Biology subjects

Gutierrez-Franco, A.

Publications and source records attributed to Gutierrez-Franco, A..

3 recordsLinked to original sources

bioRxiv2025

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro

RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly understood. Here, we investigate for the first time the role of the double-stranded RBP Staufen2 (STAU2) in human neurogenesis. Characterization of STAU2 knockout iPSC derived cells using scRNA-seq shows that loss of STAU2 disrupts neuroepithelial cell identity and accelerates neural differentiation by altering the activity of key transcription factors and driving early metabolic transitions. Additionally, STAU2 regulates the expression of miRNA host genes and alters miRNA-mediated post- transcriptional control in progenitor cells, which exerts additional effects on STAU2 regulated gene regulatory networks. These changes result in neural progenitor exhaustion, unstructured neural rosettes, and reduced organoid size. Together, our work uncovers a previously unrecognized role for STAU2 as a central regulator of early human neurogenesis, acting through both miRNA-mediated and transcriptional pathways to coordinate progenitor maintenance and neuronal fate specification.

molecular biology↗

bioRxiv2024

Quantification of transcript isoforms at the single-cell level using SCALPEL

Single-cell RNA sequencing (scRNA-seq) has facilitated the study of gene expression and the development of new tools to quantify transcript in individual cells. Yet, most of these methods have low sensitivity and accuracy. Here we present SCALPEL, a Nextflow-based tool to quantify and characterize transcript isoforms at the single-cell level using standard 3 based scRNA-seq data. SCALPEL predictions have higher sensitivity than other tools and can be validated experimentally. We have used SCALPEL to study the changes in isoform usage during mouse spermatogenesis and in the differentiation of induced pluripotent stem cells (iPSCs) to neural progenitors. These analyses allow the identification of novel cell populations that cannot be defined using conventional gene expression profiles, confirm known changes in 3 UTR length during cell differentiation, and identify cell-type specific miRNA signatures controlling isoform expression in individual cells. Together, our work highlights how SCALPEL expands the current scRNA-seq toolset to explore post-transcriptional gene regulation in individual cells from different species, tissues, and technologies to investigate the variability and the specificity of gene regulatory mechanisms at the single-cell level.

bioinformatics↗

bioRxiv2022

Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells

Single-cell transcriptomics methods have become very popular to study the cellular composition of organs and tissues and characterize the expression profiles of the individual cells that compose them. The main critical step in single-cell transcriptomics is sample preparation. Several methods have been developed to preserve cells after sample dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the types of cells to be processed. In this project, we perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq (scRNA-seq) on neural and glial cells derived from induced pluripotent stem cells (iPSCs) and highlight their strengths and weaknesses. We compared the cellular composition and expression profile of single-cell suspensions from fresh NPCs with that of NPCs preserved with Dimethyl Sulfoxide (DMSO), Methanol, vivoPHIX and Acetil-methanol (ACME). Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell, it strongly affects the cellular composition and the expression profile of the resulting datasets. In contrast, methanol fixed samples display a cellular composition like that of fresh samples while providing a good cell quality and smaller expression biases. Taken together, our results show that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations.

genomics↗