Cholesterol and lipid-associated transcriptional signature in chronic myeloid leukemia patients with nilotinib-induced hypercholesterolemia

Abstract The efficacy of nilotinib in patients with newly diagnosed Chronic Myeloid Leukemia (CML) has been extensively demonstrated in clinical trials (Sacha et al., Future Oncol. 2019). Although nilotinib provides superior overall survival and deeper molecular responses compared to other tyrosine kinase inhibitors, it has been associated with various adverse events. Among these, hypercholesterolemia (HC) is one of the most frequently reported (Rea et al., Haematologica 2014). Indeed, nilotinib can exacerbate vascular risk factors by increasing low-density lipoprotein cholesterol levels (Minson et al., Blood Advances 2019).In our study, we investigated 22 newly diagnosed CML patients who received first-line treatment with nilotinib at a dose of 300mg BID. During treatment, 13 of these patients developed HC. No Ph+ nuclei were detected in any patients after 12 months of nilotinib treatment (Trojani et al., Cancers 2025).Bone marrow (BM) Lin+ and BM CD34+/Lin- cells were isolated at diagnosis and after 12 months of treatment, along with the same cell subsets from 10 healthy donors (CTRLs), using Miltenyi Microbeads. The CD34+/Lin- cells represent the hematopoietic stem and progenitor cell population, whereas the Lin+ fraction includes lymphocytes (B and T), natural killer cells, granulocytes, and monocytes/macrophages.We performed gene expression profiling of BM Lin+ cells from patients at diagnosis, comparing them to the BM Lin+ cells from the same patients after 12 months of nilotinib treatment and to the BM Lin+ cells from CTRLs, using Affymetrix HTA 2.0 array. A parallel analysis was conducted on BM CD34+/Lin- cells from the same individuals.We aimed to explore a possible correlation between a set of genes associated with lipid and cholesterol metabolism pathways and the transcriptional profiles of BM Lin+ and BM CD34+/Lin- cells in patients who developed HC following nilotinib treatment.To this end, we focused on a predefined set of 2,687 genes selected from the literature that investigated the role of Lin+ cells in the pathological development of human atherosclerotic plaques, which are strongly influenced by HC (Bashore et al., Arterioscler. Thromb. Vasc. Biol.2024; Depuydt et al., Circ. Res. 2020; Lu et al., Biomolecules 2024). Gene Set Enrichment Analysis was performed on this set using the clusterProfiler package in R (Yu et al., OMICS.2012).The gene set resulted significantly enriched (adjusted p-value < 10-20) with 456 genes (out of 2,687) belonging to the leading-edge subset, i.e. the core group of genes within the gene set that contribute most strongly to the Normalized Enrichment Scores in the Lin+ cells analysis. These genes, although not significantly differentially expressed, lie at the extremes of the genes ranked by fold change and are upregulated in patients who developed HC. Mainly, we found that 41 genes belonged to the KEGG Lipid and atherosclerosis pathway (hsa05417), 20 genes were included in the Fluid shear stress and atherosclerosis (hsa05418), and 7 genes were associated with Cholesterol metabolism (hsa04979). Particularly, CAMK2D and APOB were associated with both HC and coronary artery disease (CAD) whereas CYP51A1 to cholesterol biosynthesis (Anlar et al., Biomol. and Biomed. 2025).From the CD34+/Lin- cells analysis, the gene set was significantly enriched (adjusted p-value < 10-30) with 863 genes (out of 2,687) belonging to the leading-edge subset and upregulated in patients who developed HC. Consistent with Lin+ cells findings, we identified 43 genes mapping to hsa05417, 27 genes associated with hsa05418, and 7 genes linked to hsa04979. Notably, RAC1 was involved in in HC-induced atherosclerotic plaques calcification (Healy et al., Arterioscler. Thromb. Vasc. Biol. 2020), while CD36 upregulation promoted atherosclerotic plaque development via cJUN activation (Sozen et al., Redox Biol. 2014).In conclusion, we identified the overexpression of a set of 24 genes including SOAT1 (hsa04979), JUN, HSP90AA1, HSP90B1, LYN, and VDAC3 which unravelled a signature of atherosclerotic development and CAD in both BM Lin+Ph- cells and BM CD34+/Lin-Ph- cells from CML patients who developed nilotinib-induced HC (Uyy et al., Sci. Rep. 2022).To the best of our knowledge, this is the first enrichment-based signature with potential utility for CML patient stratification. Future studies involving larger cohorts and refined gene panels may improve its predictive value and guide personalized therapeutic approaches.