-related biomarkers by employing a machine learning (ML) approach and experimental validation. The gene expression profile of CRC patients with liver metastasis was obtained using the GSE41568 dataset, and the differentially expressed genes between primary and metastatic samples were screened. Subsequently, we carried out feature selection to identify the most relevant DEGs using LASSO and Penalized-SVM methods. DEGs commonly selected by these methods were selected for further analysis. Finally, the experimental validation was done through qRT-PCR. 11 genes were commonly selected by LASSO and P-SVM algorithms, among which seven had prognostic value in colorectal cancer. It was found that the expression of the MMP3 gene decreases in stage IV of colorectal cancer compared to other stages (P value < 0.01). Also, the expression level of the WNT11 gene was observed to increase significantly in this stage (P value < 0.001). It was also found that the expression of WNT5a, TNFSF11, and MMP3 is significantly lower, and the expression level of WNT11 is significantly higher in liver metastasis samples compared to primary tumors. In summary, this study has identified a set of potential biomarkers for CRC metastasis using ML algorithms. The findings of this research may provide new insights into identifying biomarkers for CRC metastasis and may potentially lay the groundwork for innovative therapeutic strategies for treatment of this disease.
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Affiliation(s)
- Amirhossein Ahmadieh-Yazdi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Mahdavinezhad
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Leili Tapak
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fatemeh Nouri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran.
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
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Han Y, Akhtar J, Liu G, Li C, Wang G. Early warning and diagnosis of liver cancer based on dynamic network biomarker and deep learning. Comput Struct Biotechnol J 2023; 21:3478-3489. [PMID: 38213892 PMCID: PMC10782000 DOI: 10.1016/j.csbj.2023.07.002] [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: 04/12/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 01/13/2024] Open
Abstract
Background Early detection of complex diseases like hepatocellular carcinoma remains challenging due to their network-driven pathology. Dynamic network biomarkers (DNB) based on monitoring changes in molecular correlations may enable earlier predictions. However, DNB analysis often overlooks disease heterogeneity. Methods We integrated DNB analysis with graph convolutional neural networks (GCN) to identify critical transitions during hepatocellular carcinoma development in a mouse model. A DNB-GCN model was constructed using transcriptomic data and gene expression levels as node features. Results DNB analysis identified a critical transition point at 7 weeks of age despite histological examinations being unable to detect cancerous changes at that time point. The DNB-GCN model achieved 100% accuracy in classifying healthy and cancerous mice, and was able to accurately predict the health status of newly introduced mice. Conclusion The integration of DNB analysis and GCN demonstrates potential for the early detection of complex diseases by capturing network structures and molecular features that conventional biomarker discovery methods overlook. The approach warrants further development and validation.
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Affiliation(s)
- Yukun Han
- Institute of Modern Biology, Nanjing University, Nanjing 210023, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Javed Akhtar
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guozhen Liu
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chenzhong Li
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guanyu Wang
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Creating a More Welcoming Home for Your Work at The American Journal of Pathology. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:2-3. [PMID: 36521959 DOI: 10.1016/j.ajpath.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022]
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Artificial Intelligence in Cancer Research: Trends, Challenges and Future Directions. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121991. [PMID: 36556356 PMCID: PMC9786074 DOI: 10.3390/life12121991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The World Health Organization (WHO), in their 2022 report, identified cancer as one of the leading causes of death, accounting for about 16% of deaths worldwide. The Cancer-Moonshot community aims to reduce the cancer death rate by half in the next 25 years and wants to improve the lives of cancer-affected people. Cancer mortality can be reduced if detected early and treated appropriately. Cancers like breast cancer and cervical cancer have high cure probabilities when treated early in accordance with best practices. Integration of artificial intelligence (AI) into cancer research is currently addressing many of the challenges where medical experts fail to bring cancer to control and cure, and the outcomes are quite encouraging. AI offers many tools and platforms to facilitate more understanding and tackling of this life-threatening disease. AI-based systems can help pathologists in diagnosing cancer more accurately and consistently, reducing the case error rates. Predictive-AI models can estimate the likelihood for a person to get cancer by identifying the risk factors. Big data, together with AI, can enable medical experts to develop customized treatments for cancer patients. The side effects from this kind of customized therapy will be less severe in comparison with the generalized therapies. However, many of these AI tools will remain ineffective in fighting against cancer and saving the lives of millions of patients unless they are accessible and understandable to biologists, oncologists, and other medical cancer researchers. This paper presents the trends, challenges, and future directions of AI in cancer research. We hope that this paper will be of help to both medical experts and technical experts in getting a better understanding of the challenges and research opportunities in cancer diagnosis and treatment.
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