Biology subjects

Morgan, D. C.

Publications and source records attributed to Morgan, D. C..

4 recordsLinked to original sources

bioRxiv2025

The molecular mechanism of uptake and cell-to-cell transmission of arginine-containing dipeptide repeat proteins.

Micro-satellite repeat expansion of the 5 GGGGCC 3 sequence in the C9orf72 gene is the most common monogenic form of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Dipeptide repeat proteins (DPRs) translated from the mutant allele can be detected in postmortem brains of afflicted individuals. The arginine containing peptides, poly-PR and poly-GR, are particularly noxious to cells. Both have been shown to undergo cell-cell transmission, but the underlying mechanisms are not understood. We found rapid internalization and nucleolar localization of bath-applied hemagglutinin (HA) tagged poly-PR with twenty repeats (HA-PR20) in cell lines and neurons. Small molecule and RNAi approaches implicated a temperature-dependent, fluid phase endocytosis mechanism in HA-PR20 uptake. We sought to identify DPR-related cell surface uptake factors using a high-resolution proximity labeling technique developed in the MacMillan group, termed {micro}Map. DPR-iridium conjugates identified candidate cell-surface proteins which were interrogated in an RNAi screen. Focusing on our strongest candidate, chondroitin sulfate proteoglycan 4 (CSPG4), we showed that cellular uptake of HA-PR20 is blocked by inhibition of glycosaminoglycan chain synthesis (using drugs or RNAi) and knockdown or ablation of CSPG4 (using RNAi or CRISPR editing). Reduction of CSPG4 protected PR20-induced neuronal toxicity. We used a dual reporter system to interrogate in vitro neuron-to-neuron transmission of PR50 and found that PR50 synthesized by one neuron readily spread to neighboring neurons. Transmission was significantly reduced when CSPG4 was knocked down. These results suggest CSPG4 is an important factor in poly-PR internalization and transmission and therefore may be a therapeutic target to slow DPR transmission and disease progression. Significance StatementA GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is the most common monogenic form of ALS/FTD. This expansion leads to dipeptide repeat protein (DPR) production through non-canonical translation of repeat-containing RNA. DPRs have been shown to transmit between cells, but how this occurs is not well understood. We identified the cell surface protein chondroitin sulfate proteoglycan 4 (CSPG4) as a mediator of the uptake and intercellular spread of toxic arginine-rich DPRs. Targeting CSPG4 may provide a strategy to block DPR transmission and slow disease progression.

neuroscience↗

bioRxiv2025

Micromapping (μMap) of HER2 Across Human Breast Cancers: Photocatalytic Proximity Labeling Identifies Primary Resistance Mechanisms and Functional Interactors

Interactions among receptor tyrosine kinases (RTKs), particularly HER2, are critical in driving the growth of certain breast cancer subtypes. However, the mechanisms of HER2 dependency and resistance to targeted therapies remain unclear. Using photocatalytic micromapping ({micro}Map) proximity labeling, we profiled the HER2 interactome across human breast cancer lines. We identify galectin family proteins as uniquely enriched in trastuzumab-resistant models, and show that genetic and pharmacological inhibition of galectins restores trastuzumab sensitivity. Mechanistically, galectin inhibition destabilized HER2 and other RTKs and enhanced antibody-mediated receptor degradation. Galectin inhibition in combination with trastuzumab triggered mitochondrial and endoplasmic reticulum stress pathways, revealing new mechanisms underlying HER2 signaling, dependency, and resistance in breast cancer. We also identified protein tyrosine phosphatase F (PTPRF) as a pan-cancer HER2 interactor, which is broadly upregulated and whose knockdown suppresses proliferation in HER2-low cancers. This work provides an extensive new interactomic resource and underscores the utility of proximity labeling for mapping complex cancer networks and identifying new therapeutic targets.

cancer biology↗

bioRxiv2025

Temporal Microenvironment Mapping (microMap) of Intracellular Trafficking Pathways of Cell-Penetrating Peptides Across the Blood-Brain Barrier

Peptides play critical roles in cellular functions such as signaling and immune regulation, and peptide-based biotherapeutics show great promise for treating various diseases. Among these, cell-penetrating peptides (CPPs) are particularly valuable for drug delivery due to their ability to cross cell membranes. However, the mechanisms underlying CPP-mediated transport, especially across the blood-brain barrier (BBB), remain poorly understood. Mapping intracellular CPP pathways is essential for advancing drug delivery systems, particularly for neurological disorders, as understanding how CPPs navigate the complex environment of the BBB could enable the development of more effective brain-targeted therapies. Here, we leverage a nanoscale proximity labeling technique, termed {micro}Map, to precisely probe the peptide- receptor interactions and intracellular trafficking mechanisms of photocatalyst-tagged CPPs. The unique advantage of the Map platform lies in the ability to control the timing of light exposure, which enables the collection of time-gated data, depending on when the blue light is applied to the cells. By harnessing this spatiotemporal precision, we can uncover key peptide-receptor interactions and cellular processes, setting the stage for new innovations in drug design and brain-targeted therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/633151v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1585958org.highwire.dtl.DTLVardef@151b288org.highwire.dtl.DTLVardef@a03efeorg.highwire.dtl.DTLVardef@87d6a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit

Gene regulatory network inference allows for the study of transcriptional control to identify the alteration of cellular processes in human diseases. Our group has developed several tools to model a variety of regulatory processes, including transcriptional (PANDA, SPIDER) and post-transcriptional (PUMA) gene regulation, and gene regulation in individual samples (LIONESS). These methods work by performing repeated operations on data matrices in order to integrate information across multiple lines of biological evidence. This limits their use for large-scale genomic studies due to the associated high computational burden. To address this limitation, we developed gpuZoo, which includes GPU-accelerated implementations of these algorithms. The runtime of the gpuZoo implementation in MATLAB and Python is up to 61 times faster and 28 times less expensive than the multi-core CPU implementation of the same methods. gpuZoo takes advantage of the modern multi-GPU device architecture to build a population of sample-specific gene regulatory networks with similar runtime and cost improvements by combining GPU acceleration with an efficient on-line derivation. Taken together, gpuZoo allows parallel and on-line gene regulatory network inference in large-scale genomic studies with cost-effective performance. gpuZoo is available in MATLAB through the netZooM package https://github.com/netZoo/netZooM and in Python through the netZooPy package https://github.com/netZoo/netZooPy.

systems biology↗