Relationship between donor-derived cell-free DNA and tissue-based rejection-related transcripts in heart transplantation.

BACKGROUND: Endomyocardial biopsy (EMB)-based traditional microscopy remains the gold standard for the detection of cardiac allograft rejection, despite its limitation of inherent subjectivity leading to inter-reader variability. Alternative techniques now exist to surveil for allograft injury and classify rejection. Donor-derived cell-free DNA (dd-cfDNA) testing is now a validated blood-based assay used to surveil for allograft injury. The molecular microscope diagnostic system (MMDx) utilizes intragraft rejection-associated transcripts (RATs) to classify allograft rejection and identify injury. The use of dd-cfDNA and MMDx together provides objective molecular insight into allograft injury and rejection. The aim of this study was to measure the diagnostic agreement between dd-cfDNA and MMDx and assess the relationship between dd-cfDNA and MMDx-derived RATs, which may provide further insight into the pathophysiology of allograft rejection and injury. METHODS: This is a retrospective observational study of 156 EMB evaluated with traditional microscopy and MMDx. All samples were paired with dd-cfDNA from peripheral blood before EMB (up to 9 days). Diagnostic agreement between traditional histopathology, MMDx, and dd-cfDNA (threshold of 0.20%) was compared for assessment of allograft injury. In addition, the relationship between dd-cfDNA and individual RAT expression levels from MMDx was evaluated. RESULTS: MMDx characterized allograft tissue as no rejection (62.8%), antibody-mediated rejection (ABMR) (26.9%), T-cell-mediated rejection (TCMR) (5.8%), and mixed ABMR/TCMR (4.5%). For the diagnosis of any type of rejection (TCMR, ABMR, and mixed rejection), there was substantial agreement between MMDx and dd-cfDNA (76.3% agreement). All transcript clusters (group of gene sets designated by MMDx) and individual transcripts considered abnormal from MMDx had significantly elevated dd-cfDNA. In addition, a positive correlation between dd-cfDNA levels and certain MMDx-derived RATs was observed. Tissue transcript clusters were correlated with dd-cfDNA scores, including DSAST, GRIT, HT1, QCMAT, and S4. For individual transcripts, tissue ROBO4 was significantly correlated with dd-cfDNA in both nonrejection and rejection as assessed by MMDx. CONCLUSIONS: Collectively, we have shown substantial diagnostic agreement between dd-cfDNA and MMDx. Furthermore, based on the findings presented, we postulate a common pathway between the release of dd-cfDNA and expression of ROBO4 (a vascular endothelial-specific gene that stabilizes the vasculature) in the setting of antibody-mediated rejection, which may provide a mechanistic rationale for observed elevations in dd-cfDNA in AMR, compared to acute cellular rejection.

Tension Causes Unfolding of Intracellular Vimentin Intermediate Filaments.

Intermediate filament (IF) proteins are a class of proteins that constitute different filamentous structures in mammalian cells. As such, IF proteins are part of the load-bearing cytoskeleton and support the nuclear envelope. Molecular dynamics simulations show that IF proteins undergo secondary structural changes to compensate mechanical loads, which is confirmed by experimental in vitro studies on IF hydrogels. However, the structural response of intracellular IF to mechanical load is yet to be elucidated in cellulo. Here, in situ nonlinear Raman imaging combined with multivariate data analysis is used to quantify the intracellular secondary structure of the IF cytoskeletal protein vimentin under different states of cellular tension. It is found that cells under native cellular tension contain more unfolded vimentin than chemically or physically relaxed specimens. This indicates that the unfolding of IF proteins occurs intracellularly when sufficient forces are applied, suggesting that IF structures act as local force sensors in the cell to mark locations under large mechanical tension.

RNA Nanostructure Molecular Imaging.

Atomic force and transmission electron microscopies (AFM/TEM) are powerful tools to analyze RNA-based nanostructures. While cryo-TEM analysis allows the determination of near-atomic resolution structures of large RNA complexes, this chapter intends to present how RNA nanostructures can be analyzed at room temperature on surfaces. Indeed, TEM and AFM analyses permit the conformation of a large population of individual molecular structures to be observed, providing a statistical basis for the variability of these nanostructures within the population. Nevertheless, if double-stranded DNA molecular imaging has been described extensively, only a few investigations of single-stranded DNA and RNA filaments have been conducted so far. Indeed, technique for spreading and adsorption of ss-molecules on AFM surfaces or TEM grids is a crucial step to avoid disturbing RNA conformation on the surface. In this chapter, we present a specific method to analyze RNA assemblies and RNA-protein complexes for molecular microscopies.