RNA-seq dataset of subcutaneous adipose tissue: Transcriptional differences between obesity and healthy women

In this data article, we present the dataset from the RNA-Seq analysis of subcutaneous adipose tissue collected from 5 healthy normal weight women (NW, age 37 +/- 6.7 years, BMI 24.3 +/- 0.9 kg/m(2)) and 5 obese women (OBF, age 41 +/- 12.5 years, BMI 38.2 +/- 4.6 kg/m(2)). Raw data obtained from Illumina NextSeq 500 sequencer were processed through BlueBee (R) Genomics Platform while differential expression analysis was performed with the DESeq2 R package and deposited in the GEO public repository with GSE166047 as accession number. Specifically, 20 samples divided between NW (control), OBF (obese women), OBM (obese male) and OBT2D (obese women with diabetes) are deposited in the GSE166047. We hereby describe only 10 samples (5 healthy normal weight women reported as NW and 5 obese women reported as OBF) because we refer to the data published in the article "Transcriptional characterization of Subcutaneous Adipose Tissue in obesity affected women highlights metabolic dysfunction and implications for lncRNAs" (DOI: 10.1016/j.ygeno.2021.09.014). Pathways analyses were performed on g:Profiler, Enrichr, ClueGO and GSEA to gain biological insights on gene expression. Raw data reported in GEO database along with detailed methods description reported in this data article could be reused for comparisons with other datasets on the topic to obtain transcriptional differences in a wider co-hort. Moreover, detailed pathways analysis along with cross-referenced data with other datasets will allow to identify novel dysregulated pathways and genes responsible for this regulation. The biological interpretation of this dataset, along with related in vitro experiments, is reported by Rey et al., in Genomics (DOI: 10.1016/j.ygeno.2021.09.014). (C) 2021 Published by Elsevier Inc

Therapeutic effect of neural progenitor cells expanded in the 3D nano-engineered Nichoid substrate in a Parkinson’s disease preclinical model

3D microscaffoldsare becoming more and more relevant in regenerative medicine, as they lead to the creation of a structure similar to a physiologicalniche. An example is the nano-engineered Nichoid, a 3D structure in which the cells are able to proliferate. In this work,we investigated the proliferation and stemness properties of Er-NPCswhen grown inside the Nichoid, and their potential therapeutic application in the treatment of Parkinson\u2019s Disease.3D microscaffolds are becoming more and more relevant in regenerative medicine, as they lead to the creation of a structure similar to a physiological niche. An example is the nano-engineered Nichoid, a 3D structure in which the cells are able to proliferate. In this work, we investigated the proliferation and stemness properties of Er-NPCs when grown inside the Nichoid, and their potential therapeutic application in the treatment of Parkinson\u2019s Disease

Bone Marrow Mesenchymal Stem Cells Expanded Inside the Nichoid Micro-Scaffold: a Focus on Anti-Inflammatory Response

Purpose Mesenchymal stem cells (MSCs) represent a promising source for stem cell therapies in numerous diseases, including pediatric respiratory system diseases. Characterized by low immunogenicity, high anti-inflammatory, and immunoregulatory features, MSCs demonstrated an excellent therapeutic profile in numerous in vitro and preclinical models. MSCs reside in a specialized physiologic microenvironment, characterized by a unique combination of biophysical, biochemical, and cellular properties. The exploitation of the 3D micro-scaffold Nichoid, which simulates the native niche, enhanced the anti-inflammatory potential of stem cells through mechanical stimulation only, overcoming the limitation of biochemical and xenogenic growth factors application.Materials and Methods In this work, we expanded pediatric bone marrow MSCs (BM-MSCs) inside the Nichoid and performed a complete cellular characterization with different approaches including viability assays, immunofluorescence analyses, RNA sequencing, and gene expression analysis.Results We demonstrated that BM-MSCs inside the scaffold remain in a stem cell quiescent state mimicking the condition of the in vivo environment. Moreover, the gene expression profile of these cells shows a significant up-regulation of genes involved in immune response when compared with the flat control.Conclusion The significant changes in the expression profile of anti-inflammatory genes could potentiate the therapeutic effect of BM-MSCs, encouraging the possible clinical translation for the treatment of pediatric congenital and acquired pulmonary disorders, including post-COVID lung manifestations

Neural precursor cells expanded inside the 3d micro-scaffold nichoid present different non-coding rnas profiles and transcript isoforms expression: Possible epigenetic modulation by 3d growth

Non-coding RNAs show relevant implications in various biological and pathological processes. Thus, understanding the biological implications of these molecules in stem cell biology still represents a major challenge. The aim of this work is to study the transcriptional dysregulation of 357 non-coding genes, found through RNA-Seq approach, in murine neural precursor cells expanded inside the 3D micro-scaffold Nichoid versus standard culture conditions. Through weighted co-expression network analysis and functional enrichment, we highlight the role of non-coding RNAs in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Moreover, as non-coding RNAs are poorly conserved between species, we focus on those with human homologue sequences, performing further computational characterization. Lastly, we looked for isoform switching as possible mechanism in altering coding and non-coding gene expression. Our results provide a comprehensive dissection of the 3D scaffold Nichoid’s influence on the biological and genetic response of neural precursor cells. These findings shed light on the possible role of non-coding RNAs in 3D cell growth, indicating that also non-coding RNAs are implicated in cellular response to mechanical stimuli

Sistema otticamente accessibile per studi su uova embrionate

Sistema otticamente accessibile per studi su uova embrionate caratterizzato dal fatto di comprendere un disco di forma circolare e con bordi interni leggermente inclinati; detto disco comprende un foro passante centrale; detto foro è chiuso da una piastrina trasparente; detto foro passante è atto ad essere accostato alla membrana respiratoria di un uovo embrionato

Dissecting the effect of a 3D microscaffold on the transcriptome of neural stem cells with computational approaches: A focus on mechanotransduction

3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds, we focus on the Nichoid, a miniaturized scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular responses simply by subjecting the cells to mechanical stimuli. This kind of influence results in different cellular morphology and organization, but the molecular bases of these changes remain largely unknown. Through RNA-Seq approach on murine neural precursors stem cells expanded inside the Nichoid, we investigated the deregulated genes and pathways showing that the Nichoid causes alteration in genes strongly connected to mechanobiological functions. Moreover, we fully dissected this mechanism highlighting how the changes start at a membrane level, with subsequent alterations in the cytoskeleton, signaling pathways, and metabolism, all leading to a final alteration in gene expression. The results shown here demonstrate that the Nichoid influences the biological and genetic response of stem cells thorough specific alterations of cellular signaling. The characterization of these pathways elucidates the role of mechanical manipulation on stem cells, with possible implications in regenerative medicine applications

Advances in Tissue Engineering and Innovative Fabrication Techniques for 3-D-Structures: Translational Applications in Neurodegenerative Diseases

In the field of regenerative medicine applied to neurodegenerative diseases, one of the most important challenges is the obtainment of innovative scaffolds aimed at improving the development of new frontiers in stem-cell therapy. In recent years, additive manufacturing techniques have gained more and more relevance proving the great potential of the fabrication of precision 3-D scaffolds. In this review, recent advances in additive manufacturing techniques are presented and discussed, with an overview on stimulus-triggered approaches, such as 3-D Printing and laser-based techniques, and deposition-based approaches. Innovative 3-D bioprinting techniques, which allow the production of cell/molecule-laden scaffolds, are becoming a promising frontier in disease modelling and therapy. In this context, the specific biomaterial, stiffness, precise geometrical patterns, and structural properties are to be considered of great relevance for their subsequent translational applications. Moreover, this work reports numerous recent advances in neural diseases modelling and specifically focuses on pre-clinical and clinical translation for scaffolding technology in multiple neurodegenerative diseases

Expansion and characterization of human adipose derived stem cells in the 3D nano-engineered Nichoid substrate

The use of 3D microscaffolds, such as the Nichoid, in regenerative medicine is becoming more and more relevant, as they mimic an architectural environment that recreates the physiological stem cells niche. In this work, we investigated the proliferation and stemness properties of hADSCs when grown inside the Nichoid

Therapeutic effect of neural progenitor cells expanded in the 3D nano-engineered Nichoid substrate in a Parkinson’s disease preclinical model

INTRODUCTION: In regenerative medicine, biomaterials have been used to create 3D micro scaffolds, such as the one named \u201cNichoid\u201d, which mimics the biomechanical characteristics of stem cell niches. The aim of this study was to investigate: i) the proliferation, differentiation and stemness properties of neural precursor cells (NPCs) following their cultivation inside the Nichoid substrate; ii) the therapeutic effect and safety in vivo of NPCs cultivated inside the Nichoid in preclinical experimental model of Parkinson\u2019s Disease (PD). METHODS: Nichoids were fabricated by two photon laser polymerization using a photosensitive resin. NPCs were grown for different periods inside the Nichoid (1x104 cells at plating). Growth curves were performed and cells features were characterized by immunofluorescence, Western Blot, and Real Time PCR analysis. Parkinsonism was induced by the intraperitoneal administration of MPTP in C57/black mice by using an acute protocol. NPCs were transplanted in a murine experimental model of PD after a 7 days\u2019 growth inside the Nichoid. RESULTS: NPCs grown inside the Nichoid create a 3D carpet expanding inside the scaffold. 7 days after plating, cells grown inside the Nichoid show a significantly higher proliferation than in normal floating culture conditions. NPCs expanded inside the Nichoid maintain their biological features and show an increase in stemness potential, as demonstrated by immunofluorescence, Real Time-PCR, Western blot and methylation assay. The therapeutic effect and safety of Nichoid-grown NPCs was evaluated by their intrastriatal infusion (7x104 cells) in PD affected mice. Behavioral performances were evaluated with two different tests showing that Nichoid-grown NPCs promoted the recovery of PD symptoms and favor the expression of tyrosine hydroxylase in the pathology affected brain areas. CONCLUSIONS: Stem cells showed an increase in stemness potential when grown inside the Nichoid, showing great promise and strong application in the field of regenerative medicine applied to neurodegenerative disease

Therapeutic effect of neural progenitor cells expanded in the 3D nano-engineered Nichoid substrate in a Parkinson’s disease preclinical model

INTRODUCTION: The use of biomaterials allows to generate active biophysical signals for directing stem cell fate through 3D microscaffolds, such as the one named \u201cNichoid\u201d [1]. The aim of this study was to investigate: i) the proliferation, differentiation and stemness properties of neural precursor cells (NPCs) [2, 3] following their cultivation in the Nichoid substrate; ii) the therapeutic effect and safety in vivo of NPCs cultivated in the Nichoid in preclinical experimental model of Parkinson\u2019s Disease (PD). METHODS: Nichoids were fabricated by 2PP onto circular glass coverslips using a home-made SZ2080 photoresist. NPCs were grown inside the Nichoid for 7 days (1x104 cells/cm2), counted and characterized with immunofluorescence, western blot, and Real Time PCR analysis. NPCs were transplanted in a murine experimental model of PD after a 7 days\u2019 growth inside the Nichoid. Parkinsonism was induced by the intraperitoneal administration of MPTP in C57/bl mice (Fig.1) [3]. RESULTS: NPCs grown inside the Nichoid create a 3D carpet expanding inside the scaffold. 7 days after plating, cells grown inside the Nichoid show a significantly higher cell viability and proliferation than in normal floating culture conditions. Furthermore, after being re-plated in floating conditions for 7 more days, the cells formed smaller but more abundant neurospheres respect to control. The replated cells, analyzed by immunofluorescence, Real Time-PCR and Western blot, demonstrate an increase in stemness markers. The therapeutic potential and safety of Nichoid-grown NPCs was evaluated by their intrastriatal infusion (7x104 cells) in the brain of PD affected mice. Behavioral performances were evaluated with two different tests showing that Nichoid-grown NPCs promoted the recovery of PD symptoms better than NPCs maintained in normal floating conditions. DISCUSSION & CONCLUSIONS: Stem cells demonstrated an increase in stemness potential when grown inside the Nichoid, showing great promise and strong application in the field of regenerative medicine applied to neurodegenerative disease. ACKNOWLEDGEMENTS: Financial support was received from \u201cNeurogel-en-Marche\u201d Foundation (France) to SC; Fondazione \u201cRomeo and Enrica Invernizzi\u201d to AMDG. ERC grant NICHOID, G.A. 646990 and NICHOIDS, G.A. 754467. Patent number I0178851 registered 8 march 2019. REFERENCES [1]Raimondi et al. Acta Biomater. 2013;9(1):4579-84. [2]Carelli et al. Cell Transplant. 2015;24(4):703-19. [3]Carelli et al. Neuropharmacol. 2017;119:76-90