Smoke Tree Flavonoids Rewrite Gene Activity in Leukemia Cells, Study Finds

A trio of plant-derived flavonoids isolated from the heartwood of the smoke tree, Cotinus coggygria Scop., can profoundly rewire the genetic machinery of chronic myeloid leukemia cells, according to a new open-access study published in BMC Complementary Medicine and Therapies. The research, led by Ivana Pašić of the Institute for Oncology and Radiology of Serbia together with collaborators in Serbia and Germany, provides the most detailed picture yet of how three structurally related compounds—butin, butein, and sulfuretin—act on K562 leukemia cells at the level of the entire transcriptome. Rather than relying on a single readout of cell death, the team combined flow cytometry, caspase inhibition experiments, and three independent mRNA sequencing runs to map, gene by gene, what happens inside leukemic cells when these natural products go to work.

The smoke tree is a striking shrub best known for the wispy, smoke-like plumes that give it its common name, but its heartwood has long attracted attention from natural products chemists. Heartwood extracts of C. coggygria are rich in flavonoids, a sprawling family of plant secondary metabolites that includes many compounds with documented anticancer activity in laboratory settings. Earlier work had established that butin, butein, and sulfuretin exhibit cytotoxic effects against leukemia cells, yet the molecular mechanisms underlying these effects in K562 cells—a widely used model of chronic myeloid leukemia—remained poorly defined. The new study set out to close that gap by treating the cells with the purified compounds as well as with crude heartwood extracts prepared with ethanol, water, and a methylene chloride/methanol mixture.

The experimental design combined classical pharmacology with modern genomics. Flow cytometry was used to determine how the treatments altered cell cycle distribution and whether they triggered the activation of apoptosis, the programmed cell death pathway that many anticancer therapies seek to engage. To pin down the mode of cell death, the researchers employed caspase inhibition, a technique that reveals whether cell death depends on the caspase enzymes that execute apoptosis. The centerpiece of the study, however, was the transcriptomics: three independent mRNA sequencing experiments were performed on treated K562 cells, and the resulting data were subjected to differential gene expression analysis followed by pathway-level analyses using the Reactome and KEGG databases through gene set enrichment analysis, or GSEA. Network and pathway-cluster analyses then tied the individual enriched pathways together into coherent biological stories.

The headline finding is that all three flavonoids push leukemia cells in a broadly similar direction—toward growth suppression, a metabolic downshift, and the activation of adaptive stress-response networks—but each compound leaves its own distinctive fingerprint on the transcriptome. Butein emerged as the most transcriptionally aggressive of the three, inducing 809 differentially expressed genes. Butin followed with 439 differentially expressed genes, and sulfuretin produced 299. Despite these differences in breadth, the team identified 134 differentially expressed genes shared across all three treatments, suggesting a common core response to this family of flavonoids that may underlie their shared antileukemic activity.

Butin’s transcriptomic signature tells a story of systematic shutdown. Treatment with this compound produced a transcriptional shift marked by the suppression of RNA processing, mRNA splicing, translation initiation, and mitochondrial bioenergetics. In practical terms, the compound appears to choke off the leukemia cell’s ability to read out its genetic information, mature its messenger RNAs, and manufacture new proteins, while simultaneously starving the cell’s power plants. The enrichment analysis pointed specifically to downregulation of oxidative phosphorylation, the OXPHOS system that generates most of a cell’s ATP, and of the tricarboxylic acid cycle, or TCA cycle, which feeds that system. For rapidly dividing cancer cells, which depend heavily on coordinated protein synthesis and mitochondrial metabolism, this dual hit represents a serious metabolic and biosynthetic crisis.

Butein, the most potent transcriptional perturber, induced a strikingly coordinated downregulation of many of the same programs. Mitochondrial respiration, RNA maturation, mRNA maturation, and mRNA transport were all suppressed after butein treatment, indicating that the compound disrupts both the energy supply and the information-processing pipeline of the leukemic cell. The overlap between butin and butein is notable from a chemical biology standpoint: both compounds share a core flavonoid scaffold, and their convergent effects on mitochondrial and RNA-related pathways suggest that these processes may be particularly vulnerable targets for this class of molecules. At the same time, the fact that butein altered nearly twice as many genes as butin hints at additional, compound-specific activities that remain to be fully characterized.

Sulfuretin stood apart. Instead of the broad biosynthetic and metabolic shutdown seen with its two chemical cousins, sulfuretin displayed a distinct pattern characterized by positive enrichment of stress, inflammatory, immune, and proteasome-related pathways. In other words, treated cells mounted what looks like an adaptive stress response, ramping up programs associated with inflammation and protein quality control. Alongside this activation, the analysis revealed negative enrichment of RB1/E2F-associated G1/S transition programs—a reference to the molecular circuitry that governs the transition from the G1 phase of the cell cycle into DNA synthesis. Suppressing this program suggests that sulfuretin may hold leukemia cells at the G1 checkpoint, preventing them from committing to another round of cell division.

These findings matter because they move the field beyond the simple observation that a plant compound kills cancer cells in a dish. By resolving the transcriptomic architecture of the response, the study offers mechanistic hypotheses that can be tested directly: whether the compounds induce reactive oxygen species through mitochondrial dysfunction, whether the proteasome activation seen with sulfuretin reflects a genuine unfolded protein burden, and whether the shared 134-gene core response contains biomarkers that predict sensitivity to flavonoid treatment. The authors also emphasize that the framework they have built is not limited to leukemia. Because the transcriptomic signatures point to fundamental processes—protein synthesis, mitochondrial respiration, cell cycle control—their approach can be translated to other types of malignancy, where the same compounds might exploit different vulnerabilities depending on the tissue of origin.

The study also illustrates the power of pathway-level analysis over simple gene lists. Differential expression analysis alone can identify thousands of changed transcripts, but GSEA against curated databases such as Reactome and KEGG, combined with network and pathway-cluster analyses, revealed that the changed genes were not scattered at random. Instead, they converged on coherent biological modules—RNA processing, translation initiation, OXPHOS, TCA cycle, G1/S transition, proteasome function—that together explain how a flavonoid treatment can translate into cytotoxicity. The team’s careful handling of technical variation, documented in supplementary analyses showing sample clustering before and after batch correction, adds confidence that the observed signatures reflect biology rather than experimental noise.

For now, the work remains at the level of cell culture, and the usual caveats apply: concentrations that are cytotoxic in a dish do not automatically translate into safe and effective drugs, and the pharmacokinetics of flavonoids in the human body are notoriously complex. But the study delivers something that earlier cytotoxicity screens could not—a transcriptomic framework for further investigation of the antileukemic properties of butin, butein, and sulfuretin. As interest in natural products as sources of anticancer lead compounds continues to grow, the smoke tree’s heartwood chemistry has just become considerably more interesting, and the road from Balkan shrub to molecular medicine has gained a well-marked first milestone.

Subject of Research: Transcriptomic effects of Cotinus coggygria flavonoids on K562 myeloid leukemia cells

Article Title: Transcriptome analysis of K562 myeloid leukemia cells treated with butin, butein, and sulfuretin from the heartwood of Cotinus coggygria Scop.

Article References: Transcriptome analysis of K562 myeloid leukemia cells treated with butin, butein, and sulfuretin from the heartwood of Cotinus coggygria Scop.. (n.d.). https://doi.org/10.1186/s12906-026-05570-5

Image Credits: AI Generated

DOI: 10.1186/s12906-026-05570-5

Keywords: Cotinus coggygria, flavonoids, butin, butein, sulfuretin, K562 leukemia cells, transcriptome analysis, RNA sequencing, gene set enrichment analysis, apoptosis, mitochondrial respiration, natural products