Biology subjects

Cross, A. J.

Publications and source records attributed to Cross, A. J..

4 recordsLinked to original sources

bioRxiv2021

Mapping origins of variation in neural trajectories of human pluripotent stem cells

Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. We identified differences in the early lineage emergence across hPSC lines that mapped on the antero-posterior axis of embryonic development. RNA-seq analysis revealed dynamic transcriptomic patterns that defined the emergence of mesendodermal versus neuroectodermal lineages conserved across hPSC lines and cell line-specific transcriptional signatures that were invariant across differentiation. The stable cell line-specific transcriptomic patterns predicted the retinoic acid (RA) response of the cell lines, resulting in distinct bias towards fore-versus hind-brain fates. Replicate hPSC lines and paired adult donor tissue demonstrated that cells from individual humans expressed unique and long-lasting transcriptomic signatures associated with evolutionarily recent genes. In addition to this genetic contribution, we found that replicate lines from a single donor showed divergent brain regional fates linked to distinct chromatin states, indicating that epigenetic mechanisms also contribute to neural fate differences. This variation in lineage bias and its correlation with RA responsive gene expression was also observed in a large collection of hPSC lines. These results define transcriptomic differences in hPSCs that initiate a critical early step specifying anterior or posterior neural fates.

neuroscience↗

bioRxiv2019

Human cortical neural stem cells generate regional organizer states in vitro before committing to excitatory neuronal fates

Better understanding the progression of neural stem cells (NSCs) in the developing cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of neuropsychiatric disorders. Here we used RNA-sequencing, cell imaging and lineage tracing of mouse and human in vitro NSCs to model the generation of cortical neuronal fates. We show that conserved signaling mechanisms regulate the acute transition from proliferative NSCs to committed glutamatergic excitatory neurons. As human telencephalic NSCs developed from pluripotency in vitro, they first transitioned through organizer states that spatially pattern the cortex before generating glutamatergic precursor fates. NSCs derived from multiple human pluripotent lines varied in these early patterning states leading differentially to dorsal or ventral telencephalic fates. This work furthers systematic analysis of the earliest patterning events that generate the major neuronal trajectories of the human telencephalon.

neuroscience↗

bioRxiv2018

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

High-throughput sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of the biases associated with small RNA sequencing have focused on adapter ligation bias with limited evaluation of reverse transcription or amplification biases. Furthermore, evaluations of the accuracy of quantifications of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited and no study has yet evaluated differences in the quantification of isomiRs of altered length. In addition, no studies have yet compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.

genomics↗

bioRxiv2018

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

Human induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across nine time points over 5 broad conditions: self-renewal, early neuronal differentiation, neural precursor cells (NPCs), assembled rosettes, and differentiated neuronal cells that were validated using electrophysiology. We identified widespread changes in the expression of individual transcript features and their splice variants, gene networks, and global patterns of transcription. We next demonstrated that co-culturing human NPCs with rodent astrocytes resulted in mutually synergistic maturation, and that cell type-specific expression data can be extracted using only sequencing read alignments without potentially disruptive cell sorting. We lastly developed and validated a computational tool to estimate the relative neuronal maturity of iPSC-derived neuronal cultures and human brain tissue, which were maturationally heterogeneous but contained subsets of cells most akin to adult human neurons.

genomics↗