Biology subjects

Macchi, F.

Publications and source records attributed to Macchi, F..

7 recordsLinked to original sources

bioRxiv2026

A multilayered in silico analysis links UHRF1, DNA methylation and developmental chromatin memory to lineage-dependent prognosis in gastric, renal and adrenal cancers

Aberrant DNA methylation is a hallmark of cancer, but its clinical interpretation remains debated. UHRF1, a key epigenetic adaptor for DNA methylation maintenance and chromatin bivalency regulation in embryonic stem cells, is frequently overexpressed yet shows context-dependent prognostic behaviour. By integrating bulk and single-cell transcriptomics, CpG-resolution methylation, developmental chromatin states, immune profiling and clinical outcomes across gastric (STAD), clear-cell renal (KIRC) and adrenal (ACC) carcinomas, we identified a four-class UHRF1-embryonic morphogenesis (UHRF1-EM) framework resolving this paradox. This axis revealed an inverse prognostic pattern: whilst across all three tumours EM-low and EM-high states mark better or worse prognosis, respectively, UHRF1-high levels associate with favourable outcome in STAD (UH-EML), and unfavourable in KIRC and ACC (UH-EMH). The classification proved reproducible and independently prognostic after adjustment for stage and molecular subtypes, outperforming existing classifiers and exceeding pathological stage in KIRC and ACC. Multivariable models incorporating UHRF1-EM yielded uniformly positive {Delta}C-indices. Hypermethylation associated with the UHRF1-EM axis was enriched at ESC bivalent developmental loci (EM and oncofoetal genes), but not at housekeeping cell-cycle sites. In STAD, this pattern was related to oncofoetal gene downregulation and best prognosis, whereas in KIRC and ACC it matched with gene-body/enhancer methylation, higher EM expression, immunosuppressive microenvironments and worst prognosis. Together, these findings establish the UHRF1-EM axis as a clinically robust molecular classifier and support a mechanistic model in which tumour-specific epigenetic engagement of developmental loci may contribute to the prognostic inversion, providing a foundation for further mechanistic experimental validation.

cancer biology↗

bioRxiv2025

UHRF1 Overexpression Generates Distinct Senescent States with Different Tp53 Dependencies

SummarySenescence is a pleiotropic phenotype that alternatively suppresses or promotes cancer. The tumor suppressive roles are linked to clearance of damaged cells by the immune system, while cells with tumor promoting functions resist apoptosis, evade immune clearance and either persist and support the tumor microenvironment, or escape and proliferate. What generates these diverse populations is unclear. We investigated this in preneoplastic zebrafish livers where the epigenetic regulator, UHRF1, is overexpressed in hepatocytes. Double strand breaks, DNA methylation repatterning, retrotransposon expression, cell cycle withdrawal and activation of Atm and Tp53 dependent senescence were early responses to UHRF1 overexpression. This evolved to generate diverse populations of senescent cells, some which expressed immune and senescence signatures plus anti-apoptotic markers, and others co-expressed proliferative genes. The fate of these populations was dictated by UHRF1 levels and Tp53, as Tp53 loss enabled proliferation of cells with reduced UHRF1 expression but not in cells expressing high UHRF1. The senolytic Navitoclax targeted only a subset of senescent cells. Thus, the diversity of senescent cells driven by epigenetic changes can generate divergent outcomes. Short summaryUHRF1 overexpression in zebrafish hepatocytes induces DNA damage leading to Atm-tp53-dependent senescence with UHRF1 levels dictating whether hepatocytes remain senescent, escape, or undergo senolytic elimination.

cancer biology↗

bioRxiv2025

Altered cortical network in Parkinson's Disease: the central role of PV interneuron and synaptic remodelling

Parkinson's disease (PD) is traditionally defined by the progressive degeneration of nigrostriatal dopaminergic neurons; however, accumulating evidence highlights extensive cortical dysfunctions as key contributors to motor and non-motor symptoms. Despite this growing recognition, the precise mechanisms underlying cortical network disruptions and their contribution to PD pathophysiology remain poorly understood, particularly in relation to parvalbumin-positive interneurons (PV-INs) and maladaptive plasticity. Here, we investigate the dysregulation of cortical network homeostasis in PD using a 6-hydroxydopamine (6-OHDA) mouse model, focusing on the progressive disruption of parvalbumin-positive interneuron (PV-IN) connectivity, excitatory/inhibitory balance, and neuroinflammatory responses. Using a multimodal approach integrating longitudinal electrophysiology, wide-field calcium imaging, and histological analyses, we revealed striking alterations in cortical activity and connectivity. Specifically, we observed pathological high-gamma hyperactivity during movement, accompanied by severe disruptions in PV-IN connectivity across motor and somatosensory cortices. Histological analyses further revealed synaptic imbalances and microglial dysregulation, suggesting an extensive cortical response to dopaminergic loss. These findings indicate that PV-IN dysfunction drives cortical maladaptive plasticity, leading to network desynchronization and motor deficits. By reframing PD as a disorder of cortical network homeostasis, this study provides novel mechanistic insights and identifies cortical plasticity as a promising therapeutic target for disease modification.

neuroscience↗

bioRxiv2024

Epigenetic Disordering Drives Stemness, Senescence Escape and Tumor Heterogeneity

Tumor heterogeneity is the substrate for tumor evolution and the linchpin of treatment resistance. Cancer cell heterogeneity is largely attributed to distinct genetic changes within each cell population. However, the widespread epigenome repatterning that characterizes most cancers is also highly heterogenous within tumors and could generate cells with diverse identities and malignant features. We show that high levels of the epigenetic regulator and oncogene, UHRF1, in zebrafish hepatocytes rapidly induced methylome disordering, loss of heterochromatin, and DNA damage, resulting in cell cycle arrest, senescence, and acquisition of stemness. Reducing UHRF1 expression transitions these cells from senescent to proliferation-competent. The expansion of these damaged cells results in hepatocellular carcinomas (HCC) that have immature cancer cells intermingled with fibroblasts, immune and senescent cells expressing high UHRF1 levels, which serve as reservoirs for new cancer cells. This defines a distinct and heterogenous HCC subtype resulting from epigenetic changes, stemness and senescence escape.

cancer biology↗

bioRxiv2024

Combining Gamma Neuromodulation and Robotic Rehabilitation Restores Parvalbimin-mediated Gamma Function and Boosts Motor Recovery in Stroke Mice

Stroke is a leading cause of long-term disability, often characterized by compromised motor function. Gamma band is known to be related to Parvalbumin interneurons (PV-IN) synchronous discharge and it has been found to be affected after stroke in humans and animals. Both Gamma band and PV-IN also play a key role in motor function, thus representing a promising target for post-stroke neurorehabilitation. Non-Invasive neuromodulatory approaches are considered a safe intervention and can be used for this purpose. This study presents a novel, clinically relevant, non-invasive and well-tolerated sub-acute treatment combining robotic rehabilitation with advanced neuromodulation techniques, validated in a mouse model of ischemic injury. In the sub-acute phase after stroke, we scored profound deficits in motor-related Gamma band regulation on the perilesional cortex. Accordingly, both at the perilesional and at the whole-cortex levels, the damage results in impaired PV-IN activity, with reduced firing rate and increased functional connectivity levels. Therefore, we tested the therapeutic potential of coupling robotic rehabilitation with optogenetic PV-driven Gamma band stimulation in a subacute post-stroke phase during motor training to reinforce the efficacy of the treatment. Frequency-specific movement-related Gamma band stimulation, when combined with physical training, significantly improved forelimb motor function. More importantly, by pairing robotic rehabilitation with a clinical-like non-invasive 40 Hz transcranial Alternating Current Stimulation, we achieved similar motor improvements mediated by the effective restoring of movement-related Gamma band power and increased PV-IN connections in premotor cortex. Our research introduces a new understanding of the role of parvalbumin-interneurons in post-stroke impairment and recovery. These results highlight the synergistic potential of combining perilesional Gamma band stimulation with robotic rehabilitation as a promising and realistic therapeutic approach for stroke patients. SummaryStroke-induced motor deficits are accompanied by alteration of Gamma modulation and PV-interneurons activity and restored by a combination of non-invasive Gamma stimulation and robotic therapy.

neuroscience↗

bioRxiv2021

Epigenetic machinery is functionally conserved in cephalopods

Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet little is known about the epigenome in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental and regenerative processes, but using molecular approaches in such studies is hindered by the lack of knowledge about genome organization and gene regulation in these animals. We combined bioinformatic and molecular analysis of Octopus bimaculoides to identify gene expression signatures for 12 adult tissues and a hatchling, and investigate the presence and pattern of DNA methylation and histone methylation marks across tissues. This revealed a dynamic gene expression profile encoding several epigenetic regulators, including DNA methylation maintenance factors that were highly conserved and functional in cephalopods, as shown by detection of 5-methyl-cytosine in multiple tissues of octopus, squid and bobtail squid. WGBS of octopus brain and RRBS from a hatchling revealed that less than 10% of CpGs are methylated, highlighting a non-random distribution in the genome of all tissues, with enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Each DNA methylation pattern encompassed genes with distinct functions and, strikingly, many of these genes showed similar expression levels across tissues. In contrast to the static pattern of DNA methylation, the histone marks H3K27me3, H3K9me3 and H3K4me3 were detected at different levels in diverse cephalopod tissues. This suggests the methylome and histone code cooperate to regulate tissue specific gene expression in a way that may be unique to cephalopods.

genomics↗

bioRxiv2021

Permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver

Proteostatic stress initiates a transcriptional response that is unique to the stress condition, yet the regulatory mechanisms underlying the distinct gene expression patterns observed in stressed cells remains unknown. Using a functional genomic approach, we investigated how activating transcription factor 6 (ATF6), a key transcription factor in the unfolded protein response (UPR), regulates target genes. We first designed a computational strategy to define Atf6 target genes based on the evolutionary conservation of predicted ATF6 binding in gene promoters, identifying 652 conserved putative Atf6 target (CPAT) genes. CPATs were overrepresented for genes functioning in the UPR, however, the majority functioned in cellular processes unrelated to proteostasis, including small molecule metabolism and development. Functional studies of stress-independent and toxicant based Atf6 activation in zebrafish livers showed that the pattern of CPAT expression in response to Atf6 overexpression, alcohol and arsenic was unique. Only 34 CPATs were differentially expressed in all conditions, indicating that Atf6 is sufficient to regulate a small subset of CPATs. Blocking Atf6 using Ceapins in zebrafish demonstrated that Atf6 is necessary for activation of these genes in response to arsenic. We investigated CPAT during physiologically mediated hepatocyte stress using liver regeneration in mice as a model. Over half of all CPATs were differentially expressed during this process. This was attributed to the permissive chromatin environment in quiescent livers on the promoters of these genes, characterized by the absence of H3K27me3 and enrichment of H3K4me3. Taken together, these data uncover a complex transcriptional response to Atf6 activation and implicate a permissive epigenome as a mechanism by which distinct transcriptional responses are regulated by Atf6.

genomics↗