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Li J, Tian J, Liu Y, Liu Z, Tong M. Personalized analysis of human cancer multi-omics for precision oncology. Comput Struct Biotechnol J 2024; 23:2049-2056. [PMID: 38783900 PMCID: PMC11112262 DOI: 10.1016/j.csbj.2024.05.011] [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: 01/30/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Multi-omics technologies, encompassing genomics, proteomics, and transcriptomics, provide profound insights into cancer biology. A fundamental computational approach for analyzing multi-omics data is differential analysis, which identifies molecular distinctions between cancerous and normal tissues. Traditional methods, however, often fail to address the distinct heterogeneity of individual tumors, thereby neglecting crucial patient-specific molecular traits. This shortcoming underscores the necessity for tailored differential analysis algorithms, which focus on particular patient variations. Such approaches offer a more nuanced understanding of cancer biology and are instrumental in pinpointing personalized therapeutic strategies. In this review, we summarize the principles of current individualized techniques. We also review their efficacy in analyzing cancer multi-omics data and discuss their potential applications in clinical practice.
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Affiliation(s)
- Jiaao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Jingyi Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Yachen Liu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Zan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
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Cai H, Chen L, Yang S, Jiang R, Guo Y, He M, Luo Y, Hong G, Li H, Song K. Personalized differential expression analysis in triple-negative breast cancer. Brief Funct Genomics 2024; 23:495-506. [PMID: 38197537 DOI: 10.1093/bfgp/elad057] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.
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Affiliation(s)
- Hao Cai
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Liangbo Chen
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Shuxin Yang
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Ronghong Jiang
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Ming He
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yun Luo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Guini Hong
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Hongdong Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Kai Song
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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Gillman R, Field MA, Schmitz U, Karamatic R, Hebbard L. Identifying cancer driver genes in individual tumours. Comput Struct Biotechnol J 2023; 21:5028-5038. [PMID: 37867967 PMCID: PMC10589724 DOI: 10.1016/j.csbj.2023.10.019] [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: 07/28/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Cancer is a heterogeneous disease with a strong genetic component making it suitable for precision medicine approaches aimed at identifying the underlying molecular drivers within a tumour. Large scale population-level cancer sequencing consortia have identified many actionable mutations common across both cancer types and sub-types, resulting in an increasing number of successful precision medicine programs. Nonetheless, such approaches fail to consider the effects of mutations unique to an individual patient and may miss rare driver mutations, necessitating personalised approaches to driver-gene prioritisation. One approach is to quantify the functional importance of individual mutations in a single tumour based on how they affect the expression of genes in a gene interaction network (GIN). These GIN-based approaches can be broadly divided into those that utilise an existing reference GIN and those that construct de novo patient-specific GINs. These single-tumour approaches have several limitations that likely influence their results, such as use of reference cohort data, network choice, and approaches to mathematical approximation, and more research is required to evaluate the in vitro and in vivo applicability of their predictions. This review examines the current state of the art methods that identify driver genes in single tumours with a focus on GIN-based driver prioritisation.
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Affiliation(s)
- Rhys Gillman
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Matt A. Field
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Ulf Schmitz
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Rozemary Karamatic
- Gastroenterology and Hepatology, Townsville University Hospital, PO Box 670, Townsville, Queensland 4810, Australia
- College of Medicine and Dentistry, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Lionel Hebbard
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
- Australian Institute for Tropical Health and Medicine, Townsville, Queensland, Australia
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Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers (Basel) 2023; 15:cancers15051557. [PMID: 36900348 PMCID: PMC10001303 DOI: 10.3390/cancers15051557] [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: 01/06/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Targeting glioblastoma (GBM) stem-like cells (GSCs) is a common interest in both the laboratory investigation and clinical treatment of GBM. Most of the currently applied GBM stem-like markers lack validation and comparison with common standards regarding their efficiency and feasibility in various targeting methods. Using single-cell RNA sequencing datasets from 37 GBM patients, we obtained a large pool of 2173 GBM stem-like marker candidates. To evaluate and select these candidates quantitatively, we characterized the efficiency of the candidate markers in targeting the GBM stem-like cells by their frequencies and significance of being the stem-like cluster markers. This was followed by further selection based on either their differential expression in GBM stem-like cells compared with normal brain cells or their relative expression level compared with other expressed genes. The cellular location of the translated protein was also considered. Different combinations of selection criteria highlight different markers for different application scenarios. By comparing the commonly used GSCs marker CD133 (PROM1) with markers selected by our method regarding their universality, significance, and abundance, we revealed the limitations of CD133 as a GBM stem-like marker. Overall, we propose BCAN, PTPRZ1, SOX4, etc. for laboratory-based assays with samples free of normal cells. For in vivo targeting applications that require high efficiency in targeting the stem-like subtype, the ability to distinguish GSCs from normal brain cells, and a high expression level, we recommend the intracellular marker TUBB3 and the surface markers PTPRS and GPR56.
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Hiort P, Hugo J, Zeinert J, Müller N, Kashyap S, Rajapakse JC, Azuaje F, Renard BY, Baum K. DrDimont: explainable drug response prediction from differential analysis of multi-omics networks. Bioinformatics 2022; 38:ii113-ii119. [PMID: 36124784 PMCID: PMC9486584 DOI: 10.1093/bioinformatics/btac477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. RESULTS We present DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e. molecular differences that are the source of high differential drug scores can be retrieved. We predict differential drug response in breast cancer using transcriptomics, proteomics, phosphosite and metabolomics measurements and contrast estrogen receptor positive and receptor negative patients. DrDimont performs better than drug prediction based on differential protein expression or PageRank when evaluating it on ground truth data from cancer cell lines. We find proteomic and phosphosite layers to carry most information for distinguishing drug response. AVAILABILITY AND IMPLEMENTATION DrDimont is available on CRAN: https://cran.r-project.org/package=DrDimont. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pauline Hiort
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
| | - Julian Hugo
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
| | - Justus Zeinert
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
| | - Nataniel Müller
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
| | - Spoorthi Kashyap
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
| | - Jagath C Rajapakse
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | | | - Bernhard Y Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
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Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer’s disease drug repurposing. PLoS Comput Biol 2022; 18:e1010367. [PMID: 35951653 PMCID: PMC9398009 DOI: 10.1371/journal.pcbi.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 08/23/2022] [Accepted: 07/08/2022] [Indexed: 11/19/2022] Open
Abstract
Predictive modeling of drug-induced gene expressions is a powerful tool for phenotype-based compound screening and drug repurposing. State-of-the-art machine learning methods use a small number of fixed cell lines as a surrogate for predicting actual expressions in a new cell type or tissue, although it is well known that drug responses depend on a cellular context. Thus, the existing approach has limitations when applied to personalized medicine, especially for many understudied diseases whose molecular profiles are dramatically different from those characterized in the training data. Besides the gene expression, dose-dependent cell viability is another important phenotype readout and is more informative than conventional summary statistics (e.g., IC50) for characterizing clinical drug efficacy and toxicity. However, few computational methods can reliably predict the dose-dependent cell viability. To address the challenges mentioned above, we designed a new deep learning model, MultiDCP, to predict cellular context-dependent gene expressions and cell viability on a specific dosage. The novelties of MultiDCP include a knowledge-driven gene expression profile transformer that enables context-specific phenotypic response predictions of novel cells or tissues, integration of multiple diverse labeled and unlabeled omics data, the joint training of the multiple prediction tasks, and a teacher-student training procedure that allows us to utilize unreliable data effectively. Comprehensive benchmark studies suggest that MultiDCP outperforms state-of-the-art methods with unseen cell lines that are dissimilar from the cell lines in the supervised training in terms of gene expressions. The predicted drug-induced gene expressions demonstrate a stronger predictive power than noisy experimental data for downstream tasks. Thus, MultiDCP is a useful tool for transcriptomics-based drug repurposing and compound screening that currently rely on noisy high-throughput experimental data. We applied MultiDCP to repurpose individualized drugs for Alzheimer’s disease in terms of efficacy and toxicity, suggesting that MultiDCP is a potentially powerful tool for personalized drug discovery. Conventional target-based compound screening that follows the one-drug-one-gene drug discovery paradigm has a low success rate in tackling multi-genic systemic diseases such as Alzheimer’s disease. A systems pharmacology strategy is needed to target gene regulatory networks. To enable systems pharmacology-oriented phenotypic screening, it is critical to utilize a mechanistic phenotype readout to link drug responses in a model system to drug toxicity and efficacy in an individual. Chemical-induced dose-dependent gene expression profiles provide critical information on drug mode of action and off-target effects and can identify drug candidates that reverse disease phenotypes. However, state-of-the-art machine learning methods for predicting chemical-induced gene expressions are all trained using data from a limited number of cancer cell lines and can only achieve suboptimal performance when applied to new cell types or patient samples. Here, we have developed a new deep learning framework to address this challenge and demonstrated its potential in personalized drug repurposing using Alzheimer’s disease as a case study.
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Liu Y, Lin Y, Yang W, Lin Y, Wu Y, Zhang Z, Lin N, Wang X, Tong M, Yu R. Application of individualized differential expression analysis in human cancer proteome. Brief Bioinform 2022; 23:6562685. [DOI: 10.1093/bib/bbac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Liquid chromatography–mass spectrometry-based quantitative proteomics can measure the expression of thousands of proteins from biological samples and has been increasingly applied in cancer research. Identifying differentially expressed proteins (DEPs) between tumors and normal controls is commonly used to investigate carcinogenesis mechanisms. While differential expression analysis (DEA) at an individual level is desired to identify patient-specific molecular defects for better patient stratification, most statistical DEP analysis methods only identify deregulated proteins at the population level. To date, robust individualized DEA algorithms have been proposed for ribonucleic acid data, but their performance on proteomics data is underexplored. Herein, we performed a systematic evaluation on five individualized DEA algorithms for proteins on cancer proteomic datasets from seven cancer types. Results show that the within-sample relative expression orderings (REOs) of protein pairs in normal tissues were highly stable, providing the basis for individualized DEA for proteins using REOs. Moreover, individualized DEA algorithms achieve higher precision in detecting sample-specific deregulated proteins than population-level methods. To facilitate the utilization of individualized DEA algorithms in proteomics for prognostic biomarker discovery and personalized medicine, we provide Individualized DEP Analysis IDEPAXMBD (XMBD: Xiamen Big Data, a biomedical open software initiative in the National Institute for Data Science in Health and Medicine, Xiamen University, China.) (https://github.com/xmuyulab/IDEPA-XMBD), which is a user-friendly and open-source Python toolkit that integrates individualized DEA algorithms for DEP-associated deregulation pattern recognition.
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Affiliation(s)
- Yachen Liu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
| | - Yalan Lin
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
| | - Wenxian Yang
- Aginome Scientific, Xiamen, Fujian 316005, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yujuan Wu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
| | - Zheyang Zhang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Nuoqi Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xianlong Wang
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Mengsha Tong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Rongshan Yu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- Aginome Scientific, Xiamen, Fujian 316005, China
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Mohamed RI, Bargal SA, Mekawy AS, El-Shiekh I, Tuncbag N, Ahmed AS, Badr E, Elserafy M. The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PLoS One 2021; 16:e0247837. [PMID: 33662042 PMCID: PMC7932549 DOI: 10.1371/journal.pone.0247837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/14/2021] [Indexed: 12/22/2022] Open
Abstract
In the era of precision medicine, analyzing the transcriptomic profile of patients is essential to tailor the appropriate therapy. In this study, we explored transcriptional differences between two invasive breast cancer subtypes; infiltrating ductal carcinoma (IDC) and lobular carcinoma (LC) using RNA-Seq data deposited in the TCGA-BRCA project. We revealed 3854 differentially expressed genes between normal ductal tissues and IDC. In addition, IDC to LC comparison resulted in 663 differentially expressed genes. We then focused on DNA repair genes because of their known effects on patients' response to therapy and resistance. We here report that 36 DNA repair genes are overexpressed in a significant number of both IDC and LC patients' samples. Despite the upregulation in a significant number of samples, we observed a noticeable variation in the expression levels of the repair genes across patients of the same cancer subtype. The same trend is valid for the expression of miRNAs, where remarkable variations between patients' samples of the same cancer subtype are also observed. These individual variations could lie behind the differential response of patients to treatment. The future of cancer diagnostics and therapy will inevitably depend on high-throughput genomic and transcriptomic data analysis. However, we propose that performing analysis on individual patients rather than a big set of patients' samples will be necessary to ensure that the best treatment is determined, and therapy resistance is reduced.
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Affiliation(s)
- Ruwaa I. Mohamed
- Center for Informatics Sciences (CIS), Nile University, Giza, Egypt
| | - Salma A. Bargal
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Asmaa S. Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nurcan Tuncbag
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Alaa S. Ahmed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
- * E-mail: (EB); (ME)
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- * E-mail: (EB); (ME)
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