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Kori M, Demirtas TY, Comertpay B, Arga KY, Sinha R, Gov E. A 19-Gene Signature of Serous Ovarian Cancer Identified by Machine Learning and Systems Biology: Prospects for Diagnostics and Personalized Medicine. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:90-101. [PMID: 38320250 DOI: 10.1089/omi.2023.0273] [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: 02/08/2024]
Abstract
Ovarian cancer is a major cause of cancer deaths among women. Early diagnosis and precision/personalized medicine are essential to reduce mortality and morbidity of ovarian cancer, as with new molecular targets to accelerate drug discovery. We report here an integrated systems biology and machine learning (ML) approach based on the differential coexpression analysis to identify candidate systems biomarkers (i.e., gene modules) for serous ovarian cancer. Accordingly, four independent transcriptome datasets were statistically analyzed independently and common differentially expressed genes (DEGs) were identified. Using these DEGs, coexpressed gene pairs were unraveled. Subsequently, differential coexpression networks between the coexpressed gene pairs were reconstructed so as to identify the differentially coexpressed gene modules. Based on the established criteria, "SOV-module" was identified as being significant, consisting of 19 genes. Using independent datasets, the diagnostic capacity of the SOV-module was evaluated using principal component analysis (PCA) and ML techniques. PCA showed a sensitivity and specificity of 96.7% and 100%, respectively, and ML analysis showed an accuracy of up to 100% in distinguishing phenotypes in the present study sample. The prognostic capacity of the SOV-module was evaluated using survival and ML analyses. We found that the SOV-module's performance for prognostics was significant (p-value = 1.36 × 10-4) with an accuracy of 63% in discriminating between survival and death using ML techniques. In summary, the reported genomic systems biomarker candidate offers promise for personalized medicine in diagnosis and prognosis of serous ovarian cancer and warrants further experimental and translational clinical studies.
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Affiliation(s)
- Medi Kori
- Faculty of Health Sciences, Acibadem Mehmet Ali Aydinlar University, İstanbul, Türkiye
| | - Talip Yasir Demirtas
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Betul Comertpay
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, İstanbul, Türkiye
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, İstanbul, Türkiye
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Esra Gov
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
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Li Y, Li X, Chen H, Sun K, Li H, Zhou Y, Wang J, Bai F, Yang F. Single‐cell RNA sequencing reveals the multi‐cellular ecosystem in different radiological components of pulmonary part‐solid nodules. Clin Transl Med 2022; 12:e723. [PMID: 35184398 PMCID: PMC8858630 DOI: 10.1002/ctm2.723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 11/24/2022] Open
Abstract
Background Early‐stage lung adenocarcinoma that radiologically manifests as part‐solid nodules, consisting of both ground‐glass and solid components, has distinctive growth patterns and prognosis. The characteristics of the tumour microenvironment and transcriptional features of the malignant cells of different radiological phenotypes remain poorly understood. Methods Twelve treatment‐naive patients with radiological part‐solid nodules were enrolled. After frozen pathology was confirmed as lung adenocarcinoma, two regions (ground‐glass and solid) from each of the 12 part‐solid nodules and 5 normal lung tissues from 5 of the12 patients were subjected to single‐cell sequencing by 10x Genomics. We used Seurat v3.1.5 for data integration and analysis. Results We comprehensively dissected the multicellular ecosystem of the ground‐glass and solid components of part‐solid nodules at the single‐cell resolution. In tumours, these components had comparable proportions of malignant cells. However, the angiogenesis, epithelial‐to‐mesenchymal transition, KRAS, p53, and cell‐cycle signalling pathways were significantly up‐regulated in malignant cells within solid components compared to those within ground‐glass components. For the tumour microenvironment, the relative abundance of myeloid and NK cells tended to be higher in solid components than in ground‐glass components. Slight subtype composition differences existed between the ground‐glass and solid components. The T/NK cell subsets’ cytotoxic function and the macrophages’ pro‐inflammation function were suppressed in solid components. Moreover, pericytes in solid components had a stronger communication related to angiogenesis promotion with endothelial cells and tumour cells. Conclusion The cellular landscape of ground‐glass components is significantly different from that of normal tissue and similar to that of solid components. However, transcriptional differences exist in the vital signalling pathways of malignant and immune cells within these components.
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Affiliation(s)
- Yanmeng Li
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
| | - Xiao Li
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
| | - Haiming Chen
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
| | - Kunkun Sun
- Department of Pathology Peking University People's Hospital Beijing China
| | - Hao Li
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
| | - Ying Zhou
- Department of Pathology Peking University People's Hospital Beijing China
| | - Jun Wang
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
- Beijing Advanced Innovation Center for Genomics (ICG) Peking University Beijing China
| | - Fan Yang
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences & Department of Thoracic Surgery People's Hospital, Peking University Beijing China
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Jolly MK, Murphy RJ, Bhatia S, Whitfield HJ, Redfern A, Davis MJ, Thompson EW. Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications. Cells Tissues Organs 2021; 211:110-133. [PMID: 33902034 DOI: 10.1159/000515289] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 11/19/2022] Open
Abstract
The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.
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Affiliation(s)
- Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ryan J Murphy
- Queensland University of Technology, School of Mathematical Sciences, Brisbane, Queensland, Australia
| | - Sugandha Bhatia
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Redfern
- Department of Medicine, School of Medicine, University of Western Australia, Fiona Stanley Hospital Campus, Perth, Washington, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Erik W Thompson
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
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Riemann A, Rauschner M, Gießelmann M, Reime S, Thews O. The Acidic Tumor Microenvironment Affects Epithelial-Mesenchymal Transition Markers as Well as Adhesion of NCI-H358 Lung Cancer Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1269:179-183. [PMID: 33966214 DOI: 10.1007/978-3-030-48238-1_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Epithelial-mesenchymal transition (EMT), which is involved in metastasis formation, requires reprogramming of gene expression mediated by key EMT transcription factors. However, signals from the cellular microenvironment, including hypoxia, can also modulate the process of EMT. Hypoxia is often associated with a reduction in the extracellular pH of the tumor microenvironment (acidosis). Whether acidosis alone has an impact on the expression of the EMT markers E-cadherin, N-cadherin, and vimentin was studied in NCI-H358 lung cancer cells. Reducing extracellular pH decreased E-cadherin mRNA, while vimentin and N-cadherin mRNA were doubled. However, at the protein level, E-cadherin and N-cadherin were both reduced, and only vimentin was upregulated. E-cadherin and N-cadherin expression at the cell surface, which is the relevant parameter for cell-cell and cell-matrix interaction, decreased too. The reduction of cell surface proteins was due to diminished protein expression and not changes in cellular localization, since localization of EMT markers in general was not affected by acidosis. Acidosis also affected NCI-H358 cells functionally. Adhesion was decreased when the cells were primed in an acidic medium before measuring cell adherence, which is in line with the reduced expression of cadherins at the cell surface. Additionally, migration was decreased after acidic priming. A possible mechanism for the regulation of EMT markers involves the action of microRNA-203a (miR-203a). In NCI-H358 lung cancer cells, miR-203a expression was repressed by acidosis. Since a decrease in the level of miR-203a has been shown to induce EMT, it might be involved in the modulation of EMT marker expression, adhesion, and migration by the acidic tumor microenvironment in NCI-H358 lung cancer cells.
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Affiliation(s)
- Anne Riemann
- Julius Bernstein Institute of Physiology, University of Halle-Wittenberg, Halle (Saale), Germany.
| | - M Rauschner
- Julius Bernstein Institute of Physiology, University of Halle-Wittenberg, Halle (Saale), Germany
| | - M Gießelmann
- Julius Bernstein Institute of Physiology, University of Halle-Wittenberg, Halle (Saale), Germany
| | - S Reime
- Julius Bernstein Institute of Physiology, University of Halle-Wittenberg, Halle (Saale), Germany
| | - O Thews
- Julius Bernstein Institute of Physiology, University of Halle-Wittenberg, Halle (Saale), Germany
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Wang Y, Yi N, Hu Y, Zhou X, Jiang H, Lin Q, Chen R, Liu H, Gu Y, Tong C, Lu M, Zhang J, Zhang B, Peng L, Li L. Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:696-711. [PMID: 32769060 PMCID: PMC7412763 DOI: 10.1016/j.omtn.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/05/2020] [Accepted: 07/06/2020] [Indexed: 12/23/2022]
Abstract
Cardiomyocyte differentiation derived from embryonic stem cells (ESCs) is a complex process involving molecular regulation of multiple levels. In this study, we first identify and compare differentially expressed gene (DEG) signatures of ESC-derived cardiomyocyte differentiation (ESCDCD) in humans and mice. Then, the multiscale embedded gene co-expression network analysis (MEGENA) of the human ESCDCD dataset is performed to identify 212 significantly co-expressed gene modules, which capture well the regulatory information of cardiomyocyte differentiation. Three modules respectively involved in the regulation of stem cell pluripotency, Wnt, and calcium pathways are enriched in the DEG signatures of the differentiation phase transition in the two species. Three human-specific cardiomyocyte differentiation phase transition modules are identified. Moreover, the potential regulation mechanisms of transcription factors during cardiomyocyte differentiation are also illustrated. Finally, several novel key drivers of ESCDCD are identified with the evidence of their expression during mouse embryonic cardiomyocyte differentiation. Using an integrative network analysis, the core molecular signatures and gene subnetworks (modules) underlying cardiomyocyte lineage commitment are identified in both humans and mice. Our findings provide a global picture of gene-gene co-regulation and identify key regulators during ESCDCD.
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Affiliation(s)
- Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Na Yi
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yi Hu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hanyu Jiang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Qin Lin
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Rou Chen
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Huan Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yanqiong Gu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Chang Tong
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Min Lu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Junfang Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
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