Biology subjects

De Vittorio, M.

Publications and source records attributed to De Vittorio, M..

9 recordsLinked to original sources

bioRxiv2026

p53 knockout drives stage-specific long non-coding RNA reprogramming during human neural differentiation and glioma organoid tumorigenesis.

Background: Long non-coding RNAs (lncRNAs) are emerging regulators of tumor initiation and progression through their effects on stemness, lineage commitment, and transcriptional plasticity. The contribution of lncRNA reprogramming during early p53-deficient gliomagenesis remains poorly understood. Methods: Human induced pluripotent stem cells (iPSCs) carrying a complete TP53 knockout were differentiated into neural progenitor cells (NPCs) and cerebral organoids. Bulk RNA sequencing was performed at multiple differentiation stages and compared with established glioblastoma cell lines (U87 and U118) to identify lncRNA expression changes associated with p53 loss and tumor-like transformation. Results: p53 deficiency induced a progressive and stage-specific remodeling of the lncRNA landscape, with the most pronounced transcriptional shift observed in 40-day NPCs. This late-stage profile partially overlapped with glioblastoma-like cell lines and was characterized by the upregulation of five lncRNAs enriched in both p53-deficient neural models and glioma cells. Principal component analysis showed that these lncRNAs clustered with tumor-associated samples and were strongly co-expressed with mitotic cell-cycle genes. In particular, LINC00973 and LINC01583 were highly expressed in primary glioblastoma datasets, while RP5-875H18.9 and RP11-1094H24.4 emerged as previously unrecognized glioma-associated transcripts. Conclusion: Loss of p53 drives stage-dependent lncRNA reprogramming during neural differentiation and promotes the emergence of glioma-associated transcriptional features. These findings identify candidate lncRNAs that may contribute to early gliomagenesis and represent potential biomarkers or therapeutic targets in glioblastoma.

cancer biology↗

bioRxiv2025

Depth-resolved fiber photometry of amyloid plaque signals in freely behaving Alzheimer's disease mice

Alzheimers disease pathology typically manifests itself across multiple brain regions yet assessment at this scale in mouse models remains a challenge. This hinders the development of novel therapeutic approaches. Here we introduce a novel fiber photometry approach to monitor amyloid pathology in freely behaving mice. We first demonstrated that flat fiber-based photometry can detect amyloid signals across multiple brain regions under anesthesia after injecting a blood-brain barrier permeable tracer, Methoxy-X04. The depth profile of in vivo fluorescent signals was correlated with postmortem histological plaque signals. After confirming its feasibility ex vivo, we chronically implanted a tapered fiber for depth-resolved fiber photometry in freely behaving mice. After injecting Methoxy-X04, fluorescent signals increased in a depth-specific manner in Alzheimers mice, but not in wild-type littermates. While fiber photometry has been widely adopted to monitor neuronal and non-neuronal activity, our approach expands the capabilities to monitor molecular pathologies such as amyloid plaques, even in a freely behaving condition.

neuroscience↗

bioRxiv2022

Deep brain cancer metastasis detection with wide-volume Raman spectroscopy through a single tapered fiber

We propose a low-invasive method to enable implantable, large volume Raman spectroscopy in arbitrarily deep brain regions of the mouse brain. Using a single tapered fiber as thin as 1 m at the tip, we identified diagnostic markers of brain metastasis - the most frequent brain tumor in human adults - with overall accuracy [≥] 90%. We view our approach as a promising complement to the existing palette of tools for optical interrogation of the brain.

neuroscience↗

bioRxiv2021

Influence of anatomical features of different brain regions on the spatial localization of fiber photometry signals

Fiber photometry is widely used in neuroscience labs for in vivo detection of functional fluorescence from optical indicators of neuronal activity with a simple optical fiber. The fiber is commonly placed next to the region of interest to both excite and collect the fluorescence signal. However, the path of both excitation and fluorescence photons is altered by the uneven optical properties of the brain, due to local variation of the refractive index, different cellular types, densities and shapes. Nonetheless, the effect of the local anatomy on the actual shape and extent of the volume of tissue that interfaces with the fiber has received little attention so far. To fill this gap, we measured the size and shape of fiber photometry efficiency field in the primary motor and somatosensory cortex, in the hippocampus and in the striatum of the mouse brain, highlighting how their substructures determine the detected signal and the depth at which photons can be mined. Importantly, we show that the information on the spatial expression of the fluorescent probes alone is not sufficient to account for the contribution of local subregions to the overall collected signal, and it must be combined with the optical properties of the tissue adjacent to the fiber tip.

neuroscience↗

bioRxiv2021

Numerical calculation of the light propagation in tapered optical fibers for optical neural interfaces

As implantable optical systems recently enabled new approaches to study the brain with optical radiations, tapered optical fibers emerged as promising implantable waveguides to deliver and collect light from sub-cortical structures of the mouse brain. They rely on a specific feature of multimodal fiber optics: as the waveguide narrows, the number of guided modes decreases and the radiation can gradually couple with the environment. This happens along a taper segment whose length can be tailored to match with the depth of functional structures of the mouse brain, and can extend for a few millimeters. This anatomical requirement results in optical systems which have an active area that is very long compared to the wavelength of the light they guide and their behavior is typically estimated by ray tracing simulations, because finite element methods are too computationally demanding. Here we present a computational technique that exploits the beam-envelope method and the cylindrical symmetry of the fibers to provide an efficient and exact calculation of the electric field along the fibers, which may enable the design of neural interfaces optimized to meet different goals.

neuroscience↗

bioRxiv2020

Ray tracing models for estimating light collection properties of microstructured tapered optical fibers for optical neural interfaces

Tapered optical fibers (TFs) were recently employed for depth-resolved monitoring of functional fluorescence in sub-cortical brain structures, enabling light collection from groups of a few cells through small optical windows located on the taper edge [1]. Here we present a numerical model to estimate light collection properties of microstructured TFs implanted in scattering brain tissue. Ray tracing coupled with Henyey-Greenstein scattering model enables the estimation of both light collection and fluorescence excitation fields in three dimensions, whose combination is employed to retrieve the volume of tissue probed by the device.

bioengineering↗

bioRxiv2018

Multipoint and large volume fiber photometry with a single tapered optical fiber implant

Techniques to monitor functional fluorescence signal from the brain are increasingly popular in the neuroscience community. However, most implementations are based on flat cleaved optical fibers (FFs) that can only interface with shallow tissue volumes adjacent to the fiber opening. To circumvent this limitation, we exploit modal properties of tapered optical fibers (TFs) to structure light collection over the wide optically active area of the fiber taper, providing an approach to efficiently and selectively collect light from the region(s) of interest. While being less invasive than FFs, TF probes can uniformly collect light over up to 2 mm of tissue and allow for multisite photometry along the taper. Furthermore, by micro-structuring the non-planar surface of the fiber taper, collection volumes from TFs can also be engineered arbitrarily in both shape and size. Owing to the abilities offered by these probes, we envision that TFs can set a novel, powerful paradigm in optically targeting not only the deep brain, but, more in general, any biological system or organ where light collection from the deep tissues is beneficial but challenging because of tissue scattering and absorption.

neuroscience↗

bioRxiv2017

Exploiting modal demultiplexing properties of tapered optical fibers for tailored optogenetic stimulation

Optogenetic control of neural activity in deep brain regions requires precise and flexible light delivery with non-invasive devices. To this end, Tapered Optical Fibers (TFs) represent a minimally-invasive tool that can deliver light over either large brain volumes or spatially confined subregions. This work links the emission properties of TFs with the modal content injected into the fiber, finding that the maximum transversal propagation constant (kt) and the total number of guided modes sustained by the waveguide are key parameters for engineering the mode demultiplexing properties of TFs. Intrinsic features of the optical fiber (numerical aperture and core/cladding diameter) define the optically active segment of the taper (up to [~]3mm), along which a linear relation between the propagating set of kt values and the emission position exists. These site-selective light-delivery properties are preserved at multiple wavelengths, further extending the range of applications expected for tapered fibers for optical control of neural activity.

neuroscience↗

bioRxiv2016

Dynamically controlled light delivery over large brain volumes through tapered optical fibers

Optogenetics promises spatiotemporal precise control of neural processes using light. However, the spatial extent of illumination within the brain is difficult to control and cannot be adjusted using standard fiber optics. We demonstrate that optical fibers with tapered tips can be used to illuminate either large brain volumes or dynamically selectable subregions. Remotely adjusting the light input angle to the fiber varies the light-emitting portion of the taper over several millimeters without movement of the implant. We use this mode to activate dorsal versus ventral striatum of individual mice and reveal different effects of each manipulation on motor behavior. Conversely injecting light over the full numerical aperture of the fiber results in light emission from the entire taper surface, achieving broader and more efficient optogenetic activation of neurons when compared to the standard flat-faced fiber stimulation. Thus, tapered fibers permit focal or broad illumination that can be precisely and dynamically matched to experimental needs.

neuroscience↗