# Targeted lipidomics meets transcriptomics: how cinobufagin rewires fatty acid, sphingolipid, and glycerophospholipid metabolism to combat hepatoma cell growth

**Authors:** Wanjun Shao, Congying Yu, Rufei Xu, Xiaoqian Rong, Ailin Yang

PMC · DOI: 10.3389/fphar.2025.1664915 · Frontiers in Pharmacology · 2026-02-09

## TL;DR

This study shows how the compound cinobufagin fights liver cancer by altering key lipid metabolism pathways, offering new insights for cancer treatment.

## Contribution

The study reveals novel lipid metabolism pathways targeted by cinobufagin in hepatoma cells.

## Key findings

- Cinobufagin disrupts fatty acid, sphingolipid, and glycerophospholipid metabolism in hepatoma cells.
- Transcriptomics and metabolomics integration identifies specific lipid pathways affected by cinobufagin.
- The compound's anti-HCC activity is partially mediated through lipid metabolic rewiring.

## Abstract

Hepatocellular carcinoma (HCC) is a common malignant tumor, is characterized by an early stage that is not easy to diagnose and a high mortality rate in the late stage, which is a serious threat to patients' lives. Abnormalities in lipid metabolism are closely related to the development of HCC. Integrating transcriptomics and metabolomics analyses can help in the study of drug mechanism of action. Cinobufagin, is the main active ingredient for chinese medicine Chansu to exert anti-tumor effects, but the effects of cinobufagin on abnormal lipid metabolism in tumor cells are not clear.

We employed targeted lipid metabolomics to profile alterations in key lipid classes. Furthermore, integrated transcriptomics and metabolomics analyses were conducted to identify critical pathways involved in cinobufagin's action.

In this study, we demonstrate through the results of targeted lipid metabolomics that cinobufagin interferes with fatty acyls, sphingolipids, glycerophospholipids, glycerolipids, saccharolipids, and sterol lipids. The results of integration of transcriptomics and metabolomics identified that intervention in fatty acid metabolism (including biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, fatty acid degradation, and fatty acid elongation), sphingolipid metabolism (including sphingolipid metabolism, glycosphingolipid biosynthesis-globo and isoglobo series, glycosphingolipid biosynthesis-lacto and neolacto series, glycosphingolipid biosynthesis-ganglio series), and glycerophospholipid metabolism (including glycerophospholipid metabolism, ether lipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis) may be partially responsible for the effect of anti-hepatoma cell growth induced by cinobufagin.

Our findings demonstrate that cinobufagin exerts anti-HCC activity partially through lipid metabolism, particularly by targeting fatty acid, sphingolipid, and glycerophospholipid pathways. This study is of great significance for the application of cinobufagin and chansu in clinical HCC treatment and promotes the development of new drugs from traditional Chinese medicine in the field of antitumor.

## Linked entities

- **Chemicals:** cinobufagin (PubChem CID 11969542)
- **Diseases:** Hepatocellular carcinoma (MONDO:0007256), HCC (MONDO:0007256)

## Full-text entities

- **Genes:** B3GNT3 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) [NCBI Gene 10331] {aka B3GAL-T8, B3GN-T3, B3GNT-3, HP10328, TMEM3, beta3Gn-T3}, B4galnt1 (beta-1,4-N-acetyl-galactosaminyl transferase 1) [NCBI Gene 14421] {aka 4933429D13Rik, Gal-NAc-T, GalNAc-T, GalNAcT, Galgt1, Ggm-2}, DECR1 (2,4-dienoyl-CoA reductase 1) [NCBI Gene 1666] {aka DECR, NADPH, SDR18C1}, ETNPPL (ethanolamine-phosphate phospho-lyase) [NCBI Gene 64850] {aka AGXT2L1}, FOXM1 (forkhead box M1) [NCBI Gene 2305] {aka FKHL16, FOXM1A, FOXM1B, FOXM1C, HFH-11, HFH11}, B3GALT4 (beta-1,3-galactosyltransferase 4) [NCBI Gene 8705] {aka BETA3GALT4, GALT2, GALT4}, Gal3st1 (galactose-3-O-sulfotransferase 1) [NCBI Gene 53897] {aka Cst, Gcst}, EHHADH (enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase) [NCBI Gene 1962] {aka ECHD, FRTS3, L-PBE, LBFP, MFE1, PBFE}, Kdsr (3-ketodihydrosphingosine reductase) [NCBI Gene 70750] {aka 6330410P18Rik, 9430079B08Rik, Fvt1}, AGPAT1 (1-acylglycerol-3-phosphate O-acyltransferase 1) [NCBI Gene 10554] {aka 1-AGPAT1, G15, LPAAT-alpha, LPAATA, LPLAT1}, EZR (ezrin) [NCBI Gene 7430] {aka CVIL, CVL, HEL-S-105, VIL2}, ACOT8 (acyl-CoA thioesterase 8) [NCBI Gene 10005] {aka HNAACTE, NAP1, PTE-1, PTE-2, PTE1, PTE2}, Gba1 (glucosylceramidase beta 1) [NCBI Gene 14466] {aka GC, GCase, GLUC, Gba, betaGC}, PISD (phosphatidylserine decarboxylase) [NCBI Gene 23761] {aka DJ858B16, LIBF, PSDC, PSSC, dJ858B16.2}, ECHS1 (enoyl-CoA hydratase, short chain 1) [NCBI Gene 1892] {aka ECHS1D, SCEH, mECH, mECH1}, LDAH (lipid droplet associated hydrolase) [NCBI Gene 60526] {aka C2orf43, hLDAH}, FOSB (FosB proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 2354] {aka AP-1, G0S3, GOS3, GOSB}, GNPAT (glyceronephosphate O-acyltransferase) [NCBI Gene 8443] {aka DAP-AT, DAPAT, DHAPAT, RCDP2}, Kdr (kinase insert domain protein receptor) [NCBI Gene 16542] {aka 6130401C07, Flk-1, Flk1, Krd-1, Ly73, VEGFR-2}, FUT1 (fucosyltransferase 1 (H blood group)) [NCBI Gene 2523] {aka H, HH, HSC}, SGMS2 (sphingomyelin synthase 2) [NCBI Gene 166929] {aka CDL, SMS2}, AFP (alpha fetoprotein) [NCBI Gene 174] {aka AFPD, FETA, HPAFP}, ACADM (acyl-CoA dehydrogenase medium chain) [NCBI Gene 34] {aka ACAD1, MCAD, MCADH}, Neu3 (neuraminidase 3) [NCBI Gene 50877], Sphk2 (sphingosine kinase 2) [NCBI Gene 56632] {aka Sk2, Spk2}, CPT1B (carnitine palmitoyltransferase 1B) [NCBI Gene 1375] {aka CPT1-M, CPT1M, CPTI, CPTI-M, M-CPT1, MCCPT1}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, Cers1 (ceramide synthase 1) [NCBI Gene 93898] {aka Lass1, Uog-1, to}, PC (pyruvate carboxylase) [NCBI Gene 5091] {aka PCB}, ACAA2 (acetyl-CoA acyltransferase 2) [NCBI Gene 10449] {aka DSAEC, T1}, ELOVL2 (ELOVL fatty acid elongase 2) [NCBI Gene 54898] {aka SSC2}, BCL2 (BCL2 apoptosis regulator) [NCBI Gene 596] {aka Bcl-2, PPP1R50}, Ugcg (UDP-glucose ceramide glucosyltransferase) [NCBI Gene 22234] {aka Epcs21, GlcT-1, Ugcgl}, CPT1C (carnitine palmitoyltransferase 1C) [NCBI Gene 126129] {aka CATL1, CPT I-C, CPT1-B, CPT1P, CPTI-B, CPTIC}, GLB1 (galactosidase beta 1) [NCBI Gene 2720] {aka EBP, ELNR1, MPS4B}, LPCAT2 (lysophosphatidylcholine acyltransferase 2) [NCBI Gene 54947] {aka AGPAT11, AYTL1, LPLAT9, LysoPAFAT}, MCAT (malonyl-CoA-acyl carrier protein transacylase) [NCBI Gene 27349] {aka FASN2C, MCT, MCT1, MT, NET62, OPA15}, STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774] {aka ADMIO, ADMIO1, APRF, HIES}, Sgpp2 (sphingosine-1-phosphate phosphatase 2) [NCBI Gene 433323] {aka SPPase2, Spp2}, PARP1 (poly(ADP-ribose) polymerase 1) [NCBI Gene 142] {aka ADPRT, ADPRT 1, ADPRT1, ARTD1, PARP, PARP-1}, LPCAT4 (lysophosphatidylcholine acyltransferase 4) [NCBI Gene 254531] {aka AGPAT7, AYTL3, LPAAT-eta, LPEAT2, LPLAT10}, BAX (BCL2 associated X, apoptosis regulator) [NCBI Gene 581] {aka BCL2L4}, PLA2G4B (phospholipase A2 group IVB) [NCBI Gene 100137049] {aka HsT16992, cPLA2-beta}, SLC7A11 (solute carrier family 7 member 11) [NCBI Gene 23657] {aka CCBR1, xCT}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, CPT1A (carnitine palmitoyltransferase 1A) [NCBI Gene 1374] {aka CPT I, CPT1, CPT1-L, CPTI-L, L-CPT1}, FASN (fatty acid synthase) [NCBI Gene 2194] {aka FAS, OA-519, SDR27X1}, GCNT2 (glucosaminyl (N-acetyl) transferase 2 (I blood group)) [NCBI Gene 2651] {aka CCAT, CTRCT13, GCNT2C, GCNT5, IGNT, II}, Oga (O-GlcNAcase) [NCBI Gene 76055] {aka Hy5, Mgea5, Ncoat}, ACACA (acetyl-CoA carboxylase alpha) [NCBI Gene 31] {aka ACAC, ACACAD, ACACalpha, ACC, ACC1, ACCA}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, SIRT1 (sirtuin 1) [NCBI Gene 23411] {aka SIR2, SIR2L1, SIR2alpha}, CPT2 (carnitine palmitoyltransferase 2) [NCBI Gene 1376] {aka CPT1, CPTASE, IIAE4}, ST3GAL3 (ST3 beta-galactoside alpha-2,3-sialyltransferase 3) [NCBI Gene 6487] {aka DEE15, EIEE15, MRT12, SIAT6, ST3GALII, ST3Gal III}, AURKA (aurora kinase A) [NCBI Gene 6790] {aka AIK, ARK1, AURA, BTAK, PPP1R47, STK15}, Acer1 (alkaline ceramidase 1) [NCBI Gene 171168] {aka 2310024P18Rik, Alkcdase1, Asah3, Cer1}, Cerk (ceramide kinase) [NCBI Gene 223753] {aka D330016D08Rik, mKIAA1646}, CD82 (CD82 molecule) [NCBI Gene 3732] {aka 4F9, C33, GR15, IA4, KAI1, R2}, ST3GAL1 (ST3 beta-galactoside alpha-2,3-sialyltransferase 1) [NCBI Gene 6482] {aka Gal-NAc6S, SIAT4A, SIATFL, ST3GalA, ST3GalA.1, ST3GalIA}
- **Diseases:** cytotoxicity (MESH:D064420), intestinal tumors (MESH:D007414), liver fibrosis (MESH:D008103), NAFLD (MESH:D065626), peritoneal carcinoma (MESH:D010534), Cancer (MESH:D009369), esophageal adenocarcinoma (MESH:D000230), diabetes (MESH:D003920), acute lymphoblastic leukemia (MESH:D054198), thyroid tumors (MESH:D013964), mitochondrial dysfunction (MESH:D028361), colon cancer (MESH:D015179), colonic inflammation (MESH:D007249), liver disease (MESH:D008107), liver metastasis (MESH:D009362), cirrhosis (MESH:D005355), melanoma (MESH:D008545), HCV infection (MESH:D006526), prostate cancer (MESH:D011471), RCC (MESH:D002292), non-small cell lung cancer (MESH:D002289), squamous cell carcinoma of the head and neck (MESH:D000077195), liver tumors (MESH:D008113), colon tumor (MESH:D003110), HCC (MESH:D006528), esophageal cancer (MESH:D004938), UVM (MESH:C536494), hepatitis (MESH:D056486), tumorigenesis (MESH:D063646), OV (MESH:D010051), LGG (MESH:D008228), fatty liver (MESH:D005234), triple-negative (MESH:D064726), breast cancer (MESH:D001943), lung adenocarcinoma (MESH:D000077192), obesity (MESH:D009765)
- **Chemicals:** CE (MESH:D002788), coenzyme A (MESH:D003065), PA (MESH:D010712), Acar (MESH:C116917), acetonitrile (MESH:C032159), TAG (MESH:D014280), Sia (MESH:D019158), carbohydrate (MESH:D002241), FA (MESH:D005227), PC (MESH:D010713), streptomycin (MESH:D013307), DHS (MESH:C005682), carbon (MESH:D002244), PS (MESH:D010718), Phosphatidylethanol (MESH:C051521), Resolvin D1 (MESH:C518399), n-3 polyunsaturated fatty acid (MESH:D015525), benzoic acid (MESH:D019817), acyl-coenzyme A (MESH:D000214), glycan (MESH:D011134), amino acid (MESH:D000596), butylcarnitine (MESH:C427065), UDP-glucose (MESH:D014532), Cinobufagin (MESH:C002471), Bufadienolides (MESH:D002018), Glycosphingolipid (MESH:D006028), prostaglandin (MESH:D011453), EDTA (MESH:D004492), PI (MESH:D010716), FC (MESH:C095424), Palmitoylcarnitine (MESH:D010172), Glycerophospholipid (MESH:D020404), sugars (MESH:D000073893), ganglioside (MESH:D005732), PUFAs (MESH:D005231), formic acid (MESH:C030544), PGA2 (MESH:C100008), C1P (MESH:C065576), cinobufotalin (MESH:C063451), carnitine (MESH:D002331), N-Oleoyl taurine (MESH:C581016), penicillin (MESH:D010406), 3-ketodihydrosphingosine (MESH:C002882), Hemibismonoacylglycerophosphate (-), PE (MESH:C483858), SM (MESH:D013109), Chansu (MESH:C095591), palmitate (MESH:D010168), Methanol (MESH:D000432), Arenobufagin (MESH:C055393), DMSO (MESH:D004121), cholesterol (MESH:D002784), 15-keto PGE2 (MESH:C026346), Ether (MESH:D004986), glucose (MESH:D005947), fucose (MESH:D005643), ganglioside GM3 (MESH:D005679), LPA (MESH:C032881), ROS (MESH:D017382), BMP (MESH:C012786)
- **Species:** Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116], Mus musculus (house mouse, species) [taxon 10090], Duttaphrynus melanostictus (Asian common toad, species) [taxon 30335], Bufo gargarizans (Asiatic toad, species) [taxon 30331]
- **Cell lines:** A549 — Homo sapiens (Human), Lung adenocarcinoma, Cancer cell line (CVCL_0023), HepG2 — Homo sapiens (Human), Hepatoblastoma, Cancer cell line (CVCL_0027)

## Full text

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## Figures

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## References

97 references — full list in the complete paper: https://tomesphere.com/paper/PMC12926493/full.md

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Source: https://tomesphere.com/paper/PMC12926493