2022
The role of FYCO1-dependent autophagy in lens fiber cell differentiation
Khan SY, Ali M, Kabir F, Na CH, Delannoy M, Ma Y, Qiu C, Costello MJ, Hejtmancik JF, Riazuddin SA. The role of FYCO1-dependent autophagy in lens fiber cell differentiation. Autophagy 2022, 18: 2198-2215. PMID: 35343376, PMCID: PMC9397473, DOI: 10.1080/15548627.2022.2025570.Peer-Reviewed Original ResearchConceptsAutophagic vesiclesLens fiber cell differentiationMouse lensesAutophagic fluxFiber cell differentiationHuman embryonic stem cellsCoiled-coil domainOrganelle-free zoneEmbryonic stem cellsHuman lens epithelial cellsAutophagy-associated genesSingle guide RNAsQuantitative real-time PCRLens epithelial cellsAdaptor proteinRNA-seqGuide RNARNA sequencingCellular organellesLens morphogenesisCataract phenotypeWild typeFYCO1Cell differentiationEndoplasmic reticulum
2019
Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies
Ali M, Kabir F, Thomson JJ, Ma Y, Qiu C, Delannoy M, Khan SY, Riazuddin SA. Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies. Scientific Reports 2019, 9: 18552. PMID: 31811247, PMCID: PMC6898283, DOI: 10.1038/s41598-019-54258-z.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsComparative transcriptome analysisTranscriptome analysisLentoid bodiesPluripotent stem cellsBody transcriptomeRNA sequencingStem cellsNext-generation RNA sequencingEmbryonic stem cellsFiber-like cellsSimilar expression profilesTranscriptome datasetsTranscriptome profilingCell transcriptomeLens morphogenesisExcellent systemMouse lensExpression profilesTranscriptomeMechanism of cataractogenesisLens-like structuresUltrastructure analysisGenesOcular lens
2016
Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family
Hysolli E, Tanaka Y, Su J, Kim KY, Zhong T, Janknecht R, Zhou XL, Geng L, Qiu C, Pan X, Jung YW, Cheng J, Lu J, Zhong M, Weissman SM, Park IH. Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family. Stem Cell Reports 2016, 7: 43-54. PMID: 27373925, PMCID: PMC4945581, DOI: 10.1016/j.stemcr.2016.05.014.Peer-Reviewed Original ResearchConceptsDNA methylation stateEmbryonic stem cellsInduced pluripotent stem cellsHuman somatic cell reprogrammingSomatic cell reprogrammingMethylation stateCell reprogrammingMiR-29 familyDNA methylation landscapeImportant epigenetic regulatorsStem cellsOverexpression of Oct4Global DNA methylationMiRNA-based approachesPluripotent stem cellsMethylation landscapeHistone modificationsDNA demethylationEpigenomic changesEarly reprogrammingEpigenetic regulatorsEpigenetic differencesDNA methylationHydroxymethylation analysisReprogramming
2013
Small-Diameter Vascular Graft Engineered Using Human Embryonic Stem Cell-Derived Mesenchymal Cells
Sundaram S, Echter A, Sivarapatna A, Qiu C, Niklason L. Small-Diameter Vascular Graft Engineered Using Human Embryonic Stem Cell-Derived Mesenchymal Cells. Tissue Engineering Part A 2013, 20: 740-750. PMID: 24125588, PMCID: PMC3926168, DOI: 10.1089/ten.tea.2012.0738.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsHuman embryonic stem cell-derived mesenchymal cellsSmooth muscle cellsSMC marker expressionMesenchymal cellsEmbryonic stem cellsMarkers of cartilageLineage commitmentNew cell sourceGrowth factor betaStem cellsDifferentiation capabilityCell populationsNative counterpartsMuscle cellsHuman vessel wallStringent analysisFactor betaCell sourceCellsMarker expressionSmooth muscle actinMuscle actinVascular constructsCell sourcing
2012
High‐Efficiency Transfection and siRNA‐Mediated Gene Knockdown in Human Pluripotent Stem Cells
Ma Y, Lin H, Qiu C. High‐Efficiency Transfection and siRNA‐Mediated Gene Knockdown in Human Pluripotent Stem Cells. Current Protocols In Stem Cell Biology 2012, 21: 5c.2.1-5c.2.9. PMID: 22605647, DOI: 10.1002/9780470151808.sc05c02s21.Peer-Reviewed Original ResearchConceptsHigh transfection efficiencyPluripotent stem cellsTransfection efficiencyTransfection reagent Lipofectamine 2000Human embryonic stem cellsStem cellsHuman pluripotent stem cellsEmbryonic stem cellsPluripotent cell linesLipofectamine 2000SiRNA-mediated gene knockdownPluripotent cellsExpensive equipmentPluripotent genesGene knockdownProtocolEfficiencyPrimary cellsGenesCell linesCarriersCellsApplicationsTransfection
2010
High-efficiency siRNA-based gene knockdown in human embryonic stem cells
Ma Y, Jin J, Dong C, Cheng EC, Lin H, Huang Y, Qiu C. High-efficiency siRNA-based gene knockdown in human embryonic stem cells. RNA 2010, 16: 2564-2569. PMID: 20978109, PMCID: PMC2995416, DOI: 10.1261/rna.2350710.Peer-Reviewed Original ResearchDynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing
Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 5254-5259. PMID: 20194744, PMCID: PMC2841935, DOI: 10.1073/pnas.0914114107.Peer-Reviewed Original ResearchConceptsNeural differentiationUndifferentiated hESCsNeural fate specificationCell identity maintenanceStage-specific regulationHuman embryonic stem cellsTypes of genesPaired-end sequencingDifferentiation of hESCsEmbryonic stem cellsPaired-end readsNeural cell differentiationSplicing dynamicsFate specificationDynamic transcriptomeIsoform diversityTranscriptome changesUnannotated transcriptsGene transcriptionRNA sequencingStages of differentiationNeural lineagesCell differentiationDifferential expressionGliogenic potential
2009
Lin28-mediated post-transcriptional regulation of Oct4 expression in human embryonic stem cells
Qiu C, Ma Y, Wang J, Peng S, Huang Y. Lin28-mediated post-transcriptional regulation of Oct4 expression in human embryonic stem cells. Nucleic Acids Research 2009, 38: 1240-1248. PMID: 19966271, PMCID: PMC2831306, DOI: 10.1093/nar/gkp1071.Peer-Reviewed Original ResearchConceptsRNA helicase APost-transcriptional regulationHuman embryonic stem cellsEmbryonic stem cellsLin28-dependent stimulationOct4 expressionPost-transcriptional regulatory factorsPluripotency factor OCT4Subset of mRNAsPost-transcriptional levelStem cellsTarget mRNA expressionMicroRNA processingFactors OCT4Observed regulationReporter systemRegulatory factorsEfficient translationLin28Novel mechanismMRNARegulationFirst evidenceExpressionMRNA expressionDevelopmentally regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus
Lathrop MJ, Hsu M, Richardson CA, Olivier EN, Qiu C, Bouhassira EE, Fiering S, Lowrey CH. Developmentally regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus. Experimental Hematology 2009, 37: 807-813.e2. PMID: 19460471, PMCID: PMC3792488, DOI: 10.1016/j.exphem.2009.04.005.Peer-Reviewed Original ResearchConceptsAdult erythroid cellsCpG island genesHistone modificationsGene expressionDNA hypomethylationErythroid cellsDNA methylationBeta-like globin gene expressionBeta-globin gene regulationIsland genesActive histone marksBeta-globin locusGamma-globin promoterGlobin gene expressionHuman embryonic stem cellsDNA methylation patternsSpecific gene expressionEmbryonic stem cellsPrimary human erythroblastsHuman β-globinHistone marksGene regulationMethylation stateBisulfite sequencingCpG islands