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Ouyang D, Liang Y, Li L, Ai N, Lu S, Yu M, Liu X, Xie S. Integration of multi-omics data using adaptive graph learning and attention mechanism for patient classification and biomarker identification. Comput Biol Med 2023; 164:107303. [PMID: 37586201 DOI: 10.1016/j.compbiomed.2023.107303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/08/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
With the rapid development and accumulation of high-throughput sequencing technology and omics data, many studies have conducted a more comprehensive understanding of human diseases from a multi-omics perspective. Meanwhile, graph-based methods have been widely used to process multi-omics data due to its powerful expressive ability. However, most existing graph-based methods utilize fixed graphs to learn sample embedding representations, which often leads to sub-optimal results. Furthermore, treating embedding representations of different omics equally usually cannot obtain more reasonable integrated information. In addition, the complex correlation between omics is not fully taken into account. To this end, we propose an end-to-end interpretable multi-omics integration method, named MOGLAM, for disease classification prediction. Dynamic graph convolutional network with feature selection is first utilized to obtain higher quality omic-specific embedding information by adaptively learning the graph structure and discover important biomarkers. Then, multi-omics attention mechanism is applied to adaptively weight the embedding representations of different omics, thereby obtaining more reasonable integrated information. Finally, we propose omic-integrated representation learning to capture complex common and complementary information between omics while performing multi-omics integration. Experimental results on three datasets show that MOGLAM achieves superior performance than other state-of-the-art multi-omics integration methods. Moreover, MOGLAM can identify important biomarkers from different omics data types in an end-to-end manner.
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Affiliation(s)
- Dong Ouyang
- Peng Cheng Laboratory, Shenzhen, 518055, China; School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Yong Liang
- Peng Cheng Laboratory, Shenzhen, 518055, China.
| | - Le Li
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Ning Ai
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Shanghui Lu
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Mingkun Yu
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Xiaoying Liu
- Computer Engineering Technical College, Guangdong Polytechnic of Science and Technology, Zhuhai, 519090, China
| | - Shengli Xie
- Guangdong-HongKong-Macao Joint Laboratory for Smart Discrete Manufacturing, Guangzhou, 510000, China
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Inoue C, Miki Y, Suzuki T. New Perspectives on Sex Steroid Hormones Signaling in Cancer-Associated Fibroblasts of Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:3620. [PMID: 37509283 PMCID: PMC10377312 DOI: 10.3390/cancers15143620] [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: 04/30/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The importance of sex hormones, especially estrogen, in the pathogenesis of non-small-cell lung cancer (NSCLC) has attracted attention due to its high incidence among young adults and nonsmokers, especially those who are female. Cancer-associated fibroblasts (CAFs) reside in the cancer stroma and influence cancer growth, invasion, metastasis, and acquisition of drug resistance through interactions with cancer cells and other microenvironmental components. Hormone-mediated cell-cell interactions are classic cell-cell interactions and well-known phenomena in breast cancer and prostate cancer CAFs. In cancers of other organs, including NSCLC, the effects of CAFs on hormone-receptor expression and hormone production in cancer tissues have been reported; however, there are few such studies. Many more studies have been performed on breast and prostate cancers. Recent advances in technology, particularly single-cell analysis techniques, have led to significant advances in the classification and function of CAFs. However, the importance of sex hormones in cell-cell interactions of CAFs in NSCLC remains unclear. This review summarizes reports on CAFs in NSCLC and sex hormones in cancer and immune cells surrounding CAFs. Furthermore, we discuss the prospects of sex-hormone research involving CAFs in NSCLC.
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Affiliation(s)
- Chihiro Inoue
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Yasuhiro Miki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takashi Suzuki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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Shen J, Xie M, Xu Y, Qian Q, Qiu T, Shi W, Ren D, Ji J, Huang J. Identification of the deubiquitinase USP28 as a novel molecular therapeutic target of ovarian cancer. Biochem Biophys Res Commun 2023; 638:184-191. [PMID: 36462492 DOI: 10.1016/j.bbrc.2022.11.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Ubiquitin specific proteinase 28 (USP28) is a member of the deubiquitylating enzymes, which are mainly involved in cell cycle, apoptosis and DNA damage repair. Although USP28 has been found to be upregulated in some tumors, its role in ovarian cancer (OV) remains unclear. Here we show that USP28 was highly expressed in OV samples compared with normal ovarian tissue, and OV patients with higher USP28 levels had a worse prognosis. We found that the abnormal expression of USP28 mRNA in OV was related to the activation of β-catenin signaling pathway, and USP28 was a transcriptional target gene of the β-catenin/YAP1/TBX5 complex. In addition, genetic ablation or pharmacological inhibition of USP28 impaired the proliferation ability of OV cells in vitro and in vivo. In conclusion, our findings show that β-catenin/YAP1/TBX5-mediated aberrant expression of USP28 promotes the malignant phenotype of OV, suggesting that USP28 may be a therapeutic target for OV.
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Affiliation(s)
- Jing Shen
- Department of Obstetrics and Gynecology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei, China
| | - Mengru Xie
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yuxin Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Qilan Qian
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Teng Qiu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Wen Shi
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Dexu Ren
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jing Ji
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
| | - Jinling Huang
- Department of Obstetrics & Gynecology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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Panahi-Moghadam S, Hassani S, Farivar S, Vakhshiteh F. Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer. Noncoding RNA 2022; 8:ncrna8050066. [PMID: 36287118 PMCID: PMC9607539 DOI: 10.3390/ncrna8050066] [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: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Enhancers are distal cis-acting elements that are commonly recognized to regulate gene expression via cooperation with promoters. Along with regulating gene expression, enhancers can be transcribed and generate a class of non-coding RNAs called enhancer RNAs (eRNAs). The current discovery of abundant tissue-specific transcription of enhancers in various diseases such as cancers raises questions about the potential role of eRNAs in disease diagnosis and therapy. This review aimed to demonstrate the current understanding of eRNAs in cancer research with a focus on the potential roles of eRNAs as prognostic and diagnostic biomarkers in cancers.
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Affiliation(s)
- Somayeh Panahi-Moghadam
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Shokoufeh Hassani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran
| | - Shirin Farivar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Faezeh Vakhshiteh
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran 1449614535, Iran
- Correspondence:
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Wang L, Zhou SQ, Zhou Y, Lu JX. A Two-eRNA-Based Signature Can Impact the Immune Status and Predict the Prognosis and Drug Sensitivity of Lung Adenocarcinoma. J Immunol Res 2022; 2022:8069858. [PMID: 35600050 PMCID: PMC9115606 DOI: 10.1155/2022/8069858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
Enhancer RNAs (eRNAs) are intergenic long noncoding RNAs (lncRNAs) participating in the development of malignant cancers via targeting cancer-associated genes and immune checkpoints. Immune infiltration of the tumor microenvironment was positively associated with overall survival (OS) in lung adenocarcinoma (LUAD). In this study, we aimed to explore the clinical significance of PCBP1-AS1 in LUAD and developed a novel prognostic signature based on two eRNAs. Our team discovered that the expression of PCBP1-AS1 was distinctly downregulated in LUAD specimens compared with nontumor specimens. Lower PCBP1-AS1 expression was related to advanced clinical stages and poor prognosis. KEGG analysis unveiled that the coexpression genes of PCBP1-AS1 were involved in the regulation of several tumor-related pathways. In addition, remarkable associations were observed between the expression of PCBP1-AS1 and the levels of several immune cells. Then, we used PCBP1-AS1 and TBX5-AS1 to develop a prognostic model. Survival assays unveiled that patients with higher risk scores exhibited a shorter OS in contrast to patients with lower risk scores. In addition, multivariable Cox regressive analysis indicated that the risk score was an independent prediction factor in LUAD sufferers. The anticancer drug sensitivity analysis indicated that risk score had a positive relationship with several anticancer drugs. Taken together, our findings indicated PCBP1-AS1 as a function modulator in LUAD development. In addition, we constructed a robust immune-related eRNA signature which might be a clinical prognosis factor for LUAD patients.
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Affiliation(s)
- Li Wang
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Shao-quan Zhou
- Department of Radiology, Chongqing General Hospital, Chongqing, China
| | - Yu Zhou
- Department of Respiratory Critical Care Medicine, Chongqing Fuling People's Hospital, Chongqing, China
| | - Jia-xi Lu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
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Enhancer RNA AL928768.3 from the IGH Locus Regulates MYC Expression and Controls the Proliferation and Chemoresistance of Burkitt Lymphoma Cells with IGH/MYC Translocation. Int J Mol Sci 2022; 23:ijms23094624. [PMID: 35563017 PMCID: PMC9103539 DOI: 10.3390/ijms23094624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/10/2022] Open
Abstract
Chromosomal rearrangements leading to the relocation of proto-oncogenes into transcription-active regions are found in various types of tumors. In particular, the transfer of proto-oncogenes to the locus of heavy chains of immunoglobulins (IGH) is frequently observed in B-lymphomas. The increased expression of the MYC proto-oncogene due to IGH/MYC translocation is detected in approximately 85% of Burkitt lymphoma cases. The regulatory mechanisms affecting the oncogenes upon translocation include non-coding enhancer RNAs (eRNAs). We conducted a search for the eRNAs that may affect MYC transcription in the case of IGH/MYC translocation in Burkitt lymphoma, looking for potentially oncogenic eRNAs located at the IGH locus and predominantly expressed in B cells. Overexpression and knockdown of our primary candidate eRNA AL928768.3 led to the corresponding changes in the expression of MYC proto-oncogene in Burkitt lymphoma cells. Furthermore, we demonstrated that AL928768.3 knockdown decreased lymphoma cell proliferation and resistance to chemotherapy. Significant effects were observed only in cell lines bearing IGH/MYC abnormality but not in B-cell lines without this translocation nor primary B-cells. Our results indicate that AL928768.3 plays an important role in the development of Burkitt’s lymphoma and suggest it and similar, yet undiscovered eRNAs as potential tissue-specific targets for cancer treatment.
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