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Crossley ER, Fedorova L, Mulyar O, Freeman R, Khuder S, Fedorov A. Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing. NAR Genom Bioinform 2024; 6:lqae074. [PMID: 38962254 PMCID: PMC11217675 DOI: 10.1093/nargab/lqae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Thousands of prolonged sequences of human ultra-conserved non-coding elements (UCNEs) share only one common feature: peculiarities in the unique composition of their dinucleotides. Here we investigate whether the numerous weak signals emanating from these dinucleotide arrangements can be used for computational identification of UCNEs within the human genome. For this purpose, we analyzed 4272 UCNE sequences, encompassing 1 393 448 nucleotides, alongside equally sized control samples of randomly selected human genomic sequences. Our research identified nine different features of dinucleotide arrangements that enable differentiation of UCNEs from the rest of the genome. We employed these nine features, implementing three Machine Learning techniques - Support Vector Machine, Random Forest, and Artificial Neural Networks - to classify UCNEs, achieving an accuracy rate of 82-84%, with specific conditions allowing for over 90% accuracy. Notably, the strongest feature for UCNE identification was the frequency ratio between GpC dinucleotides and the sum of GpG and CpC dinucleotides. Additionally, we investigated the entire pool of 31 046 SNPs located within UCNEs for their representation in the ClinVar database, which catalogs human SNPs with known phenotypic effects. The presence of UCNE-associated SNPs in ClinVar aligns with the expectation of a random distribution, emphasizing the enigmatic nature of UCNE phenotypic manifestation.
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Affiliation(s)
- Emily R Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
| | | | | | | | - Sadik Khuder
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
| | - Alexei Fedorov
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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Li S, Cai X, Chen L, Lin M, Zhu Z, Xiao H, Nie P, Chen Q, Yang X. Inhibition of hepatocellular carcinoma growth via modulation of the miR-221/SOX11 axis by curcumin and berberine. PeerJ 2023; 11:e16593. [PMID: 38084140 PMCID: PMC10710771 DOI: 10.7717/peerj.16593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal malignancy that has limited treatment options. This study focused on the potential therapeutic effects of curcumin (CUR) and berberine (BBR) on the miR-221/SRY-box transcription factor 11 (SOX11) axis in HCC. We investigated the combined effects of CUR and BBR on HEPG2 and Huh7 cell survival and miR-221 expression using Cell Counting Kit-8 assays and RT-qPCR, respectively. Western blotting was used to detect changes in the apoptosis-related caspase-3/9 protein levels. We performed bioinformatics analysis and dual-luciferase assays and measured apoptotic protein levels to assess the role of the miR-221/SOX11 axis in mediating the effects of CUR-BBR. Both CUR and BBR suppressed HCC cell growth in a dose-dependent manner, with the most potent combined effect observed at a 2:1 ratio. CUR-BBR treatment significantly downregulated miR-221 expression, and miR-221 overexpression partially reversed the CUR-BBR-mediated decrease in cell survival. In addition, SOX11 was found to be a direct target of miR-221. CUR-BBR treatment upregulated SOX11 expression, and overexpression of SOX11 restored the inhibitory effects of CUR-BBR on cell growth, migration, and invasion and promoted apoptosis in the presence of miR-221. Furthermore, CUR-BBR activated pro-apoptotic proteins caspase-3/9 through the miR-221/SOX11 axis. The combined effect of CUR-BBR played an important role in inhibiting the growth of HCC cells. This combined effect was achieved by regulating the miR-221/SOX11 axis and activating the synthesis of pro-apoptotic proteins. Our findings highlight a promising combined therapeutic approach for HCC and underscore the importance of targeting the miR-221/SOX11 axis.
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Affiliation(s)
- Sheng Li
- Department of Internal Medicine, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoliang Cai
- Department of Internal Medicine, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Liang Chen
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Manbian Lin
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Ziqi Zhu
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Huihuang Xiao
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Pingping Nie
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Quanwen Chen
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoyu Yang
- Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
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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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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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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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