Cell-resolved pharmacodynamic profiling reveals tissue- and cell-population-specific activity of antisense oligonucleotide chemical conjugates in vivo

Chemical conjugation can modulate antisense oligonucleotide (ASO) pharmacology and improve organ-specific delivery, yet whole-tissue measurements provide limited information on cell-specific activity. Here, we used metastasis-associated lung adenocarcinoma transcript 1 (Malat1) knockdown as a pharmacodynamic readout to compare whole-tissue and cell-resolved activity of chemically conjugated ASOs in platelet-derived growth factor receptor alpha-enhanced green fluorescent protein (PDGFRα-eGFP) mouse model to assess their in vivo uptake in PDGFRα-expressing (GFP+) cells. This reporter mouse model uses PDGFRα as an exemplar cellular marker and provides an accessible tool for evaluating ASO conjugate activity within mesenchymal stromal and progenitor populations, mainly tissue fibroblasts. Following subcutaneous administration, Malat1 was quantified in whole tissues and cell-sorted PDGFRα+/GFP⁺ or PDGFRα-/GFP⁻ populations. ASO-mediated Malat1 reduction varied by tissue and conjugate chemistry, with palmitate conjugation producing the broadest extrahepatic activity and pronounced whole-tissue activity in heart and skeletal muscle. Cell-resolved analysis further revealed preferential palmitate-ASO activity within PDGFRα⁺ skeletal-muscle populations. Preliminary safety assessment also showed conjugate-dependent differences, with body-weight loss and ALT elevation in tocopherol-ASO-treated male mice and spleen enlargement in both sexes. These findings present an in vivo modelling system for evaluating cell-specific ASO activity and demonstrate the advantages of cell-resolved assessment over whole-tissue measurements.