Biology subjects

Guthrie, M.

Publications and source records attributed to Guthrie, M..

4 recordsLinked to original sources

bioRxiv2026

Spatiotemporal Proteome Remodeling Directs Human Hematopoietic Stem Cells via a Metabolic-Cytoskeletal Axis

Hematopoietic stem cells (HSCs) sustain the lifelong production of all blood and immune cells and are central to transplantation and gene therapies. However, the clinical use of these approaches remains limited due to the functional attrition of HSCs during ex vivo adaptation and expansion in culture. As these transitions are executed at the protein and structural level, the primary drivers of cellular adaptation have remained elusive in transcriptional studies. Here, we overcome the technical resolution limits of rare primary cells by integrating a scalable, ultra-low input proteomics pipeline with 3D super-resolution imaging to map the proteomic and spatial organization of primary human HSCs during ex vivo expansion. Our analysis reveals a previously unrecognized, metabolic-cytoskeletal axis that coordinates organelle reorganization and structural polarity. Perturbation of this axis preserves structural polarity while uncoupling it from biomass expansion, demonstrating that growth and functional deterioration are separable processes in ex vivo HSC culture. These findings establish a framework for understanding ex vivo HSC adaptation and expansion and inform the rational development of next-generation cellular therapies.

cell biology↗

bioRxiv2025

WS6 enables scalable ex vivo expansion and gene editing of epithelial basal stem cells

Modeling human epithelial diseases and developing cell-based therapies require robust methods to expand and manipulate epithelial stem and progenitor cells in vitro. Basal stem/progenitor cells from stratified epithelia can be expanded in 3T3-J2 fibroblast feeder cell co-culture systems, and the addition of the ROCK inhibitor Y-27632 enhances proliferation and culture longevity, a phenomenon described as conditional reprogramming. Here, we present a method incorporating the small molecule WS6 to further improve the proliferation and lifespan of cultured epithelial cells from multiple tissues, including airway, skin, and thymus. Cells maintained in this medium ( EpMED; FAD+Y+WS6) retain basal stem/progenitor cell identity and function, including the capacity to differentiate. We demonstrate their capacity to engraft in vivo in a tracheal transplantation model. In a second application, we generate clonal CRISPR-Cas9 genome edited nasal cultures, introducing targeted knockouts of DNAH5 or DNAI2 to create primary ciliary dyskinesia disease models. We anticipate that our method will have broad applications in epithelial cell biology, disease modeling, and regenerative medicine, while reducing reliance on immortalized or cancer cell lines and animal experimentation.

cell biology↗

bioRxiv2025

Argonaute-siRNA loading via the RNA-binding protein RDE-4 in C. elegans

Small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), associate with Argonaute proteins to control gene expression, impacting a wide range of cellular processes, such as antiviral defense, transposon silencing, and development1. Plants and animals typically have several classes of small RNAs, along with multiple Argonautes2. These Argonautes often confer distinct functionality to the various classes of small RNAs3. But how small RNAs are selectively loaded into the appropriate Argonaute is not well understood. miRNAs and siRNAs are typically generated from double-stranded RNA (dsRNA) precursors by the endoribonuclease Dicer4. siRNAs are often processed from fully base-paired precursors derived from various endogenous and exogenous sources, whereas miRNAs typically originate from genetically encoded partially base-paired hairpins1. In C. elegans, Dicer/DCR-1 processing of siRNAs and a related small RNA class, known as 26G- RNAs, is mediated by the dsRNA-binding protein RDE-45-7. Here, we show that RDE-4 also facilitates loading of siRNAs (but not miRNAs) into the Argonaute RDE-1, but not into ALG-1, and loading of 26G-RNAs into the Argonaute ERGO-1. Although we do not find evidence that ALG-3/4 associated 26G-RNAs require RDE-4 for Argonaute loading, their levels are strongly reduced in rde-4 mutants indicating that RDE-4 is broadly required for their formation or stability. Our findings reveal a role for RDE-4 as a critical determinant of small RNA loading specificity and provide insight into the mechanisms by which small RNAs are selectively paired with their corresponding Argonautes.

biochemistry↗

bioRxiv2020

Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA clusters in cancer

Oncogenic extrachromosomal DNA elements (ecDNAs) promote intratumoral heterogeneity, creating a barrier for successful cancer treatments. The underlying mechanisms are poorly understood and studies are hampered in part by a lack of adequate tools enabling studies of ecDNA behavior. Here, we show that single-cell ecDNA copy numbers follow a Gaussian distribution across tumor cells in vitro and in patient glioblastoma specimens, suggesting uneven ecDNA segregation during mitosis. We established a CRISPR-based approach which leverages unique ecDNA breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying this method during mitosis revealed disjointed ecDNA inheritance patterns, providing an explanation for rapid ecDNA accumulation in cancer. Post-mitosis, ecDNAs tended to cluster and clustered ecDNAs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and shed new lights of mechanisms through which ecDNAs contribute to oncogenesis.

cancer biology↗