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Michelatti D, Beyes S, Bernardis C, Negri ML, Morelli L, Bediaga NG, Poli V, Fagnocchi L, Lago S, D'Annunzio S, Cona N, Gaspardo I, Bianchi A, Jovetic J, Gianesello M, Turdo A, D'Accardo C, Gaggianesi M, Dori M, Forcato M, Crispatzu G, Rada-Iglesias A, Sosa MS, Timmers HTM, Bicciato S, Todaro M, Tiberi L, Zippo A. Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory. Nat Commun 2024; 15:2198. [PMID: 38503727 PMCID: PMC10951355 DOI: 10.1038/s41467-024-46524-0] [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: 01/09/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
Metastasis arises from disseminated tumour cells (DTCs) that are characterized by intrinsic phenotypic plasticity and the capability of seeding to secondary organs. DTCs can remain latent for years before giving rise to symptomatic overt metastasis. In this context, DTCs fluctuate between a quiescent and proliferative state in response to systemic and microenvironmental signals including immune-mediated surveillance. Despite its relevance, how intrinsic mechanisms sustain DTCs plasticity has not been addressed. By interrogating the epigenetic state of metastatic cells, we find that tumour progression is coupled with the activation of oncogenic enhancers that are organized in variable interconnected chromatin domains. This spatial chromatin context leads to the activation of a robust transcriptional response upon repeated exposure to retinoic acid (RA). We show that this adaptive mechanism sustains the quiescence of DTCs through the activation of the master regulator SOX9. Finally, we determine that RA-stimulated transcriptional memory increases the fitness of metastatic cells by supporting the escape of quiescent DTCs from NK-mediated immune surveillance. Overall, these findings highlight the contribution of oncogenic enhancers in establishing transcriptional memories as an adaptive mechanism to reinforce cancer dormancy and immune escape, thus amenable for therapeutic intervention.
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Negri ML, D'Annunzio S, Vitali G, Zippo A. May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions. Bioessays 2023; 45:e2300075. [PMID: 37530178 DOI: 10.1002/bies.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.
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Dalle Nogare M, D'Annunzio S, Vazza G, Regazzo D, Picello L, Denaro L, Voltan G, Scaroni C, Ceccato F, Occhi G. The Methylation Analysis of the Glucose-Dependent Insulinotropic Polypeptide Receptor (GIPR) Locus in GH-Secreting Pituitary Adenomas. Int J Mol Sci 2023; 24:ijms24119264. [PMID: 37298217 DOI: 10.3390/ijms24119264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The glucose-dependent insulinotropic polypeptide receptor (GIPR) is aberrantly expressed in about one-third of GH-secreting pituitary adenomas (GH-PAs) and has been associated with a paradoxical increase of GH after a glucose load. The reason for such an overexpression has not yet been clarified. In this work, we aimed to evaluate whether locus-specific changes in DNA methylation patterns could contribute to this phenomenon. By cloning bisulfite-sequencing PCR, we compared the methylation pattern of the GIPR locus in GIPR-positive (GIPR+) and GIPR-negative (GIPR-) GH-PAs. Then, to assess the correlation between Gipr expression and locus methylation, we induced global DNA methylation changes by treating the lactosomatotroph GH3 cells with 5-aza-2'-deoxycytidine. Differences in methylation levels were observed between GIPR+ and GIPR- GH-PAs, both within the promoter (31.9% vs. 68.2%, p < 0.05) and at two gene body regions (GB_1 20.7% vs. 9.1%; GB_2 51.2% vs. 65.8%, p < 0.05). GH3 cells treated with 5-aza-2'-deoxycytidine showed a ~75% reduction in Gipr steady-state level, possibly associated with the observed decrease in CpGs methylation. These results indicate that epigenetic regulation affects GIPR expression in GH-PAs, even though this possibly represents only a part of a much more complex regulatory mechanism.
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Scalisi S, Ahmad A, D'Annunzio S, Rousseau D, Zippo A. Quantitative Analysis of PcG-Associated Condensates by Stochastic Optical Reconstruction Microscopy (STORM). Methods Mol Biol 2023; 2655:183-200. [PMID: 37212997 DOI: 10.1007/978-1-0716-3143-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The polycomb group (PcG) proteins play a central role in the maintenance of a repressive state of gene expression. Recent findings demonstrate that PcG components are organized into nuclear condensates, contributing to the reshaping of chromatin architecture in physiological and pathological conditions, thus affecting the nuclear mechanics. In this context, direct stochastic optical reconstruction microscopy (dSTORM) provides an effective tool to achieve a detailed characterization of PcG condensates by visualizing them at a nanometric level. Furthermore, by analyzing dSTORM datasets with cluster analysis algorithms, quantitative information can be yielded regarding protein numbers, grouping, and spatial organization. Here, we describe how to set up a dSTORM experiment and perform the data analysis to study PcG complexes' components in adhesion cells quantitatively.
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Ahmad A, Sala F, Paiè P, Candeo A, D'Annunzio S, Zippo A, Frindel C, Osellame R, Bragheri F, Bassi A, Rousseau D. On the robustness of machine learning algorithms toward microfluidic distortions for cell classification via on-chip fluorescence microscopy. LAB ON A CHIP 2022; 22:3453-3463. [PMID: 35946995 DOI: 10.1039/d2lc00482h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-cell imaging and sorting are critical technologies in biology and clinical applications. The power of these technologies is increased when combined with microfluidics, fluorescence markers, and machine learning. However, this quest faces several challenges. One of these is the effect of the sample flow velocity on the classification performances. Indeed, cell flow speed affects the quality of image acquisition by increasing motion blur and decreasing the number of acquired frames per sample. We investigate how these visual distortions impact the final classification task in a real-world use-case of cancer cell screening, using a microfluidic platform in combination with light sheet fluorescence microscopy. We demonstrate, by analyzing both simulated and experimental data, that it is possible to achieve high flow speed and high accuracy in single-cell classification. We prove that it is possible to overcome the 3D slice variability of the acquired 3D volumes, by relying on their 2D sum z-projection transformation, to reach an efficient real time classification with an accuracy of 99.4% using a convolutional neural network with transfer learning from simulated data. Beyond this specific use-case, we provide a web platform to generate a synthetic dataset and to investigate the effect of flow speed on cell classification for any biological samples and a large variety of fluorescence microscopes (https://www.creatis.insa-lyon.fr/site7/en/MicroVIP).
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De Nunzio C, Cicione A, Di Giacomo F, Disabato G, Nacchia A, Gravina C, Voglino O, Franco A, Lombardo R, Rovesti L, Baldassarri V, D'Annunzio S, Turchi B, Gallo G, Stira J, Guercio A, Guarnotta G, Tubaro A. Cardiovascular adverse events-related to GnRH agonists and GnRH antagonists: Analysis of real-life data from Eudra-Vigilance database. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00290-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Franco A, Nacchia A, Disabato G, Voglino O, Baldassarri V, Lombardo R, D'Annunzio S, Cicione A, Rovesti L, Mancini E, Guarnotta G, Guercio A, Gallo G, Turchi B, Gravina C, Stira J, Tubaro A, De Nunzio C. Medications mostly associated with urinary retention: Assessment of the Eudravigilance (EV) and the Food and Drug Administration (FDA) Pharmacovigilance database entries. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00670-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lombardo R, Nacchia A, Cicione A, Turchi B, Gallo G, Guercio A, Stira J, Rovesti L, Franco A, Gravina C, Guarnotta G, Mancini E, Voglino O, Baldassarri V, D'Annunzio S, Riolo S, Tubaro A, De Nunzio C. Real-life adverse events related to PDE-5 I treatment: Analysis of the EudraVigilance database. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)01245-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Rovesti L, Nacchia A, Di Giacomo F, Disabato G, Gravina C, Gallo G, Stira J, Turchi B, Guercio A, Lombardo R, Cicione A, Voglino O, Baldassarri V, Guarnotta G, Mancini E, Franco A, D'Annunzio S, Tubaro A, De Nunzio C. Medications mostly associated with haematuria: Assessment of the EudraVigilance (EV) and Food and Drug Administration (FDA) Pharmacovigilance databases entries. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00193-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ciato D, Li R, Monteserin Garcia JL, Papst L, D'Annunzio S, Hristov M, Tichomirowa MA, Belaya Z, Rozhinskaya L, Buchfelder M, Theodoropoulou M, Paez-Pereda M, Stalla GK. Inhibition of Heat Shock Factor 1 Enhances Repressive Molecular Mechanisms on the POMC Promoter. Neuroendocrinology 2019; 109:362-373. [PMID: 30995664 DOI: 10.1159/000500200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/02/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Cushing's disease (CD) is caused by adrenocorticotropic hormone (ACTH)-secreting pituitary tumours. They express high levels of heat shock protein 90 and heat shock factor 1 (HSF1) in comparison to the normal tissue counterpart, indicating activated cellular stress. AIMS Our objectives were: (1) to correlate HSF1 expression with clinical features and hormonal/radiological findings of CD, and (2) to investigate the effects of HSF1 inhibition as a target for CD treatment. PATIENTS/METHODS We examined the expression of total and pSer326HSF1 (marker for its transcriptional activation) by Western blot on eight human CD tumours and compared to the HSF1 status of normal pituitary. We screened a cohort of 45 patients with CD for HSF1 by immunohistochemistry and correlated the HSF1 immunoreactivity score with the available clinical data. We evaluated the effects of HSF1 silencing with RNA interference and the HSF1 inhibitor KRIBB11 in AtT-20 cells and four primary cultures of human corticotroph tumours. RESULTS We show that HSF1 protein is highly expressed and transcriptionally active in CD tumours in comparison to normal pituitary. The immunoreactivity score for HSF1 did not correlate with the typical clinical features of the disease. HSF1 inhibition reduced proopiomelanocortin (Pomc) transcription in AtT-20 cells. The HSF1 inhibitor KRIBB11 suppressed ACTH synthesis from 75% of human CD tumours in primary cell culture. This inhibitory action on Pomc transcription was mediated by increased glucocorticoid receptor and suppressed Nurr77/Nurr1 and AP-1 transcriptional activities. CONCLUSIONS These data show that HSF1 regulates POMC transcription. Pharmacological targeting of HSF1 may be a promising treatment option for the control of excess ACTH secretion in CD.
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Viola S, Antonacci R, D'Annunzio S, Faricelli A, Aquilone L, Gambi D, Malatesta G. Three-dimensional transcranial Doppler in acute ischemic stroke in the territory of the middle cerebral artery: clinical and CT correlation. ITALIAN JOURNAL OF NEUROLOGICAL SCIENCES 1991; 12:545-55. [PMID: 1783532 DOI: 10.1007/bf02336950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We studied 34 patients with acute ischemic stroke in the territory of the middle cerebral artery (MCA) by three-dimensional transcranial Doppler (TCD-3D). The parameters analyzed were: mean blood flow velocity, systolic and diastolic velocities; indices of pulsatility, hemisphere asymmetry and pulsatility transmission. Of the 34 patients 11 presented marked slowing of flow velocity in the MCA on the infarct side with an asymmetry index (AI) of over 40%, 8 patients with slightly reduced flow velocity in the MCA and an AI of 25-40%, 2 patients in whom there was indirect evidence of collateral circulations in the anterior cerebral artery distribution together with slowing of MCA flow; 5 patients had stenosis of the MCA, 9 patients showed no alterations of the Doppler parameters. The correlation between neurological symptom pattern and AI was significant (r = 0.76). Noninvasive, easy to perform, performable at once and reliable, TCD-3D is a great improvement on traditional transcranial Doppler and is especially useful in assessing the hemodynamics of the cerebral circulation in ischemic stroke.
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