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Long E, Patel H, Golden A, Antony M, Yin J, Funderburk K, Feng J, Song L, Hoskins JW, Amundadottir LT, Hung RJ, Amos CI, Shi J, Rothman N, Lan Q, Choi J. High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility. Am J Hum Genet 2024; 111:1405-1419. [PMID: 38906146 PMCID: PMC11267514 DOI: 10.1016/j.ajhg.2024.05.021] [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: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024] Open
Abstract
Genome-wide association studies (GWASs) have identified numerous lung cancer risk-associated loci. However, decoding molecular mechanisms of these associations is challenging since most of these genetic variants are non-protein-coding with unknown function. Here, we implemented massively parallel reporter assays (MPRAs) to simultaneously measure the allelic transcriptional activity of risk-associated variants. We tested 2,245 variants at 42 loci from 3 recent GWASs in East Asian and European populations in the context of two major lung cancer histological types and exposure to benzo(a)pyrene. This MPRA approach identified one or more variants (median 11 variants) with significant effects on transcriptional activity at 88% of GWAS loci. Multimodal integration of lung-specific epigenomic data demonstrated that 63% of the loci harbored multiple potentially functional variants in linkage disequilibrium. While 22% of the significant variants showed allelic effects in both A549 (adenocarcinoma) and H520 (squamous cell carcinoma) cell lines, a subset of the functional variants displayed a significant cell-type interaction. Transcription factor analyses nominated potential regulators of the functional variants, including those with cell-type-specific expression and those predicted to bind multiple potentially functional variants across the GWAS loci. Linking functional variants to target genes based on four complementary approaches identified candidate susceptibility genes, including those affecting lung cancer cell growth. CRISPR interference of the top functional variant at 20q13.33 validated variant-to-gene connections, including RTEL1, SOX18, and ARFRP1. Our data provide a comprehensive functional analysis of lung cancer GWAS loci and help elucidate the molecular basis of heterogeneity and polygenicity underlying lung cancer susceptibility.
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Affiliation(s)
- Erping Long
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyxandra Golden
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Michelle Antony
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karen Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jason W Hoskins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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2
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Calistri NL, Liby TA, Hu Z, Zhang H, Dane M, Gross SM, Heiser LM. TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.596911. [PMID: 38895265 PMCID: PMC11185620 DOI: 10.1101/2024.06.04.596911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Paclitaxel is a standard of care neoadjuvant therapy for patients with triple negative breast cancer (TNBC); however, it shows limited benefit for locally advanced or metastatic disease. Here we used a coordinated experimental-computational approach to explore the influence of paclitaxel on the cellular and molecular responses of TNBC cells. We found that escalating doses of paclitaxel resulted in multinucleation, promotion of senescence, and initiation of DNA damage induced apoptosis. Single-cell RNA sequencing (scRNA-seq) of TNBC cells after paclitaxel treatment revealed upregulation of innate immune programs canonically associated with interferon response and downregulation of cell cycle progression programs. Systematic exploration of transcriptional responses to paclitaxel and cancer-associated microenvironmental factors revealed common gene programs induced by paclitaxel, IFNB, and IFNG. Transcription factor (TF) enrichment analysis identified 13 TFs that were both enriched based on activity of downstream targets and also significantly upregulated after paclitaxel treatment. Functional assessment with siRNA knockdown confirmed that the TFs FOSL1, NFE2L2 and ELF3 mediate cellular proliferation and also regulate nuclear structure. We further explored the influence of these TFs on paclitaxel-induced cell cycle behavior via live cell imaging, which revealed altered progression rates through G1, S/G2 and M phases. We found that ELF3 knockdown synergized with paclitaxel treatment to lock cells in a G1 state and prevent cell cycle progression. Analysis of publicly available breast cancer patient data showed that high ELF3 expression was associated with poor prognosis and enrichment programs associated with cell cycle progression. Together these analyses disentangle the diverse aspects of paclitaxel response and identify ELF3 upregulation as a putative biomarker of paclitaxel resistance in TNBC.
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Affiliation(s)
- Nicholas L Calistri
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Tiera A. Liby
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Zhi Hu
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Hongmei Zhang
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Mark Dane
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Sean M. Gross
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
| | - Laura M. Heiser
- Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland Oregon
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3
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Lin J, Hou L, Zhao X, Zhong J, Lv Y, Jiang X, Ye B, Qiao Y. Switch of ELF3 and ATF4 transcriptional axis programs the amino acid insufficiency-linked epithelial-to-mesenchymal transition. Mol Ther 2024; 32:1956-1969. [PMID: 38627967 PMCID: PMC11184330 DOI: 10.1016/j.ymthe.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) that endows cancer cells with increased invasive and migratory capacity enables cancer dissemination and metastasis. This process is tightly associated with metabolic reprogramming acquired for rewiring cell status and signaling pathways for survival in dietary insufficiency conditions. However, it remains largely unclear how transcription factor (TF)-mediated transcriptional programs are modulated during the EMT process. Here, we reveal that depletion of a key epithelial TF, ELF3 (E74-like factor-3), triggers a transforming growth factor β (TGF-β) signaling activation-like mesenchymal transcriptomic profile and metastatic features linked to the aminoacyl-tRNA biogenesis pathway. Moreover, the transcriptome alterations elicited by ELF3 depletion perfectly resemble an ATF4-dependent weak response to amino acid starvation. Intriguingly, we observe an exclusive enrichment of ELF3 and ATF4 in epithelial and TGF-β-induced or ELF3-depletion-elicited mesenchymal enhancers, respectively, with rare co-binding on altered enhancers. We also find that the upregulation of aminoacyl-tRNA synthetases and some mesenchymal genes upon amino acid deprivation is diminished in ATF4-depleted cells. In sum, the loss of ELF3 binding on epithelial enhancers and the gain of ATF4 binding on the enhancers of mesenchymal factors and amino acid deprivation responsive genes facilitate the loss of epithelial cell features and the gain of TGF-β-signaling-associated mesenchymal signatures, which further promote lung cancer cell metastasis.
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Affiliation(s)
- Jianxiang Lin
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Linjun Hou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin Zhao
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Jingli Zhong
- College of Life Science, Guangzhou University, Guangzhou 510006, China
| | - Yilv Lv
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaohua Jiang
- Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China.
| | - Bo Ye
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Yunbo Qiao
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China.
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4
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Ju Y, Fang S, Liu L, Ma H, Zheng L. The function of the ELF3 gene and its mechanism in cancers. Life Sci 2024; 346:122637. [PMID: 38614305 DOI: 10.1016/j.lfs.2024.122637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
E74-like factor 3 (ELF3) is an important member of the E-twenty-six (ETS) transcription factor family. ELF3 is expressed in various types of cells and regulates a variety of biological behaviors, such as cell proliferation, differentiation, apoptosis, migration, and invasion, by binding to DNA to regulate the expression of other genes. In recent years, studies have shown that ELF3 plays an important role in the occurrence and development of many tumors and inflammation and immune related diseases. ELF3 has different functions and expression patterns in different tumors; it can function as a tumor suppressor gene or an oncogene, highlighting its dual effects of tumor promotion and inhibition. ELF3 also affects the levels of tumor immunity-related cytokines and is involved in the regulation and expression of multiple signaling pathways. In tumor therapy, ELF3 is a complex and multifunctional gene and has become a key focus of targeted treatment research. An in-depth study of the biological function of ELF3 can help to elucidate its role in biological processes and provide ideas and a basis for the development and clinical application of ELF3-related therapeutic methods. This review introduces the structure and physiological and cellular functions of the ELF3 gene, summarizes the mechanisms of action of ELF3 in different types of malignant tumors and its role in immune regulation, inflammation, etc., and discusses treatment methods for ELF3-related diseases, providing significant reference value for scholars studying the ELF3 gene and related diseases.
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Affiliation(s)
- Yiheng Ju
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Sheng Fang
- Yantai Penglai People's Hospital, Yantai, China
| | - Lei Liu
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Ma
- Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Longbo Zheng
- Affiliated Hospital of Qingdao University, Qingdao, China.
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5
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Lei Y, Huang XT, Guo X, Hang Katie Chan K, Gao L. DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations. Brief Bioinform 2024; 25:bbae334. [PMID: 38980373 PMCID: PMC11232306 DOI: 10.1093/bib/bbae334] [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: 03/11/2024] [Revised: 06/03/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.
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Affiliation(s)
- Yahui Lei
- School of Computer Science and Technology, Xidian University, Xi’an 710071, Shaanxi, China
| | - Xiao-Tai Huang
- School of Computer Science and Technology, Xidian University, Xi’an 710071, Shaanxi, China
| | - Xingli Guo
- School of Computer Science and Technology, Xidian University, Xi’an 710071, Shaanxi, China
| | - Kei Hang Katie Chan
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Epidemiology and Center for Global Cardiometabolic Health, Brown University, Providence, RI, United States
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi’an 710071, Shaanxi, China
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6
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Fujii M, Sekine S, Sato T. Decoding the basis of histological variation in human cancer. Nat Rev Cancer 2024; 24:141-158. [PMID: 38135758 DOI: 10.1038/s41568-023-00648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Molecular abnormalities that shape human neoplasms dissociate their phenotypic landscape from that of the healthy counterpart. Through the lens of a microscope, tumour pathology optically captures such aberrations projected onto a tissue slide and has categorized human epithelial neoplasms into distinct histological subtypes based on the diverse morphogenetic and molecular programmes that they manifest. Tumour histology often reflects tumour aggressiveness, patient prognosis and therapeutic vulnerability, and thus has been used as a de facto diagnostic tool and for making clinical decisions. However, it remains elusive how the diverse histological subtypes arise and translate into pleiotropic biological phenotypes. Molecular analysis of clinical tumour tissues and their culture, including patient-derived organoids, and add-back genetic reconstruction of tumorigenic pathways using gene engineering in culture models and rodents further elucidated molecular mechanisms that underlie morphological variations. Such mechanisms include genetic mutations and epigenetic alterations in cellular identity codes that erode hard-wired morphological programmes and histologically digress tumours from the native tissues. Interestingly, tumours acquire the ability to grow independently of the niche-driven stem cell ecosystem along with these morphological alterations, providing a biological rationale for histological diversification during tumorigenesis. This Review comprehensively summarizes our current understanding of such plasticity in the histological and lineage commitment fostered cooperatively by molecular alterations and the tumour environment, and describes basic and clinical implications for future cancer therapy.
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Affiliation(s)
- Masayuki Fujii
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
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7
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Wu T, Liu S, Chen W, Zhao D, Lu Z. Huaier suppresses cell viability, migration and invasion in human non-small cell lung cancer via lncRNA DLEU2/miR-212-5p/ELF3 axis. Int J Med Sci 2024; 21:319-331. [PMID: 38169645 PMCID: PMC10758155 DOI: 10.7150/ijms.89308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Accumulating studies suggest that Huaier exerts anti-tumor effects through intricate mechanisms. Despite extensive research on its efficacy in lung cancer, further investigation is required to elucidate the molecular mechanism of Huaier. The involvement of long noncoding RNAs (lncRNAs) in the anti-lung cancer effects of Huaier remains unknown. In this study, we found Huaier suppressed cell viability, migration and invasion in non-small cell lung cancer (NSCLC) cells. LncRNA sequencing analysis revealed Deleted in lymphocytic leukemia 2 (DLEU2) to be significantly downregulated in Huaier-treated NSCLC cells. Furthermore, DLEU2 silencing was observed to suppress NSCLC progression, while DLEU2 overexpression attenuated the anti-tumor effects of Huaier in NSCLC, thereby promoting cell viability, migration and invasion of NSCLC. The ceRNA role of DLEU2 had been demonstrated in NSCLC, which directly interacted with miR-212-5p to rescue the repression of E74 Like ETS Transcription Factor 3 (ELF3) by this microRNA. Additionally, Huaier was found to regulate the expression of miR-212-5p and ELF3. Functionally, miR-212-5p inhibitor or ELF3 overexpression reversed the effects of DLEU2 silencing or Huaier treatment, resulting in increased colony formation, migration and invasion in NSCLC. Taken together, these results illuminate the mechanism underlying Huaier's anti-tumor effects via the DLEU2/miR-212-5p/ELF3 signaling pathway, which offers novel insights into the anti-tumor effects of Huaier and constitutes a promising therapeutic target for the treatment in NSCLC.
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Affiliation(s)
- Tangwei Wu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Shuiyi Liu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Weiqun Chen
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
- Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Dan Zhao
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Zhongxin Lu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
- Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
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8
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Gutiérrez M, Zamora I, Freeman MR, Encío IJ, Rotinen M. Actionable Driver Events in Small Cell Lung Cancer. Int J Mol Sci 2023; 25:105. [PMID: 38203275 PMCID: PMC10778712 DOI: 10.3390/ijms25010105] [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: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Small cell lung cancer (SCLC) stands out as the most aggressive form of lung cancer, characterized by an extremely high proliferation rate and a very poor prognosis, with a 5-year survival rate that falls below 7%. Approximately two-thirds of patients receive their diagnosis when the disease has already reached a metastatic or extensive stage, leaving chemotherapy as the remaining first-line treatment option. Other than the recent advances in immunotherapy, which have shown moderate results, SCLC patients cannot yet benefit from any approved targeted therapy, meaning that this cancer remains treated as a uniform entity, disregarding intra- or inter-tumoral heterogeneity. Continuous efforts and technological improvements have enabled the identification of new potential targets that could be used to implement novel therapeutic strategies. In this review, we provide an overview of the most recent approaches for SCLC treatment, providing an extensive compilation of the targeted therapies that are currently under clinical evaluation and inhibitor molecules with promising results in vitro and in vivo.
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Affiliation(s)
- Mirian Gutiérrez
- Department of Health Sciences, Public University of Navarre, 31008 Pamplona, Spain; (M.G.); (I.Z.)
| | - Irene Zamora
- Department of Health Sciences, Public University of Navarre, 31008 Pamplona, Spain; (M.G.); (I.Z.)
| | - Michael R. Freeman
- Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA;
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ignacio J. Encío
- Department of Health Sciences, Public University of Navarre, 31008 Pamplona, Spain; (M.G.); (I.Z.)
- IdiSNA, Navarre Institute for Health Research, 31006 Pamplona, Spain
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, 31008 Pamplona, Spain; (M.G.); (I.Z.)
- IdiSNA, Navarre Institute for Health Research, 31006 Pamplona, Spain
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9
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Vega AA, Marshall EA, Noonan AJC, Filho FSL, Yang J, Stewart GL, Johnson FD, Vucic EA, Pewarchuk ME, Shah PP, Clem BF, Nislow C, Lam S, Lockwood WW, Hallam SJ, Leung JM, Beverly LJ, Lam WL. Methionine-producing tumor micro(be) environment fuels growth of solid tumors. Cell Oncol (Dordr) 2023; 46:1659-1673. [PMID: 37318751 DOI: 10.1007/s13402-023-00832-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Recent studies have uncovered the near-ubiquitous presence of microbes in solid tumors of diverse origins. Previous literature has shown the impact of specific bacterial species on the progression of cancer. We propose that local microbial dysbiosis enables certain cancer phenotypes through provisioning of essential metabolites directly to tumor cells. METHODS 16S rDNA sequencing of 75 patient lung samples revealed the lung tumor microbiome specifically enriched for bacteria capable of producing methionine. Wild-type (WT) and methionine auxotrophic (metA mutant) E. coli cells were used to condition cell culture media and the proliferation of lung adenocarcinoma (LUAD) cells were measured using SYTO60 staining. Further, colony forming assay, Annexin V Staining, BrdU, AlamarBlue, western blot, qPCR, LINE microarray and subcutaneous injection with methionine modulated feed were used to analyze cellular proliferation, cell-cycle, cell death, methylation potential, and xenograft formation under methionine restriction. Moreover, C14-labeled glucose was used to illustrate the interplay between tumor cells and bacteria. RESULTS/DISCUSSION Our results show bacteria found locally within the tumor microenvironment are enriched for methionine synthetic pathways, while having reduced S-adenosylmethionine metabolizing pathways. As methionine is one of nine essential amino acids that mammals are unable to synthesize de novo, we investigated a potentially novel function for the microbiome, supplying essential nutrients, such as methionine, to cancer cells. We demonstrate that LUAD cells can utilize methionine generated by bacteria to rescue phenotypes that would otherwise be inhibited due to nutrient restriction. In addition to this, with WT and metA mutant E. coli, we saw a selective advantage for bacteria with an intact methionine synthetic pathway to survive under the conditions induced by LUAD cells. These results would suggest that there is a potential bi-directional cross-talk between the local microbiome and adjacent tumor cells. In this study, we focused on methionine as one of the critical molecules, but we also hypothesize that additional bacterial metabolites may also be utilized by LUAD. Indeed, our radiolabeling data suggest that other biomolecules are shared between cancer cells and bacteria. Thus, modulating the local microbiome may have an indirect effect on tumor development, progression, and metastasis.
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Affiliation(s)
- Alexis A Vega
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
- Brown Cancer Center, University of Louisville School of Medicine, 505 S. Hancock St. Rm 204, Louisville, KY, 40202, USA
| | - Erin A Marshall
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Avery J C Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | | | - Julia Yang
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Greg L Stewart
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Fraser D Johnson
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | | | - Michelle E Pewarchuk
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Parag P Shah
- Brown Cancer Center, University of Louisville School of Medicine, 505 S. Hancock St. Rm 204, Louisville, KY, 40202, USA
| | - Brian F Clem
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
- Brown Cancer Center, University of Louisville School of Medicine, 505 S. Hancock St. Rm 204, Louisville, KY, 40202, USA
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - William W Lockwood
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada
- Biofactorial High-Throughput Biology Facility, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Levi J Beverly
- Brown Cancer Center, University of Louisville School of Medicine, 505 S. Hancock St. Rm 204, Louisville, KY, 40202, USA.
| | - Wan L Lam
- Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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10
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Chen Y, Pan Y, Gao H, Yi Y, Qin S, Ma F, Zhou X, Guan M. Mechanistic insights into super-enhancer-driven genes as prognostic signatures in patients with glioblastoma. J Cancer Res Clin Oncol 2023; 149:12315-12332. [PMID: 37432454 DOI: 10.1007/s00432-023-05121-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is one of the most common malignant brain tumors in adults and is characterized by high aggressiveness and rapid progression, poor treatment, high recurrence rate, and poor prognosis. Although super-enhancer (SE)-driven genes haven been recognized as prognostic markers for several cancers, whether it can be served as effective prognostic markers for patients with GBM has not been evaluated. METHODS We first combined histone modification data with transcriptome data to identify SE-driven genes associated with prognosis in patients with GBM. Second, we developed a SE-driven differentially expressed genes (SEDEGs) risk score prognostic model by univariate Cox analysis, KM survival analysis, multivariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression. Its reliability in predicting was verified by two external data sets. Third, through mutation analysis, immune infiltration, we explored the molecular mechanisms of prognostic genes. Next, Genomics of Drug Sensitivity in Cancer (GDSC) and the Connectivity Map (cMap) database were employed to assess different sensitivities to chemotherapeutic agents and small-molecule drug candidates between high- and low-risk patients. Finally, SEanalysis database was chosen to identify SE-driven transcription factors (TFs) regulating prognostic markers which will reveal a potential SE-driven transcriptional regulatory network. RESULTS First, we developed a 11-gene risk score prognostic model (NCF2, MTHFS, DUSP6, G6PC3, HOXB2, EN2, DLEU1, LBH, ZEB1-AS1, LINC01265, and AGAP2-AS1) selected from 1,154 SEDEGs, which is not only an independent prognostic factor for patients, but also can effectively predict the survival rate of patients. The model can effectively predict 1-, 2- and 3-year survival of patients and was validated in external Chinese Glioma Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) datasets. Second, the risk score was positively correlated with the infiltration of regulatory T cell, CD4 memory activated T cell, activated NK cell, neutrophil, resting mast cell, M0 macrophage, and memory B cell. Third, we found that high-risk patients showed higher sensitivity than low-risk patients to both 27 chemotherapeutic agents and 4 small-molecule drug candidates which might benefit further precision therapy for GBM patients. Finally, 13 potential SE-driven TFs imply how SE regulates GBM patient's prognosis. CONCLUSION The SEDEG risk model not only helps to elucidate the impact of SEs on the course of GBM, but also provides a bright future for prognosis determination and choice of treatment for GBM patients.
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Affiliation(s)
- Youran Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yi Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Hanyu Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yunmeng Yi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Shijie Qin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Fei Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Xue Zhou
- School of Chemistry and Biological Engineering, Nanjing Normal University Taizhou College, Taizhou, 225300, China.
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China.
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11
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Lu J, Zhang Q, Mo L, Chen W, Mao L. Comprehensive analysis of E47‑like factors and verification of ELF4 in clear cell renal cell carcinoma. Oncol Lett 2023; 26:395. [PMID: 37600328 PMCID: PMC10433703 DOI: 10.3892/ol.2023.13981] [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: 02/05/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prominent subtype of renal cancer and E47-like factors (ELFs) are important in tumorigenesis; however, the specific role of key ELFs in ccRCC remains unclear. The present study comprehensively analyzed RNA sequencing and clinical data from multiple databases, and identified differentially expressed ELFs (ELF3-5) in ccRCC. The DNA promoter methylation, genetic variation and clinical significance of ELF3-5 in ccRCC were analyzed using the cBioPortal and UALCAN databases. The association between ELF3-5 and multiple immune cell infiltration was analyzed using Tumor Immune Estimation Resource. Subsequently, ELF4 was selected and its association with biological functions was assessed. Cell counting kit-8 (CCK-8), colony formation, Transwell, macrophage chemotaxis and polarization assays were conducted to validate the functions of ELF4. Notably, the mRNA expression levels of ELF4 were significantly upregulated in ccRCC, whereas ELF3 and ELF5 mRNA expression levels were significantly downregulated. Clinical significance analysis revealed that ELF4 showed a high clinical significance with tumor grade, clear cell type A and B subtypes, and incidence rates of amplification in genetic variation. Further analyses indicated that ELF4 may be involved in multiple immune cell differentiation. Additionally, cell experiments revealed that ELF4 inhibition downregulated 769-P and 786-O proliferation, migration and invasion. Knockdown of ELF4 in cancer cells also inhibited M2 macrophage polarization and chemotaxis towards 769-P and 786-O cells. Conclusively, the present findings indicated the clinical significance of ELF4 in ccRCC, and verified its key role in driving cell proliferation, migration and invasion, and promoting M2 macrophage polarization and chemotaxis in ccRCC.
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Affiliation(s)
- Jun Lu
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
| | - Qianqian Zhang
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
| | - Licai Mo
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
| | - Weiying Chen
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
| | - Linghong Mao
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
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12
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Nakamura T, Nishikawa Y, Shiokawa M, Takeda H, Yokode M, Matsumoto S, Muramoto Y, Ota S, Yoshida H, Okada H, Kuwada T, Marui S, Matsumori T, Maruno T, Uza N, Kodama Y, Hatano E, Seno H. ELF3 suppresses gallbladder cancer development through downregulation of the EREG/EGFR/mTOR complex 1 signalling pathway. J Pathol 2023; 261:28-42. [PMID: 37345534 DOI: 10.1002/path.6144] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
The prognosis of gallbladder cancer (GBC) remains poor, and a better understanding of GBC molecular mechanisms is important. Genome sequencing of human GBC has demonstrated that loss-of-function mutations of E74-like ETS transcription factor 3 (ELF3) are frequently observed, with ELF3 considered to be a tumour suppressor in GBC. To clarify the underlying molecular mechanisms by which ELF3 suppresses GBC development, we performed in vivo analysis using a combination of autochthonous and allograft mouse models. We first evaluated the clinical significance of ELF3 expression in human GBC tissues and found that low ELF3 expression was associated with advanced clinical stage and deep tumour invasion. For in vivo analysis, we generated Pdx1-Cre; KrasG12D ; Trp53R172H ; Elf3f/f (KPCE) mice and Pdx1-Cre; KrasG12D ; Trp53R172H ; Elf3wt/wt (KPC) mice as a control and analysed their gallbladders histologically. KPCE mice developed larger papillary lesions in the gallbladder than those developed by KPC mice. Organoids established from the gallbladders of KPCE and KPC mice were analysed in vitro. RNA sequencing showed upregulated expression of epiregulin (Ereg) in KPCE organoids, and western blotting revealed that EGFR/mechanical targets of rapamycin complex 1 (mTORC1) were upregulated in KPCE organoids. In addition, ChIP assays on Elf3-overexpressing KPCE organoids showed that ELF3 directly regulated Ereg. Ereg deletion in KPCE organoids (using CRISPR/Cas9) induced EGFR/mTORC1 downregulation, indicating that ELF3 controlled EGFR/mTORC1 activity through regulation of Ereg expression. We also generated allograft mouse models using KPCE and KPC organoids and found that KPCE organoid allograft tumours exhibited poorly differentiated structures with mTORC1 upregulation and mesenchymal phenotype, which were suppressed by Ereg deletion. Furthermore, EGFR/mTORC1 inhibition suppressed cell proliferation and epithelial-mesenchymal transition in KPCE organoids. Our results suggest that ELF3 suppresses GBC development via downregulation of EREG/EGFR/mTORC1 signalling. EGFR/mTORC1 inhibition is a potential therapeutic option for GBC with ELF3 mutation. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Takeharu Nakamura
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshihiro Nishikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masahiro Shiokawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masataka Yokode
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shimpei Matsumoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuya Muramoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sakiko Ota
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroyuki Yoshida
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirokazu Okada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Kuwada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Saiko Marui
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomoaki Matsumori
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahisa Maruno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimitsu Uza
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuzo Kodama
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Etsuro Hatano
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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13
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Wu Y, Li Z, Lin H, Wang H. Identification of Tumor Antigens and Immune Subtypes of High-grade Serous Ovarian Cancer for mRNA Vaccine Development. J Cancer 2023; 14:2655-2669. [PMID: 37779866 PMCID: PMC10539400 DOI: 10.7150/jca.87184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 10/03/2023] Open
Abstract
High-grade serous ovarian cancer (HGSC) is the most common pathology of ovarian cancer and has aggressive characteristics and poor prognosis. mRNA vaccines are a novel tool for cancer immune treatment and may play an important role in HGSC therapy. Our study aimed to explore tumour antigens for vaccine development and identify potential populations amenable to vaccine treatment. Based on transcription data from The Cancer Genome Atlas (TCGA), we identified four tumour-specific antigens for vaccine production: ARPC1B, ELF3, VSTM2L, and IL27RA. In addition to being associated with HGSC patient prognosis, the expression of these antigens was positively correlated with the abundances of antigen-presenting cells (APCs). Furthermore, we stratified HGSC samples into three immune subtypes (IS1-IS3) with different immune characteristics. A corhort from ICGC (International Cancer Genome Consortium) was used to validate. Patients of IS3 had the best prognosis, while patients of IS1 were most likely to benefit from vaccination. There was substantial heterogeneity in immune signatures and immune-associated molecule expression in HGSC. Finally, weighted gene coexpression network analysis (WGCNA) was employed to cluster immune-related genes and explore potential biomarkers related to vaccination. In conclusion, we identified four potential tumour antigens for mRNA vaccine production for HGSC treatment, and the immune subtype could be an important indicator to select suitable HGSC patients to receive vaccination.
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Affiliation(s)
- Yanxuan Wu
- Department of Radiation Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhifeng Li
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hong Lin
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongbiao Wang
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
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14
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Lei J, Xu JY, Hu M, Wu SG, Zhou J. MOB kinase activator 1A acts as an oncogene by targeting PI3K/AKT/mTOR in ovarian cancer. Discov Oncol 2023; 14:100. [PMID: 37314589 DOI: 10.1007/s12672-023-00705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND To illuminate the precise roles of MOB Kinase Activator 1 A (MOB1A) in the development of ovarian cancer (OC). METHODS MOB1A expression and clinical data of OC were obtained from the public database on gene expression and proteomics. Meanwhile, verification of expression was carried out in Gene Expression Omnibus, the Human Protein Atlas, and OC cell lines. The prognosis of MOB1A was explored in the Kaplan-Meier plotter. RNA interference and lentivirus vectors were applied to construct knockdown and overexpressed cell models. Changes in the malignant behaviors of OC cells were detected by cholecystokinin octopeptide cell counting kit, wound healing, colony formation assay, transwell, flow cytometry assays, and in vivo experiments. Changes in proteins in the PI3K and autophagy-related makers were detected by western blot analysis. RESULTS The expression of MOB1A was significantly upregulated and accompanied by an inferior survival rate in OC. Knockdown of MOB1A inhibited the proliferation, invasion, migration, and cell cycle of OC cells, whereas induced cell autophagy. MOB1A upregulation had the opposite effects. In addition, bioinformatics analysis and western blot experiments showed that MOB1A plays an important role in the PI3K/AKT/mTOR pathway. CONCLUSIONS Our findings indicated that MOB1A is highly expressed and related to poor prognosis in OC. MOB1A plays a role in promoting the malignant biological behavior of tumor cells through PI3K/AKT/mTOR signaling pathway.
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Affiliation(s)
- Jian Lei
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
- Department of Obstetrics and Gynecology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jing-Ying Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Min Hu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - San-Gang Wu
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
| | - Juan Zhou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
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15
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Yang L, Wang H, Guo M, He M, Zhang W, Zhan M, Liu Y. ELF3 promotes gemcitabine resistance through PKMYT1/CDK1 signaling pathway in gallbladder cancer. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00799-5. [PMID: 36988891 DOI: 10.1007/s13402-023-00799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Gemcitabine is the standard treatment for gallbladder cancer (GBC) patients, and the development of resistance frequently limits its efficacy. However, the molecular features and mechanisms of gemcitabine resistance (Gem-R) in GBC cells remain unknown. Herein, we aimed to explore the role of ELF3 in Gem-R of GBC, including the underlying mechanisms. METHODS RNA sequencing was used to screen the essential genes related to the generation of Gem-R in GBC tissues. The correlation between Gem-R and ELF3 expression was identified in GDSC, GEO database, GBC tissues, and 3 GBC cell lines. Immunohistochemical staining, quantitative real-time polymerase chain reaction, and western blot were used to examine the expression of ELF3, PKMYT1, and CDK1. Luciferase reporter assays were used to identify the binding site of ELF3 in the PKMYT1 promoter region. CCK-8 assay and clonogenic survival assays were used to evaluate the sensitivity of gemcitabine in GBC cells. A GBC xenograft model was used to evaluate the influence of ELF3 on the therapeutic effect of gemcitabine. RESULTS A consistently positive correlation between ELF3 expression and Gem-R, both in newly generated GBC RNA-seq data and in the datasets from GDSC and GEO. Gem-R in GBC cells was facilitated by ELF3 overexpression, whereas ELF3 knockdown had the opposite effect. In vivo experiments further proved that reducing ELF3 expression promoted the gemcitabine sensitivity of GBC cells and extended the survival time of mice that received orthotopic xenografted tumors. Mechanistically, ELF3 upregulated PKMYT1 expression by interacting with the DNA binding region of PKMYT1 in GBC cells, thereby promoting the phosphorylation of CDK1 and inducing Gem-R. Treatment with a combination of the PKMYT1 shRNA and gemcitabine significantly reduced the growth of GBC cells induced by overexpression of ELF3 in vitro and in vivo. CONCLUSIONS ELF3/PKMYT1/CDK1 axis significantly regulates Gem-R to GBC cells and may represent a promising drug target for treating GBC patients.
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Affiliation(s)
- Linhua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Research Center of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200011, China
| | - Hui Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Research Center of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200011, China
| | - Miaomiao Guo
- The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Min He
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Research Center of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200011, China
| | - Wei Zhang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Research Center of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200011, China
| | - Ming Zhan
- The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Research Center of Biliary Tract Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200011, China.
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16
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Subbalakshmi AR, Sahoo S, Manjunatha P, Goyal S, Kasiviswanathan VA, Mahesh Y, Ramu S, McMullen I, Somarelli JA, Jolly MK. The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition. J Biol Eng 2023; 17:17. [PMID: 36864480 PMCID: PMC9983220 DOI: 10.1186/s13036-023-00333-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal plasticity (EMP) involves bidirectional transitions between epithelial, mesenchymal and multiple intermediary hybrid epithelial/mesenchymal phenotypes. While the process of epithelial-mesenchymal transition (EMT) and its associated transcription factors are well-characterised, the transcription factors that promote mesenchymal-epithelial transition (MET) and stabilise hybrid E/M phenotypes are less well understood. RESULTS Here, we analyse multiple publicly-available transcriptomic datasets at bulk and single-cell level and pinpoint ELF3 as a factor that is strongly associated with an epithelial phenotype and is inhibited during EMT. Using mechanism-based mathematical modelling, we also show that ELF3 inhibits the progression of EMT. This behaviour was also observed in the presence of an EMT inducing factor WT1. Our model predicts that the MET induction capacity of ELF3 is stronger than that of KLF4, but weaker than that of GRHL2. Finally, we show that ELF3 levels correlates with worse patient survival in a subset of solid tumour types. CONCLUSION ELF3 is shown to be inhibited during EMT progression and is also found to inhibit the progression of complete EMT suggesting that ELF3 may be able to counteract EMT induction, including in the presence of EMT-inducing factors, such as WT1. The analysis of patient survival data indicates that the prognostic capacity of ELF3 is specific to cell-of-origin or lineage.
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Affiliation(s)
- Ayalur Raghu Subbalakshmi
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Sarthak Sahoo
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Prakruthi Manjunatha
- grid.444321.40000 0004 0501 2828Department of Medical Electronics, M S Ramaiah Institute of Technology, 560054 Bangalore, India
| | - Shaurya Goyal
- grid.429017.90000 0001 0153 2859Department of Humanities and Social Sciences, Indian Institute of Technology, 721302 Kharagpur, India
| | - Vignesh A Kasiviswanathan
- grid.512757.30000 0004 1761 9897Department of Biotechnology, JSS Science and Technology University, 570006 Mysore, India
| | - Yeshwanth Mahesh
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Soundharya Ramu
- grid.419655.a0000 0001 0008 3668Department of Biotechnology, National Institute of Technology Warangal, 506004 Warangal, India
| | - Isabelle McMullen
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA
| | - Jason A. Somarelli
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA ,grid.26009.3d0000 0004 1936 7961Duke Cancer Institute, Duke University, NC 27708 Durham, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012, Bangalore, India.
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Wang Y, Huang Z, Sun M, Huang W, Xia L. ETS transcription factors: Multifaceted players from cancer progression to tumor immunity. Biochim Biophys Acta Rev Cancer 2023; 1878:188872. [PMID: 36841365 DOI: 10.1016/j.bbcan.2023.188872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.
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Affiliation(s)
- Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zhao Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
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18
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Horie M, Tanaka H, Suzuki M, Sato Y, Takata S, Takai E, Miyashita N, Saito A, Nakatani Y, Yachida S. An integrative epigenomic approach identifies ELF3 as an oncogenic regulator in ASCL1-positive neuroendocrine carcinoma. Cancer Sci 2023. [PMID: 36840413 DOI: 10.1111/cas.15764] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/16/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Neuroendocrine carcinoma (NEC) is a highly aggressive subtype of the neuroendocrine tumor with an extremely poor prognosis. We have previously conducted a comprehensive genomic analysis of over 100 cases of NEC of the gastrointestinal system (GIS-NEC) and unraveled its unique and organ-specific genomic drivers. However, the epigenomic features of GIS-NEC remain unexplored. In this study, we have described the epigenomic landscape of GIS-NEC and small cell lung carcinoma (SCLC) by integrating motif enrichment analysis from the assay of transposase-accessible chromatin sequencing (ATAC-seq) and enhancer profiling from a novel cleavage under targets and tagmentation (CUT&Tag) assay for H3K27ac and identified ELF3 as one of the super-enhancer-related transcriptional factors in NEC. By combining CUT&Tag and knockdown RNA sequencing for ELF3, we uncovered the transcriptional network regulated by ELF3 and defined its distinctive gene signature, including AURKA, CDC25B, CLDN4, ITGB6, and YWAHB. Furthermore, a loss-of-function assay revealed that ELF3 depletion led to poor cell viability. Finally, using gene expression of clinical samples, we successfully divided GIS-NEC patients into two subgroups according to the ELF3 signature and demonstrated that tumor-promoting pathways were activated in the ELF3 signature-high group. Our findings highlight the transcriptional regulation of ELF3 as an oncogenic transcription factor and its tumor-promoting properties in NEC.
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Affiliation(s)
- Masafumi Horie
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidenori Tanaka
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masami Suzuki
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yoshihiko Sato
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - So Takata
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Naoya Miyashita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoichiro Nakatani
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.,Division of Genomic Medicine, National Cancer Center Research Institute, Tokyo, Japan
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19
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Elf3 deficiency during zebrafish development alters extracellular matrix organization and disrupts tissue morphogenesis. PLoS One 2022; 17:e0276255. [DOI: 10.1371/journal.pone.0276255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
E26 transformation specific (ETS) family transcription factors are expressed during embryogenesis and are involved in various cellular processes such as proliferation, migration, differentiation, angiogenesis, apoptosis, and survival of cellular lineages to ensure appropriate development. Dysregulated expression of many of the ETS family members is detected in different cancers. The human ELF3, a member of the ETS family of transcription factors, plays a role in the induction and progression of human cancers is well studied. However, little is known about the role of ELF3 in early development. Here, the zebrafish elf3 was cloned, and its expression was analyzed during zebrafish development. Zebrafish elf3 is maternally deposited. At different developmental stages, elf3 expression was detected in different tissue, mainly neural tissues, endoderm-derived tissues, cartilage, heart, pronephric duct, blood vessels, and notochord. The expression levels were high at the tissue boundaries. Elf3 loss-of-function consequences were examined by using translation blocking antisense morpholino oligonucleotides, and effects were validated using CRISPR/Cas9 knockdown. Elf3-knockdown produced short and bent larvae with notochord, craniofacial cartilage, and fin defects. The extracellular matrix (ECM) in the fin and notochord was disorganized. Neural defects were also observed. Optic nerve fasciculation (bundling) and arborization in the optic tectum were defective in Elf3-morphants, and fragmentation of spinal motor neurons were evident. Dysregulation of genes encoding ECM proteins and matrix metalloprotease (MMP) and disorganization of ECM may play a role in the observed defects in Elf3 morphants. We conclude that zebrafish Elf3 is required for epidermal, mesenchymal, and neural tissue development.
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20
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Chen P, Quan Z, Song X, Gao Z, Yuan K. MDFI is a novel biomarker for poor prognosis in LUAD. Front Oncol 2022; 12:1005962. [PMID: 36300089 PMCID: PMC9589366 DOI: 10.3389/fonc.2022.1005962] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background Approximately 80% of lung cancers are non-small cell lung cancers (NSCLC). Lung adenocarcinoma (LUAD) is the main subtype of NSCLC. The incidence and mortality of lung cancer are also increasing yearly. Myogenic differentiation family inhibitor (MDFI) as a transcription factor, its role in lung cancer has not yet been clarified. Methods LUAD data were downloaded from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO), analyzed and plotted using the R language. Associations between Clinical information and MDFI expression were assessed using logistic regression analyses to explore the effects of MDFI on LUAD. Two sets of tissue microarrays (TMAs) further confirmed the overexpression of MDFI in LUAD and its impact on prognosis. In addition, we examined the correlation between MDFI and immune infiltration. To investigate the effect of MDFI on the biological behavior of LUAD tumor cells by GSEA and GO/KEGG analysis. The survival status and somatic mutational characteristics of patients according to MDFI levels were depicted and analyzed. Results Expression of high MDFI in LUAD tissues via analyzing TCGA dataset (P <0.001). Kaplan-Meier survival analysis indicated a poor prognosis for those patients with LUAD who had upregulated MDFI expression levels (P <0.001). This was also verified by two groups of TMAs (P=0.024). Using logistic statistics analysis, MDFI was identified as an independent predictive factor and was associated with poor prognosis in LUAD (P <0.001, P =0.021). Assessment of clinical characteristics, tumor mutation burden (TMB), and tumor microenvironment (TME) between high- and low-expression score groups showed lower TMB, richer immune cell infiltration, and better prognosis in the low-risk group. Conclusion This study showed that MDFI was overexpressed in LUAD and was significantly associated with poor prognosis, indicating that MDFI may be used as a potential novel biomarker for the diagnosis and prognosis of LUAD. MDFI is associated with immune infiltration of LUAD and it is reasonable to speculate that it plays an important role in tumor proliferation and spread. In view of the significant differences in MDFI expression between different biological activities, LUAD patients with MDFI overexpression may obtain more precise treatment strategies in the clinic.
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Affiliation(s)
- Pengyu Chen
- Division of Thoracic Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
- School of Medicine, Dalian Medical University, Dalian, China
| | - Zhen Quan
- Division of Thoracic Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
- School of Medicine, Dalian Medical University, Dalian, China
| | - Xueyu Song
- Division of Thoracic Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
- School of Medicine, Dalian Medical University, Dalian, China
| | - Zhaojia Gao
- Division of Thoracic Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
| | - Kai Yuan
- Division of Thoracic Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, China
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21
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Xu L, Huang Z, Zeng Z, Li J, Xie H, Xie C. An integrative analysis of DNA methylation and gene expression to predict lung adenocarcinoma prognosis. Front Genet 2022; 13:970507. [PMID: 36105089 PMCID: PMC9465336 DOI: 10.3389/fgene.2022.970507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 12/09/2022] Open
Abstract
Background: Abnormal DNA methylation of gene promoters is an important feature in lung adenocarcinoma (LUAD). However, the prognostic value of DNA methylation remains to be further explored. Objectives. We sought to explore DNA methylation characteristics and develop a quantifiable criterion related to DNA methylation to improve survival prediction for LUAD patients. Methods: Illumina Human Methylation450K array data, level 3 RNA-seq data and corresponding clinical information were obtained from TCGA. Cox regression analysis and the Akaike information criterion were used to construct the best-prognosis methylation signature. Receiver operating characteristic curve analysis was used to validate the prognostic ability of the DNA methylation-related feature score. qPCR was used to measure the transcription levels of the identified genes upon methylation. Results: We identified a set of DNA methylation features composed of 11 genes (MYEOV, KCNU1, SLC27A6, NEUROD4, HMGB4, TACR3, GABRA5, TRPM8, NLRP13, EDN3 and SLC34A1). The feature score, calculated based on DNA methylation features, was independent of tumor recurrence and TNM stage in predicting overall survival. Of note, the combination of this feature score and TNM stage provided a better overall survival prediction than either of them individually. The transcription levels of all the hypermethylated genes were significantly increased after demethylation, and the expression levels of 3 hypomethylated proteins were significantly higher in tumor tissues than in normal tissues, as indicated by immunohistochemistry data from the Human Protein Atlas. Our results suggested that these identified genes with prognostic features were regulated by DNA methylation of their promoters. Conclusion: Our studies demonstrated the potential application of DNA methylation markers in the prognosis of LUAD.
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Affiliation(s)
- Liexi Xu
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Hongxin Xie
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie,
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22
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Lin Z, Liu Y, Lin P, Li J, Gan J. Clinical significance of STING expression and methylation in lung adenocarcinoma based on bioinformatics analysis. Sci Rep 2022; 12:13951. [PMID: 35978045 PMCID: PMC9385651 DOI: 10.1038/s41598-022-18278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/09/2022] [Indexed: 02/05/2023] Open
Abstract
The role of stimulator of interferon genes [STING, also known as transmembrane protein 173 (TMEM173)] in various human cancers has begun to emerge. However, the clinical value of STING in lung adenocarcinoma (LUAD) remains elusive. This study aims to elucidate the clinical significance of STING expression and methylation in LUAD. Here, through analyzing data from public resources, we found that both the mRNA and protein expression of STING were reduced in lung cancer. Moreover, lower expression of STING was associated with a worse prognosis in LUAD, but not lung squamous cell carcinoma (LUSC). Of note, higher methylation of STING was found in LUAD and had the potential to distinguish LUAD tissues from adjacent non-tumor lung tissues and correlated with unfavorable outcomes. Furthermore, the methylation of STING could serve as an independent prognostic indicator for both the overall survival (OS) and disease-free survival (DFS) of LUAD patients. Additionally, the constructed nomogram exhibited a favorable predictive accuracy in predicting the probability of 1- and 2-year OS. Our findings suggest that the mRNA expression, and especially the DNA methylation of STING, have the potential to be prognostic indicators for LUAD patients.
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Affiliation(s)
- Ze Lin
- Department of Biochemistry, Shantou University Medical College, Shantou, People's Republic of China
| | - Yu Liu
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, People's Republic of China
| | - Peng Lin
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Jinping Li
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, People's Republic of China
| | - Jinfeng Gan
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, People's Republic of China
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, People's Republic of China
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23
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Qiu WR, Qi BB, Lin WZ, Zhang SH, Yu WK, Huang SF. Predicting the Lung Adenocarcinoma and Its Biomarkers by Integrating Gene Expression and DNA Methylation Data. Front Genet 2022; 13:926927. [PMID: 35846148 PMCID: PMC9280023 DOI: 10.3389/fgene.2022.926927] [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: 04/25/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
The early symptoms of lung adenocarcinoma patients are inapparent, and the clinical diagnosis of lung adenocarcinoma is primarily through X-ray examination and pathological section examination, whereas the discovery of biomarkers points out another direction for the diagnosis of lung adenocarcinoma with the development of bioinformatics technology. However, it is not accurate and trustworthy to diagnose lung adenocarcinoma due to omics data with high-dimension and low-sample size (HDLSS) features or biomarkers produced by utilizing only single omics data. To address the above problems, the feature selection methods of biological analysis are used to reduce the dimension of gene expression data (GSE19188) and DNA methylation data (GSE139032, GSE49996). In addition, the Cartesian product method is used to expand the sample set and integrate gene expression data and DNA methylation data. The classification is built by using a deep neural network and is evaluated on K-fold cross validation. Moreover, gene ontology analysis and literature retrieving are used to analyze the biological relevance of selected genes, TCGA database is used for survival analysis of these potential genes through Kaplan-Meier estimates to discover the detailed molecular mechanism of lung adenocarcinoma. Survival analysis shows that COL5A2 and SERPINB5 are significant for identifying lung adenocarcinoma and are considered biomarkers of lung adenocarcinoma.
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Affiliation(s)
- Wang-Ren Qiu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
- *Correspondence: Wang-Ren Qiu, ; Shun-Fa Huang,
| | - Bei-Bei Qi
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Wei-Zhong Lin
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Shou-Hua Zhang
- Department of General Surgery, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wang-Ke Yu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Shun-Fa Huang
- School of Information Engineering, Jingdezhen University, Jingdezhen, China
- *Correspondence: Wang-Ren Qiu, ; Shun-Fa Huang,
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24
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Du L, Liu Y, Li C, Deng J, Sang Y. The interaction between ETS transcription factor family members and microRNAs: A novel approach to cancer therapy. Biomed Pharmacother 2022; 150:113069. [PMID: 35658214 DOI: 10.1016/j.biopha.2022.113069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
In cancer biology, ETS transcription factors promote tumorigenesis by mediating transcriptional regulation of numerous genes via the conserved ETS DNA-binding domain. MicroRNAs (miRNAs) act as posttranscriptional regulators to regulate various tumor-promoting or tumor-suppressing factors. Interactions between ETS factors and miRNAs regulate complex tumor-promoting and tumor-suppressing networks. This review discusses the progress of ETS factors and miRNAs in cancer research in detail. We focused on characterizing the interaction of the miRNA/ETS axis with competing endogenous RNAs (ceRNAs) and its regulation in posttranslational modifications (PTMs) and the tumor microenvironment (TME). Finally, we explore the prospect of ETS factors and miRNAs in therapeutic intervention. Generally, interactions between ETS factors and miRNAs provide fresh perspectives into tumorigenesis and development and novel therapeutic approaches for malignant tumors.
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Affiliation(s)
- Liwei Du
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yuchen Liu
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China; Stomatology College of Nanchang University, Nanchang, China
| | - Chenxi Li
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Jinkuang Deng
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China.
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25
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Guan X, Sun N. E74-Like Factor 3 Promotes Endometrial Cancer Cell Proliferation, Migration and Invasion via Regulating Mucin 1/Hypoxia-Inducible Factor 1α Pathway. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.2981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
High expression of E74-like factor 3 (ELF3) has been reported in type 1 endometrial cancer (EC). Bioinformatics analysis predicted a positive correlation with ELF3 and mucin 1 (MUC1)/hypoxiainducible factor 1α (HIF-1α), a previously identified cancer-promoting
pathway. This study focused on the MUC1/HIF-1α-involved action mechanism of ELF3 in EC. ELF3 expression in EC cell lines was measured by RT-qPCR and western blot analysis. Following the expression of ELF3 was silent, cell proliferation was examined using CCK-8 and colony formation
assay, cell migration and invasion were observed using wound healing and transwell assays. The effect of ELF1 silencing on MUC1/HIF-1α expression was detected by western blot. Rescue experiments incorporating pcDNA3.1(+)/MUC1 explored the interaction between ELF3 and MUC1/HIF-1α
in EC cell proliferation, migration and invasion. ELF3 was found to be expressed at a high level in EC cell lines, and the silencing of it effectively inhibited EC cell proliferation. Moreover, ELF silencing also inhibited the migration and invasion of EC cells. Consistent with the database
prediction, a positive correlation between ELF3 and MUC1/HIF-1α was observed. More importantly, MUC1 overexpression abated the promotive effect of ELF3 silencing on EC cell proliferation, migration and invasion. ELF3 promotes EC cell proliferation, migration and invasion by regulating
MUC1/HIF-1α pathway. Thus, ELF3 as well as MUC1/HIF-1α pathway may be particle targets in the treatment of EC.
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Affiliation(s)
- Xin Guan
- Department of Gynecology, Third People’s Hospital, Dalian City, Liaoning Province, 116033, P. R. China
| | - Ning Sun
- Department of Medical Laboratory, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing City, Jiangsu Province, 210004, P. R. China
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26
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Yao Z, Zhu G, Too J, Duan M, Wang Z. Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches. Front Genet 2022; 12:793629. [PMID: 35350819 PMCID: PMC8957794 DOI: 10.3389/fgene.2021.793629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022] Open
Abstract
OMIC datasets have high dimensions, and the connection among OMIC features is very complicated. It is difficult to establish linkages among these features and certain biological traits of significance. The proposed ensemble swarm intelligence-based approaches can identify key biomarkers and reduce feature dimension efficiently. It is an end-to-end method that only relies on the rules of the algorithm itself, without presets such as the number of filtering features. Additionally, this method achieves good classification accuracy without excessive consumption of computing resources.
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Affiliation(s)
- Zhaomin Yao
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Gancheng Zhu
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Jingwei Too
- Faculty of Electrical Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, Melaka, Malaysia
| | - Meiyu Duan
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Zhiguo Wang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
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27
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Liu X, Ma X, Li H, Wang Y, Mao M, Liang C, Hu Y. LINC00472 suppresses oral squamous cell carcinoma growth by targeting miR-455-3p/ELF3 axis. Bioengineered 2022; 13:1162-1173. [PMID: 35258410 PMCID: PMC8805930 DOI: 10.1080/21655979.2021.2018092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
LINC00472 is reported to play a role in suppressing tumors in cancers such as lung cancer and hepatocellular carcinoma, among others. We made investigations into the effects of LINC00472 in oral squamous cell carcinoma (OSCC) progression to explore the underlying molecular mechanisms. By qRT-PCR, we assessed the LINC00472 expression in OSCC tissues and cells and performed functional analysis to investigate how LINC00472/miR-455-3p/ELF3 impacts OSCC cell proliferation, apoptosis, and cell cycle. The role that LINC00472 plays in OSCC tumor growth was examined by establishing a xenograft model. Down-regulation of LINC00472 occurred in tissues and cells of an OSCC tumor. LINC00472 overexpression caused OSCC cell proliferation to be inhibited, cell apoptosis to be promoted, and cell cycle arrest to be induced. As a competing endogenous RNA (ceRNA), LINC00472 can block miR-455-3p function and further promote ELF3 expression. The overexpression of miR-455-3p or ELF3 knockdown was shown to be capable of reversing the anti-tumor effects of LINC00472 in OSCC. In vivo experiments confirmed the tumor-suppressing role of LINC00472 in the progression of OSCC. In short, we found that the novel LINC00472 inhibits OSCC growth via the miR-455-3p/ELF3 axis. LINC00472 and its targeted miR-455-3p/ELF3 axis may represent valuable targets for treating OSCC.
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Affiliation(s)
- Xiu Liu
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Xinrong Ma
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Hongyu Li
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Yu Wang
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Minghui Mao
- Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Chao Liang
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Ying Hu
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
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28
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Genome-wide mapping of somatic mutation rates uncovers drivers of cancer. Nat Biotechnol 2022; 40:1634-1643. [PMID: 35726091 PMCID: PMC9646522 DOI: 10.1038/s41587-022-01353-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/10/2022] [Indexed: 01/12/2023]
Abstract
Identification of cancer driver mutations that confer a proliferative advantage is central to understanding cancer; however, searches have often been limited to protein-coding sequences and specific non-coding elements (for example, promoters) because of the challenge of modeling the highly variable somatic mutation rates observed across tumor genomes. Here we present Dig, a method to search for driver elements and mutations anywhere in the genome. We use deep neural networks to map cancer-specific mutation rates genome-wide at kilobase-scale resolution. These estimates are then refined to search for evidence of driver mutations under positive selection throughout the genome by comparing observed to expected mutation counts. We mapped mutation rates for 37 cancer types and applied these maps to identify putative drivers within intronic cryptic splice regions, 5' untranslated regions and infrequently mutated genes. Our high-resolution mutation rate maps, available for web-based exploration, are a resource to enable driver discovery genome-wide.
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29
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Lee JS, Choi YE, Kim S, Han JY, Goh SH. ELF3 Is a Target That Promotes Therapeutic Efficiency in EGFR Tyrosine Kinase Inhibitor-Resistant Non-Small Cell Lung Cancer Cells via Inhibiting PKCί. Int J Mol Sci 2021; 22:ijms222212287. [PMID: 34830169 PMCID: PMC8620479 DOI: 10.3390/ijms222212287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Mutations in epidermal growth factor receptor (EGFR) proteins account for many non-small cell lung cancers (NSCLCs), and EGFR tyrosine kinase inhibitors (TKIs) are being used as targeted therapeutics. However, resistance to TKIs continues to increase owing to additional mutations in more than half of the patients receiving EGFR TKI therapy. In addition to targeting new mutations with next-generation therapeutics, it is necessary to find an alternative target to overcome the challenges associated with resistance. (2) Methods: To identify potential alternative targets in patients with NSCLC undergoing targeted therapy, putative targets were identified by transcriptome profiling and validated for their biological and therapeutic effects in vitro and in vivo. (3) Results: ELF3 was found to be differentially expressed in NSCLC, and ELF3 knockdown significantly increased cell death in K-Ras mutant as well as in EGFR L858R/T790M mutation harboring lung cancer cells. We also found that auranofin, an inhibitor of protein kinase C iota (PKCί), a protein upstream of ELF3, effectively induced cell death. (4) Conclusions: Our study suggests that blocking ELF3 is an effective way to induce cell death in NSCLC with K-Ras and EGFR T790M/L858R mutations and thus advocates the use of auranofin as an effective alternative drug to overcome EGFR TKI resistance.
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Affiliation(s)
- Jeon-Soo Lee
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
| | - Young Eun Choi
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
| | - Sunshin Kim
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (S.K.); (J.-Y.H.)
| | - Ji-Youn Han
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (S.K.); (J.-Y.H.)
| | - Sung-Ho Goh
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
- Correspondence: ; Tel.: +82-31-920-2477
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Song S, He X, Wang J, Wang R, Wang L, Zhao W, Wang Y, Zhang Y, Yu Z, Miao D, Xue Y. ELF3-AS1 contributes to gastric cancer progression by binding to hnRNPK and induces thrombocytosis in peripheral blood. Cancer Sci 2021; 112:4553-4569. [PMID: 34418240 PMCID: PMC8586678 DOI: 10.1111/cas.15104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023] Open
Abstract
Numerous studies have reported that a variety of long noncoding RNAs (lncRNAs) can promote the proliferation, invasion, and migration of different tumor cells. However, different lncRNAs regulate cell functions in various forms, and the exact mechanisms are not clear. Here, we investigated the effect of the lncRNA ELF3-AS1 on gastric cancer (GC) cell function and explored the exact mechanism. Quantitative real-time polymerase chain reaction was used to detect the expression of ELF3-AS1 in GC tissues and adjacent nontumor tissues. Knockdown and overexpression of ELF3-AS1 was used to detect the effect of ELF3-AS1 on cell function. Potential downstream target genes were identified using RNA transcriptome sequencing, while RNA immunoprecipitation, chromatin immunoprecipitation, and Western blotting were performed to explore the tumor promotion mechanisms of ELF3-AS1. We observed that ELF3-AS1 was highly expressed in GC tissues, and high ELF3-AS1 expression predicted poor prognosis. The knockdown of ELF3-AS1 significantly inhibited cell proliferation, migration, and epithelial-mesenchymal transition and promoted apoptosis. Mechanistic investigations revealed that ELF3-AS1 may regulate the downstream target gene, C-C motif chemokine 20, by binding with the RNA-binding protein hnRNPK. Additionally, we found that high ELF3-AS1 expression was associated with thrombocytosis. Interleukin-6 and thrombopoietin may be involved in ELF3-AS1-induced paraneoplastic thrombocytosis. Together, our results demonstrate that aberrantly expressed ELF3-AS1 in GC may play important roles in oncogenesis and progression and is expected to become a new target for the diagnosis and treatment of GC.
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Affiliation(s)
- Shubin Song
- Department of gastrointestinal surgeryHarbin Medical University Cancer HospitalHarbinChina
- Department of Breast SurgeryShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Xuezhi He
- Department of Nutrition and Food HygieneSchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Jing Wang
- Department of Anatomy, Histology and EmbryologyState Key Laboratory of Reproductive MedicineThe Research Center for Bone and Stem CellsNanjing Medical UniversityNanjingChina
| | - Rong Wang
- Department of Anatomy, Histology and EmbryologyThe Research Center for Bone and Stem CellsNanjing Medical UniversityNanjingChina
| | - Leilei Wang
- Department of Breast SurgeryShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Wei Zhao
- Department of Breast SurgeryShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Yimin Wang
- Department of gastrointestinal surgeryHarbin Medical University Cancer HospitalHarbinChina
| | - Yongle Zhang
- Department of gastrointestinal surgeryHarbin Medical University Cancer HospitalHarbinChina
| | - Zhiyong Yu
- Department of Breast SurgeryShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Dengshun Miao
- The Research Center for AgingFriendship Affiliated Plastic Surgery Hospital of Nanjing Medical UniversityNanjingChina
| | - Yingwei Xue
- Department of gastrointestinal surgeryHarbin Medical University Cancer HospitalHarbinChina
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. A protein interaction landscape of breast cancer. Science 2021; 374:eabf3066. [PMID: 34591612 PMCID: PMC9040556 DOI: 10.1126/science.abf3066] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Minkyu Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Jisoo Park
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kyumin Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Ajda Rojc
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Margaret Soucheray
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Patrick O'Leary
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Denise Wolf
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Dominique Mitchell
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Kari A Herrington
- Department of Biochemistry and Biophysics, Center for Advanced Light Microscopy, University of California, San Francisco, CA, USA
| | - Denise P Muñoz
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kuei-Ho Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Fan Zheng
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Jason F Kreisberg
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Morgan E Diolaiti
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - John D Gordan
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Laura van 't Veer
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Alan Ashworth
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trey Ideker
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Department of Bioengineering, University of California, San Diego, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
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Xu H, Wang H, Li G, Jin X, Chen B. The Immune-Related Gene ELF3 is a Novel Biomarker for the Prognosis of Ovarian Cancer. Int J Gen Med 2021; 14:5537-5548. [PMID: 34531679 PMCID: PMC8439714 DOI: 10.2147/ijgm.s332320] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ovarian cancer (OC) is a fatal gynaecological malignancy. The study aimed to conduct a comprehensive study to determine the role of ELF3 in OC through bioinformatic analysis. Methods Kruskal-Wallis test, Wilcoxon sign-rank test, and logistic regression were used to evaluate the relationship between clinical characteristics and ELF3 expression. Kaplan-Meier method and Cox regression analysis were used to evaluate the prognostic factors. Gene set enrichment analysis (GSEA) and immuno-infiltration analysis were used to evaluate the significant involvement of ELF3 in function. Results High ELF3 expression in OC was associated with age (P< 0.001). High ELF3 expression predicted a poorer overall survival (OS) (HR: 1.37; 95% CI: 1.05-1.78; P=0.019) and disease specific survival (DSS) (HR: 1.43; 95% CI: 1.08-1.89; P=0.013). And ELF3 expression (HR: 1.779; 95% CI: 1.281-2.472; P<0.001) was independently correlated with OS in OC patients. GSEA demonstrated that pathways including GPCR-ligand binding, neuronal system, signaling by WNT, translation, neuroactive ligand-receptor interaction, and TCF dependent signaling in response to WNT were differentially enriched in ELF3 low expression phenotype. Immune infiltration analysis showed that ELF3 expression was correlated with immune infiltrates. Conclusion ELF3 expression in OC patients was significantly associated with poor survival and immune infiltration and a promising prognostic biomarker in OC.
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Affiliation(s)
- Hao Xu
- Department of Gynecology, Huangshi Love & Health Hospital Affiliated to Hubei Polytechnic University, Huangshi, 435000, Hubei, People's Republic of China
| | - Haihong Wang
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Guilin Li
- Department of Gynecology, Maternal and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Xin Jin
- Department of Gynecology, Maternal and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Buze Chen
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China.,Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
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Huangfu L, He Q, Han J, Shi J, Li X, Cheng X, Guo T, Du H, Zhang W, Gao X, Luan F, Xing X, Ji J. MicroRNA-135b/CAMK2D Axis Contribute to Malignant Progression of Gastric Cancer through EMT Process Remodeling. Int J Biol Sci 2021; 17:1940-1952. [PMID: 34131397 PMCID: PMC8193265 DOI: 10.7150/ijbs.58062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/26/2021] [Indexed: 01/10/2023] Open
Abstract
There is a continued need for investigating the roles of microRNAs (miRNAs) and their targets on the progression of gastric cancer (GC), especially metastasis. Here, we performed an integrated study to identify dysregulated miRNAs critical for GC development and progression. miR-135b was determined as a promising biomarker for GC. The expression level of miR-135b was increased among GC cell lines, patient tumor tissues, serum samples, and correlation with aggravation of the GC patients. The in vitro functional assays demonstrated overexpression of miR-135b promoted cell proliferation, migration and invasion in GC, while miR-135b inhibition led to the opposite results. CAMK2D was found to be the direct target of miR-135b, serving as a tumor suppressor in GC cells. Based on our and public datasets, we confirmed the attenuation of CAMK2D expression in GC tissues. And, the expression levels of miR-135b and CAMK2D were closely associated with prognosis of GC patients. Ectopic expression of miR-135b resulted in the down-regulation of CAMK2D. Additionally, CAMK2D was a prerequisite for miR-135b to promote GC cells proliferation and migration by regulating the EMT process, which was confirmed by the in vivo experiments. Importantly, in vivo injection of miR-135b antagomir significantly repressed the tumor growth and metastasis of xenograft models, which suggested that the miR-135b antagomir were promising for clinical applications. Taken together, these results indicate that miR-135b/CAMK2D axis drives GC progression by EMT process remodeling, suggesting that miR-135b may be utilized as a new therapeutic target and prognostic marker for GC patients.
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Affiliation(s)
- Longtao Huangfu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Qifei He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China.,Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518000, China
| | - Jing Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Jingyao Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Xiaomei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Xiaojing Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Ting Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Hong Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Wanhong Zhang
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital, Beijing, Fu-Cheng Road, Beijing, 100142, China.,Center of Minimally Invasive Gastrointestinal Surgery, Shanxi Cancer Hospital, Zhigong New Street, Taiyuan, Shanxi, China
| | - Xiangyu Gao
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital, Beijing, Fu-Cheng Road, Beijing, 100142, China
| | - Fengming Luan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Xiaofang Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital, Fu-Cheng Road, Beijing, 100142, China.,Department of Gastrointestinal Surgery, Peking University Cancer Hospital, Beijing, Fu-Cheng Road, Beijing, 100142, China
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Kuang L, Li L. E74-like factor 3 suppresses microRNA-485-5p transcription to trigger growth and metastasis of ovarian cancer cells with the involvement of CLDN4/Wnt/β-catenin axis. Saudi J Biol Sci 2021; 28:4137-4146. [PMID: 34354393 PMCID: PMC8324996 DOI: 10.1016/j.sjbs.2021.04.093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
Ovarian cancer (OC) is one of the most prevailing gynecological malignancies with high mortality rate, while E74 like ETS transcription factor 3 (ELF3) is reported to be associated with tumorigenesis. This work aims to analyze the role of ELF3 on the suppression of miR-485-5p transcription in OC. Expression of ELF3 in OC and its correlation with overall survival were predicted on a bioinformation system GEPIA. Then, the level of ELF3 in OC tissues and cells and in normal ones was evaluated. Binding relationships between ELF3 and microRNA (miR)-485-5p, and between miR-485-5p and claudin-4 (CLND4) were predicted through Bioinformatics tools. Altered expression of ELF3, miR-485-5p and CLND4 was introduced alone or jointly to probe their influences on OC cell growth. ELF3 was suggested to be highly expressed in OC, which was linked to poor prognosis in patients. Abundant expression of ELF3 was identified in OC tissues and cell lines as relative to the normal ones. ELF3 inhibition suppressed growth and metastasis of OC cells. ELF3 transcriptionally suppressed miR-485-5p expression to further enhance CLDN4 expression. Overexpression of miR-485-5p led to similar trends as ELF3 inhibition did. Importantly, upregulation of CLDN4 was found to block the roles of ELF3 inhibition in OC cells. In addition, the Wnt/signaling pathway suppressed by miR-485-5p mimic was reactivated following CLDN4 overexpression. This study evidenced that ELF3 suppresses miR-485-5p transcription to enhance CLDN4 expression, leading to Wnt/β-catenin activation and promoting OC cell growth and metastasis. This work may provide new ideas for gene-based therapies for OC.
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Affiliation(s)
- Lei Kuang
- Department of Gynecology, Lianyungang First People's Hospital, Lianyungang 222000, Jiangsu, PR China
| | - Li'an Li
- Department of Gynecology and Obstetrics, First Medical Center of PLA General Hospital, Beijing 100853, PR China
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Pulmonary Inflammation and KRAS Mutation in Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33788188 DOI: 10.1007/978-3-030-63046-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2023]
Abstract
Chronic lung infection and lung cancer are two of the most important pulmonary diseases. Respiratory infection and its associated inflammation have been increasingly investigated for their role in increasing the risk of respiratory diseases including chronic obstructive pulmonary disease (COPD) and lung cancer. Kirsten rat sarcoma viral oncogene (KRAS) is one of the most important regulators of cell proliferation, differentiation, and survival. KRAS mutations are among the most common drivers of cancer. Lung cancer harboring KRAS mutations accounted for ~25% of the incidence but the relationship between KRAS mutation and inflammation remains unclear. In this chapter, we will describe the roles of KRAS mutation in lung cancer and how elevated inflammatory responses may increase KRAS mutation rate and create a vicious cycle of chronic inflammation and KRAS mutation that likely results in persistent potentiation for KRAS-associated lung tumorigenesis. We will discuss in this chapter regarding the studies of KRAS gene mutations in specimens from lung cancer patients and in animal models for investigating the role of inflammation in increasing the risk of lung tumorigenesis driven primarily by oncogenic KRAS.
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Lei J, He ZY, Wang J, Hu M, Zhou P, Lian CL, Hua L, Wu SG, Zhou J. Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis. Cancer Med 2021; 10:2924-2939. [PMID: 33742531 PMCID: PMC8026926 DOI: 10.1002/cam4.3854] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background To investigate the potential molecular mechanism of ovarian cancer (OC) evolution and immunological correlation using the integrated bioinformatics analysis. Methods Data from the Gene Expression Omnibus was used to gain differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Gene and Genome pathway analysis were completed by utilizing the Database for Annotation, Visualization, and Integrated Discovery. After multiple validations via The Cancer Genome Atlas (TCGA), Genotype‐Tissue Expression (GTEx) projects, the Human Protein Atlas, Kaplan–Meier (KM) plotter, and immune logical relationships of the key gene SOBP were evaluated based on Tumor Immune Estimation Resource, and Gene Set Enrichment Analysis (GSEA) software. Finally, the lncRNAs‐miRNAs‐mRNAs subnetwork was predicted by starBase, TargetScan, miRBD, and LncBase, individually. Correlation of expression and prognosis for mRNAs, miRNAs, and lncRNAs were confirmed by TCGA, Gene Expression Profiling Interactive Analysis 2 (GEPIA 2), starBase, and KM. Results A total of 192 shared DEGs were discovered from the four data sets, including 125 upregulated and 67 downregulated genes. Functional enrichment analysis presented that they were mainly enriched in cartilage development, pathway in PI3 K‐Akt signaling pathway. Lower expression of SOBP was the independent prognostic factor for inferior prognosis in OC patients. The downregulation of SOBP enhanced the infiltration levels of B cells, CD8+ T cells, Macrophage, Neutrophil, and Dendritic cells. GSEA also disclosed low SOBP showed a significantly associated with the activation of various immune‐related pathways. Finally, we first reported that the MEG8/miR‐378d/SOBP axis was linked to the development and prognosis of OC through regulating the cytokines pathway. Conclusions Our study establishes a novel MEG8/miR‐378d/SOBP axis in the development and prognosis of OC, and the triple subnetwork probably affects the progression of the OC by regulating the cytokines pathway.
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Affiliation(s)
- Jian Lei
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Zhen-Yu He
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, People's Republic of China
| | - Jun Wang
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Min Hu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Ping Zhou
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Chen-Lu Lian
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Li Hua
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - San-Gang Wu
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Juan Zhou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
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He D, Wang D, Lu P, Yang N, Xue Z, Zhu X, Zhang P, Fan G. Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations. Oncogene 2021; 40:355-368. [PMID: 33144684 PMCID: PMC7808940 DOI: 10.1038/s41388-020-01528-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/03/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022]
Abstract
Lung adenocarcinoma (LUAD) harboring EGFR mutations prevails in Asian population. However, the inter-patient and intra-tumor heterogeneity has not been addressed at single-cell resolution. Here we performed single-cell RNA sequencing (scRNA-seq) of total 125,674 cells from seven stage-I/II LUAD samples harboring EGFR mutations and five tumor-adjacent lung tissues. We identified diverse cell types within the tumor microenvironment (TME) in which myeloid cells and T cells were the most abundant stromal cell types in tumors and adjacent lung tissues. Within tumors, accompanied by an increase in CD1C+ dendritic cells, the tumor-associated macrophages (TAMs) showed pro-tumoral functions without signature gene expression of defined M1 or M2 polarization. Tumor-infiltrating T cells mainly displayed exhausted and regulatory T-cell features. The adenocarcinoma cells can be categorized into different subtypes based on their gene expression signatures in distinct pathways such as hypoxia, glycolysis, cell metabolism, translation initiation, cell cycle, and antigen presentation. By performing pseudotime trajectory, we found that ELF3 was among the most upregulated genes in more advanced tumor cells. In response to secretion of inflammatory cytokines (e.g., IL1B) from immune infiltrates, ELF3 in tumor cells was upregulated to trigger the activation of PI3K/Akt/NF-κB pathway and elevated expression of proliferation and anti-apoptosis genes such as BCL2L1 and CCND1. Taken together, our study revealed substantial heterogeneity within early-stage LUAD harboring EGFR mutations, implicating complex interactions among tumor cells, stromal cells and immune infiltrates in the TME.
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Affiliation(s)
- Di He
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Pulmonary Hospital, Department of Thoracic Surgery, School of Life Sciences and Technology, Tongji University, Shanghai, 200433, China
| | - Di Wang
- Shanghai Pulmonary Hospital, Department of Thoracic Surgery, School of Life Sciences and Technology, Tongji University, Shanghai, 200433, China
| | - Ping Lu
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Nan Yang
- PharmaLegacy Laboratories (Shanghai) Co, Zhangjiang High-Tech Park Ltd, Building 7, 388 Jialilue Road, Shanghai, 201203, China
| | - Zhigang Xue
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xianmin Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Pulmonary Hospital, Department of Thoracic Surgery, School of Life Sciences and Technology, Tongji University, Shanghai, 200433, China.
| | - Peng Zhang
- Shanghai Pulmonary Hospital, Department of Thoracic Surgery, School of Life Sciences and Technology, Tongji University, Shanghai, 200433, China.
| | - Guoping Fan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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Suzuki M, Saito-Adachi M, Arai Y, Fujiwara Y, Takai E, Shibata S, Seki M, Rokutan H, Maeda D, Horie M, Suzuki Y, Shibata T, Kiyono T, Yachida S. E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer. Cancer Res 2020; 81:489-500. [PMID: 33293429 DOI: 10.1158/0008-5472.can-19-2988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/28/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
The transcription factor E74-like factor 3 (ELF3) is inactivated in a range of cancers, including biliary tract cancer (BTC). Here, we investigated the tumor-suppressive role of ELF3 in bile duct cells by identifying several previously unknown direct target genes of ELF3 that appear to be implicated in biliary duct carcinogenesis. ELF3 directly repressed ZEB2, a key regulator of epithelial-mesenchymal transition, and upregulated the expression of CGN, an integral element in lumen formation. Loss of ELF3 led to decreased cell-cell junctions and enhanced cell motility. ALOX5 and CXCL16 were also identified as additional direct targets of ELF3; their corresponding proteins 5-lipoxygenase and CXCL16 play a role in the immune response. Conditioned medium from cells overexpressing ELF3 significantly enhanced the migration of natural killer cells and CD8+ T cells toward the conditioned medium. Gene expression profiling for BTC expressing high levels of ELF3 revealed significant enrichment of the ELF3-related genes. In a BTC xenograft model, activation of ELF3 increased expression of ELF3-related genes, enhanced the tubular structure of the tumors, and led to a loss of vimentin. Overall, our results indicate that ELF3 is a key regulator of both epithelial integrity and immune responses in BTC. SIGNIFICANCE: Thease finding shows that ELF3 regulates epithelial integrity and host immune responses and functions as a tumor suppressor in biliary tract cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/2/489/F1.large.jpg.
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Affiliation(s)
- Masami Suzuki
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuko Fujiwara
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Rokutan
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Daichi Maeda
- Department of Clinical Genomics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masafumi Horie
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.
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Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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Aberrant super-enhancer landscape reveals core transcriptional regulatory circuitry in lung adenocarcinoma. Oncogenesis 2020; 9:92. [PMID: 33070167 PMCID: PMC7568720 DOI: 10.1038/s41389-020-00277-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/25/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Lung adenocarcinoma (LUAD) relies on dysregulated gene expression to sustain its infinite growth and progression. Emerging evidence indicates that aberrant transcriptional program results from core transcriptional regulatory circuitry (CRC) which is driven by super-enhancers (SEs). In this study, by integrating profiles of H3K27Ac chromatin immunoprecipitation sequencing (ChIP-seq) from normal adult lung and LUAD cell lines, we revealed that widespread alterations of the super-enhancer were presence during lung carcinogenesis. With SE-based modeling of regulatory circuits and assessments of transcription factor (TF) dependencies, we reconstructed an interconnected transcriptional regulation network formed by three master TFs, including ELF3, EHF, and TGIF1, all of which promoted each other’s expression that confirmed by ChIP-qPCR and western blot. Loss-of function assay revealed that each of them is essential for LUAD cells survival, invasion and metastasis. Meanwhile, the rescue assay also illustrated the transacting transcriptional regulatory circuitry. In addition, the mRNA levels of ELF3, EHF, and TGIF1 were differentially expressed in LUAD tumors and peritumoral tissue. IHC of serial sections revealed that high expressions of CRC (ELF3/EHF/TGIF1-High) were closely associated with high proliferative activity in tumor tissue and poor prognosis on patients with LUAD. Finally, we used small molecular inhibitors to perturb the transcriptional circuitry, also exhibited a prominent anti-cancer effect in vitro. Our findings reveal the mechanism of the transcriptional dysregulation and addiction of LUAD.
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Improved detection of tumor suppressor events in single-cell RNA-Seq data. NPJ Genom Med 2020; 5:43. [PMID: 33083012 PMCID: PMC7541488 DOI: 10.1038/s41525-020-00151-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/17/2022] Open
Abstract
Tissue-specific transcription factors are frequently inactivated in cancer. To fully dissect the heterogeneity of such tumor suppressor events requires single-cell resolution, yet this is challenging because of the high dropout rate. Here we propose a simple yet effective computational strategy called SCIRA to infer regulatory activity of tissue-specific transcription factors at single-cell resolution and use this tool to identify tumor suppressor events in single-cell RNA-Seq cancer studies. We demonstrate that tissue-specific transcription factors are preferentially inactivated in the corresponding cancer cells, suggesting that these are driver events. For many known or suspected tumor suppressors, SCIRA predicts inactivation in single cancer cells where differential expression does not, indicating that SCIRA improves the sensitivity to detect changes in regulatory activity. We identify NKX2-1 and TBX4 inactivation as early tumor suppressor events in normal non-ciliated lung epithelial cells from smokers. In summary, SCIRA can help chart the heterogeneity of tumor suppressor events at single-cell resolution.
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