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Bouchareb E, Dallel S, De Haze A, Damon-Soubeyrand C, Renaud Y, Baabdaty E, Vialat M, Fabre J, Pouchin P, De Joussineau C, Degoul F, Sanmukh S, Gendronneau J, Sanchez P, Gonthier-Gueret C, Trousson A, Morel L, Lobaccaro JM, Kocer A, Baron S. Liver X Receptors Enhance Epithelial to Mesenchymal Transition in Metastatic Prostate Cancer Cells. Cancers (Basel) 2024; 16:2776. [PMID: 39199549 PMCID: PMC11353074 DOI: 10.3390/cancers16162776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/12/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024] Open
Abstract
Prostate cancer (PCa) is one of the most common cancers in men. Metastasis is the leading cause of death in prostate cancer patients. One of the crucial processes involved in metastatic spread is the "epithelial-mesenchymal transition" (EMT), which allows cells to acquire the ability to invade distant organs. Liver X Receptors (LXRs) are nuclear receptors that have been demonstrated to regulate EMT in various cancers, including hepatic cancer. Our study reveals that the LXR pathway can control pro-invasive cell capacities through EMT in prostate cancer, employing ex vivo and in vivo approaches. We characterized the EMT status of the commonly used LNCaP, DU145, and PC3 prostate cancer cell lines through molecular and immunohistochemistry experiments. The impact of LXR activation on EMT function was also assessed by analyzing the migration and invasion of these cell lines in the absence or presence of an LXR agonist. Using in vivo experiments involving NSG-immunodeficient mice xenografted with PC3-GFP cells, we were able to study metastatic spread and the effect of LXRs on this process. LXR activation led to an increase in the accumulation of Vimentin and Amphiregulin in PC3. Furthermore, the migration of PC3 cells significantly increased in the presence of the LXR agonist, correlating with an upregulation of EMT. Interestingly, LXR activation significantly increased metastatic spread in an NSG mouse model. Overall, this work identifies a promoting effect of LXRs on EMT in the PC3 model of advanced prostate cancer.
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Affiliation(s)
- Erwan Bouchareb
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Sarah Dallel
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
- Service d’Endocrinologie, Diabétologie et Maladies Métaboliques, CHU Clermont Ferrand, Hôpital Gabriel Montpied, 63003 Clermont-Ferrand, France
| | - Angélique De Haze
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Christelle Damon-Soubeyrand
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Yoan Renaud
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Elissa Baabdaty
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Marine Vialat
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Julien Fabre
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Pierre Pouchin
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Cyrille De Joussineau
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Françoise Degoul
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Swapnil Sanmukh
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Juliette Gendronneau
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Phelipe Sanchez
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Céline Gonthier-Gueret
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Amalia Trousson
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Laurent Morel
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Jean Marc Lobaccaro
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Ayhan Kocer
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
| | - Silvère Baron
- iGReD, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France; (E.B.); (S.D.); (C.D.-S.); (Y.R.); (E.B.); (M.V.); (J.F.); (P.P.); (C.D.J.); (F.D.); (S.S.); (J.G.); (P.S.); (C.G.-G.); (A.T.); (L.M.); (J.M.L.)
- Groupe Cancer Clermont Auvergne, 28, Place Henri Dunant, BP38, 63001 Clermont-Ferrand, France
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Billi M, De Marinis E, Gentile M, Nervi C, Grignani F. Nuclear miRNAs: Gene Regulation Activities. Int J Mol Sci 2024; 25:6066. [PMID: 38892257 PMCID: PMC11172810 DOI: 10.3390/ijms25116066] [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: 04/22/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which contribute to the regulation of many physiological and pathological processes. Conventionally, miRNAs perform their activity in the cytoplasm where they regulate gene expression by interacting in a sequence-specific manner with mature messenger RNAs. Recent studies point to the presence of mature miRNAs in the nucleus. This review summarizes current findings regarding the molecular activities of nuclear miRNAs. These molecules can regulate gene expression at the transcriptional level by directly binding DNA on the promoter or the enhancer of regulated genes. miRNAs recruit different protein complexes to these regions, resulting in activation or repression of transcription, through a number of molecular mechanisms. Hematopoiesis is presented as a paradigmatic biological process whereby nuclear miRNAs possess a relevant regulatory role. Nuclear miRNAs can influence gene expression by affecting nuclear mRNA processing and by regulating pri-miRNA maturation, thus impacting the biogenesis of miRNAs themselves. Overall, nuclear miRNAs are biologically active molecules that can be critical for the fine tuning of gene expression and deserve further studies in a number of physiological and pathological conditions.
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Affiliation(s)
- Monia Billi
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
| | - Elisabetta De Marinis
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Martina Gentile
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Clara Nervi
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Francesco Grignani
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
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Anderson EM, Anderson SK. Economy of Effort or Sophisticated Programming? The Prevalence of Bidirectional Promoter Complexes in the Human Genome. Genes (Basel) 2024; 15:252. [PMID: 38397241 PMCID: PMC10887517 DOI: 10.3390/genes15020252] [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: 01/28/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
An abundance of antisense promoters in the vicinity of the transcriptional start site of coding genes suggests that they play an important role in gene regulation. The divergent transcription of housekeeping genes by a common central promoter region allows for coordinated regulation of genes in related pathways and is also linked to higher promoter activity. However, closely positioned transcription start sites can also result in competition between overlapping promoter elements and generate a binary switch element. Furthermore, the direct competition resulting from the presence of an antisense promoter immediately downstream of the transcription start site of the gene produces an element that can exist in only one of two stable transcriptional states: sense or antisense. In this review, we summarize analyses of the prevalence of antisense transcription in higher eukaryotes and viruses, with a focus on the antisense promoters competing with the promoters of coding genes. The structures of bidirectional promoters driving the simultaneous expression of housekeeping genes are compared with examples of human bidirectional elements that have been shown to act as switches. Since many bidirectional elements contain a noncoding RNA as the divergent transcript, we describe examples of functional noncoding antisense transcripts that affect the epigenetic landscape and alter the expression of their host gene. Finally, we discuss opportunities for additional research on competing sense/antisense promoters, uncovering their potential role in programming cell differentiation.
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Affiliation(s)
- Erik M Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Stephen K Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Kalita B, Sahu S, Bharadwaj A, Panneerselvam L, Martinez-Cebrian G, Agarwal M, Mathew SJ. The Wnt-pathway corepressor TLE3 interacts with the histone methyltransferase KMT1A to inhibit differentiation in Rhabdomyosarcoma. Oncogene 2024; 43:524-538. [PMID: 38177411 DOI: 10.1038/s41388-023-02911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Rhabdomyosarcoma tumor cells resemble differentiating skeletal muscle cells, which unlike normal muscle cells, fail to undergo terminal differentiation, underlying their proliferative and metastatic properties. We identify the corepressor TLE3 as a key regulator of rhabdomyosarcoma tumorigenesis by inhibiting the Wnt-pathway. Loss of TLE3 function leads to Wnt-pathway activation, reduced proliferation, decreased migration, and enhanced differentiation in rhabdomyosarcoma cells. Muscle-specific TLE3-knockout results in enhanced expression of terminal myogenic differentiation markers during normal mouse development. TLE3-knockout rhabdomyosarcoma cell xenografts result in significantly smaller tumors characterized by reduced proliferation, increased apoptosis and enhanced differentiation. We demonstrate that TLE3 interacts with and recruits the histone methyltransferase KMT1A, leading to repression of target gene activation and inhibition of differentiation in rhabdomyosarcoma. A combination drug therapy regime to promote Wnt-pathway activation by the small molecule BIO and inhibit KMT1A by the drug chaetocin led to significantly reduced tumor volume, decreased proliferation, increased expression of differentiation markers and increased survival in rhabdomyosarcoma tumor-bearing mice. Thus, TLE3, the Wnt-pathway and KMT1A are excellent drug targets which can be exploited for treating rhabdomyosarcoma tumors.
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Affiliation(s)
- Bhargab Kalita
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Subhashni Sahu
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Anushree Bharadwaj
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Lakshmikanthan Panneerselvam
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | | | - Megha Agarwal
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sam J Mathew
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India.
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Gilyazova I, Gimalova G, Nizamova A, Galimova E, Ishbulatova E, Pavlov V, Khusnutdinova E. Non-Coding RNAs as Key Regulators in Lung Cancer. Int J Mol Sci 2023; 25:560. [PMID: 38203731 PMCID: PMC10778604 DOI: 10.3390/ijms25010560] [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: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
For several decades, most lung cancer investigations have focused on the search for mutations in candidate genes; however, in the last decade, due to the fact that most of the human genome is occupied by sequences that do not code for proteins, much attention has been paid to non-coding RNAs (ncRNAs) that perform regulatory functions. In this review, we principally focused on recent studies of the function, regulatory mechanisms, and therapeutic potential of ncRNAs including microRNA (miRNA), long ncRNA (lncRNA), and circular RNA (circRNA) in different types of lung cancer.
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Affiliation(s)
- Irina Gilyazova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Galiya Gimalova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Aigul Nizamova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
| | - Elmira Galimova
- Department of Pathological Physiology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Ekaterina Ishbulatova
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Department of Urology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
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Sharma S, Pisignano G, Merulla J, Catapano CV, Varani G. A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript. Nucleic Acids Res 2022; 50:11331-11343. [PMID: 36243981 DOI: 10.1093/nar/gkac875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Transcription of E-cadherin, a tumor suppressor that plays critical roles in cell adhesion and the epithelial-mesenchymal transition, is regulated by a promoter-associated non-coding RNA (paRNA). The sense-oriented paRNA (S-paRNA) includes a functional C/A single nucleotide polymorphism (SNP rs16260). The A-allele leads to decreased transcriptional activity and increased prostate cancer risk. The polymorphic site is known to affect binding of a microRNA-guided Argonaute 1 (AGO1) complex and recruitment of chromatin-modifying enzymes to silence the promoter. Yet the SNP is distant from the microRNA-AGO1 binding domain in both primary sequence and secondary structure, raising the question of how regulation occurs. Here we report the 3D NMR structure of the 104-nucleotide domain of the S-paRNA that encompasses the SNP and the microRNA-binding site. We show that the A to C change alters the locally dynamic and metastable structure of the S-paRNA, revealing how the single nucleotide mutation regulates the E-cadherin promoter through its effect on the non-coding RNA structure.
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Affiliation(s)
- Shrikant Sharma
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | | | - Jessica Merulla
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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Conformational effects of a cancer-linked mutation in pri-miR-30c RNA. J Mol Biol 2022; 434:167705. [PMID: 35760371 DOI: 10.1016/j.jmb.2022.167705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that mediate post-transcriptional downregulation of specific target genes. These transcripts are the products of a two-step processing pathway; primary miRNAs (pri-miRNAs) are processed by Drosha into individual precursor miRNA (pre-miRNA) hairpins, which are subsequently processed by Dicer into mature miRNAs. Single nucleotide polymorphisms (SNPs) that occur in pri-miRNAs, pre-miRNAs and mature miRNAs have been shown to affect the processing of specific target genes by modulating Drosha and Dicer processing or interactions with RNA binding proteins (RBPs). Using NMR and single-molecule optical tweezer experiments, we have investigated the conformational effects of a cancer-linked G/A mutation in the terminal loop of pri-miR-30c RNA, and how this influences binding by the SRSF3 and hnRNP A1 RBPs, which are implicated in its processing. Our results reveal that the wildtype and G/A variant pri-miR-30c RNAs adopt very similar elongated stem-loop structures, both of which are bound by SRSF3. However, while both wildtype and G/A pri-miR-30c RNAs can form dimeric kissing hairpin structures, the G to A mutation results in partial destabilization of the dimer in the variant transcript. This promotes recognition and binding by hnRNP A1, an RBP that enhances pri-miR-30c processing. Our data provide structural insight into the conformational effects of a G/A mutation in pri-miR-30c RNA and how this could affect processing and promote cancer.
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8
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Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther 2022; 7:121. [PMID: 35418578 PMCID: PMC9008121 DOI: 10.1038/s41392-022-00975-3] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
It is now well known that non-coding RNAs (ncRNAs), rather than protein-coding transcripts, are the preponderant RNA transcripts. NcRNAs, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Despite recent discoveries in cancer therapy, resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy continue to be a major setback. Recent studies have shown that ncRNAs also play a major role in resistance to different cancer therapies by rewiring essential signaling pathways. In this review, we present the intricate mechanisms through which dysregulated ncRNAs control resistance to the four major types of cancer therapies. We will focus on the current clinical implications of ncRNAs as biomarkers to predict treatment response (intrinsic resistance) and to detect resistance to therapy after the start of treatment (acquired resistance). Furthermore, we will present the potential of targeting ncRNA to overcome cancer treatment resistance, and we will discuss the challenges of ncRNA-targeted therapy—especially the development of delivery systems.
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9
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HER2-CDH1 Interaction via Wnt/B-Catenin Is Associated with Patients' Survival in HER2-Positive Metastatic Gastric Adenocarcinoma. Cancers (Basel) 2022; 14:cancers14051266. [PMID: 35267574 PMCID: PMC8909509 DOI: 10.3390/cancers14051266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary A deeper understanding of the molecular mechanisms involved in gastric cacner (GC) pathologenesis would help the identification of prognostic biomarkers and the development of new treatments. Human epidermal growth factor receptor 2 (HER2/ErbB2), a membrane-bound receptor of the EGFR family, may be overexpressed in GC. Trastuzumab is a HER2 inhibitor used to treat HER2+ metastatic gastric cancer (mGC). The present study aims to investigate the relationship between CDH1 mRNA expression and HER2-positivity in mGC using a multiplexed gene expression profile in two series of GC patients: 38 HER2+ and HER2- mGC and 36 HER2- GC with and without metastasis. Our results revealed the relationship between CDH1 and HER2 mRNA expression in mGC via the canonical WNT/β-catenin pathway and identified EGF as an independent prognostic biomarker for survival. Abstract Trastuzumab is a human epidermal growth factor receptor 2 (HER2) inhibitor used to treat HER2+ metastatic gastric cancer (mGC). The present study aims to investigate the relationship between CDH1 mRNA expression and HER2-positivity in mGC using a multiplexed gene expression profile in two series of gastric cancer (GC): Series 1 (n = 38): HER2+ and HER2- mGC; Series 2 (n = 36) HER2- GC with and without metastasis. To confirm the results, the same expression profiles were analyzed in 354 GC from The Cancer Genome Atlas (TCGA) dataset. The difference in gene expression connected HER2 overexpression with canonical wingless-type (Wnt)/β-catenin pathway and immunohistochemical (IHC) expression loss of E-cadherin (E-CAD). CDH1 mRNA expression was simultaneously associated with the rs16260-A variant and an increase in E-CAD expression. Differences in retinoic acid receptor alfa (RARA), RPL19 (coding for the 60S ribosomal L19 protein), catenin delta 1 (CTNND1), and epidermal growth factor (EGF) mRNA levels—all included in the Wnt/β-catenin pathway—were found associated with overall survival (OS). RARA, CTNND1, and EGF resulted in independent OS prognostic factors. EGF was confirmed as an independent factor along with TNM stage in HER2-overpressed mGC from TCGA collection. Our study highlighted factors involved in the WNT/β-catenin pathway that interconnected E-CAD with HER2 overexpression and patient survival.
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10
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A novel promoter-associated non-coding small RNA paGLI1 recruits FUS/P65 to transactivate GLI1 gene expression and promotes infiltrating glioma progression. Cancer Lett 2022; 530:68-84. [DOI: 10.1016/j.canlet.2022.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/29/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022]
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11
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Zhang X, Ping P, Hutvagner G, Blumenstein M, Li J. Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach. Nucleic Acids Res 2021; 49:e106. [PMID: 34291293 PMCID: PMC8631080 DOI: 10.1093/nar/gkab610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/21/2022] Open
Abstract
Raw sequencing reads of miRNAs contain machine-made substitution errors, or even insertions and deletions (indels). Although the error rate can be low at 0.1%, precise rectification of these errors is critically important because isoform variation analysis at single-base resolution such as novel isomiR discovery, editing events understanding, differential expression analysis, or tissue-specific isoform identification is very sensitive to base positions and copy counts of the reads. Existing error correction methods do not work for miRNA sequencing data attributed to miRNAs’ length and per-read-coverage properties distinct from DNA or mRNA sequencing reads. We present a novel lattice structure combining kmers, (k – 1)mers and (k + 1)mers to address this problem. The method is particularly effective for the correction of indel errors. Extensive tests on datasets having known ground truth of errors demonstrate that the method is able to remove almost all of the errors, without introducing any new error, to improve the data quality from every-50-reads containing one error to every-1300-reads containing one error. Studies on experimental miRNA sequencing datasets show that the errors are often rectified at the 5′ ends and the seed regions of the reads, and that there are remarkable changes after the correction in miRNA isoform abundance, volume of singleton reads, overall entropy, isomiR families, tissue-specific miRNAs, and rare-miRNA quantities.
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Affiliation(s)
- Xuan Zhang
- Data Science Institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Pengyao Ping
- Data Science Institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Michael Blumenstein
- Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Jinyan Li
- To whom correspondence should be addressed. Tel: +61 295149264; Fax: +61 295149264;
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12
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Xing Y, Wang Z, Lu Z, Xia J, Xie Z, Jiao M, Liu R, Chu Y. MicroRNAs: immune modulators in cancer immunotherapy. IMMUNOTHERAPY ADVANCES 2021; 1:ltab006. [PMID: 35919742 PMCID: PMC9327120 DOI: 10.1093/immadv/ltab006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/18/2021] [Accepted: 05/07/2021] [Indexed: 12/27/2022] Open
Abstract
Summary
MicroRNA (miRNA) is a class of endogenous small non-coding RNA of 18–25 nucleotides and plays regulatory roles in both physiological and pathological processes. Emerging evidence support that miRNAs function as immune modulators in tumors. MiRNAs as tumor suppressors or oncogenes are also found to be able to modulate anti-tumor immunity or link the crosstalk between tumor cells and immune cells surrounding. Based on the specific regulating function, miRNAs can be used as predictive, prognostic biomarkers, and therapeutic targets in immunotherapy. Here, we review new findings about the role of miRNAs in modulating immune responses, as well as discuss mechanisms underlying their dysregulation, and their clinical potentials as indicators of tumor prognosis or to sensitize cancer immunotherapy.
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Affiliation(s)
- Yun Xing
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Zhiqiang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Zhou Lu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Jie Xia
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Zhangjuan Xie
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Mengxia Jiao
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Ronghua Liu
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Yiwei Chu
- Shanghai Fifth People’s Hospital and Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
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He P, Zhang C, Chen G, Shen S. Loss of lncRNA SNHG8 promotes epithelial-mesenchymal transition by destabilizing CDH1 mRNA. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1858-1867. [PMID: 33754289 DOI: 10.1007/s11427-020-1895-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 10/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are widely involved in a variety of biological processes, including epithelial-mesenchymal transition (EMT). In the current study, we found that lncRNA small nucleolar RNA host gene 8 (SNHG8) was tightly correlated with EMT-associated gene signatures, and was down-regulated by Zinc finger E-box-binding homeobox 1 (ZEB1) during EMT progress. Functionally, knockdown of SNHG8 induced EMT in epithelial cells, through destabilizing the CDH1 mRNA dependent on a 17-nucleotide sequence shared by SNHG8 and CDH1. In addition, analysis with public database showed that SNHG8 tended to be down-regulated in different cancer types and the lower expression of SNHG8 predicted poorer prognosis. Taken together, our study reports a ZEB1-repressed lncRNA SNHG8 which is important for stabilizing CDH1 mRNA, thereby maintaining the epithelial status of epithelial cells.
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Affiliation(s)
- Ping He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoqiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shaoming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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14
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The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder. J Pers Med 2021; 11:jpm11030167. [PMID: 33804455 PMCID: PMC7999864 DOI: 10.3390/jpm11030167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Recent studies imply that there is a tight association between epigenetics and a molecular mechanism of major depressive disorder (MDD). Epigenetic modifications, i.e., DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA), are able to influence the severity of the disease and the outcome of the therapy. This article summarizes the most recent literature data on this topic, i.e., usage of histone deacetylases as therapeutic agents with an antidepressant effect and miRNAs or lncRNAs as markers of depression. Due to the noteworthy potential of the role of epigenetics in MDD diagnostics and therapy, we have gathered the most relevant data in this area.
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15
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Emerging Contribution of PancRNAs in Cancer. Cancers (Basel) 2020; 12:cancers12082035. [PMID: 32722129 PMCID: PMC7464463 DOI: 10.3390/cancers12082035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
“Cancer” includes a heterogeneous group of diseases characterized by abnormal growth beyond natural boundaries. Neoplastic transformation of cells is orchestrated by multiple molecular players, including oncogenic transcription factors, epigenetic modifiers, RNA binding proteins, and coding and noncoding transcripts. The use of computational methods for global and quantitative analysis of RNA processing regulation provides new insights into the genomic and epigenomic features of the cancer transcriptome. In particular, noncoding RNAs are emerging as key molecular players in oncogenesis. Among them, the promoter-associated noncoding RNAs (pancRNAs) are noncoding transcripts acting in cis to regulate their host genes, including tumor suppressors and oncogenes. In this review, we will illustrate the role played by pancRNAs in cancer biology and will discuss the latest findings that connect pancRNAs with cancer risk and progression. The molecular mechanisms involved in the function of pancRNAs may open the path to novel therapeutic opportunities, thus expanding the repertoire of targets to be tested as anticancer agents in the near future.
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16
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Mapelli SN, Napoli S, Pisignano G, Garcia-Escudero R, Carbone GM, Catapano CV. Deciphering the complexity of human non-coding promoter-proximal transcriptome. Bioinformatics 2020; 35:2529-2534. [PMID: 30535182 PMCID: PMC6662291 DOI: 10.1093/bioinformatics/bty981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/08/2018] [Accepted: 12/07/2018] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION Long non-coding RNAs (lncRNAs) have gained increasing relevance in epigenetic regulation and nuclear functional organization. High-throughput sequencing approaches have revealed frequent non-coding transcription in promoter-proximal regions. However, a comprehensive catalogue of promoter-associated RNAs (paRNAs) and an analysis of the possible interactions with neighboring genes and genomic regulatory elements are missing. RESULTS Integrating data from multiple cell types and experimental platforms we identified thousands of paRNAs in the human genome. paRNAs are transcribed in both sense and antisense orientation, are mostly non-polyadenylated and retained in the cell nucleus. Transcriptional regulators, epigenetic effectors and activating chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of both active promoters and enhancers. Promoters with paRNAs reside preferentially at chromatin loop boundaries, suggesting an involvement in anchor site recognition and chromatin looping. Importantly, these features are independent of the transcriptional state of neighboring genes. Thus, paRNAs may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. This study provides a comprehensive analysis of the promoter-proximal transcriptome and offers novel insights into the roles of paRNAs in epigenetic processes and human diseases. AVAILABILITY AND IMPLEMENTATION Genomic coordinates of predicted paRNAs are available at https://figshare.com: https://doi.org/10.6084/m9.figshare.7392791.v1 and https://doi.org/10.6084/m9.figshare.4856630.v2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sarah N Mapelli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sara Napoli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Giuseppina Pisignano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Ramon Garcia-Escudero
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Molecular Oncology Unit-CIEMAT and Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Giuseppina M Carbone
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Carlo V Catapano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne1066, Switzerland
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17
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Chellini L, Frezza V, Paronetto MP. Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:51. [PMID: 32183847 PMCID: PMC7079525 DOI: 10.1186/s13046-020-01552-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
In-depth analysis of global RNA sequencing has enabled a comprehensive overview of cellular transcriptomes and revealed the pervasive transcription of divergent RNAs from promoter regions across eukaryotic genomes. These studies disclosed that genomes encode a vast repertoire of RNAs beyond the well-known protein-coding messenger RNAs. Furthermore, they have provided novel insights into the regulation of eukaryotic epigenomes, and transcriptomes, including the identification of novel classes of noncoding transcripts, such as the promoter-associated noncoding RNAs (pancRNAs). PancRNAs are defined as transcripts transcribed within few hundred bases from the transcription start sites (TSSs) of protein-coding or non-coding genes. Unlike the long trans-acting ncRNAs that regulate expression of target genes located in different chromosomal domains and displaying their function both in the nucleus and in the cytoplasm, the pancRNAs operate as cis-acting elements in the transcriptional regulation of neighboring genes. PancRNAs are very recently emerging as key players in the epigenetic regulation of gene expression programs in development and diseases. Herein, we review the complex epigenetic network driven by pancRNAs in eukaryotic cells, their impact on physiological and pathological states, which render them promising targets for novel therapeutic strategies.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy. .,Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
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18
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Smith KN, Miller SC, Varani G, Calabrese JM, Magnuson T. Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. Genetics 2019; 213:1093-1110. [PMID: 31796550 PMCID: PMC6893379 DOI: 10.1534/genetics.119.302661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lineage specification in early development is the basis for the exquisitely precise body plan of multicellular organisms. It is therefore critical to understand cell fate decisions in early development. Moreover, for regenerative medicine, the accurate specification of cell types to replace damaged/diseased tissue is strongly dependent on identifying determinants of cell identity. Long noncoding RNAs (lncRNAs) have been shown to regulate cellular plasticity, including pluripotency establishment and maintenance, differentiation and development, yet broad phenotypic analysis and the mechanistic basis of their function remains lacking. As components of molecular condensates, lncRNAs interact with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. With functions ranging from controlling alternative splicing of mRNAs, to providing scaffolding upon which chromatin modifiers are assembled, it is clear that at least a subset of lncRNAs are far from the transcriptional noise they were once deemed. This review highlights the diversity of lncRNA interactions in the context of cell fate specification, and provides examples of each type of interaction in relevant developmental contexts. Also highlighted are experimental and computational approaches to study lncRNAs.
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Affiliation(s)
- Keriayn N Smith
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah C Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
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19
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Ramnarine VR, Kobelev M, Gibb EA, Nouri M, Lin D, Wang Y, Buttyan R, Davicioni E, Zoubeidi A, Collins CC. The evolution of long noncoding RNA acceptance in prostate cancer initiation, progression, and its clinical utility in disease management. Eur Urol 2019; 76:546-559. [PMID: 31445843 DOI: 10.1016/j.eururo.2019.07.040] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/26/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT It is increasingly evident that non-protein-coding regions of the genome can give rise to transcripts that form functional layers of the cancer genome. One of most abundant classes in these regions is long noncoding RNAs (lncRNAs). They have gained increasing attention in prostate cancer (PCa) and paved the way for a greater understanding of these cryptic regulators in cancer. OBJECTIVE To review current research exploring the functional biology of lncRNAs in PCa over the past three decades. EVIDENCE ACQUISITION A systematic review was performed using PubMed to search for reports with terms "long noncoding RNA", "prostate", and "cancer" over the past 30 yr (1988-2018). EVIDENCE SYNTHESIS We comprehensively surveyed the literature collected and summarise experiments leading to the characterisation of lncRNAs in PCa. A historical timeline of lncRNA identification is described, where each lncRNA is categorised mechanistically and within the primary areas of carcinogenesis: tumour risk and initiation, tumour promotion, tumour suppression, and tumour treatment resistance. We describe select lncRNAs that exemplify these areas. We also review whether these lncRNAs have a clinical utility in PCa diagnosis, prognosis, and prediction, and as therapeutic targets. CONCLUSIONS The biology of lncRNA is multifaceted, demonstrating a complex array of molecular and cellular functions. These studies reveal that lncRNAs are involved in every stage of PCa. Their clinical utility for diagnosis, prognosis, and prediction of PCa is well supported, but further evaluation for their therapeutic candidacy is needed. We provide a detailed resource and view inside the lncRNA landscape for other cancer biologists, oncologists, and clinicians. PATIENT SUMMARY In this study, we review current knowledge of the non-protein-coding genome in prostate cancer (PCa). We conclude that many of these regions are functional and a source of accurate biomarkers in PCa. With a strong research foundation, they hold promise as future therapeutic targets, yet clinical trials are necessary to determine their intrinsic value to PCa disease management.
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Affiliation(s)
- Varune Rohan Ramnarine
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Maxim Kobelev
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ewan A Gibb
- Decipher Biosciences Inc., Vancouver, BC, Canada
| | - Mannan Nouri
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Ralph Buttyan
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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Du X, Guo J, Cao QY, Yao W, Li QF. A haplotype variant of Hu sheep follicle-stimulating hormone receptor promoter region decreases transcriptional activity. Anim Genet 2019; 50:407-411. [PMID: 31094009 DOI: 10.1111/age.12794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
In sheep, increased expression of the follicle-stimulating hormone receptor (FSHR) in the ovary is a common feature of ewes that carry the prolific allele. In this study, we demonstrated that polymorphisms in the core promoter of the FSHR gene are associated with the reproductive performance of Hu sheep and are involved in the transcriptional activity of FSHR. An approximately 1.5-kb region of the 5' flanking sequence of the Hu sheep FSHR gene was isolated and characterized, and its core promoter was located in the 5' regulatory region, from nucleotides -580 to -342. Four variants (c.-518T>C, c.-466C>T, c.-414A>G and c.-365C>T) were detected in this region, and six genotypes and three haplotypes were found in the Hu sheep population (n = 245). An association analysis revealed that these polymorphisms are associated with the litter size of Hu ewes. Furthermore, a luciferase assay showed that the T-C-A-C- and C-T-G-T-type core promoters have higher transcriptional activity than does the T-C-G-C type. Notably, the putative binding site for the transcription factor Yin Yang 1 (YY1) was present at the A allele of nucleotide -414, but YY1 can significantly increase the transcriptional activity of the FSHR core promoter, which contains three different haplotypes. Taken together, our results establish that these variants might be involved in regulating the transcriptional activity of FSHR and litter size in Hu ewes and may provide a novel candidate marker for marker-assisted selection in sheep breeding.
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Affiliation(s)
- X Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - J Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Q Y Cao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - W Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Q F Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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21
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Shi Y, Jiang Y, Cao J, Yang W, Zhang J, Meng F, Zhong Z. Boosting RNAi therapy for orthotopic glioblastoma with nontoxic brain-targeting chimaeric polymersomes. J Control Release 2018; 292:163-171. [PMID: 30408555 DOI: 10.1016/j.jconrel.2018.10.034] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/20/2018] [Accepted: 10/30/2018] [Indexed: 12/30/2022]
Abstract
Glioblastoma with intracranial infiltrative growth remains an incurable disease mainly owing to existence of blood brain barrier (BBB) and off-target drug toxicity. RNA interference (RNAi) with a high specificity and low toxicity emerges as a new treatment modality for glioblastoma. The clinical application of RNAi technology is, however, hampered by the absence of safe and brain-targeting transfection agents. Here, we report on angiopep-2 peptide-decorated chimaeric polymersomes (ANG-CP) as a nontoxic and brain-targeting non-viral vector to boost the RNAi therapy for human glioblastoma in vivo. ANG-CP shows excellent packaging and protection of anti-PLK1 siRNA (siPLK1) in its lumen while quickly releasing payloads in a cytoplasmic reductive environment. Notably, in vitro experiments demonstrate that ANG-CP can effectively permeate the bEnd.3 monolayer, transport siRNA into the cytosol of U-87 MG glioblastoma cells via the LRP-1-mediated pathway, and significantly silence PLK1 mRNA and corresponding oncoprotein in U-87 MG cells. ANG-CP greatly prolongs the siPLK1 circulation time and enhances its accumulation in glioblastoma. RNAi with siPLK1 induces a strong anti-glioblastoma effect and significantly improves the survival time of glioblastoma carrying mice.
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Affiliation(s)
- Yanan Shi
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China
| | - Yu Jiang
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China
| | - Jinsong Cao
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China
| | - Weijing Yang
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China
| | - Jian Zhang
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China.
| | - Fenghua Meng
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China
| | - Zhiyuan Zhong
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, PR China.
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22
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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23
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Liu H, Lei C, He Q, Pan Z, Xiao D, Tao Y. Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer. Mol Cancer 2018; 17:64. [PMID: 29471827 PMCID: PMC5822656 DOI: 10.1186/s12943-018-0765-5] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain approximately 22 nucleotides. They serve as key regulators in various biological processes and their dysregulation is implicated in many diseases including cancer and autoimmune disorders. It has been well established that the maturation of miRNAs occurs in the cytoplasm and miRNAs exert post-transcriptional gene silencing (PTGS) via RNA-induced silencing complex (RISC) pathway in the cytoplasm. However, numerous studies reaffirm the existence of mature miRNA in the nucleus, and nucleus-cytoplasm transport mechanism has also been illustrated. Moreover, active regulatory functions of nuclear miRNAs were found including PTGS, transcriptional gene silencing (TGS), and transcriptional gene activation (TGA), in which miRNAs bind nascent RNA transcripts, gene promoter regions or enhancer regions and exert further effects via epigenetic pathways. Based on existing interaction rules, some miRNA binding sites prediction software tools are developed, which are evaluated in this article. In addition, we attempt to explore and review the nuclear functions of miRNA in immunity, tumorigenesis and invasiveness of tumor. As a non-canonical aspect of miRNA action, nuclear miRNAs supplement miRNA regulatory networks and could be applied in miRNA based therapies.
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Affiliation(s)
- Hongyu Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Cheng Lei
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Qin He
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Zou Pan
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China.
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
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24
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Magnani E, Macchi F, Mancini M, Lomazzi V, Cogliati S, Pistore C, Mandruzzato M, Dock-Bregeon AC, Bonapace IM. UHRF1 regulates CDH1 via promoter associated non-coding RNAs in prostate cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:258-270. [PMID: 29466696 DOI: 10.1016/j.bbagrm.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/01/2018] [Accepted: 02/15/2018] [Indexed: 01/07/2023]
Abstract
Non-coding RNAs (ncRNAs) transcribed from the promoter and the downstream region can affect the expression of the corresponding coding genes. It has been shown that sense-directed ncRNAs arising from the promoter region of the E-cadherin gene (CDH1) mediate its repression. Here, we show that an antisense-directed ncRNA (paRCDH1-AS) transcribed from the CDH1 promoter is necessary for its expression. paRCDH1-AS acts as a hooking scaffold by recruiting the epigenetic regulators, UHRF1, DNMT3A, SUV39H1 and SUZ12, involved in CDH1 repression. The binding of epigenetic regulators to paCRDH1-AS, indeed, prevents their localization to the chromatin on CDH1 promoter. Moreover, paRCDH1-AS silencing induces CDH1 repression and a switch of the epigenetic profile on the promoter towards a more closed chromatin. Using bioinformatic and experimental approaches we defined that the promoter of the paRCDH1-AS is shared with the E-cadherin gene, showing a bidirectional promoter activity. We found that UHRF1 controls both CDH1 and paRCDH1-AS by directly binding this bidirectional promoter region. Our study provides evidences, for the first time, that UHRF1 recruitment can be affected by promoter-associated non-coding RNAs, opening new perspective regarding the role of UHRF1 in these complex regulatory networks.
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Affiliation(s)
- Elena Magnani
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Filippo Macchi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Vanessa Lomazzi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Sara Cogliati
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy; IGBMC, BP10142, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christian Pistore
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Martina Mandruzzato
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | | | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy.
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25
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Caggiari L, Miolo G, Buonadonna A, Basile D, Santeufemia DA, Cossu A, Palmieri G, De Zorzi M, Fornasarig M, Alessandrini L, Canzonieri V, Lo Re G, Puglisi F, Steffan A, Cannizzaro R, De Re V. Characterizing Metastatic HER2-Positive Gastric Cancer at the CDH1 Haplotype. Int J Mol Sci 2017; 19:E47. [PMID: 29295527 PMCID: PMC5795997 DOI: 10.3390/ijms19010047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023] Open
Abstract
The CDH1 gene, coding for the E-cadherin protein, is linked to gastric cancer (GC) susceptibility and tumor invasion. The human epidermal growth factor receptor 2 (HER2) is amplified and overexpressed in a portion of GC. HER2 is an established therapeutic target in metastatic GC (mGC). Trastuzumab, in combination with various chemotherapeutic agents, is a standard treatment for these tumors leading to outcome improvement. Unfortunately, the survival benefit is limited to a fraction of patients. The aim of this study was to improve knowledge of the HER2 and the E-cadherin alterations in the context of GC to characterize subtypes of patients that could better benefit from targeted therapy. An association between the P7-CDH1 haplotype, including two polymorphisms (rs16260A-rs1801552T) and a subset of HER2-positive mGC with better prognosis was observed. Results indicated the potential evaluation of CDH1 haplotypes in mGC to stratify patients that will benefit from trastuzumab-based treatments. Moreover, data may have implications to understanding the HER2 and the E-cadherin interactions in vivo and in response to treatments.
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Affiliation(s)
- Laura Caggiari
- Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Gianmaria Miolo
- Medical Oncology, IRCCS, CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Angela Buonadonna
- Medical Oncology, IRCCS, CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Debora Basile
- Medical Oncology, IRCCS, CRO National Cancer Institute, 33081 Aviano, Italy.
- Department of Medicine, School of Medical Oncology, University of Udine, 0432 Udine, Italy.
| | | | - Antonio Cossu
- Operative Unit of Pathology Department of Surgical, Microsurgical and Medical Sciences, University of Sassari, 07100 Sassari, Italy.
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, Cancer Genetics Unit, C.N.R., 07100 Sassari, Italy.
| | - Mariangela De Zorzi
- Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Mara Fornasarig
- Gastroenterology, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Lara Alessandrini
- Pathology, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | | | - Giovanni Lo Re
- Medical Oncology Department, Santa Maria degli Angeli Hospital, 33170 Pordenone, Italy.
| | - Fabio Puglisi
- Medical Oncology, IRCCS, CRO National Cancer Institute, 33081 Aviano, Italy.
- Department of Medicine, School of Medical Oncology, University of Udine, 0432 Udine, Italy.
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Renato Cannizzaro
- Gastroenterology, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Valli De Re
- Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
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26
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Napoli S, Piccinelli V, Mapelli SN, Pisignano G, Catapano CV. Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription. RNA Biol 2017; 14:1742-1755. [PMID: 28805496 PMCID: PMC5731802 DOI: 10.1080/15476286.2017.1356564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
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Affiliation(s)
- Sara Napoli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Valentina Piccinelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Sarah N Mapelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Giuseppina Pisignano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Carlo V Catapano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland.,b Department of Oncology , Faculty of Biology and Medicine, University of Lausanne , Lausanne , Switzerland
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27
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Neppl RL, Wu CL, Walsh K. lncRNA Chronos is an aging-induced inhibitor of muscle hypertrophy. J Cell Biol 2017; 216:3497-3507. [PMID: 28855249 PMCID: PMC5674882 DOI: 10.1083/jcb.201612100] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 06/28/2017] [Accepted: 08/03/2017] [Indexed: 02/07/2023] Open
Abstract
Neppl et al. identify a long noncoding RNA named Chronos whose expression increases with age and decreases in Akt-mediated growth. Inhibition of Chronos induces myofiber hypertrophy in vitro and in vivo, in part, through the epigenetic modulation of Bmp7 signaling. Skeletal muscle exhibits remarkable plasticity in its ability to modulate its mass in response to the physiologic changes associated with functional use, systemic disease, and aging. Although a gradual loss of muscle mass normally occurs with advancing age, its increasingly rapid progression results in sarcopenia in a subset of individuals. The identities of muscle-enriched, long noncoding RNAs that regulate this process are unknown. Here, we identify a long noncoding RNA, named Chronos, whose expression in muscle is positively regulated with advancing age and negatively regulated during Akt1-mediated growth. Inhibition of Chronos induces myofiber hypertrophy both in vitro and in vivo, in part, through the epigenetic modulation of Bmp7 signaling.
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Affiliation(s)
- Ronald L Neppl
- Molecular Cardiology, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA .,Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Chia-Ling Wu
- Molecular Cardiology, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA
| | - Kenneth Walsh
- Molecular Cardiology, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA
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