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Khan MS, Hanif W, Alsakhen N, Jabbar B, Shamkh IM, Alsaiari AA, Almehmadi M, Alghamdi S, Shakoori A, Al Farraj DA, Almutairi SM, Hussein Issa Mohammed Y, Abouzied AS, Rehman AU, Huwaimel B. Isoform switching leads to downregulation of cytokine producing genes in estrogen receptor positive breast cancer. Front Genet 2023; 14:1230998. [PMID: 37900178 PMCID: PMC10611502 DOI: 10.3389/fgene.2023.1230998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Objective: Estrogen receptor breast cancer (BC) is characterized by the expression of estrogen receptors. It is the most common cancer among women, with an incidence rate of 2.26 million cases worldwide. The aim of this study was to identify differentially expressed genes and isoform switching between estrogen receptor positive and triple negative BC samples. Methods: The data were collected from ArrayExpress, followed by preprocessing and subsequent mapping from HISAT2. Read quantification was performed by StringTie, and then R package ballgown was used to perform differential expression analysis. Functional enrichment analysis was conducted using Enrichr, and then immune genes were shortlisted based on the ScType marker database. Isoform switch analysis was also performed using the IsoformSwitchAnalyzeR package. Results: A total of 9,771 differentially expressed genes were identified, of which 86 were upregulated and 117 were downregulated. Six genes were identified as mainly associated with estrogen receptor positive BC, while a novel set of ten genes were found which have not previously been reported in estrogen receptor positive BC. Furthermore, alternative splicing and subsequent isoform usage in the immune system related genes were determined. Conclusion: This study identified the differential usage of isoforms in the immune system related genes in cancer cells that suggest immunosuppression due to the dysregulation of CXCR chemokine receptor binding, iron ion binding, and cytokine activity.
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Affiliation(s)
| | - Waqar Hanif
- Department of Bioinformatics, Department of Sciences, School of Interdisciplinary Engineering & Science (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Israa M. Shamkh
- Chemo and Bioinformatics Lab, Bio Search Research Institution, Giza, Egypt
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Afnan Shakoori
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Dunia A. Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Amr S. Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NOD CAR), Giza, Egypt
| | - Aziz-Ur Rehman
- Keystone Pharmacogenomics LLC, Bensalem, PA, United States
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, Hail, Saudi Arabia
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Robust high-dimensional regression for data with anomalous responses. ANN I STAT MATH 2020. [DOI: 10.1007/s10463-020-00764-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lee W, Huang DS, Han K. Constructing cancer patient-specific and group-specific gene networks with multi-omics data. BMC Med Genomics 2020; 13:81. [PMID: 32854705 PMCID: PMC7450550 DOI: 10.1186/s12920-020-00736-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 12/26/2022] Open
Abstract
Background Cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. The same treatment for patients of the same cancer type often results in different outcomes in terms of efficacy and side effects of the treatment. Thus, the molecular characterization of individual cancer patients is increasingly important to find an effective treatment. Recently a few methods have been developed to construct cancer sample-specific gene networks based on the difference in the mRNA expression levels between the cancer sample and reference samples. Methods We constructed a patient-specific network with multi-omics data based on the difference between a reference network and a perturbed reference network by the patient. A network specific to a group of patients was obtained using the average change in correlation coefficients and node degree of patient-specific networks of the group. Results In this paper, we present a new method for constructing cancer patient-specific and group-specific gene networks with multi-omics data. The main differences of our method from previous ones are as follows: (1) networks are constructed with multi-omics (mRNA expression, copy number variation, DNA methylation and microRNA expression) data rather than with mRNA expression data alone, (2) background networks are constructed with both normal samples and cancer samples of the specified type to extract cancer-specific gene correlations, and (3) both patient individual-specific networks and patient group-specific networks can be constructed. The results of evaluating our method with several types of cancer show that it constructs more informative and accurate gene networks than previous methods. Conclusions The results of evaluating our method with extensive data of seven cancer types show that the difference of gene correlations between the reference samples and a patient sample is a more predictive feature than mRNA expression levels and that gene networks constructed with multi-omics data show a better performance than those with single omics data in predicting cancer for most cancer types. Our approach will be useful for finding genes and gene pairs to tailor treatments to individual characteristics.
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Affiliation(s)
- Wook Lee
- Department of Computer Engineering, Inha University, Incheon, 22212, South Korea
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, China
| | - Kyungsook Han
- Department of Computer Engineering, Inha University, Incheon, 22212, South Korea.
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Chen J, Liu C, Cen J, Liang T, Xue J, Zeng H, Zhang Z, Xu G, Yu C, Lu Z, Wang Z, Jiang J, Zhan X, Zeng J. KEGG-expressed genes and pathways in triple negative breast cancer: Protocol for a systematic review and data mining. Medicine (Baltimore) 2020; 99:e19986. [PMID: 32358373 PMCID: PMC7440132 DOI: 10.1097/md.0000000000019986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The incidence of triple negative breast cancer (TNBC) is at a relatively high level, and our study aimed to identify differentially expressed genes (DEGs) in TNBC and explore the key pathways and genes of TNBC. METHODS The gene expression profiling (GSE86945, GSE86946 and GSE102088) data were obtained from Gene Expression Omnibus Datasets, DEGs were identified by using R software, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were performed by the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools, and the protein-protein interaction (PPI) network of the DEGs was constructed by the STRING database and visualized by Cytoscape software. Finally, the survival value of hub DEGs in breast cancer patients were performed by the Kaplan-Meier plotter online tool. RESULTS A total of 2998 DEGs were identified between TNBC and health breast tissue, including 411 up-regulated DEGs and 2587 down-regulated DEGs. GO analysis results showed that down-regulated DEGs were enriched in gene expression (BP), extracellular exosome (CC), and nucleic acid binding, and up-regulated were enriched in chromatin assembly (BP), nucleosome (CC), and DNA binding (MF). KEGG pathway results showed that DEGs were mainly enriched in Pathways in cancer and Systemic lupus erythematosus and so on. Top 10 hub genes were picked out from PPI network by connective degree, and 7 of top 10 hub genes were significantly related with adverse overall survival in breast cancer patients (P < .05). Further analysis found that only EGFR had a significant association with the prognosis of triple-negative breast cancer (P < .05). CONCLUSIONS Our study showed that DEGs were enriched in pathways in cancer, top 10 DEGs belong to up-regulated DEGs, and 7 gene connected with poor prognosis in breast cancer, including HSP90AA1, SRC, HSPA8, ESR1, ACTB, PPP2CA, and RPL4. These can provide some guidance for our research on the diagnosis and prognosis of TNBC, and further research is needed to evaluate their value in the targeted therapy of TNBC.
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Affiliation(s)
| | - Chong Liu
- Department of Spine and Osteopathy Ward
| | | | - Tuo Liang
- Department of Spine and Osteopathy Ward
| | - Jiang Xue
- Department of Spine and Osteopathy Ward
| | | | | | | | | | | | | | - Jie Jiang
- Department of Spine and Osteopathy Ward
| | | | - Jian Zeng
- Department of Gastrointestinal Gland Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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Zhang J, Liu J, Wu J, Li W, Chen Z, Yang L. Progression of the role of CRYAB in signaling pathways and cancers. Onco Targets Ther 2019; 12:4129-4139. [PMID: 31239701 PMCID: PMC6553995 DOI: 10.2147/ott.s201799] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/07/2019] [Indexed: 01/18/2023] Open
Abstract
CRYAB is a member of the small heat shock protein family, first discovered in the lens of the eye, and involved in various diseases, such as eye and heart diseases and even cancers, for example, breast cancer, lung cancer, prostate cancer, and ovarian cancer. In addition, CRYAB proteins are involved in a variety of signaling pathways including apoptosis, inflammation, and oxidative stress. This review summarizes the recent progress concerning the role of CRYAB in signaling pathways and diseases. Therefore, the role of CRYAB in signaling pathways and cancers is urgently needed. This article reviews the regulation of CRYAB in the apoptotic inflammatory signaling pathway and its role in cancers progression and as a key role in anti-cancer therapy targeting CRYAB in an effort to improve outcomes for patients with metastatic disease.
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Affiliation(s)
- JunFei Zhang
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
| | - Jia Liu
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
| | - JiaLi Wu
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
| | - WenFeng Li
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
| | - ZhongWei Chen
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
| | - LiShan Yang
- Department of Emergency Medical, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750000, People's Republic of China
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Chen J, Qian X, He Y, Han X, Pan Y. Novel key genes in triple‐negative breast cancer identified by weighted gene co‐expression network analysis. J Cell Biochem 2019; 120:16900-16912. [PMID: 31081967 DOI: 10.1002/jcb.28948] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Jian Chen
- Department of Oncology The First Affiliated Hospital of University of Science and Technology of China Hefei China
| | - Xiaojun Qian
- Department of Oncology The First Affiliated Hospital of University of Science and Technology of China Hefei China
| | - Yifu He
- Department of Oncology The First Affiliated Hospital of University of Science and Technology of China Hefei China
| | - Xinghua Han
- Department of Oncology The First Affiliated Hospital of University of Science and Technology of China Hefei China
| | - Yueyin Pan
- Department of Oncology The First Affiliated Hospital of University of Science and Technology of China Hefei China
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Gupta I, Sareyeldin RM, Al-Hashimi I, Al-Thawadi HA, Al Farsi H, Vranic S, Al Moustafa AE. Triple Negative Breast Cancer Profile, from Gene to microRNA, in Relation to Ethnicity. Cancers (Basel) 2019; 11:cancers11030363. [PMID: 30871273 PMCID: PMC6468678 DOI: 10.3390/cancers11030363] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is the most frequent cause of cancer-related deaths among women worldwide. It is classified into four major molecular subtypes. Triple-negative breast cancers (TNBCs), a subgroup of breast cancer, are defined by the absence of estrogen and progesterone receptors and the lack of HER-2 expression; this subgroup accounts for ~15% of all breast cancers and exhibits the most aggressive metastatic behavior. Currently, very limited targeted therapies exist for the treatment of patients with TNBCs. On the other hand, it is important to highlight that knowledge of the molecular biology of breast cancer has recently changed the decision-making process regarding the course of cancer therapies. Thus, a number of new techniques, such as gene profiling and sequencing, proteomics, and microRNA analysis have been used to explore human breast carcinogenesis and metastasis including TNBC, which consequently could lead to new therapies. Nevertheless, based on evidence thus far, genomics profiles (gene and miRNA) can differ from one geographic location to another as well as in different ethnic groups. This review provides a comprehensive and updated information on the genomics profile alterations associated with TNBC pathogenesis associated with different ethnic backgrounds.
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Affiliation(s)
- Ishita Gupta
- College of Medicine, Qatar University, Doha P. O. Box:2713, Qatar.
| | | | - Israa Al-Hashimi
- College of Medicine, Qatar University, Doha P. O. Box:2713, Qatar.
| | | | - Halema Al Farsi
- College of Medicine, Qatar University, Doha P. O. Box:2713, Qatar.
| | - Semir Vranic
- College of Medicine, Qatar University, Doha P. O. Box:2713, Qatar.
| | - Ala-Eddin Al Moustafa
- College of Medicine, Qatar University, Doha P. O. Box:2713, Qatar.
- Biomedical Research Centre, Qatar University, Doha P.O Box: 2713, Qatar.
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Wright JM, Jones GB. Harnessing the Digital Exhaust: Incorporating wellness into the pharma model. Digit Biomark 2018; 2:31-46. [PMID: 30272048 PMCID: PMC6157915 DOI: 10.1159/000488132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/02/2018] [Indexed: 12/24/2022] Open
Abstract
The increasing availability of devices capable of tracking biomarkers presents major opportunities in contemporary healthcare. Herein we advocate a new role for the pharmaceutical industry to capitalize on these opportunities and in doing so incorporate wellness and patient engagement programs into their standard business models. Medical grade decision making using diagnostic, prognostic, and monitoring biomarkers will require coordinated approaches between the pharmaceutical and technology industries and the careful design of longitudinal clinical studies to validate their efficacy. These studies will also require data capture, archiving, curating and sharing on a previously unprecedented scale, and raise additional concerns with regard to data security and ownership. Concurrently, systems-based approaches to the capture and interpretation of a new class of digital biomarkers are emerging, and hold promise for heightened levels of patient engagement and remote sensing. Collectively, if these new opportunities are approached within the context of the patient-provider ecosystem, major repositioning of the pharmaceutical industry may be possible in the near term.
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Affiliation(s)
- Justin M. Wright
- Technical Research and Development, Novartis Pharmaceuticals, East Hanover, New Jersey, USA
| | - Graham Barry Jones
- Clinical and Translational Science Institute, Tufts Medical Center, Boston, Massachusetts, USA
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