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Fagnocchi, L.

Publications and source records attributed to Fagnocchi, L..

8 recordsLinked to original sources

Midbrain Tet1 dosage defines inter-individual binge-eating susceptibility

Binge-eating disorder (BED) is the most common eating disorder worldwide and carries life-altering comorbidities. While genetic and environmental risk factors have been identified, the mechanisms that determine inter-individual susceptibility to BED remain largely unknown. Here, we demonstrate that developmental dosage of the DNA hydroxymethylase Tet1 defines stable inter-individual differences in binge-eating susceptibility. In mice, midbrain dopaminergic neurons of the ventral tegmental area (VTADA) are essential for the induction of addictive binge-eating behavior, express high levels of Tet1, and undergo rapid and widespread DNA hydroxymethylation remodeling upon experimental binge eating. Strikingly, Tet1 haploinsufficiency creates pronounced inter-individual variation in binge-eating susceptibility even among genetically identical mice, which we trace to reduced connectivity between the prelimbic medial prefrontal cortex (mPFCPL) and the VTA. Chemogenetic inhibition of mPFCPL[->]VTA projections reduces binge-eating susceptibility, whereas EGR1-guided re-activation of TET1 in VTA dopaminergic neurons restores susceptibility, supporting a causal role for this axis. Importantly, TET1 promoter methylation in patients associates with binge-eating behavior and reward-circuit function, suggesting conservation of this regulatory network in humans. Collectively, these findings identify Tet1 dosage as a novel regulator of binge-eating susceptibility and provide a mechanistic basis for how inter-individual differences in behavior are established.

neuroscience↗

BifurcatoR: A Framework for Revealing Clinically Actionable Signal in Variance Masquerading as Noise

BackgroundDisease heterogeneity is a persistent challenge in medicine, complicating both research and treatment. Standard analytical pipelines often assume patient populations are homogeneous, overlooking variance patterns that may signal biologically distinct subgroups. Variance heterogeneity (VH)--including skewness, outliers, and multimodal distributions--offers a powerful but underused lens for detecting latent etiological structures relevant to prognosis and therapeutic response. MethodsA major barrier to VH analysis is the fragmented landscape of available methods, many of which rely on normality assumptions that biological data frequently violate. In addition, existing tools often require programming expertise, and clear guidance on study design considerations--such as sample size and method selection--is lacking. To address these issues, we developed BifurcatoR, an open-source software platform that simplifies the detection, modeling, and interpretation of VH. BifurcatoR integrates simulation-based method evaluation, study design recommendations, and a user-friendly web interface to support VH analysis across a range of data distributions. We benchmarked VH methods through simulation and applied BifurcatoR to two clinical datasets: acute myeloid leukemia (AML) and obesity. ResultsSimulation studies revealed that VH method performance is highly context-specific, varying with distribution shape, mean-variance coupling, and underlying subgroup structure. In AML, BifurcatoR identified two molecularly distinct subgroups with different treatment responses, including an EVI1-high group with significantly poorer prognosis (p < 0.005) among KMT2A-rearranged cases. In a separate study, VH analysis uncovered immunophenotypic subgroups in obesity based on gene-level discordance across monozygotic twin pairs, highlighting latent variation in adipose immune cell composition. ConclusionsVH is not "noise", biological variation without clinical relevance. Instead, VH is a structured signal that can reveal latent and clinically meaningful subtypes. BifurcatoR offers a practical, accessible framework for incorporating VH into biomedical research, with implications for biomarker discovery, patient stratification, and precision medicine.

bioinformatics↗

Metastatic cell plasticity is maintained by SOX9 function during mitosis in breast cancer

Disseminated tumor cells (DTCs) contribute to metastasis formation by adapting to the hostile environmental conditions encountered at the seeded secondary organs. This phenotypic plasticity is supported by the epigenetic reprogramming of cis-regulatory elements (CREs), representing a hallmark of metastatic cells. DTCs can enter a reversible state of cancer dormancy, resulting from their ability to enter quiescence after mitosis and escape immune surveillance. In this respect, mitosis may represent a window of opportunity to increase DTCs fitness by priming CREs, ensuring the reactivation of a dormancy-related transcriptional program while preserving the epigenetic information. By profiling the chromatin changes occurring during the early steps of mitosis, we found that DTCs experience fluctuations in chromatin accessibility at CREs, which are bookmarked by pro-metastatic TFs. Among these, the pro-dormancy TF SOX9 remained associated with mitotic chromatin, facilitating transcriptional reactivation upon exiting mitosis. By dissecting the consequences of degrading SOX9 before mitosis, we found that its priming of dormancy-related CREs, combined with the recruitment of the Mediator kinase module, is instrumental for metastatic cells to enter quiescence and escape NK-mediated immune surveillance. These findings indicate that cancer dormancy is primed during mitosis by pro-metastatic TFs.

molecular biology↗

Chronic obesity does not alter cancer survival in Tp53R270H/+ mice

Obesity is a complex chronic disease characterized by excessive adiposity and associations with numerous co-morbidities, including cancer. Despite extensive research, we have limited understanding of the mechanisms coupling obesity to cancer risk, and separately, of the contexts where obesity does or does not exacerbate disease. Here, we show that chronic high-fat diet induced obesity has no significant effect on the Trp53R270H/+ mouse, a model of human Li-Fraumeni multi-cancer syndrome. Surprisingly, despite inducing rapid and highly penetrant obesity and long-term differences in adiposity, greater than one year of HFD had no significant effect on survival or tumor burden. These findings were replicated in two separate cohorts totaling 359 mice and thus provide important negative data for the field. Given strong publication bias against negative data in the literature, this large murine cohort study represents a clear case where chronic diet-induced obesity does not accelerate or aggravate cancer outcomes. The data thus carry high impact for researchers, funders, and policymakers alike.

cancer biology↗

Developmental priming of cancer susceptibility

DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility states in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.

cancer biology↗

A rapid microglial metabolic response controls metabolism and improves memory

Chronic high-fat feeding triggers chronic metabolic dysfunction including obesity, insulin resistance, and diabetes. How high-fat intake first triggers these pathophysiological states remains unknown. Here, we identify an acute microglial metabolic response that rapidly translates intake of high-fat diet (HFD) to a surprisingly beneficial effect on metabolism and spatial / learning memory. High-fat intake rapidly increases palmitate levels in cerebrospinal fluid and triggers a wave of microglial metabolic activation characterized by mitochondrial membrane activation and fission as well as metabolic skewing towards aerobic glycolysis. These effects are detectable throughout the brain and can be detected within as little as 12 hours of HFD exposure. In vivo, microglial ablation and conditional DRP1 deletion show that the microglial metabolic response is necessary for the acute effects of HFD. 13C-tracing experiments reveal that in addition to processing via {beta}-oxidation, microglia shunt a substantial fraction of palmitate towards anaplerosis and re-release of bioenergetic carbons into the extracellular milieu in the form of lactate, glutamate, succinate, and intriguingly, the neuro-protective metabolite itaconate. Together, these data identify microglia as a critical nutrient regulatory node in the brain, metabolizing away harmful fatty acids and releasing the same carbons as alternate bioenergetic and protective substrates for surrounding cells. The data identify a surprisingly beneficial effect of short-term HFD on learning and memory. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/535373v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b9699corg.highwire.dtl.DTLVardef@1c48efcorg.highwire.dtl.DTLVardef@18757d0org.highwire.dtl.DTLVardef@962cf6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

Identification of two β-cell subtypes by 7 independent criteria

Despite the recent explosion in surveys of cell-type heterogeneity, the mechanisms that specify and stabilize highly related cell subtypes remain poorly understood. Here, focusing initially on exploring quantitative histone mark heterogeneity, we identify two major sub-types of pancreatic {beta}-cells ({beta}HI and {beta}LO). {beta}HI and {beta}LO cells differ in their size, morphology, cytosolic and nuclear ultrastructure, transcriptional output, epigenomes, cell surface marker, and function. Importantly, {beta}HI and {beta}LO cells can be FACS separated live into CD24+ ({beta}HI) and CD24- ({beta}LO) fractions. From an epigenetic viewpoint, {beta}HI-cells exhibit [~]4-fold higher levels of H3K27me3, more compacted chromatin, and distinct chromatin organization that associates with a specific pattern of transcriptional output. Functionally, {beta}HI cells have increased mitochondrial mass, activity, and insulin secretion both in vivo and ex vivo. Critically, Eed and Jmjd3 loss-of-function studies demonstrate that H3K27me3 dosage is a significant regulator of {beta}HI / {beta}LO cell ratio in vivo, yielding some of the first-ever specific models of {beta}-cell sub-type distortion. {beta}HI and {beta}LO sub-types are conserved in humans with {beta}HI-cells enriched in human Type-2 diabetes. These data identify two novel and fundamentally distinct {beta}-cell subtypes and identify epigenetic dosage as a novel regulator of {beta}-cell subtype specification and heterogeneity. HighlightsO_LIQuantitative H3K27me3 heterogeneity reveals 2 common {beta}-cell subtypes C_LIO_LI{beta}HI and {beta}LO cells are stably distinct by 7 independent sets of parameters C_LIO_LIH3K27me3 dosage controls {beta}HI / {beta}LO ratio in vivo C_LIO_LI{beta}HI and {beta}LO cells are conserved in humans and enriched in Type-2 diabetes C_LI

cell biology↗

MYC-driven epigenetic reprogramming favors the onset of tumorigensis by inducing a stem cell-like state

Breast cancer consists of highly heterogeneous tumors, whose cell of origin and driver oncogenes resulted difficult to be uniquely defined. Here we report that MYC acts as tumor reprogramming factor in mammary epithelial cells by inducing an alternative epigenetic program, which triggers loss of cell identity and activation of oncogenic pathways. Over-expression of MYC induces transcriptional repression of lineage-specifying transcription factors, causing decommissioning of luminal-specific enhancers. MYC-driven dedifferentiation supports the onset of a stem cell-like state by inducing the activation of de novo enhancers, which drive the transcriptional activation of oncogenic pathways. Furthermore, we demonstrate that the MYC-driven epigenetic reprogramming favors the formation and maintenance of tumor initiating cells endowed with metastatic capacity. This study supports the notion that MYC-driven tumor initiation relies on cell reprogramming, which is mediated by the activation of MYC-dependent oncogenic enhancers, thus establishing a therapeutic rational for treating basal-like breast cancers.

cancer biology↗