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Zarrella JA, Tsurumi A. Genome-wide transcriptome profiling and development of age prediction models in the human brain. Aging (Albany NY) 2024; 16:4075-4094. [PMID: 38428408 PMCID: PMC10968712 DOI: 10.18632/aging.205609] [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: 05/02/2022] [Accepted: 03/28/2023] [Indexed: 03/03/2024]
Abstract
Aging-related transcriptome changes in various regions of the healthy human brain have been explored in previous works, however, a study to develop prediction models for age based on the expression levels of specific panels of transcripts is lacking. Moreover, studies that have assessed sexually dimorphic gene activities in the aging brain have reported discrepant results, suggesting that additional studies would be advantageous. The prefrontal cortex (PFC) region was previously shown to have a particularly large number of significant transcriptome alterations during healthy aging in a study that compared different regions in the human brain. We harmonized neuropathologically normal PFC transcriptome datasets obtained from the Gene Expression Omnibus (GEO) repository, ranging in age from 21 to 105 years, and found a large number of differentially regulated transcripts in the old and elderly, compared to young samples overall, and compared female and male-specific expression alterations. We assessed the genes that were associated with age by employing ontology, pathway, and network analyses. Furthermore, we applied various established (least absolute shrinkage and selection operator (Lasso) and Elastic Net (EN)) and recent (eXtreme Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM)) machine learning algorithms to develop accurate prediction models for chronological age and validated them. Studies to further validate these models in other large populations and molecular studies to elucidate the potential mechanisms by which the transcripts identified may be related to aging phenotypes would be advantageous.
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Affiliation(s)
- Joseph A. Zarrella
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Shriner's Hospitals for Children-Boston, Boston, MA 02114, USA
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Muthamilselvan S, Palaniappan A. BrcaDx: precise identification of breast cancer from expression data using a minimal set of features. FRONTIERS IN BIOINFORMATICS 2023; 3:1103493. [PMID: 37287543 PMCID: PMC10242386 DOI: 10.3389/fbinf.2023.1103493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/15/2023] [Indexed: 06/09/2023] Open
Abstract
Background: Breast cancer is the foremost cancer in worldwide incidence, surpassing lung cancer notwithstanding the gender bias. One in four cancer cases among women are attributable to cancers of the breast, which are also the leading cause of death in women. Reliable options for early detection of breast cancer are needed. Methods: Using public-domain datasets, we screened transcriptomic profiles of breast cancer samples, and identified progression-significant linear and ordinal model genes using stage-informed models. We then applied a sequence of machine learning techniques, namely, feature selection, principal components analysis, and k-means clustering, to train a learner to discriminate "cancer" from "normal" based on expression levels of identified biomarkers. Results: Our computational pipeline yielded an optimal set of nine biomarker features for training the learner, namely, NEK2, PKMYT1, MMP11, CPA1, COL10A1, HSD17B13, CA4, MYOC, and LYVE1. Validation of the learned model on an independent test dataset yielded a performance of 99.5% accuracy. Blind validation on an out-of-domain external dataset yielded a balanced accuracy of 95.5%, demonstrating that the model has effectively reduced the dimensionality of the problem, and learnt the solution. The model was rebuilt using the full dataset, and then deployed as a web app for non-profit purposes at: https://apalania.shinyapps.io/brcadx/. To our knowledge, this is the best-performing freely available tool for the high-confidence diagnosis of breast cancer, and represents a promising aid to medical diagnosis.
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Jiawei Z, Min M, Yingru X, Xin Z, Danting L, Yafeng L, Jun X, Wangfa H, Lijun Z, Jing W, Dong H. Identification of Key Genes in Lung Adenocarcinoma and Establishment of Prognostic Mode. Front Mol Biosci 2020; 7:561456. [PMID: 33195408 PMCID: PMC7653064 DOI: 10.3389/fmolb.2020.561456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/07/2020] [Indexed: 12/23/2022] Open
Abstract
Background Materials and Methods Results Conclusion
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Affiliation(s)
- Zhou Jiawei
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Mu Min
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Safety and Health, Ministry of Education, Anhui University of Science and Technology, Huainan, China
- *Correspondence: Mu Min,
| | - Xing Yingru
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, China
| | - Zhang Xin
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Li Danting
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Liu Yafeng
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Xie Jun
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, China
| | - Hu Wangfa
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, China
| | - Zhang Lijun
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Wu Jing
- School of Medicine, Anhui University of Science and Technology, Huainan, China
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Safety and Health, Ministry of Education, Anhui University of Science and Technology, Huainan, China
- Wu Jing,
| | - Hu Dong
- School of Medicine, Anhui University of Science and Technology, Huainan, China
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Safety and Health, Ministry of Education, Anhui University of Science and Technology, Huainan, China
- Hu Dong,
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Yu DH, Huang JY, Liu XP, Ruan XL, Chen C, Hu WD, Li S. Effects of hub genes on the clinicopathological and prognostic features of lung adenocarcinoma. Oncol Lett 2020; 19:1203-1214. [PMID: 31966050 PMCID: PMC6956410 DOI: 10.3892/ol.2019.11193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is a common malignancy; however, the majority of its underlying molecular mechanisms remain unknown. In the present study, weighted gene co-expression network analysis was applied to construct gene co-expression networks for the GSE19804 dataset, in order to screen hub genes associated with the pathogenesis of LUAD. In addition, with the aid of the Database for Annotation, Visualization and Integrated Discovery, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes, pathway enrichment analyses were performed on the genes in the selected module. Using the GSE40791 dataset and The Cancer Genome Atlas database, the hub genes were identified. It was discovered that the turquoise module was the most significant module associated with the tumor stage of LUAD. After performing functional enrichment analyses, it was indicated that the turquoise module was mainly enriched in signal transduction. Additionally, at the transcriptional and translational level, nine hub genes were identified and validated: Carbonic anhydrase 4 (CA4), platelet and endothelial cell adhesion molecule 1 (PECAM1), DnaJ member B4 (DNAJB4), advanced glycosylation end-product specific receptor (AGER), GTPase, IMAP family member 6 (GIMAP6), chromosome 10 open reading frame 54 (C10orf54), dedicator of cytokinesis 4 (DOCK4), Golgi membrane protein 1 (GOLM1) and platelet activating factor acetylhydrolase 1b catalytic subunit 3 (PAFAH1B3). CA4, PECAM1, DNAJB4, AGER, GIMAP6, C10orf54 and DOCK4 were expressed at lower levels in the tumor samples, whereas GOLM1 and PAFAH1B3 were highly expressed in tumor samples. In addition, all hub genes were associated with prognosis. In conclusion, one module and nine genes were recognized to be associated with the tumor stage of LUAD. These findings may enhance the understanding of the progression and prognosis of LUAD.
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Affiliation(s)
- Dong-Hu Yu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Jing-Yu Huang
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiao-Lan Ruan
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Human Genetics Resource Preservation Center of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Wei-Dong Hu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Human Genetics Resource Preservation Center of Hubei Province, Wuhan, Hubei 430071, P.R. China
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