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Che R, Panah M, Mirani B, Knowles K, Ostapovich A, Majumdar D, Chen X, DeSimone J, White W, Noonan M, Luo H, Alexandrov A. Identification of Human Pathways Acting on Nuclear Non-Coding RNAs Using the Mirror Forward Genetic Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615073. [PMID: 39386709 PMCID: PMC11463631 DOI: 10.1101/2024.09.26.615073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Despite critical roles in diseases, human pathways acting on strictly nuclear non-coding RNAs have been refractory to forward genetics. To enable their forward genetic discovery, we developed a single-cell approach that "Mirrors" activities of nuclear pathways with cytoplasmic fluorescence. Application of Mirror to two nuclear pathways targeting MALAT1's 3' end, the pathway of its maturation and the other, the degradation pathway blocked by the triple-helical Element for Nuclear Expression (ENE), identified nearly all components of three complexes: Ribonuclease P and the RNA Exosome, including nuclear DIS3, EXOSC10, and C1D, as well as the Nuclear Exosome Targeting (NEXT) complex. Additionally, Mirror identified DEAD-box helicase DDX59 associated with the genetic disorder Oral-Facial-Digital syndrome (OFD), yet lacking known substrates or roles in nuclear RNA degradation. Knockout of DDX59 exhibits stabilization of the full-length MALAT1 with a stability-compromised ENE and increases levels of such long non-coding RNAs as NEAT1_1 and NIPBL-DT, as well as 3'-extended forms of small nuclear RNAs. It also exhibits extensive retention of minor introns, including in OFD-associated genes, suggesting a mechanism for DDX59 association with OFD. Mirror efficiently identifies pathways acting on strictly nuclear non-coding RNAs, including essential and indirectly-acting components, and, as a result, uncovers unexpected links to human disease.
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Affiliation(s)
- Rui Che
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
| | - Monireh Panah
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
| | - Bhoomi Mirani
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
| | - Krista Knowles
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
| | - Anastacia Ostapovich
- Dept. of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Debarati Majumdar
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
| | - Xiaotong Chen
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
| | - Joseph DeSimone
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
| | - William White
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
| | - Megan Noonan
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
| | - Hong Luo
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
| | - Andrei Alexandrov
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC 29631, USA
- Clemson University Center for Human Genetics, Greenwood, SC 29646, USA
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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Zhang S, Gu J, Shi LL, Qian B, Diao X, Jiang X, Wu J, Wu Z, Shen A. A pan-cancer analysis of anti-proliferative protein family genes for therapeutic targets in cancer. Sci Rep 2023; 13:21607. [PMID: 38062199 PMCID: PMC10703880 DOI: 10.1038/s41598-023-48961-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The recently discovered APRO (anti-proliferative protein) family encodes a group of trans-membrane glycoproteins and includes 6 members: TOB1, TOB2, BTG1, BTG2, BTG3 and BTG4. The APRO family is reportedly associated with the initiation and progression of cancers. This study aims to undertake a comprehensive investigation of the APRO family of proteins as a prognostic biomarker in various human tumors. We performed a pan-cancer analysis of the APRO family based on The Cancer Genome Atlas (TCGA). With the bioinformatics methods, we explored the prognostic value of the APRO family and the correlation between APRO family expression and tumor mutation burden (TMB), microsatellite instability (MSI), drug sensitivity, and immunotherapy in numerous cancers. Our results show that the APRO family was primarily down-regulated in cancer samples. The expression of APRO family members was linked with patient prognosis. In addition, APRO family genes showed significant association with immune infiltrate subtypes, tumor microenvironment, and tumor cell stemness. Finally, our study also demonstrated the relationship between APRO family genes and drug sensitivity. This study provides comprehensive information to understand the APRO family's role as an oncogene and predictor of survival in some tumor types.
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Affiliation(s)
- Siming Zhang
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jue Gu
- Affiliated Hospital of Nantong University, Nantong, China
| | - Ling-Ling Shi
- Affiliated Nantong Hospital Third of Nantong University, Nantong, China
| | - Bo Qian
- Maternal and Child Care Hospital of Qidong, Nantong, China
| | - Xun Diao
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiaohui Jiang
- Department of General Surgery, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Jindong Wu
- Department of General Surgery, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Zhijun Wu
- Department of Oncology, Nantong Traditional Chinese Medicine Hospital, Nantong, China.
| | - Aiguo Shen
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China.
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Mazarei M, Shahabi Rabori V, Ghasemi N, Salehi M, Rayatpisheh N, Jahangiri N, Saberiyan M. LncRNA MALAT1 signaling pathway and clinical applications in overcome on cancers metastasis. Clin Exp Med 2023; 23:4457-4472. [PMID: 37695391 DOI: 10.1007/s10238-023-01179-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
In spite of its high mortality rate and difficulty in finding a cure, scientific advancements have contributed to a reduction in cancer-related fatalities. Aberrant gene expression during carcinogenesis emphasizes the importance of targeting the signaling networks that control gene expression in cancer treatment. Long noncoding RNAs (lncRNAs), which are transcribed RNA molecules that play a role in gene expression regulation, are a recent innovative therapeutic approach for diagnosing and treating malignancies. MALAT1, a well-known lncRNA, functions in gene expression, RNA processing, and epigenetic control. High expression levels of MALAT1 are associated with several human disorders, including metastasis, invasion, autophagy, and proliferation of cancer cells. MALAT1 affects various signaling pathways and microRNAs (miRNAs), and this study aims to outline its functional roles in cancer metastasis and its interactions with cellular signaling pathways. Moreover, MALAT1 and its interactions with signaling pathways can be promising target for cancer treatment.
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Affiliation(s)
- Madineh Mazarei
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Nazila Ghasemi
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mehrnaz Salehi
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Najmeh Rayatpisheh
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Negin Jahangiri
- Department of Biology, Faculty of Basic Sciences and Engineering, Gonbad Kavous University, Gonbad-e Kavus, Iran
| | - Mohammadreza Saberiyan
- Department of Medical Genetics, Faculty of Medicine, School of Medical Sciences, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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