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Ng JK, Chen Y, Akinwe TM, Heins HB, Mehinovic E, Chang Y, Payne ZL, Manuel JG, Karchin R, Turner TN. Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.02.24302238. [PMID: 38352539 PMCID: PMC10863034 DOI: 10.1101/2024.02.02.24302238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level. Our hypothesis is that missense variation is present in different protein locations in the two phenotypes leading to the distinct phenotypic outcomes. We tested this hypothesis in 1D protein space using our software CLUMP. Furthermore, we newly developed 3D-CLUMP that uses 3D protein structures to spatially test clustering of missense variation for proteome-wide significance. We examined missense DNVs in 39,883 parent-child sequenced trios with NDDs and missense somatic variants from 10,543 sequenced tumors covering five TCGA cancer types and two COSMIC pan-cancer aggregates of tissue types. There were 57 proteins with proteome-wide significant missense variation clustering in NDDs when compared to cancers and 79 proteins with proteome-wide significant missense clustering in cancers compared to NDDs. While our main objective was to identify differences in patterns of missense variation, we also identified a novel NDD protein BLTP2. Overall, our study is innovative, provides new insights into differential missense variation in NDDs and cancer at the protein-level, and contributes necessary information toward building a framework for thinking about prognostic and therapeutic aspects of these proteins.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yilin Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Titilope M. Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hillary B. Heins
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoonhoo Chang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Human & Statistical Genetics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary L. Payne
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juana G. Manuel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
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Liu Y, Ding W, Wang J, Ao X, Xue J. Non-coding RNAs in lung cancer: molecular mechanisms and clinical applications. Front Oncol 2023; 13:1256537. [PMID: 37746261 PMCID: PMC10514911 DOI: 10.3389/fonc.2023.1256537] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Lung cancer (LC) is a heterogeneous disease with high malignant degree, rapid growth, and early metastasis. The clinical outcomes of LC patients are generally poor due to the insufficient elucidation of pathological mechanisms, low efficiency of detection and assessment methods, and lack of individualized therapeutic strategies. Non-coding RNAs (ncRNAs), including microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA), are endogenous regulators that are widely involved in the modulation of almost all aspects of life activities, from organogenesis and aging to immunity and cancer. They commonly play vital roles in various biological processes by regulating gene expression via their interactions with DNA, RNA, or protein. An increasing amount of studies have demonstrated that ncRNAs are closely correlated with the initiation and development of LC. Their dysregulation promotes the progression of LC via distinct mechanisms, such as influencing protein activity, activating oncogenic signaling pathways, or altering specific gene expression. Furthermore, some ncRNAs present certain clinical values as biomarker candidates and therapeutic targets for LC patients. A complete understanding of their mechanisms in LC progression may be highly beneficial to developing ncRNA-based therapeutics for LC patients. This review mainly focuses on the intricate mechanisms of miRNA, lncRNA, and circRNA involved in LC progression and discuss their underlying applications in LC treatment.
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Affiliation(s)
- Ying Liu
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, Shandong, China
| | - Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jianxun Wang
- School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Xiang Ao
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Junqiang Xue
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Rehabilitation Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Hsa_circ_0000520 Promotes Non-Small Cell Lung Cancer Progression through the miR-1258/AKT3 Axis. JOURNAL OF ONCOLOGY 2022; 2022:3676685. [PMID: 36593867 PMCID: PMC9805391 DOI: 10.1155/2022/3676685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/09/2022] [Accepted: 11/05/2022] [Indexed: 12/25/2022]
Abstract
Background There are several previous studies suggesting that circular RNAs (circRNAs) are involved in tumorigenesis of non-small cell lung cancer (NSCLC). Nevertheless, the role of circRNA_0000520 (circ_0000520) in this disease has not yet been studied. Methods circ_0000520, microRNA (miR)-1258, and AKT serine/threonine kinase 3 (AKT3) mRNA expression levels were detected by qPCR. CCK-8, EdU, and Transwell assays were utilized to detect NSCLC cells' malignant biological behaviors. The targeted relationship between miR-1258 and AKT3 3'-UTR or circ_0000520 was verified through the dual-luciferase reporter gene assay. Western blotting was utilized to measure the AKT3 expression after circ_0000520 and miR-1258 were selectively regulated. Results circ_0000520 was upregulated in NSCLC. Highly expressed circ_0000520 is linked to the NSCLC patient's advanced TNM stage and lymph node metastasis. circ_0000520 overexpression facilitated NSCLC cell growth, migration, and invasion. miR-1258 was identified as the downstream target of circ_0000520. miR-1258 overexpression weakened the effect of circ_0000520 overexpression on NSCLC cells. miR-1258 targeted and inhibited AKT3. circ_0000520 positively regulated the AKT3 expression in NSCLC cells by sponging miR-1258. Conclusion circ_0000520 upregulates AKT3 by competitively binding with miR-1258 to facilitate NSCLC progression.
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