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Artikel ; Online: Linking Aging to Cancer: The Role of Chromatin Biology.

Corveleyn, Laura / Sen, Payel / Adams, Peter / Sidoli, Simone

The journals of gerontology. Series A, Biological sciences and medical sciences

2024

Abstract: Epigenetic changes have been established to be a hallmark of aging, which implies that aging science requires collaborating with the field of chromatin biology. DNA methylation patterns, changes in relative abundance of histone post-translational ... ...

Abstract	Epigenetic changes have been established to be a hallmark of aging, which implies that aging science requires collaborating with the field of chromatin biology. DNA methylation patterns, changes in relative abundance of histone post-translational modifications (PTMs), and chromatin remodeling are the central players in modifying chromatin structure. Aging is commonly associated with an overall increase in chromatin instability, loss of homeostasis and decondensation. However, numerous publications have highlighted that the link between aging and chromatin changes is not nearly as linear as previously expected. This complex interplay of these epigenetics elements during the lifetime of an organism likely contribute to cellular senescence, genomic instability, and disease susceptibility. Yet, the causal links between these phenomena still need to be fully unraveled. In this perspective article, we discuss potential future directions of aging chromatin biology.
Sprache	Englisch
Erscheinungsdatum	2024-05-18
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	1223643-3
ISSN	1758-535X ; 1079-5006
ISSN (online)	1758-535X
ISSN	1079-5006
DOI	10.1093/gerona/glae133
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Middle-Down MS is Ready to Answer Complex Questions in Chromatin Biology.

Sidoli, Simone

Proteomics

2018 Band 18, Heft 13, Seite(n) e1800131

Abstract: Histones are the most abundant protein family in the cells of complex organisms such as mammals and, together with DNA, they define the backbone of chromatin. Histone PTMs are key players of chromatin biology, as they function as anchors for proteins ... ...

Abstract	Histones are the most abundant protein family in the cells of complex organisms such as mammals and, together with DNA, they define the backbone of chromatin. Histone PTMs are key players of chromatin biology, as they function as anchors for proteins that bind and modulate chromatin readout, including gene expression. Middle-down mass spectrometry (MS) has been optimized for about 10 years to study histone N-terminal tails, but it has been rarely applied to identify the role of coexisting histone marks in biology. In this work, Jiang et al. used middle-down MS to study the dynamics of coexisting PTMs on histone H4 in two breast cancer cell lines. They found that overall serine 1 phosphorylation (S1ph) is mildly regulated during the cell cycle, but S1ph coexistence frequency with acetylations and methylations on the lysine residues of the N-terminal tail is remarkably tuned during S phase and G2/M phase. Together, the team placed another benchmark proving that MS analysis of combinatorial histone PTMs provides a more comprehensive view on chromatin state than studying individual marks. We should then constantly question ourselves regarding the limitations of analyzing single PTMs when we attempt to define their effect on protein functions.
Mesh-Begriff(e)	Animals ; Chromatin ; Histone Code ; Histones/genetics ; Mass Spectrometry ; Protein Processing, Post-Translational
Chemische Substanzen	Chromatin ; Histones
Sprache	Englisch
Erscheinungsdatum	2018-06-07
Erscheinungsland	Germany
Dokumenttyp	Journal Article ; Comment
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201800131
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells.

Flores, Julio C / Sidoli, Simone / Dawlaty, Meelad M

iScience

2023 Band 26, Heft 7, Seite(n) 107170

Abstract: Tet2 is a member of the Ten-eleven translocation (Tet1/2/3) family of enzymes and is expressed in embryonic stem cells (ESCs). It demethylates DNA (catalytic functions) and partners with chromatin modifiers (noncatalytic functions) to regulate genes. ... ...

Abstract	Tet2 is a member of the Ten-eleven translocation (Tet1/2/3) family of enzymes and is expressed in embryonic stem cells (ESCs). It demethylates DNA (catalytic functions) and partners with chromatin modifiers (noncatalytic functions) to regulate genes. However, the significance of these functions in ESCs is less defined. Using Tet2 catalytic mutant (
Sprache	Englisch
Erscheinungsdatum	2023-06-17
Erscheinungsland	United States
Dokumenttyp	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107170
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Ten questions to AI regarding the present and future of proteomics.

Stransky, Stephanie / Sun, Yan / Shi, Xuyan / Sidoli, Simone

Frontiers in molecular biosciences

2023 Band 10, Seite(n) 1295721

Abstract: The role of a scientist is at first not so different from a philosopher. They both need to question common thinking and evaluate whether reality is not as we always thought. Based on this, we need to design hypotheses, experiments, and analyses to prove ... ...

Abstract	The role of a scientist is at first not so different from a philosopher. They both need to question common thinking and evaluate whether reality is not as we always thought. Based on this, we need to design hypotheses, experiments, and analyses to prove our alternative vision. Artificial Intelligence (AI) is rapidly moving from an "assistant" into a proper "colleague" for literature mining, data analysis and interpretation, and literally having (almost) real scientific conversations. However, being AI based on existing information, if we rely on it excessively will we still be able to question the
Sprache	Englisch
Erscheinungsdatum	2023-11-23
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1295721
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5.

Yheskel, Matanel / Sidoli, Simone / Secombe, Julie

Epigenetics & chromatin

2023 Band 16, Heft 1, Seite(n) 8

Abstract: Background: KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to ... ...

Abstract	Background: KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. Results: Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. Conclusions: Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
Mesh-Begriff(e)	Animals ; Cell Nucleus/metabolism ; Drosophila melanogaster/genetics ; Drosophila Proteins/metabolism ; Gene Expression Regulation ; Histone Demethylases/metabolism
Chemische Substanzen	Drosophila Proteins ; Histone Demethylases (EC 1.14.11.-) ; Lid protein, Drosophila (EC 1.14.11.-)
Sprache	Englisch
Erscheinungsdatum	2023-02-18
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-023-00481-y
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: The role of histone H3 lysine demethylases in glioblastoma.

Young, Dejauwne / Guha, Chandan / Sidoli, Simone

Cancer metastasis reviews

2023 Band 42, Heft 2, Seite(n) 445–454

Abstract: Glioblastoma (GBM) is the most aggressive primary brain tumor in adults with an average survival of 15-18 months. Part of its malignancy derives from epigenetic regulation that occurs as the tumor develops and after therapeutic treatment. Specifically, ... ...

Abstract	Glioblastoma (GBM) is the most aggressive primary brain tumor in adults with an average survival of 15-18 months. Part of its malignancy derives from epigenetic regulation that occurs as the tumor develops and after therapeutic treatment. Specifically, enzymes involved in removing methylations from histone proteins on chromatin, i.e., lysine demethylases (KDMs), have a significant impact on GBM biology and reoccurrence. This knowledge has paved the way to considering KDMs as potential targets for GBM treatment. For example, increases in trimethylation of histone H3 on the lysine 9 residue (H3K9me3) via inhibition of KDM4C and KDM7A has been shown to lead to cell death in Glioblastoma initiating cells. KDM6 has been shown to drive Glioma resistance to receptor tyrosine kinase inhibitors and its inhibition decreases tumor resistance. In addition, increased expression of the histone methyltransferase MLL4 and UTX histone demethylase are associated with prolonged survival in a subset of GBM patients, potentially by regulating histone methylation on the promoter of the mgmt gene. Thus, the complexity of how histone modifiers contribute to glioblastoma pathology and disease progression is yet to be fully understood. To date, most of the current work on histone modifying enzymes in GBM are centered upon histone H3 demethylase enzymes. In this mini-review, we summarize the current knowledge on the role of histone H3 demethylase enzymes in Glioblastoma tumor biology and therapy resistance. The objective of this work is to highlight the current and future potential areas of research for GBM epigenetics therapy.
Mesh-Begriff(e)	Humans ; Histones/genetics ; Histones/metabolism ; Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Glioblastoma/genetics ; Glioblastoma/pathology ; Lysine/genetics ; Lysine/metabolism ; Epigenesis, Genetic ; Jumonji Domain-Containing Histone Demethylases/genetics ; Jumonji Domain-Containing Histone Demethylases/metabolism
Chemische Substanzen	Histones ; Histone Demethylases (EC 1.14.11.-) ; Lysine (K3Z4F929H6) ; KDM4C protein, human ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; KDM7A protein, human (EC 1.14.11.-)
Sprache	Englisch
Erscheinungsdatum	2023-06-08
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	604857-2
ISSN	1573-7233 ; 0167-7659
ISSN (online)	1573-7233
ISSN	0167-7659
DOI	10.1007/s10555-023-10114-1
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Characterization of the intracellular neurexin interactome by in vivo proximity ligation suggests its involvement in presynaptic actin assembly.

Schaan Profes, Marcos / Tiroumalechetty, Araven / Patel, Neel / Lauar, Stephanie S / Sidoli, Simone / Kurshan, Peri T

PLoS biology

2024 Band 22, Heft 1, Seite(n) e3002466

Abstract: Neurexins are highly spliced transmembrane cell adhesion molecules that bind an array of partners via their extracellular domains. However, much less is known about the signaling pathways downstream of neurexin's largely invariant intracellular domain ( ... ...

Abstract	Neurexins are highly spliced transmembrane cell adhesion molecules that bind an array of partners via their extracellular domains. However, much less is known about the signaling pathways downstream of neurexin's largely invariant intracellular domain (ICD). Caenorhabditis elegans contains a single neurexin gene that we have previously shown is required for presynaptic assembly and stabilization. To gain insight into the signaling pathways mediating neurexin's presynaptic functions, we employed a proximity ligation method, endogenously tagging neurexin's intracellular domain with the promiscuous biotin ligase TurboID, allowing us to isolate adjacent biotinylated proteins by streptavidin pull-down and mass spectrometry. We compared our experimental strain to a control strain in which neurexin, endogenously tagged with TurboID, was dispersed from presynaptic active zones by the deletion of its C-terminal PDZ-binding motif. Selection of this control strain, which differs from the experimental strain only in its synaptic localization, was critical to identifying interactions specifically occurring at synapses. Using this approach, we identified both known and novel intracellular interactors of neurexin, including active zone scaffolds, actin-binding proteins (including almost every member of the Arp2/3 complex), signaling molecules, and mediators of RNA trafficking, protein synthesis and degradation, among others. Characterization of mutants for candidate neurexin interactors revealed that they recapitulate aspects of the nrx-1(-) mutant phenotype, suggesting they may be involved in neurexin signaling. Finally, to investigate a possible role for neurexin in local actin assembly, we endogenously tagged its intracellular domain with actin depolymerizing and sequestering peptides (DeActs) and found that this led to defects in active zone assembly. Together, these results suggest neurexin's intracellular domain may be involved in presynaptic actin-assembly, and furthermore highlight a novel approach to achieving high specificity for in vivo proteomics experiments.
Mesh-Begriff(e)	Animals ; Actins ; Neurexins ; Microfilament Proteins ; Actin-Related Protein 2-3 Complex ; Caenorhabditis elegans/genetics ; Cell Adhesion Molecules, Neuronal ; Caenorhabditis elegans Proteins/genetics
Chemische Substanzen	Actins ; Neurexins ; Microfilament Proteins ; Actin-Related Protein 2-3 Complex ; nrx-1 protein, C elegans ; Cell Adhesion Molecules, Neuronal ; Caenorhabditis elegans Proteins
Sprache	Englisch
Erscheinungsdatum	2024-01-22
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002466
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Decoding cocaine-induced proteomic adaptations in the mouse nucleus accumbens.

Mews, Philipp / Sosnick, Lucas / Gurung, Ashik / Sidoli, Simone / Nestler, Eric J

Science signaling

2024 Band 17, Heft 832, Seite(n) eadl4738

Abstract: Cocaine use disorder (CUD) is a chronic neuropsychiatric condition that results from enduring cellular and molecular adaptations. Among substance use disorders, CUD is notable for its rising prevalence and the lack of approved pharmacotherapies. The ... ...

Abstract	Cocaine use disorder (CUD) is a chronic neuropsychiatric condition that results from enduring cellular and molecular adaptations. Among substance use disorders, CUD is notable for its rising prevalence and the lack of approved pharmacotherapies. The nucleus accumbens (NAc), a region that is integral to the brain's reward circuitry, plays a crucial role in the initiation and continuation of maladaptive behaviors that are intrinsic to CUD. Leveraging advancements in neuroproteomics, we undertook a proteomic analysis that spanned membrane, cytosolic, nuclear, and chromatin compartments of the NAc in a mouse model. The results unveiled immediate and sustained proteomic modifications after cocaine exposure and during prolonged withdrawal. We identified congruent protein regulatory patterns during initial cocaine exposure and reexposure after withdrawal, which contrasted with distinct patterns during withdrawal. Pronounced proteomic shifts within the membrane compartment indicated adaptive and long-lasting molecular responses prompted by cocaine withdrawal. In addition, we identified potential protein translocation events between soluble-nuclear and chromatin-bound compartments, thus providing insight into intracellular protein dynamics after cocaine exposure. Together, our findings illuminate the intricate proteomic landscape that is altered in the NAc by cocaine use and provide a dataset for future research toward potential therapeutics.
Mesh-Begriff(e)	Mice ; Animals ; Nucleus Accumbens/metabolism ; Proteomics ; Cocaine/pharmacology ; Cocaine-Related Disorders/genetics ; Cocaine-Related Disorders/metabolism ; Cocaine-Related Disorders/psychology ; Chromatin/metabolism
Chemische Substanzen	Cocaine (I5Y540LHVR) ; Chromatin
Sprache	Englisch
Erscheinungsdatum	2024-04-16
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2417226-1
ISSN	1937-9145 ; 1945-0877
ISSN (online)	1937-9145
ISSN	1945-0877
DOI	10.1126/scisignal.adl4738
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Evidence for negative selection in human primary fibroblasts to tolerate high somatic mutation loads upon treatment with multiple low doses of N-ethyl-N-nitrosourea.

Heid, Johanna / Cutler, Ronald / Sun, Shixiang / Lee, Moonsook / Maslov, Alexander Y / Dong, Xiao / Sidoli, Simone / Vijg, Jan

bioRxiv : the preprint server for biology

2024

Abstract: High-throughput sequencing at the single-cell and single-molecule level has shown that mutation rate is much higher in somatic cells than in the germline, with thousands of mutations accumulating with age in most human tissues. While there is now ample ... ...

Abstract	High-throughput sequencing at the single-cell and single-molecule level has shown that mutation rate is much higher in somatic cells than in the germline, with thousands of mutations accumulating with age in most human tissues. While there is now ample evidence that some of these mutations can clonally amplify and lead to disease, most notably cancer, the total burden of mutations a cell can tolerate without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts multiple times to low doses of N-ethyl-N-nitrosourea (ENU) and quantitatively analyzing somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain ∼60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate. We found evidence for selection against potentially deleterious variants in gene coding regions as well as depletion of mutations in sequences associated with genetic pathways expressed in these human fibroblasts, most notably those relevant for maintaining basic cellular function and growth. However, no evidence of negative selection was found for variants in non-coding regions. We conclude that actively proliferating fibroblasts can tolerate very high levels of somatic mutations without major adverse effects on growth rate via negative selection against damaging coding mutations. Since most tissues in adult organisms have very limited capacity to select against mutations based on a growth disadvantage, these results suggest that a causal effect of somatic mutations in aging and disease cannot be ruled out.
Sprache	Englisch
Erscheinungsdatum	2024-04-07
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2024.04.07.588286
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model.

Stransky, Stephanie / Cutler, Ronald / Aguilan, Jennifer / Nieves, Edward / Sidoli, Simone

Epigenetics & chromatin

2022 Band 15, Heft 1, Seite(n) 35

Abstract: Background: Three-dimensional (3D) cell culture has emerged as an alternative approach to 2D flat culture to model more accurately the phenotype of solid tissue in laboratories. Culturing cells in 3D more precisely recapitulates physiological conditions ...

Abstract	Background: Three-dimensional (3D) cell culture has emerged as an alternative approach to 2D flat culture to model more accurately the phenotype of solid tissue in laboratories. Culturing cells in 3D more precisely recapitulates physiological conditions of tissues, as these cells reduce activities related to proliferation, focusing their energy consumption toward metabolism and homeostasis. Results: Here, we demonstrate that 3D liver spheroids are a suitable system to model chromatin dynamics and response to epigenetics inhibitors. To delay necrotic tissue formation despite proliferation arrest, we utilize rotating bioreactors that apply active media diffusion and low shearing forces. We demonstrate that the proteome and the metabolome of our model resemble typical liver functions. We prove that spheroids respond to sodium butyrate (NaBut) treatment, an inhibitor of histone deacetylases (HDACi), by upregulating histone acetylation and transcriptional activation. As expected, NaBut treatment impaired specific cellular functions, including the energy metabolism. More importantly, we demonstrate that spheroids reestablish their original proteome and transcriptome, including pre-treatment levels of histone acetylation, metabolism, and protein expression once the standard culture condition is restored after treatment. Given the slow replication rate (> 40 days) of cells in 3D spheroids, our model enables to monitor the recovery of approximately the same cells that underwent treatment, demonstrating that NaBut does not have long-lasting effects on histone acetylation and gene expression. These results suggest that our model system can be used to quantify molecular memory on chromatin. Conclusion: Together, we established an innovative cell culture system that can be used to model anomalously decondensing chromatin in physiological cell growth and rule out epigenetics inheritance if cells recover the original phenotype after treatment. The transient epigenetics effects demonstrated here highlight the relevance of using a 3D culture model system that could be very useful in studies requiring long-term drug treatment conditions that would not be possible using a 2D cell monolayer system.
Mesh-Begriff(e)	Acetylation ; Histones ; Proteome ; Liver ; Protein Processing, Post-Translational ; Chromatin
Chemische Substanzen	Histones ; Proteome ; Chromatin
Sprache	Englisch
Erscheinungsdatum	2022-11-21
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-022-00470-7
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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