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Dai A, Zhang X, Wang X, Liu G, Wang Q, Yu F. Transcription factors in chimeric antigen receptor T-cell development. Hum Cell 2024; 37:571-581. [PMID: 38436882 DOI: 10.1007/s13577-024-01040-7] [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: 11/07/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a new and innovative approach to treating cancers that has shown promising results in the treatment of lymphoma. However, it has been found to be less effective in the treatment of solid tumors. To overcome the limitation, researchers have explored the use of combined CAR-T therapy with other complementary regimens that target specific genes or biomarkers, which would enhance the synergistic therapeutic effects. Transcription factors (TFs) have been identified as potential markers that can regulate gene expression in CAR-T cells to enhance their cytotoxicity and safety. TFs are known to bind DNA specifically and recruit cofactor proteins to regulate the expression of target genes. By targeting TFs, it is possible to improve the anti-tumor response of CAR-T cells by altering their phenotype and transcriptional map, thereby increasing their effector function, such as reducing the exhaustion, enhancing the survival, and cytotoxicity of CAR-T cells. This review summarizes the application of transcription factors in CART therapy to enhance the synergistic therapeutic effect of CAR-T cells in the treatment of solid tumors and improve their anti-tumor responses.
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Affiliation(s)
- Anran Dai
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xiangzhi Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaoyan Wang
- Department of Gastroenterology, Suqian First People's Hospital, Suqian, 223800, Jiangsu, China
| | - Guodong Liu
- Department of General Surgery, Suqian First People's Hospital, Suqian, 223800, Jiangsu, China
| | - Qiang Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Feng Yu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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2
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de Oliveira JC. Transcribed Ultraconserved Regions: New regulators in cancer signaling and potential biomarkers. Genet Mol Biol 2023; 46:e20220125. [PMID: 36622962 PMCID: PMC9829027 DOI: 10.1590/1678-4685-gmb-2022-0125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/06/2022] [Indexed: 01/11/2023] Open
Abstract
The ultraconserved regions (UCRs) are 481 genomic elements, longer than 200 bp, 100% conserved in human, mouse, and rat genomes. Usually, coding regions are more conserved, but more than 80% of UCRs are either intergenic or intronic, and many of them produce long non-coding RNAs (lncRNAs). Recently, the deregulated expression of transcribed UCRs (T-UCRs) has been associated with pathological conditions. But, differently from many lncRNAs with recognized crucial effects on malignant cell processes, the role of T-UCRs in the control of cancer cell networks is understudied. Furthermore, the potential utility of these molecules as molecular markers is not clear. Based on this information, the present review aims to organize information about T-UCRs with either oncogenic or tumor suppressor role associated with cancer cell signaling, and better describe T-UCRs with potential utility as prognosis markers. Out of 481 T-UCRs, 297 present differential expression in cancer samples, 23 molecules are associated with tumorigenesis processes, and 12 have more clear potential utility as prognosis markers. In conclusion, T-UCRs are deregulated in several tumor types, highlighted as important molecules in cancer networks, and with potential utility as prognosis markers, although further investigation for translational medicine is still needed.
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3
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Yu TX, Kalakonda S, Liu X, Han N, Chung HK, Xiao L, Rao JN, He TC, Raufman JP, Wang JY. Long noncoding RNA uc.230/CUG-binding protein 1 axis sustains intestinal epithelial homeostasis and response to tissue injury. JCI Insight 2022; 7:156612. [PMID: 36214222 PMCID: PMC9675575 DOI: 10.1172/jci.insight.156612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/31/2022] [Indexed: 01/16/2023] Open
Abstract
Intestinal epithelial integrity is commonly disrupted in patients with critical disorders, but the exact underlying mechanisms are unclear. Long noncoding RNAs transcribed from ultraconserved regions (T-UCRs) control different cell functions and are involved in pathologies. Here, we investigated the role of T-UCRs in intestinal epithelial homeostasis and identified T-UCR uc.230 as a major regulator of epithelial renewal, apoptosis, and barrier function. Compared with controls, intestinal mucosal tissues from patients with ulcerative colitis and from mice with colitis or fasted for 48 hours had increased levels of uc.230. Silencing uc.230 inhibited the growth of intestinal epithelial cells (IECs) and organoids and caused epithelial barrier dysfunction. Silencing uc.230 also increased IEC vulnerability to apoptosis, whereas increasing uc.230 levels protected IECs against cell death. In mice with colitis, reduced uc.230 levels enhanced mucosal inflammatory injury and delayed recovery. Mechanistic studies revealed that uc.230 increased CUG-binding protein 1 (CUGBP1) by acting as a natural decoy RNA for miR-503, which interacts with Cugbp1 mRNA and represses its translation. These findings indicate that uc.230 sustains intestinal mucosal homeostasis by promoting epithelial renewal and barrier function and that it protects IECs against apoptosis by serving as a natural sponge for miR-503, thereby preserving CUGBP1 expression.
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Affiliation(s)
- Ting-Xi Yu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sudhakar Kalakonda
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Xiangzheng Liu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Naomi Han
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hee K. Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Jaladanki N. Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Tong-Chuan He
- Department of Surgery, The University of Chicago Medical Center, Chicago, Illinois, USA
| | - Jean-Pierre Raufman
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA.,Department of Medicine and
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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4
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Gao SS, Zhang ZK, Wang XB, Ma Y, Yin GQ, Guo XB. Role of transcribed ultraconserved regions in gastric cancer and therapeutic perspectives. World J Gastroenterol 2022; 28:2900-2909. [PMID: 35978878 PMCID: PMC9280734 DOI: 10.3748/wjg.v28.i25.2900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/08/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is the fourth leading cause of cancer-related death. The occurrence and development of GC is a complex process involving multiple biological mechanisms. Although traditional regulation modulates molecular functions related to the occurrence and development of GC, the comprehensive mechanisms remain unclear. Ultraconserved region (UCR) refers to a genome sequence that is completely conserved in the homologous regions of the human, rat and mouse genomes, with 100% identity, without any insertions or deletions, and often located in fragile sites and tumour-related genes. The transcribed UCR (T-UCR) is transcribed from the UCR and is a new type of long noncoding RNA. Recent studies have found that the expression level of T-UCRs changes during the occurrence and development of GC, revealing a new mechanism underlying GC. Therefore, this article aims to review the relevant research on T-UCRs in GC, as well as the function of T-UCRs and their regulatory role in the occurrence and development of GC, to provide new strategies for GC diagnosis and treatment.
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Affiliation(s)
- Shen-Shuo Gao
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
| | - Zhi-Kai Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
| | - Xu-Bin Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| | - Yan Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| | - Guo-Qing Yin
- Department of Anus and Intestine Surgery, Qingzhou Hospital Affiliated to Shandong First Medical University, Qingzhou 262500, Shandong Province, China
| | - Xiao-Bo Guo
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
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5
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Gibert MK, Sarkar A, Chagari B, Roig-Laboy C, Saha S, Bednarek S, Kefas B, Hanif F, Hudson K, Dube C, Zhang Y, Abounader R. Transcribed Ultraconserved Regions in Cancer. Cells 2022; 11:1684. [PMID: 35626721 PMCID: PMC9139194 DOI: 10.3390/cells11101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.
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Affiliation(s)
- Myron K. Gibert
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Aditya Sarkar
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Bilhan Chagari
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Christian Roig-Laboy
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Shekhar Saha
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Sylwia Bednarek
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Benjamin Kefas
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Farina Hanif
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Kadie Hudson
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Collin Dube
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
- Department of Neurology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- NCI Designated Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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6
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Yoon JH, Byun H, Ivan C, Calin GA, Jung D, Lee S. lncRNAs UC.145 and PRKG1-AS1 Determine the Functional Output of DKK1 in Regulating the Wnt Signaling Pathway in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14102369. [PMID: 35625973 PMCID: PMC9140071 DOI: 10.3390/cancers14102369] [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: 04/11/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
DKK1 inhibits the canonical Wnt signaling pathway that is known to be involved in various cancers. However, whether DKK1 acts as an oncogene or tumor suppressor gene remains controversial. Furthermore, the DKK1-regulating mechanism in gastric cancer has not yet been defined. The aim of this study was to explore whether the ultraconserved region UC.145 regulates epigenetic changes in DKK1 expression in gastric cancer. Microarray analysis revealed that UC.145 exhibited the highest binding affinity to EZH2, a histone methyltransferase. The effects of UC.145 inactivation were assessed in gastric cancer cell lines using siRNA. The results indicated that UC.145 triggers DKK1 methylation via interaction with EZH2 and is involved in the canonical Wnt signaling pathway. Additionally, interaction between UC.145 and another long non-coding RNA adjacent to DKK1, PRKG1-AS1, induced a synergistic effect on Wnt signaling. The regulation of these three genes was closely associated with patient overall survival. Inactivation of UC.145 induced apoptosis and inhibited the growth and migratory, invasive, and colony-forming abilities of gastric cancer cells. The study findings provide insights into Wnt signaling in gastric cancer and support UC.145 as a potential novel predictive biomarker for the disease.
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Affiliation(s)
- Jung-ho Yoon
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Severance Hospital, Seoul 03722, Korea; (J.-h.Y.); (H.B.)
| | - Hyojoo Byun
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Severance Hospital, Seoul 03722, Korea; (J.-h.Y.); (H.B.)
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Dahyun Jung
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Severance Hospital, Seoul 03722, Korea; (J.-h.Y.); (H.B.)
- Correspondence: (D.J.); (S.L.); Tel.: +82-2-2228-1996 (S.L.)
| | - Sangkil Lee
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Severance Hospital, Seoul 03722, Korea; (J.-h.Y.); (H.B.)
- Correspondence: (D.J.); (S.L.); Tel.: +82-2-2228-1996 (S.L.)
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7
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Zambalde EP, Adamoski D, Gradia DF, Rabinovich I, Rodrigues AC, Ivan C, Ribeiro EMSF, Calin GA, Carvalho de Oliveira J. Transcribed Ultraconserved Regions Are Associated with Clinicopathological Features in Breast Cancer. Biomolecules 2022; 12:214. [PMID: 35204715 PMCID: PMC8961524 DOI: 10.3390/biom12020214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 01/27/2023] Open
Abstract
Ultraconserved regions (UCRs) are 481 genome segments, with length longer than 200 bp, that are 100% conserved among humans, mice, and rats. The majority of UCRs are transcriptionally active (T-UCRs) as many of them produce non-coding RNAs. In a previous study, we evaluated the expression level of T-UCRs in breast cancer (BC) patients and found that 63% of transcripts correlated with some clinical and/or molecular parameter of BC. In this study, we delved into the expression levels of 12 T-UCRs and correlated them with clinicopathological parameters, immunohistochemical markers, and overall survival in two breast cancer cohorts: TCGA and Brazilian patients. We found that uc.268 is more expressed in TCGA patients under 40 years of age, associated with progesterone receptor (PR) and estrogen receptor (ER), and its high expression is found in luminal A. Lower uc.84 and uc.376 were respectively observed in metastatic and stage IV tumors associated with good prognostic in luminal B. Moreover, uc.84 was only related to the HER2+, while uc.376 was related to ER+ and PR+, and HER2+. A panel composed of uc.147, uc.271, and uc.427 distinguished luminal A from triple negative patients with an AUC of 0.9531 (sensitivity 92.19% and specificity 86.76%). These results highlight the potential role of T-UCRs in BC and provide insights into the potential application of T-UCRs as biomarkers.
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Affiliation(s)
- Erika Pereira Zambalde
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil;
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Iris Rabinovich
- Hospital Nossa Senhora das Graças, Centro de Doenças da Mama, Curitiba 80810-040, PR, Brazil;
| | - Ana Carolina Rodrigues
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Cristina Ivan
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, TX 77230, USA; (C.I.); (G.A.C.)
| | - Enilze M. S. F. Ribeiro
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - George Adrian Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, TX 77230, USA; (C.I.); (G.A.C.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
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Shi X, Huang X, Chen R, Li Y, Xu Y, Zhang W, Zhu Q, Zha X, Wang J. The transcribed ultraconserved element uc.51 promotes the proliferation and metastasis of breast cancer by stabilizing NONO. Clin Exp Metastasis 2021; 38:551-571. [PMID: 34714466 DOI: 10.1007/s10585-021-10128-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/15/2021] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs have recently emerged as significant contributors to cancers, including breast cancer (BC). One class of long noncoding RNAs called transcribed ultraconserved regions (T-UCRs) is highly conserved in many species and closely related to diverse physiological and pathological processes. However, the function of T-UCRs in BC remains largely unclear. In this study, we identified uc.51, a T-UCR that is overexpressed in both BC tissues and cell lines and is correlated with larger tumor size. Loss- and gain-of-function assays were performed in vitro and demonstrated that uc.51 promotes the proliferation, migration, and invasion of BC cells. Mechanistically, non-POU domain-containing octamer-binding protein (NONO) was found to physically interact with uc.51 by RNA pulldown followed by mass spectrometry. This interaction was further verified by RNA immunoprecipitation. Moreover, uc.51 positively regulated the expression of NONO, maintained its stability through the ubiquitin-proteasome system, and activated the phosphorylation of CREB. Rescue experiments demonstrated that NONO overexpression compensated for the attenuated influence on BC progression resulting from downregulation of uc.51, indicating that NONO functions downstream of uc.51. In vivo functional experiments also revealed a positive correlation between uc.51 expression and tumor size. Ki-67 and NONO levels in the lv-uc.51-shRNA group were decreased compared with those in the lv-con-shRNA group, according to the immunohistochemical staining results, and a decreased incidence of distant metastasis was observed in the lv-uc.51-shRNA group in the xenograft model. Collectively, our results reveal a substantial role for the uc.51-NONO axis in BC progression and indicate that the uc.51-NONO axis has potential to be a therapeutic target for BC.
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Affiliation(s)
- Xiaoqing Shi
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Xiaofeng Huang
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Rui Chen
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Yan Li
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Yinggang Xu
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Weiwei Zhang
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Qiannan Zhu
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China
| | - Xiaoming Zha
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 210000, China.
| | - Jue Wang
- Department of Breast Disease, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210000, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 210000, China.
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9
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Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue. Cancers (Basel) 2021; 13:cancers13040681. [PMID: 33567603 PMCID: PMC7914980 DOI: 10.3390/cancers13040681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary DNA regions having high sequence similarity among human, rat and mouse genomes are defined as Ultraconserved Regions. Non-coding RNA transcripts originating by these regions may play relevant roles in the onset and progression of multiple cancer types. We recently found that ultra-conserved-transcript-8+ (uc.8+) levels correlate with the grading and staging of bladder cancer. The aim of this study is to systematically evaluate the expression of ultra-conserved-transcript-8+ (uc.8+) in biopsies and assess its intracellular localization. Furthermore, we aimed to correlate uc.8+ levels with clinical parameters and patient survival. Our analysis indicates that uc.8+ can localize both in the cytoplasm and nucleus of bladder cells at early stages of tumorigenesis, while in tumors at advanced stages, uc.8+ has a prevalent cytoplasmic localization. These data provide relevant information about uc.8+ localization as a hallmark of tumor stage. Finally, using advanced computer-based techniques, we predicted the binding of uc.8+ to RNA-binding proteins. Our study overall suggests that uc.8+ localization can be used as a prognostic biomarker for bladder cancer. Abstract Non-coding RNA transcripts originating from Ultraconserved Regions (UCRs) have tissue-specific expression and play relevant roles in the pathophysiology of multiple cancer types. Among them, we recently identified and characterized the ultra-conserved-transcript-8+ (uc.8+), whose levels correlate with grading and staging of bladder cancer. Here, to validate uc.8+ as a potential biomarker in bladder cancer, we assessed its expression and subcellular localization by using tissue microarray on 73 human bladder cancer specimens. We quantified uc.8+ by in-situ hybridization and correlated its expression levels with clinical characteristics and patient survival. The analysis of subcellular localization indicated the simultaneous presence of uc.8+ in the cytoplasm and nucleus of cells from the Low-Grade group, whereas a prevalent cytoplasmic localization was observed in samples from the High-Grade group, supporting the hypothesis of uc.8+ nuclear-to-cytoplasmic translocation in most malignant tumor forms. Moreover, analysis of uc.8+ expression and subcellular localization in tumor-surrounding stroma revealed a marked down-regulation of uc.8+ levels compared to the paired (adjacent) tumor region. Finally, deep machine-learning approaches identified nucleotide sequences associated with uc.8+ localization in nucleus and/or cytoplasm, allowing to predict possible RNA binding proteins associated with uc.8+, recognizing also sequences involved in mRNA cytoplasm-translocation. Our model suggests uc.8+ subcellular localization as a potential prognostic biomarker for bladder cancer.
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Abstract
Long noncoding RNAs (lncRNAs) are involved in many regulatory mechanisms in practically every step of the RNA cycle, from transcription to RNA stability and translation. They are a highly heterogeneous class of molecules in terms of site of production, interaction networks, and functions. More and more databases are available on the web with the aim to make public information about lncRNA accessible to the scientific community. Here we review the most interesting resources with the purpose to organize a compendium of useful tools to interrogate before studying a lncRNA of interest.
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Zhao X, Sun W, Ren Y, Lu Z. Therapeutic potential of p53 reactivation in cervical cancer. Crit Rev Oncol Hematol 2020; 157:103182. [PMID: 33276182 DOI: 10.1016/j.critrevonc.2020.103182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/23/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022] Open
Abstract
Cervical cancer (CC) is one of most common malignancies affecting women worldwide. To date, surgical resection is the only effective radical remedy for CC at its early stages, while the prognosis of metastatic or recurrent CC is very poor. Dysfunction of the tumor suppressor p53 due to aberrant expression, post-translational modification, mutations, SNPs, and LOH as well as sequestration by viral antigens and MDM2/HDM2-mediated degradation is closely associated with the therapeutic insensitivity and relapse of many malignancies, including CC. Accumulating studies have demonstrated that restoration of p53 activity can induce cell cycle arrest and apoptosis, eliminate radio- and chemotherapy resistance, and inhibit tumor growth in CC cells. Therefore, activation of wild-type p53 as well as restoration of p53 function seems appealing as a therapeutic strategy. In this review, we focus on the potential roles of p53 reactivation in CC treatment and their underlying molecular mechanisms towards the development of novel therapies.
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Affiliation(s)
- Xiangxuan Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, LN, China.
| | - Wei Sun
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, LN, China
| | - Ying Ren
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, LN, China
| | - Zaiming Lu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, LN, China
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Chen J, Miao W, Yang S, Yin M, Zhao J, Song D. LncRNA NR_027471 Functions as a ceRNA for miRNA-8055 Leading to Suppression of Osteosarcoma by Regulating the Expression of TP53INP1. Front Oncol 2020; 10:563255. [PMID: 33117693 PMCID: PMC7550745 DOI: 10.3389/fonc.2020.563255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022] Open
Abstract
Osteosarcoma is a malignancy with high aggressiveness and poor prognosis, which occurs mainly in children. The therapeutic strategy against osteosarcoma includes surgery combined with chemotherapy and radiotherapy. Although the treatment of osteosarcoma has been improved in recent years, there is a large proportion of patients with incurable osteosarcoma. Investigation of the mechanism of osteosarcoma progression would be of great help in discovering therapeutic targets for this disease. Long non-coding RNAs play critical roles in the pathogenesis of different types of cancer. The current study showed that long non-coding RNA NR_027471 was downregulated in osteosarcoma cells. In vitro and in vivo studies indicated that upregulation of NR_027471 impeded the viability, proliferation, and invasion of osteosarcoma, as well as induced cell cycle arrest at G1. In addition, binding of miR-8055 to NR_027471 was demonstrated, thereby influencing the expression of tumor protein p53 inducible nuclear protein 1 (TP53INP1). Knockdown of NR_027471 promoted epithelial–mesenchymal transition by inhibiting E-cadherin and increasing the expression of zinc finger E-box-binding homeobox 1 (ZEB1), Snail, and fibronectin. These results suggested that overexpression of NR_027471 upregulated TP53INP1 by sponging to miR-8055, leading to suppression of osteosarcoma cell proliferation and progression.
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Affiliation(s)
- Jiajia Chen
- Department of Spine Surgery, The Second Affiliated Hospital of Nantong University, Nantong, China.,Department of Orthopedics, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Wujun Miao
- Department of Orthopedics, School of Medicine, Jinling Hospital, Nanjing University, Nanjing, China
| | - Saishuai Yang
- Department of Anesthesiology, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Mengchen Yin
- Department of Orthopaedics, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianning Zhao
- Department of Orthopedics, School of Medicine, Jinling Hospital, Nanjing University, Nanjing, China
| | - Dianwen Song
- Department of Orthopedics, Shanghai General Hospital of Nanjing Medical University, Shanghai, China.,Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Wang Y, Zhou D, Feng Y, Chen G, Li N. T-UCRs with digestive and respiratory diseases. Bioorg Med Chem Lett 2020; 30:127306. [PMID: 32631526 DOI: 10.1016/j.bmcl.2020.127306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
From the perspective of histoembryology, the lung, gaster, and intestines that derived from the endoderm of the gastrula are structurally homologous. The interplay of intestines and lung in many pathologic changes is called the gut-lung axis. RNAs transcribed from ultraconserved regions (T-UCRs) are highly evolutionarily conserved in many mammalian genomes and have been found to be important in the pathogenesis and diagnosis of many diseases. More and more studies in recent years have shown that T-UCRs play important roles both in digestive and respiratory diseases. Taking the gut-lung axis as the entry point, this review summarizes the T-UCRs related to digestive and respiratory diseases in recent years. Meanwhile, these T-UCRs and their targets can lay a foundation for future drug research.
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Affiliation(s)
- Yajun Wang
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Differentially Methylated Ultra-Conserved Regions Uc160 and Uc283 in Adenomas and Adenocarcinomas Are Associated with Overall Survival of Colorectal Cancer Patients. Cancers (Basel) 2020; 12:cancers12040895. [PMID: 32272654 PMCID: PMC7226527 DOI: 10.3390/cancers12040895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
: Deregulation of the transcribed ultra-conserved regions (T-UCRs) Uc160, Uc283, and Uc346 has been reported in colorectal cancer (CRC) recently. Here, we investigated promoter methylation of these T-UCRs during the adenoma-carcinoma sequence and their clinical significance in CRC patients. Methylation levels were assessed in CRC, adenomas, infiltrated lymph nodes, and metastatic tissue specimens. In situ hybridization was performed in representative tissue specimens. T-UCRs expression levels were also evaluated in HT-29 colon cancer cells before and after the acquired resistance to 5-fluorouracil (5-FU) and oxaliplatin. A gradual increase in T-UCRs methylation levels from hyperplastic polyps to adenomas and to in situ carcinomas (ISC) and a gradual decrease from ISC to infiltrative and metastatic carcinomas was observed (p < 0.001 for Uc160 and Uc283, p = 0.018 for Uc346). Uc160 and Uc283 methylation was associated with the grade of dysplasia in adenoma specimens (p = 0.034 and p = 0.019, respectively). Furthermore, higher Uc160 methylation, mainly in stage III and IV patients, was related to improved overall survival (OS) in univariate (p = 0.009; HR, 0.366) and multivariate analysis (p = 0.005; HR, 0.240). Similarly, higher methylation of Uc283 was associated with longer OS (p = 0.030). Finally, T-UCRs expression was significantly reduced in HT-29 cells after resistance to chemotherapy. This study suggests that promoter methylation of Uc160, Uc283, and Uc346 is altered during CRC development and that Uc160 and Uc283 methylation may have prognostic significance for CRC patients.
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