Background <p>Mesenchymal stem cells (MSC) play a vital role in bone regeneration. Poly-(l-lactide-co-ε-caprolactone) scaffolds functionalised with modified rhamnogalacturonan-I (RG-I) potato pectin, can modulate inflammation and promote bone regeneration in-vitro and in-vivo by modulating the action of the galactoside-binding galectin-3. In this study, we determined the binding affinity to galectin-3 of potato unmodified RG-I (PU) and its arabinose-deficient form (PA) and investigated the transcriptomic effects of PA treatment on human MSCs evaluated through in-silico pathway analysis in relation to galectin-3.</p> Methods <p>The binding affinity of RG-I (PU and PA) to galectin-3 was assessed by tryptophan fluorescence spectroscopy. Human MSC (hMSC) isolated from the bone marrow of elderly patients (&gt; 60yrs), were analysed by transcriptomic profiling. The effect of PA surface coating on gene expression was assessed in-silico by the ingenuity pathway analysis (IPA).</p> Results <p>RG-I binds to galectin-3 with a binding affinity of 8.66 × 10^− 6 M. Galactose sidechains of PA resulted in ~ 10-fold increased binding of RG-I to galectin-3 compared with PU. Forty-two genes were found to be differentially expressed (DE) in hMSCs cultured on PA surface coating, with a false-discovery rate (FDR) &lt; 0.1. IPA of these DE genes including LGALS3, encoding for galectin-3, showed enrichment for organismal disorders-abnormalities, connective tissue and skeletal muscular disorders, immunological and inflammatory diseases, and identified three gene networks: infectious diseases, immune &amp; inflammatory response and cell cycle control.</p> Conclusions <p>This study indicates that modified potato pectin (PA) can regulate the expression of a broad range of genes, including galectin-3, that are involved in cellular, inflammatory, and immunological functions of hMSCs and may potentially be used to promote bone regeneration via modulation of inflammation.</p>