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Santoro, R.

Publications and source records attributed to Santoro, R..

14 recordsLinked to original sources

Rewired mRNA homeostasis enforces cell-size associated senescence

Cellular senescence refers to a permanent state of cell cycle exit and plays a key role in blocking the proliferation of compromised cells. Despite diverse drivers, senescent cells often share common features, one of which is their increased size. Though previously viewed as a passive outcome of cell growth during senescence, recent work shows that excess cell size can actively promote senescence via the p53-p21 pathway, making it both a consequence and a cause of cell cycle arrest. How cells sense their own size and communicate this information to the cell cycle control apparatus remains unresolved. Using genome-wide proximity mapping, we show that excess cell size globally redistributes chromatin between nuclear speckles and the nuclear lamina. These changes correspond with altered gene expression profiles, including the de-repression of typically silenced lamina-associated genes, some of which are involved in the senescence-associated secretory phenotype (SASP). Consistent with altered nuclear speckle function, we find that excess cell size perturbs normal splice isoform usage. In particular, MDM4, a negative regulator of p53 signaling, is differentially spliced when cells become enlarged to yield a non-functional variant, MDM4-S. Re-introducing correctly spliced MDM4 transcripts restores G1 cell cycle progression, thereby reverting senescent phenotypes in enlarged cells. Together, these data indicate that excess cell size is sensed via changes in mRNA homeostasis associated with a reorganized genome, driving both the secretory phenotype and permanent cell cycle exit that are characteristic of cellular senescence.

cell biology↗

Nucleolar buffering of lamina-associated heterochromatin restrains Progerin-induced ageing programs

Nucleolar enlargement is a conserved hallmark of physiological and premature ageing, including Hutchinson-Gilford Progeria Syndrome (HGPS), a disorder caused by LMNA mutations that produce Progerin and profoundly disrupt nuclear architecture. Although both the nuclear lamina and nucleolus organize repressive chromatin, how nucleolar remodelling contributes to genome reorganization during ageing driven by lamina dysfunction remains unclear. Here, we identify the nucleolus as a stress-responsive chromatin-organizing compartment that buffers the initial events of Progerin-induced ageing programs by sequestering lamina-associated domains (LADs). Despite widespread nuclear reorganization and robust transcriptional ageing signatures following Progerin expression, repression of LADs is preserved. This preservation results from an increased nucleolar association of lamina-released LADs, which can retain H3K9me2 and remain transcriptionally silent. Disrupting this compensatory pathway by depleting NPM1, a nucleolar factor required for nucleolar genome association, abolishes nucleolar buffering, leading to loss of H3K9me2 at relocated LADs, derepression of LAD-associated genes, exacerbation of transcriptional ageing programs, and increased DNA damage. Together, these findings establish the nucleolus as a structural fail-safe that preserves heterochromatin integrity and reveal stress-responsive nuclear compartmentalization as a fundamental mechanism safeguarding epigenome stability.

molecular biology↗

Targeting FOXA1 and FOXA2 Disrupts the Lineage-Specific Oncogenic Output Program in Prostate Cancer

Activation of the androgen receptor (AR) is the key lineage-specific oncogenic pathway and the primary therapeutic target in prostate cancer. While AR signaling is enabled by the pioneer transcription factor FOXA1, its homolog FOXA2 is specifically expressed in advanced lineage plasticity prostate cancers that have lost the AR signaling axis. However, their roles and utility as drug targets remain incompletely characterized. Here, we show an unexpected collaboration of FOXA1 and FOXA2 in mediating AR-independent cell proliferation in different lineage plasticity cancer subtypes. Conversely, joint loss-of-function or pharmacologic disruption of FOXA1 and FOXA2 leads to the collapse of lineage-specific oncogenic transcription factors followed by cell cycle arrest. In summary, our findings uncover a druggable dependency for AR-positive and - negative prostate cancers.

cancer biology↗

LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis

In most eukaryotic cells, euchromatin is localized in the nuclear interior, whereas heterochromatin is enriched at the nuclear envelope (NE). This conventional chromatin organization is established by heterochromatin tethering to the NE, however its importance for cellular homeostasis is largely unexplored. Peripheral heterochromatin localization relies on redundant NE-tethering systems. One tether is constituted by the lamin B receptor (LBR) in mammals, but the enigmatic nature of the other tethers has hampered functional analyses. Here we demonstrate that the downregulation of abundant, ubiquitous NE proteins can induce the global detachment of heterochromatin from the NE. Among these factors, we identify LBR and LAP2 as major players in bulk heterochromatin attachment to the NE in pluripotent and differentiated mammalian cells. Their loss leads to repositioning of heterochromatin to the nuclear interior, changes in chromatin accessibility, deregulation of gene expression including activation of antiviral innate immunity, and defects in cell fate determination.

cell biology↗

TCF3::HLF Orchestrates an Enhancer-Promoter Network with Activation of MEF2C to Promote Immature HSC gene Expression in Leukemia

Oncogenic fusion transcription factors (TFs) frequently drive hematopoietic malignancies by altering gene expression in key developmental programs. TCF3::HLF is a fusion TF that characterizes a rare, treatment-resistant subtype of B-cell acute lymphoblastic leukemia (t(17;19) TCF3::HLF-positive B-ALL). Despite its clinical significance, the mechanisms by which TCF3::HLF induces leukemia are unclear. We used HiChIP mapping and genetic interference to analyze TCF3::HLF at the 3D-genome level, revealing enhancer-promoter interactions that control gene activation or repression. Notably, TCF3::HLF directly regulates MEF2C expression through its enhancer, as interference disrupted MEF2C transcription and inhibited leukemia propagation. This disruption also diminished embryonal hematopoietic stem cell (HSC) gene signatures and restored mature HSC and B-lymphoid markers. These findings highlight MEF2C as a critical component of the transcriptional network reprogrammed by TCF3::HLF. Our study provides insight into how TCF3::HLF rewires the 3D genome to drive leukemia and serves as a resource for further exploration of the TCF3::HLF regulome. TeaserUnraveling the 3D genomic interactions mediated by TCF3::HLF fusion protein in t(17;19) positive acute lymphoblastic leukemia.

cancer biology↗

NPM1 mediates genome-nucleolus interactions and the establishment of their repressive chromatin states

Repressive chromatin domains are often located at the nuclear lamina (NL) or nucleolus. Although nucleolar associated domains (NADs) have been recently mapped, the mechanisms of NAD association with nucleoli and the functional significance of their localization remain unclear. Here, we show that NAD association with nucleoli is mediated by nucleophosmin (NPM1), a factor located within the granular component, the outer layer of the nucleolus. NPM1 binds NADs, interacts with the histone lysine methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of NPM1 mutant lacking the DNA binding domain (NPM1{Delta}DBD) caused NAD dissociation from nucleoli and H3K9me2 reduction specifically at NADs. G9a is dispensable for NAD contacts with nucleoli and interacts with NPM1{Delta}DBD, indicating that NADs acquire G9a-mediated H3K9me2 only after associating with NPM1 at nucleoli. The results provide mechanistic insights into how genomic domains associate with nucleoli and acquire their repressive chromatin state. Additionally, our findings suggest that the nucleolus not only serves as a scaffold for positioning repressive chromatin domains but also plays a direct role in establishing these chromatin states.

molecular biology↗

Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

Gene position in the nuclear space plays an important role in gene regulation. This is exemplified by repressive chromatin domains frequently contacting nuclear lamina or nucleoli. The nucleolus undergoes structural changes in response to various cellular states, potentially impacting genome organization. However, how the 3D-genome organization responds to nucleolar states has remained underinvestigated due to the lack of methods able to identify nucleolar associated domains (NADs) in single cells and under nucleolar stress. To address this, we developed NoLMseq, a method combining laser-capture microdissection and DNA sequencing to map NADs in single cells. NoLMseq identified many unexplored features of chromosome organization around single nucleoli such as NAD heterogeneity among ESCs, culminating in two major populations with distinct chromatin states. NADs prevalently contact nucleoli in a monoallelic manner and allelic nucleolar contact frequency mirrors gene expression and chromatin states. NoLMseq also revealed how chromosomes reorganise around nucleoli under nucleolar stress conditions, highlighting the importance of nucleolus integrity in genome organization and 3D-genome response to nucleolar stress. The results demonstrated that NoLMseq accurately measures chromosome contacts around single healthy and stressed nucleoli and it will be a critical tool to study NADs within biological populations and determine how the 3D-genome responds to nucleolar stress in healthy and disease states.

genomics↗

Neuroendocrine control of catch-up growth in Drosophila

Children and other vertebrate animals stunted due to malnutrition can compensate for this deficit by resuming growth at a higher-than-normal rate via a still ill-defined mechanism. High mortality and adverse effects later in life may offset the positive effects of catch-up growth. Here we report that the invertebrate Drosophila melanogaster also experiences catch-up growth following a period of starvation, and the relaxin receptor Lgr4 instigates this catch-up growth. Starved larvae compensate for weight loss by growing two or more times faster and starting maturation within the same time as the non-starved sibling by preventing a rise in insulin-like growth (IGF)-induced ecdysone under Lgr4 control. Our data reveal that catch-up growth is associated with a surge of insulin, not IGF, which may clarify how catch-up growth often leads to metabolic problems and obesity.

developmental biology↗

PRAMEL7/CUL2 axis regulates NuRD stability to establish ground-state pluripotency in embryonic stem cells

Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, they only partially resemble the gene expression signature of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by causing DNA hypomethylation and gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets for proteasomal degradation regulators of repressive chromatin, including NuRD complex. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generate in vitro models to reproduce the in vivo ground-state pluripotency.

developmental biology↗

ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells

The Argonaute proteins (AGO) are well-known for their essential role in post-transcriptional gene silencing in the microRNA (miRNA) biogenesis pathway. Only two AGOs (AGO1 and AGO2) are expressed in mouse embryonic stem cells (mESCs). The transcriptome of Ago mutant mESCs revealed a large and specific set of misregulated genes, compared to other miRNA biogenesis factor mutant cells, suggesting additional functions for the AGOs in stem cells. In this study, we endeavored to understand miRNA-independent roles of the AGOs in gene expression regulation through the integration of multiple datasets. Correlation of Ago mutant differential gene expression with ENCODE histone modification data of WT mESCs revealed that affected genes were regulated by the repressive histone modification H3K27me3. We validated this observation by performing chromatin immunoprecipitation followed by sequencing and observed a global loss of H3K27me3 in Ago mutant cells. Nevertheless, this reduction explains only a small part of the specific differential gene expression observed in Ago mutant mESCs. By integrating chromatin accessibility data in conjunction with prediction of transcription factor binding sites, we identified differential binding for five transcription factors, including KLF4 as a key modulator of more than half of the specific misregulation of gene expression in the absence of AGO proteins. Our findings illustrate that in addition to chromatin state, information about transcription factor binding is more revelatory in understanding the multi-layered mechanism adopted by cells to regulate gene expression. These data also highlight the importance of an integrative approach to unravel the variety of noncanonical functions of AGOs in mESCs.

molecular biology↗

BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer

BAZ2A is the repressor of rRNA genes that are transcribed by RNA Polymerase I. In prostate cancer (PCa), however, BAZ2A function goes beyond this role since it can also repress other genes that are frequently silenced in metastatic disease. However, the mechanisms of BAZ2A-mediated repression in PCa remain elusive. Here we show that BAZ2A represses genes implicated in PCa through its RNA-binding TAM domain using mechanisms differing from rRNA gene silencing. While TAM domain mediates BAZ2A recruitment to rRNA genes, in PCa cells this is not required for BAZ2A association with target genes. Instead, BAZ2A-TAM domain in association with RNA mediates the interaction with topoisomerase 2A (TOP2A) and histone demethylase KDM1A, whose expression positively correlates with BAZ2A levels in both localized and aggressive PCa. Pharmacological inhibition of TOP2A and KDM1A activities upregulates the expression of BAZ2A-repressed genes that are regulated by a class of inactive enhancers bound by BAZ2A whereas rRNA genes are not affected. Our findings showed a novel RNA-based mechanism of gene regulation in PCa. Further, the data indicate that RNA-mediated interactions between BAZ2A and TOP2A and KDM1A repress genes critical to PCa and may prove to be useful to stratify prostate cancer risk and treatment in patients.

molecular biology↗

Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

Eukaryotic chromosomes are folded into hierarchical domains, enabling the organization of the genome into functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks thought to contribute to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for genome-wide maps of nucleolar associated domains (NADs). Here we established a method based on a Dam-fused engineered nucleolar histone H2B that marks DNA contacting the nucleolus. NAD-maps of ESCs and neural progenitors revealed layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs showed higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation, chromosomes around the nucleolus acquire a more compact, rigid architecture whereas NADs specific for ESCs decrease their interaction strength within the repressive B-compartment strength, unlocking neural genes from repressive nuclear environment. The methodologies here developed will make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function.

genomics↗

BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state

Prostate cancer (PCa) is one of the most prevalent cancers in men. Cancer stem cells are thought to be associated with PCa relapse. Here we show that BAZ2A is required for the transition of PCa cells into a cancer stem-like state. BAZ2A genomic occupancy in PCa cells coincides with H3K14ac enriched chromatin regions. This association is mediated by BAZ2A-bromodomain (BAZ2A-BRD) that specifically binds H3K14ac. BAZ2A associates with inactive enhancers marked by H3K14ac and repressing transcription of genes frequently silenced in aggressive and poorly differentiated PCa. BAZ2A-mediated repression is also linked to EP300 that acetylates H3K14ac. BAZ2A-BRD mutations or treatment with inhibitors abrogating BAZ2A-BRD/H3K14ac interaction impair the transition of PCa cells into a stem-like state. Furthermore, pharmacological inactivation of BAZ2A-BRD impairs Pten-loss oncogenic transformation of prostate organoids. Our findings indicate a role of BAZ2A-BRD in PCa stem cell features and suggest potential epigenetic-reader therapeutic strategies to target BAZ2A in aggressive PCa.

molecular biology↗

TIP5 safeguards genome architecture of ground-state pluripotent stem cells

Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. However, how genome compartmentalization is regulated remains elusive. We analyzed two closely and developmentally related pluripotent cell types: ground-state ESCs that have an open and active chromatin and developmentally advanced ESCs that display a more closed and repressed state. We show that these two ESC types differ in their regulation of genome organization due to their differential dependency on TIP5, a component of the chromatin remodeling complex NoRC. We show that TIP5 interacts on ESC chromatin with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. TIP5 associates with sub-domains within the active A compartment that strongly intersect through long-range contacts in ESCs. We found that only ground-state chromatin requires TIP5 to limit the invasion of active domains into repressive compartments. Depletion of TIP5 increased chromatin accessibility particularly at B compartments and decreased their repressive features. Furthermore, TIP5 acts as a barrier for the repressive H3K27me3 spreading, a process that also requires TOP2A activity. Finally, ground-state ESCs require TIP5 for growth, differentiation capacity, and correct expression of developmental genes. Our results revealed the propensity of open and active chromatin domains to invade repressive domains, an action counteracted by chromatin remodeling and the relief of chromatin torsional stress. This effort in controlling open/active chromatin domains is required to establish active and repressed genome partitioning and preserves cell function and identity.

molecular biology↗