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Di Giorgio E, Ranzino L, Tolotto V, Dalla E, Burelli M, Gualandi N, Brancolini C. Transcription of endogenous retroviruses in senescent cells contributes to the accumulation of double-stranded RNAs that trigger an anti-viral response that reinforces senescence. Cell Death Dis 2024; 15:157. [PMID: 38383514 PMCID: PMC10882003 DOI: 10.1038/s41419-024-06548-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
An important epigenetic switch marks the onset and maintenance of senescence. This allows transcription of the genetic programs that arrest the cell cycle and alter the microenvironment. Transcription of endogenous retroviruses (ERVs) is also a consequence of this epigenetic switch. In this manuscript, we have identified a group of ERVs that are epigenetically silenced in proliferating cells but are upregulated during replicative senescence or during various forms of oncogene-induced senescence, by RAS and Akt, or after HDAC4 depletion. In a HDAC4 model of senescence, removal of the repressive histone mark H3K27me3 is the plausible mechanism that allows the transcription of intergenic ERVs during senescence. We have shown that ERVs contribute to the accumulation of dsRNAs in senescence, which can initiate the antiviral response via the IFIH1-MAVS signaling pathway and thus contribute to the maintenance of senescence. This pathway, and MAVS in particular, plays an active role in shaping the microenvironment and maintaining growth arrest, two essential features of the senescence program.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Matteo Burelli
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Nicolò Gualandi
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy.
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Di Giorgio E, Cortolezzis Y, Gualandi N, Agostini F, Rapozzi V, Xodo LE. NRF2 interacts with distal enhancer and inhibits nitric oxide synthase 2 expression in KRAS-driven pancreatic cancer cells. Biochim Biophys Acta Mol Cell Res 2024; 1871:119606. [PMID: 37852325 DOI: 10.1016/j.bbamcr.2023.119606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Nitric oxide is a pleiotropic free radical produced by three nitric oxide synthases (NOS1-3), of which inducible NOS2 is involved in tumor initiation and progression. In this study, RNA-seq, ChIP-seq and qRT-PCR experiments combined with bioinformatic analyses showed that NRF2 is a repressor of NOS2 gene by maintaining a distal enhancer located 22 kb downstream of TSS in an inactive state. Deletion of NRF2 leads to activation of the enhancer, which exerts a pioneering function before it is fully activated. Specifically, NRF2 controls the expression of NOS2 in response to intracellular oxidative stress and extracellular oxygen pressure. We found that abrogation of NOS2 expression by siRNAs partially reduced the ability of WT Panc-1 cells to form 3D spheroids, but strongly reduced the formation of 3D spheroids by NRF2-depleted Panc-1 cells. Mechanistically, this effect correlates with the finding that NOS2 and nitric oxide stimulate epithelial-to-mesenchymal transition in NRF2-depleted Panc-1 and MIA PaCa-2 cells. We also found that knockdown of NOS2 leads to blockade of 3D matrigel invasion of NRF2-depleted PDAC cells, demonstrating that a short-circuit in the reciprocal regulation of NOS2 and NRF2 attenuates the malignancy of PDAC cells. In summary, we show for the first time that: (i) NRF2 is a suppressor of NOS2 in pancreatic cancer cells; (ii) NRF2 binds to and inactivates an enhancer located 22 kb downstream of TSS of the NOS2 gene; (iii) activation of NOS2 requires suppression of NRF2; (iv) NOS2 is required for NRF2-depleted Panc-1 cells to maintain their malignancy and invasiveness.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
| | - Ylenia Cortolezzis
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Nicolò Gualandi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Francesca Agostini
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Valentina Rapozzi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Luigi E Xodo
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
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Gualandi N, Fracarossi D, Riommi D, Sollitto M, Greco S, Mardirossian M, Pacor S, Hori T, Pallavicini A, Gerdol M. Unveiling the Impact of Gene Presence/Absence Variation in Driving Inter-Individual Sequence Diversity within the CRP-I Gene Family in Mytilus spp. Genes (Basel) 2023; 14:genes14040787. [PMID: 37107545 PMCID: PMC10138031 DOI: 10.3390/genes14040787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Mussels (Mytilus spp.) tolerate infections much better than other species living in the same marine coastal environment thanks to a highly efficient innate immune system, which exploits a remarkable diversification of effector molecules involved in mucosal and humoral responses. Among these, antimicrobial peptides (AMPs) are subjected to massive gene presence/absence variation (PAV), endowing each individual with a potentially unique repertoire of defense molecules. The unavailability of a chromosome-scale assembly has so far prevented a comprehensive evaluation of the genomic arrangement of AMP-encoding loci, preventing an accurate ascertainment of the orthology/paralogy relationships among sequence variants. Here, we characterized the CRP-I gene cluster in the blue mussel Mytilus edulis, which includes about 50 paralogous genes and pseudogenes, mostly packed in a small genomic region within chromosome 5. We further reported the occurrence of widespread PAV within this family in the Mytilus species complex and provided evidence that CRP-I peptides likely adopt a knottin fold. We functionally characterized the synthetic peptide sCRP-I H1, assessing the presence of biological activities consistent with other knottins, revealing that mussel CRP-I peptides are unlikely to act as antimicrobial agents or protease inhibitors, even though they may be used as defense molecules against infections from eukaryotic parasites.
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Affiliation(s)
- Nicolò Gualandi
- Area of Neuroscience, International School for Advanced Studies, 34136 Trieste, Italy;
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Davide Fracarossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Damiano Riommi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Marco Sollitto
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Sabrina Pacor
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Tiago Hori
- Atlantic Aqua Farms Ltd., Vernon Bridge, PE C0A 2E0, Canada;
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Anton Dohrn Zoological Station, 80121 Naples, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Correspondence:
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Esposito M, Gualandi N, Spirito G, Ansaloni F, Gustincich S, Sanges R. Transposons Acting as Competitive Endogenous RNAs: In-Silico Evidence from Datasets Characterised by L1 Overexpression. Biomedicines 2022; 10:biomedicines10123279. [PMID: 36552034 PMCID: PMC9776036 DOI: 10.3390/biomedicines10123279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
LINE L1 are transposable elements that can replicate within the genome by passing through RNA intermediates. The vast majority of these element copies in the human genome are inactive and just between 100 and 150 copies are still able to mobilize. During evolution, they could have been positively selected for beneficial cellular functions. Nonetheless, L1 deregulation can be detrimental to the cell, causing diseases such as cancer. The activity of miRNAs represents a fundamental mechanism for controlling transcript levels in somatic cells. These are a class of small non-coding RNAs that cause degradation or translational inhibition of their target transcripts. Beyond this, competitive endogenous RNAs (ceRNAs), mostly made by circular and non-coding RNAs, have been seen to compete for the binding of the same set of miRNAs targeting protein coding genes. In this study, we have investigated whether autonomously transcribed L1s may act as ceRNAs by analyzing public dataset in-silico. We observed that genes sharing miRNA target sites with L1 have a tendency to be upregulated when L1 are overexpressed, suggesting the possibility that L1 might act as ceRNAs. This finding will help in the interpretation of transcriptomic responses in contexts characterized by the specific activation of transposons.
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Affiliation(s)
- Mauro Esposito
- Computational Genomics Laboratory, Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Nicolò Gualandi
- Computational Genomics Laboratory, Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Giovanni Spirito
- Computational Genomics Laboratory, Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- CMP3vda, via Lavoratori Vittime del Col Du Mont 28, 11100 Aosta, Italy
| | - Federico Ansaloni
- Computational Genomics Laboratory, Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia, 16132 Genova, Italy
| | - Stefano Gustincich
- CMP3vda, via Lavoratori Vittime del Col Du Mont 28, 11100 Aosta, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia, 16132 Genova, Italy
| | - Remo Sanges
- Computational Genomics Laboratory, Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia, 16132 Genova, Italy
- Correspondence:
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Ansaloni F, Gualandi N, Esposito M, Gustincich S, Sanges R. TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. Bioinformatics 2022; 38:4430-4433. [PMID: 35876845 PMCID: PMC9477521 DOI: 10.1093/bioinformatics/btac526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. AVAILABILITY AND IMPLEMENTATION The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Nicolò Gualandi
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | - Mauro Esposito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | | | - Remo Sanges
- To whom correspondence should be addressed. or
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