Biology subjects

Neto, N.

Publications and source records attributed to Neto, N..

4 recordsLinked to original sources

bioRxiv2023

2P-FLIM unveils time-dependent metabolic shifts during osteogenic differentiation with a key role of lactate to fuel osteogenesis via glutaminolysis identified

Human mesenchymal stem cells (hMSCs) fuel discrete biosynthetic pathways to multiply and differentiate into specific cell lineages; with undifferentiated hMSCs showing reliance on glycolysis. hMSCs differentiating towards an osteogenic phenotype rely on oxidative phosphorylation as an energy source. Here, the metabolic profile of hMSCs was profiled during osteogenic differentiation over 14 days using a non-invasive live-cell imaging platform- two-photon fluorescence lifetime imaging microscopy (2P-FLIM) which images and measures NADH fluorescence. During osteogenesis, we observe a higher dependence on oxidative phosphorylation for cellular energy; concomitant with an increased reliance on anabolic pathways. We validated this metabolic profile using qPCR and extracellular metabolite analysis and observed a higher reliance on glutaminolysis in the earlier time-points of osteogenic differentiation. Based on the results obtained, we sought to promote glutaminolysis further during osteogenic differentiation. An indirect method of promoting glutaminolysis was explored so as to not impact cellular differentiation. As Lactate has been shown to promote glutamine uptake via c-Myc activation triggering expression of glutamine transmembrane transporters and glutaminase 1; we chose to increase extracellular lactate concentrations to drive increased glutaminolysis rates leading to higher levels of mineral deposition and osteogenic gene expression. Lactate supplementation of osteogenic medium also promoted upregulation of lactate metabolism and increased the expression of transmembrane cellular lactate transporters. Higher rates of lactate dehydrogenase gene expression coupled with higher NADH fluorescence intensity demonstrate a conversion of lactate to pyruvate. During this conversion, NADH is formed by the reverse enzymatic reaction of lactate dehydrogenase resulting in increased NADH fluorescence intensity. In order to evaluate the importance of glutaminolysis and lactate metabolism in osteogenic differentiation, these metabolic pathways were shut down using BPTES and -CHC respectively which led to reduced hMSC mineralisation. In summary, we demonstrate that hMSCs osteogenic differentiation has a temporal metabolic profile and shift that is observed as early as day 3 of cell culture. Osteogenic differentiation was demonstrated to be directly dependent on OxPhos and on glutaminolysis and validated using biochemical assays. Furthermore, extracellular lactate is an essential metabolite to ensure osteogenic differentiation as a metabolic fuel and signalling molecule to promote glutaminolysis. These findings have significant impact in generating potent approaches towards bone tissue engineering in vitro and in vivo by engaging directly with metabolite driven osteogenesis.

bioengineering↗

bioRxiv2020

Intracellular label-free detection of mesenchymal stem cell metabolism within a perivascular niche-on-a-chip

The stem cell niche at the perivascular space in human tissue plays a pivotal role in dictating the overall fate of stem cells within it. Mesenchymal stem cells (MSCs), in particular, experience influential microenvironmental conditions, which induce specific metabolic profiles that affect processes such as cell differentiation and dysregulation of the immunomodulatory funtion. Reports focusing specifically on the metabolic status of MSCs under the effect of pathophysiological stimuli - in terms of flow velocities, shear stresses or oxygen tension - do not model heterogenous gradients, highlighting the need of more advanced models reproducing the metabolic niche. Organ-on-a-chip technology offers the most advanced tools for stem cell niche modelling thus allowing for controlled dynamic culture conditions while profiling tunable oxygen tension gradients. However, current systems for live cell detection of metabolic activity inside microfluidic devices require the integration of microsensors that allow for extracellular measurments only, giving innacurate and indirect information about the metabolic state of cells. Here, we present a metabolic toolbox coupling a miniatuirzed in vitro system for human-MSCs dynamic culture, that mimics microenvironmental conditions of the perivascular niche, with high-resolution imaging of intracellular metabolism. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we monitor the spatial metabolic machinery and correlate it with experimentally validated intracellular oxygen concentration after designing the oxygen tension decay along the fluidic chamber by in silico models prediction. Our platform allows for the subjection of a metabolic profile to MSCs, mimicking the physiological niche in space and time, and its real-time monitoring representing a functional tool for modelling perivascular niches, relevant diseases and metabolic-related uptake of pharmaceuticals.

bioengineering↗

bioRxiv2019

A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses

Stem cells and the niche in which they reside feature a complex microenvironment with tightly regulated homeostasis, cell-cell interactions and dynamic regulation of metabolism. A significant number of organoid models has been described over the last decade, yet few methodologies can enable single cell level resolution analysis of the stem cell niche metabolic demands, in real-time and without perturbing integrity. Here, we studied the redox metabolism of Lgr5-GFP intestinal organoids by two emerging microscopy approaches based on luminescence lifetime measurement - fluorescence-based FLIM for NAD(P)H, and phosphorescence-based PLIM for real-time oxygenation. We found that exposure of stem (Lgr5-GFP) and differentiated (no GFP) cells to high and low glucose concentrations resulted in measurable shifts in oxygenation and redox status. NAD(P)H-FLIM and O2-PLIM both indicated that at high basal glucose conditions, Lgr5-GFP cells had lower activity of oxidative phosphorylation when compared with cells lacking Lgr5. However, when exposed to low (0.5 mM) glucose, stem cells utilized oxidative metabolism more dynamically than non-stem cells. The high heterogeneity of complex 3D architecture and energy production pathways of Lgr5-GFP organoids were also confirmed by the extracellular flux (XF) analysis. Our data reveals that combined analysis of NAD(P)H-FLIM and organoid oxygenation by PLIM represents promising approach for studying stem cell niche metabolism in a live readout.

cell biology↗

bioRxiv2018

Improving Metagenomic Assemblies Through Data Partitioning: a GC content approach

Assembling metagenomic data sequenced by NGS platforms poses significant computational challenges, especially due to large volumes of data, sequencing errors, and variations in size, complexity, diversity and abundance of organisms present in a given metagenome. To overcome these problems, this work proposes an open-source, bioinfor-matic tool called GCSplit, which partitions metagenomic sequences into subsets using a computationally inexpensive metric: the GC content. Experiments performed on real data show that preprocessing short reads with GCSplit prior to assembly reduces memory consumption and generates higher quality results, such as an increase in the N50 metric and the reduction in both the L50 value and the total number of contigs produced in the assembly. GCSplit is available at https://github.com/mirand863/gcsplit.

bioinformatics↗