Biology subjects

Caldwell, M. A.

Publications and source records attributed to Caldwell, M. A..

7 recordsLinked to original sources

bioRxiv2026

Targeted Analysis of >1500 Plasma Proteoforms via Individual Ion Mass Spectrometry

Plasma proteomics has long sought to accessibly sense human biology, precisely detect disease states, and advance diagnostics through clinical translation. In recent years, companies with defined panels such as Olink and Somascan have entered the field to complement bottom-up mass spectrometry (BUP). This study leverages a novel mass spectrometry platform to capture targeted proteoform information lost by mainline antibody-, aptamer-, and BUP-driven workflows. The Plasma Proteoform Assay (PPA) uses Individual Ion Mass Spectrometry (I{superscript 2}MS) to resolve mixtures of intact proteins presented by direct injection. Two proteoform panels, PPA 526 and PPA 1514, were defined from human plasma samples obtained from 81 individuals. The panels quantify 526 proteoforms derived from 59 genes and 1,514 proteoforms from 155 genes, respectively. Reproducibility for both panels showed coefficients of variation below 20% for most proteoforms (59-80%). PPA was benchmarked in studies including subjects with hepatic cirrhosis (N=30) and resilient agers carrying a SERPINE1 (PAI 1) mutation (N=27). PPA signatures distinguished SERPINE1 mutation carriers from affected individuals and provided sufficient resolution to discriminate among cirrhosis disease stages. In summary, we present PPA 526 and PPA 1514, the first scalable plasma proteoform panels capable of tracking hundreds to thousands of targets in a few minutes per sample.

biochemistry↗

bioRxiv2026

Biomimetic miR-133a inhibitor activated scaffolds optimised for spinal cord repair promote neurite outgrowth and angiogenesis via neuronal cytoskeletal remodelling

Significant challenges in spinal cord injury include the loss of neural tissue, disruption of local vasculature, and intrinsic suppression of actin mobilisation in neurons, together preventing axonal regrowth. Here, we develop an implantable biomimetic microRNA (miR) inhibitor-activated scaffold that combines optimised matrix cues with transcriptomically defined RNA-based modulation of intrinsic neuronal pathways as a platform to support neuronal cell delivery and promote neurovascular repair. First, hyaluronic acid macroporous scaffolds functionalized with collagen-IV and fibronectin supported iPSC-derived neuronal spheroid formation and neurite extension. To identify a neurotrophic target, we performed analysis of public miRNA-mRNA interaction datasets, revealing that miR-133a regulates pathways involved in neuronal actin cytoskeletal organisation. MiR-133a inhibitors were complexed with the cell-penetrating peptide RALA to form nanoparticles, demonstrated >95% scaffold loading efficiency, sustained localised release over 28 days and enhanced neurite outgrowth from motor neurons and iPSC neurons. Bulk RNA-sequencing and transcriptomic analysis of iPSC neurons within the scaffolds demonstrated coordinated upregulation of actin-remodelling, cell-matrix adhesion and metabolic pathways, indicative of a cytoskeletally adaptable neuron. When employed in an ex vivo dorsal root ganglia model, scaffold-mediated miR-133a inhibition promoted neurite extension and integration of delivered iPSC neurons with injured neural tissue. Finally, miR-133a-inhibitor-activated scaffolds upregulated neurovascular genes, increased endothelial cell migration and enhanced blood vessel formation in vivo in a chick embryo assay. These findings identify miR-133a as a neurotrophic target, elucidate the underlying mechanisms of action through transcriptomic analysis and demonstrate that biomimetic scaffold-mediated inhibition of miR-133a can enhance neuronal delivery for multifaceted spinal cord repair applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/719922v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@13fcb26org.highwire.dtl.DTLVardef@13239c3org.highwire.dtl.DTLVardef@6e6f5eorg.highwire.dtl.DTLVardef@51ad93_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

PolyGraph - Flexible, Biocompatible & Electrically Optimised Graphene-Polymer Composites for Next-Generation Neural Interfaces

Neural interfacing materials must deliver exceptional electrochemical performance, while integrating safely with the central nervous system. In this study we develop PolyGraph, a flexible, conductive, and biocompatible graphene-polycaprolactone (PCL) nanocomposite designed to strike this balance, which enables fabrication of conformable multichannel microelectrode arrays. Optimised liquid-phase exfoliation produces conductive, biocompatible PVP-stabilised graphene nanosheets, which are incorporated into PCL to form flexible, processable composites - PolyGraph. This material demonstrates bio- and immuno-compatibility with sensitive primary and iPSC-derived neuronal and glial cells. PolyGraph achieves low impedance ([~]1.6 {Omega} cm2 @ 1 kHz) and high charge injection capacity (11.7 mC/cm2 for a 100 ms pulse), enhanced by NaOH surface roughening and AuPd coating. Leveraging their processability, PolyGraph composites are fabricated into flexible, individually isolated microneedle electrode arrays with biomimetic soft hyaluronic acid backings. These arrays demonstrate bidirectional neural interfacing capabilities, enabling both the delivery of controlled stimulation pulses in physiological buffer and high-resolution neuronal recording in murine brain slices, with machine learning-based event classification. Together, these advances establish PolyGraph as an optimal material platform for next-generation brain-computer interfaces and soft bioelectronic devices. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/673516v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@9beea5org.highwire.dtl.DTLVardef@150be08org.highwire.dtl.DTLVardef@1ec24d2org.highwire.dtl.DTLVardef@658209_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract & TOC Text PolyGraph, a flexible graphene-polycaprolactone nanocomposite, unites conductivity, biocompatibility, and processability for next-generation neural interfaces. Fabricated into microneedle arrays with ultra-flexible backings, PolyGraph enables bidirectional neuronal recording and stimulation in brain tissue, advancing brain-computer interface (BCI) and soft bioelectronic applications.

bioengineering↗

bioRxiv2025

Next-Generation Protein Sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6

The vast complexity of the proteome currently overwhelms any single analytical technology in capturing the full spectrum of proteoform diversity. In this study, we evaluated the complementarity of two cutting-edge proteomic technologies--single-molecule protein sequencing and individual ion mass spectrometry--for analyzing recombinant human IL-6 (rhIL-6) at the amino acid, peptide, and intact proteoform levels. For single-molecule protein sequencing, we employ the recently released Platinum(R) instrument. Next-Generation Protein Sequencing (NGPS) on Platinum utilizes cycles of N-terminal amino acid recognizer binding and aminopeptidase cleavage to enable parallelized sequencing of single peptide molecules. We found that NGPS produces single amino acid coverage of multiple key regions of IL-6, including two peptides within helices A and C which harbor residues that reportedly impact IL-6 function. For top-down proteoform evaluation, we use individual ion mass spectrometry (I2MS), a highly parallelized orbitrap-based charge detection MS platform. Single ion detection of gas-phase fragmentation products (I2MS2) gives significant sequence coverage in key regions in IL-6, including two regions within helices B and D that are involved in IL-6 signaling. Together, these complementary technologies deliver a combined 52% sequence coverage, offering a more complete view of IL-6 structural and functional diversity than either technology alone. This study highlights the synergy of complementary protein detection methods to more comprehensively cover protein segments relevant to biological interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/637157v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@82d72aorg.highwire.dtl.DTLVardef@1fc39f3org.highwire.dtl.DTLVardef@40a677org.highwire.dtl.DTLVardef@70f6c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics

The dynamic range challenge for detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundant proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between [~]1 {micro}g/mL and [~]10 pg/mL in absolute abundance, providing up to 105-fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 {micro}g/mL) were detected. The ability to monitor medium and some low abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.

biochemistry↗

bioRxiv2024

Lineage-specific CDK activity dynamics characterize early mammalian development

Cyclin-dependent kinases (CDK) are key regulatory enzymes that regulate proliferation dynamics and cell fate in response to extracellular inputs. It remains largely unknown how CDK activity fluctuates and influences cell commitment in vivo during early mammalian development. Here, we generated a transgenic mouse model expressing a CDK kinase translocation reporter (KTR) that enabled quantification of CDK activity in live single cells. By examining pre- and post- implantation mouse embryos at different stages, we observed a progressive decrease in CDK activity in cells from the trophectoderm (TE) prior to implantation. This drop correlated with the establishment of an FGF4-dependent signaling gradient through the embryonic-abembryonic axis. Furthermore, we showed that CDK activity levels do not determine cell fate decisions during pre-implantation development. Finally, we uncovered the existence of conserved regulatory mechanisms in mammals by revealing lineage-specific regulation of CDK activity in TE-like human cells.

developmental biology↗

bioRxiv2023

Top-down Proteomics of 10,000 Single Brain Cells

We introduce single-cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct analysis of intact proteins to process 10,836 single cells from the rat hippocampus. This new platform addresses the throughput bottleneck for single cell proteomics using mass spectrometry, boosting cell processing rates by >20-fold in the field. We identified 169 proteoforms <70 kDa from single brain cells and classified 2758 of them as neurons, astrocytes or microglia cell types.

biochemistry↗