Siyuan Cheng
Associate Research ScientistAbout
Research
Publications
2026
HOX code–based stratification reveals RUNX1T1–HDAC reprogramming as a targetable driver of lineage plasticity across cancers
Jiang Y, Cheng S, Zhang CY, Jin X, Li L, Shin HE, Alrefai A, Luo A, Xu Y, Kim IY, Mu P. HOX code–based stratification reveals RUNX1T1–HDAC reprogramming as a targetable driver of lineage plasticity across cancers. Cancer Letters 2026, 648: 218465. DOI: 10.1016/j.canlet.2026.218465.Peer-Reviewed Original ResearchThis study investigates how HOX gene expression patterns identify therapy-resistant cancer subtypes and demonstrates RUNX1T1-HDAC3 inhibition as a potential treatment strategy for aggressive cancers.Game of clones: decipher lineage plasticity in hormone-driven cancers
Leonita A, Cheng S, Warrick J, Kim I, Deng S, Mu P. Game of clones: decipher lineage plasticity in hormone-driven cancers. Cellular And Molecular Life Sciences 2026, 83: 236. PMID: 42014520, PMCID: PMC13237331, DOI: 10.1007/s00018-026-06171-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsHormone-driven cancersFate transitionsGene regulatory circuitsIntegrative multi-omics approachCell fate transitionsLineage plasticityRegulatory programsTherapeutic vulnerabilitiesBiological consequencesMulti-omics approachNuclear hormone receptorsRegulatory modulesRegulatory circuitsCell identityCellular fatePhenotypic outcomesBiological insightsLineagesLineage fidelityEpigenetic programmingLineage identityHormone-dependent cancersSingle-cellMolecular programsRare subpopulationHOX code–based stratification reveals RUNX1T1–HDAC reprogramming as a targetable driver of lineage plasticity across cancers
Jiang Y, Cheng S, Zhang C, Jin X, Li L, Shin H, Alrefai A, Luo A, Xu Y, Kim I, Mu P. HOX code–based stratification reveals RUNX1T1–HDAC reprogramming as a targetable driver of lineage plasticity across cancers. Cancer Letters 2026, 648: 218465. PMID: 41912135, DOI: 10.1016/j.canlet.2026.218465.Peer-Reviewed Original ResearchConceptsAcute myeloid leukemiaLineage plasticityPharmacologic inhibition of HDAC3RNA-seqPharmacological inhibitionBinding partnersCancer cellsProstate cancer modelSingle-cell RNA-seqRNA-seq samplesActive enhancer marksTargetable driversMulti-omics dataDifferential expression analysisInhibition of HDAC3Prostate cancerTherapy resistanceCause of deathMyeloid leukemiaTargeted therapyCancer modelsTumor progressionLipid nanoparticlesLung cancerCancer subtypes
2025
Regulation of INSM1 Gene Expression and Neuroendocrine Differentiation in High-Risk Neuroblastoma
Chen C, Cheng S, Yu X, Lee Y, Lan M. Regulation of INSM1 Gene Expression and Neuroendocrine Differentiation in High-Risk Neuroblastoma. Biology 2025, 15: 22. PMID: 41514864, PMCID: PMC12784908, DOI: 10.3390/biology15010022.Peer-Reviewed Original ResearchRetinoic acid-induced differentiationMetabolic flux analysisZinc-finger transcription factorS-adenosylmethionineHormone-related genesSH-SY-5YSH-SY-5Y cellsTranscriptional regulationHistone methylationZinc-fingerNeuroendocrine differentiationEpigenetic controlCell fateMethionine cycle activityTranscription factorsFlux analysisEpigenetic mechanismsCell cycleTranscriptome profilingOncogenic signalingProgenitor-like phenotypeGene expressionPromoter activityPromoter assayNB aggressivenessPROX1 is an early driver of lineage plasticity in prostate cancer
Duan Z, Shi M, Kumaraswamy A, Lin D, Khokhani D, Wang Y, Zhang C, Flores D, Rodansky E, Swaim O, Storck W, Beck H, Patel R, Sayar E, Hanratty B, Xue H, Dong X, Maylin Z, Wan R, Quigley D, Sjöström M, Hu Y, Zhao F, Xia Z, Cheng S, Yu X, Feng F, Zhang L, Aggarwal R, Small E, Ravikumar V, Rao A, Bedi K, Lee J, Morrissey C, Coleman I, Nelson P, Corey E, Udager A, Rebernick R, Cieslik M, Chinnaiyan A, Yates J, Haffner M, Wang Y, Alumkal J. PROX1 is an early driver of lineage plasticity in prostate cancer. Journal Of Clinical Investigation 2025, 135: e187490. PMID: 40454483, PMCID: PMC12126232, DOI: 10.1172/jci187490.Peer-Reviewed Original ResearchConceptsNeuroendocrine prostate cancerLineage plasticityProstate cancerHistone deacetylase inhibitionHistone deacetylasesAR pathway inhibitorsPatient-derived xenograftsCancer patient tumorsPatient tumorsIntegrated analysisDrug development approachesTumorPathway inhibitorAR activityProx1 expressionProx1DNA methylationCancerCell survivalProstateLineagesFunctional importanceCell modelInhibitionWell-characterizedNotch as a Driver of Lineage Plasticity and Therapeutic Target in Enzalutamide-Resistant Prostate Cancer.
Jiang Y, Cheng S, Li L, Fraidenburg M, Kim IY, Deng S, Mu P. Notch as a Driver of Lineage Plasticity and Therapeutic Target in Enzalutamide-Resistant Prostate Cancer. BioRxiv 2025 PMID: 40501767, DOI: 10.1101/2025.05.26.656166.Peer-Reviewed Original ResearchPan-cancer Analysis Identified Ectopic RUNX1T1 Associated with Lineage Plasticity.
Jiang Y, Cheng S, Kim IY, Deng S, Mu P. Pan-cancer Analysis Identified Ectopic RUNX1T1 Associated with Lineage Plasticity. BioRxiv 2025 PMID: 40488132, DOI: 10.1101/2025.04.18.649575.Peer-Reviewed Original ResearchAndrogen Deprivation-Induced TET2 Activation Fuels Prostate Cancer Progression via Epigenetic Priming and Slow-Cycling Cancer Cells.
Li L, Cheng S, Xu Y, Deng S, Mu P, Yu X. Androgen Deprivation-Induced TET2 Activation Fuels Prostate Cancer Progression via Epigenetic Priming and Slow-Cycling Cancer Cells. BioRxiv 2025 PMID: 40196510, DOI: 10.1101/2025.03.26.645495.Peer-Reviewed Original ResearchSystematic multi-omics investigation of androgen receptor driven gene expression and epigenetics changes in prostate cancer
Li L, Cho K, Yu X, Cheng S. Systematic multi-omics investigation of androgen receptor driven gene expression and epigenetics changes in prostate cancer. Computers In Biology And Medicine 2025, 189: 110000. PMID: 40056843, DOI: 10.1016/j.compbiomed.2025.110000.Peer-Reviewed Original ResearchConceptsAndrogen deprivation therapyProstate cancer researchComprehensive multi-omics datasetsState-of-the-art bioinformatics toolsProstate cancerGene expressionActive chromatin stateTranscription factor bindingMulti-omics data analysisMulti-omics datasetsProximal promoter regionDown-regulated genesAR signalingAndrogen receptorResponse to androgen deprivation therapyGene Set Enrichment AnalysisNeuroendocrine prostate cancer developmentAndrogen-sensitive LNCaP cell lineChIPseq dataAR signaling activityChromatin stateChromatin accessibilityChromatin modificationsProstate cancer developmentDistal enhancer918 Amphicrine Prostate Carcinoma: An Intermediate Stage of Adenocarcinoma to Neuroendocrine Transdifferentiation
Yeh Y, Li L, Cheng S, Yu X. 918 Amphicrine Prostate Carcinoma: An Intermediate Stage of Adenocarcinoma to Neuroendocrine Transdifferentiation. Laboratory Investigation 2025, 105: 103151. DOI: 10.1016/j.labinv.2024.103151.Peer-Reviewed Original Research