Biology subjects

Massimino, L.

Publications and source records attributed to Massimino, L..

7 recordsLinked to original sources

bioRxiv2026

RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease

Retrospective reuse of spatial transcriptomics often starts from a deposited bin-level Seurat object rather than the inputs needed to revisit upstream molecular processing. We tested whether image segmentation could support a defensible cell-like reconstruction under this constraint in two complete H&E-stained intestinal sections from a Visium HD study of Crohn's disease-associated fibrostenosis (GSE302569). The available data comprised 18,085 genes, 988,942 original 8 {micro}m bins and 179,596,575 UMIs. We evaluated 20 segmentation configurations in the preserved image coordinate system using a common bin-centre assignment rule, without restarting Space Ranger or introducing higher-resolution expression. RNA assignment ranged from 0% to 74.68% in CD1 and 0% to 64.05% in CD2. Expansion increased recovery but did not eliminate merged regions, straight boundaries or within-bin ambiguity; approximately 70-73% of InstanSeg brightfield nuclear regions received no assigned RNA. All 38 non-empty configuration-slice combinations underwent native full-mode RCTD against the same nine-group scIBD reference. Mean slice-level RNA recovery was negatively associated with primary-component dominance across 19 configurations (descriptive Spearman {rho} = -0.77). Neither dominant-call agreement nor concentrated RCTD support validates boundaries or cell identity. The observed limitations in RNA recovery, region geometry, and compositional support did not establish any tested configuration as a reliable single-cell reconstruction from these inputs. The findings identify limitations of retrospective single-cell reconstruction from the available binned inputs, not the impossibility of cell-resolved analysis from suitable original data.

bioinformatics↗

bioRxiv2024

Prostaglandin D2 synthase controls Schwann cells metabolism

We previously reported that in the absence of Prostaglandin D2 synthase (L-PGDS) peripheral nerves are hypomyelinated in development and that with aging they present aberrant myelin sheaths. We now demonstrate that L-PGDS expressed in Schwann cells is part of a coordinated program aiming at preserving myelin integrity. In vivo and in vitro lipidomic, metabolomic and transcriptomic analyses confirmed that myelin lipids composition, Schwann cells energetic metabolism and key enzymes controlling these processes are altered in the absence of L-PGDS. Moreover, Schwann cells undergo a metabolic rewiring and turn to acetate as the main energetic source. Further, they produce ketone bodies to ensure glial cell and neuronal survival. Importantly, we demonstrate that all these changes correlate with morphological myelin alterations and describe the first physiological pathway implicated in preserving PNS myelin. Collectively, we posit that myelin lipids serve as a reservoir to provide ketone bodies, which together with acetate represent the adaptive substrates Schwann cells can rely on to sustain the axo-glial unit and preserve the integrity of the PNS.

neuroscience↗

bioRxiv2022

Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition

Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the onco-protein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that conditions in which SET is accumulated, including the severe Schinzel-Giedion Syndrome (SGS), are characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of the SET-related disorders in humans, including SGS, neurodevelopmental disorders, myeloproliferative diseases, and cancer.

developmental biology↗

bioRxiv2020

A human stem cell-derived neurosensory-epithelial circuitry on-a-chip to model herpes simplex virus reactivation

Both emerging viruses and well-known viral pathogens endowed with neurotropism can either impair directly the neuronal functions or induce physio-pathological changes by diffusing from the periphery through neurosensory-epithelial connections. However, the current lack of an in vitro system modeling the connectivity between human neurons and peripheral tissues excludes the analysis of viral latency and reactivation and the assessment of natural/artificial induced anti-viral immunity. In this study, we developed the first stable topographic neurosensory-epithelial connection on-a-chip using human stem cell derived dorsal root ganglia (DRG) sensory neurons. Bulk and single cell transcriptomics showed that different combinations of key receptors for Herpes Simplex Virus 1 (HSV-1) are expressed by each sensory neuronal cell type. This neuronal-epithelial circuitry enabled a detailed analysis of the HSV infectivity faithfully modeling its dynamics and cell type specificity. The reconstitution of an organized connectivity between human sensory neurons and keratinocytes into microfluidic chips provides for the first time a powerful in vitro platform to model viral latency and reactivation of human viral pathogens.

microbiology↗

bioRxiv2020

ZFP423 regulates early patterning and multiciliogenesis in the hindbrain choroid plexus

The choroid plexus (ChP) is a secretory tissue that produces cerebrospinal fluid (CSF) and secretes it into the ventricular system. CSF flows from the lateral to the third ventricle, and then to the fourth ventricle through the cerebral aqueduct. Recent studies have uncovered new, active roles for this structure in the regulation of neural stem cell maintenance and differentiation into neurons. Zfp423, encoding a Kruppel-type zinc finger transcription factor essential for cerebellar development and mutated in rare cases of cerebellar vermis hypoplasia / Joubert syndrome and other ciliopathies, is expressed in the hindbrain roof plate (RP), from which the IV ventricle ChP arises, and in mesenchymal cells giving rise to the stroma and leptomeninges. Zfp423 mutants display a marked reduction of the hindbrain ChP (hChP), which fails to express key markers of its secretory function and genes implicated in its development and maintenance (Lmx1a, Otx2). The mutant hChP displays a complete lack of multiciliated ependymal cells. A transcriptome analysis conducted at the earliest stages of hChP development and subsequent validations demonstrate that the mutant hChp displays a strong deregulation of pathways involved in early hindbrain patterning and multiciliated cell fate specification. Our results propose Zfp423 as a master gene and one of the earliest known determinants of hChP development.

developmental biology↗

bioRxiv2019

Whole brain delivery of an instability-prone Mecp2 transgene improves behavioral and molecular pathological defects in mouse models of Rett syndrome

Rett syndrome (RTT) is an incurable neurodevelopmental disorder caused by mutations in the gene encoding for methyl-CpG binding-protein 2 (MeCP2). Gene therapy for this disease presents inherent hurdles since MECP2 is expressed throughout the brain and its duplication leads to severe neurological conditions as well. However, the recent introduction of AAV-PHP.eB, an engineered capsid with an unprecedented efficiency in crossing the blood-brain barrier upon intravenous injection, has provided an invaluable vehicle for gene transfer in the mouse nervous system. Herein, we use AAV-PHP.eB to deliver an instability-prone Mecp2 (iMecp2) transgene cassette which, increasing RNA destabilization and inefficient protein translation of the viral Mecp2 transgene, limits supraphysiological Mecp2 protein levels in transduced neural tissues. Intravenous injections of the PHP.eB-iMecp2 virus in symptomatic male and female Mecp2 mutant mice significantly ameliorated the disease progression with improved locomotor activity, coordination, lifespan and normalization of altered gene expression and mTOR signaling. Remarkably, PHP.eB-iMecp2 administration did not result in severe toxicity effects either in female Mecp2 mutant or in wild-type animals. In contrast, we observed a strong immune response to the transgene in treated male Mecp2 mutant mice that was overcome by immunosuppression. Overall, PHP.eB-mediated delivery of the iMecp2 cassette provided widespread and efficient gene transfer maintaining physiological Mecp2 protein levels in the brain. This combination defines a novel viral system with significant therapeutic efficacy and increased safety which can contribute to overcome the hurdles that are delaying clinical applications of gene therapy for RTT.\n\nOne Sentence SummaryGlobal brain transduction of the instability-prone Mecp2 transgene by systemic AAV-PHP.eB administration is both safe and effective in protecting male and female Mecp2 mutant mice from the RTT disease phenotype.

neuroscience↗

bioRxiv2018

CRISPRa-mediated Kcna1 upregulation decreases neuronal excitability and suppresses seizures in a rodent model of temporal lobe epilepsy

Epilepsy is a major health burden, calling for new mechanistic and therapeutic insights. CRISPR-mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex-vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can effectively treat acquired focal epilepsy, focusing on ion channels because their manipulation is known be effective in changing network hyperactivity and hypersynchronisation. We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonic-clonic seizures in a model of temporal lobe epilepsy, and rescued cognitive impairment and transcriptomic alterations associated with chronic epilepsy. The focal treatment minimizes concerns about off-target effects in other organs and brain areas. This study provides the proof of principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability.

neuroscience↗