Biology subjects

Schmidt, M. D.

Publications and source records attributed to Schmidt, M. D..

5 recordsLinked to original sources

bioRxiv2024

Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation

In this study, we demonstrate that cytoskeletal state at the onset of directed differentiation is critical for the specification of human pluripotent stem cells (hPSCs) to all three germ layers. In particular, a polymerized actin cytoskeleton facilitates directed ectoderm differentiation, while depolymerizing F-actin promotes mesendoderm lineages. Applying this concept to a stem cell-derived islet (SC-islet) differentiation protocol, we show that depolymerizing F-actin with latrunculin A (latA) during the first 24 hours of definitive endoderm formation facilitates rapid exit from pluripotency and alters Activin/Nodal, BMP, JNK-JUN, and WNT pathway signaling dynamics. These signaling changes influence downstream patterning of the gut tube, leading to improved pancreatic progenitor identity and decreased expression of markers associated with other endodermal lineages. Continued differentiation generates islets containing a higher percentage of {beta} cells that exhibit improved maturation, insulin secretion, and ability to reverse hyperglycemia. Furthermore, this latA treatment reduces enterochromaffin cells in the final cell population and corrects differentiations from hPSC lines that otherwise fail to consistently produce pancreatic islets, highlighting the importance of cytoskeletal signaling at the onset of directed differentiation.

cell biology↗

bioRxiv2023

Comparative and Integrative Single Cell Analysis Reveals New Insights into the Transcriptional Immaturity of Stem Cell-Derived β Cells

Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived {beta} cells (SC-{beta} cells). However, the precise identity of SC-{beta} cells in relationship to primary fetal and adult {beta}-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-{beta} cells share a core {beta}-cell transcriptional identity with human adult and fetal {beta}-cells, however SC-{beta} cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-{beta} cells, irrespective of the derivation protocol used. Notably, fetal {beta}-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-{beta} cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.

cell biology↗

bioRxiv2022

Multiomic profiling defines cell fate plasticity of in vitro-derived islets

Transplantation of insulin-secreting {beta}-cells differentiated from human pluripotent stem cells holds great potential as a cell therapy for treating insulin-dependent diabetes. While these stem cell-derived islets (SC-islets) are able to reverse diabetes in animal models, they are not fully equivalent to their in vivo counterparts. To better define the state of the cell types generated within these SC-islets and provide a resource for identifying deficiencies in lineage specification, we used single-cell multiomic sequencing to simultaneously measure the chromatin accessibility and transcriptional profiles of SC-islets at multiple time points as well as primary human islets. The integrated analysis of both the transcriptional and chromatin landscape for each cell provided greater resolution for defining cell identity, allowing us to derive novel gene lists for identifying each islet cell type. Furthermore, this multiomic analysis revealed that the difference between SC-{beta} cells and enterochromaffin-like cells, which are a major off-target from in vitro differentiation, is a gradient of progressive cell states rather than a stark difference in identity. The chromatin landscape of primary human islets was much more restricted, suggesting that stem cell-derived cells are not fully locked into their cell fate. While long term culture of SC-islets both in vitro and in vivo does close overall chromatin state, only in vivo transplantation directs cells toward their correct identities. Collectively, our multiomic analysis demonstrates that both the chromatin and transcriptional landscapes play significant roles in islet cell identity, and these data can be used as a resource to identify specific deficiencies in the chromatin and transcriptional state of SC-islet cell types.

cell biology↗

bioRxiv2021

RNAStructViz: Graphical base pairing analysis

SummaryWe present a new graphical tool for RNA secondary structure analysis. The central feature is the ability to visually compare/contrast up to three base pairing configurations for a given sequence in a compact, standardized circular arc diagram layout. This is complemented by a built-in CT-style file viewer and radial layout substructure viewer which are directly linked to the arc diagram window via the zoom selection tool. Additional functionality includes the computation of some numerical information, and the ability to export images and data for later use. This tool should be of use to researchers seeking to better understand similarities and differences between structural alternatives for an RNA sequence. Availability and implementationhttps://github.com/gtDMMB/RNAStructViz/wiki Author contactsmschmidt34@gatech.edu, akirkpatrick3@gatech.edu, and heitsch@math.gatech.edu

bioinformatics↗

bioRxiv2018

Bumblebee visual allometry results in locally improved resolution and globally improved sensitivity

The quality of visual information that is available to an animal is limited by the size of its eyes. Differences in eye size can be observed even between closely related individuals but we understand little about how this affects visual quality. Insects are good models for exploring the effects of size on visual systems because many species exhibit size polymorphism, which modifies both the size and shape of their eyes. Previous work in this area has been limited, however, due to the challenge of determining the 3D structure of eyes. To address this, we have developed a novel method based on x-ray tomography to measure the 3D structure of insect eyes and calculate their visual capabilities. We investigated visual allometry in the bumblebee Bombus terrestris and found that size affects specific aspects of visual quality including binocular overlap, optical sensitivity across the field of view, and visual resolution in the dorsofrontal visual field. This holistic study on eye allometry reveals that differential scaling between different eye areas provides substantial flexibility for larger bumblebees to have improved visual capabilities.

neuroscience↗