2023
Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E
Boddu P, Gupta A, Roy R, De La Pena Avalos B, Herrero A, Zimmer J, Simon M, Chandhok N, King D, Neuenkirchen N, Dray E, Lin H, Kupfer G, Verma A, Neugebauer K, Pillai M. Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E. Blood 2023, 142: 714. DOI: 10.1182/blood-2023-187303.Peer-Reviewed Original ResearchSplicing factorsChIP-seqK562 cell lineKey regulatory genesCell linesSingle mutant alleleNon-denaturing gelsAlternative splicingTranscriptional kineticsRegulatory genesSpliceosome assemblySplicing efficiencyMRNA splicingCRISPR/Progenitor populationsNeomorphic functionsMolecular mechanismsMutant allelesIsoform changesGene editingNovel mechanismMutationsSF mutationsRecurrent mutationsAssembly kineticsTranscription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape
Boddu P, Gupta A, Roy R, Herrero A, Verma A, Neugebauer K, Pillai M. Transcription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape. Blood 2023, 142: 709. DOI: 10.1182/blood-2023-188083.Peer-Reviewed Original ResearchChromatin organizationSuch epigenetic changesGenome editing approachesRNA splicing factorsChromatin landscapeSingle mutant alleleEpigenetic landscapeGenomic integrityTranscription defectTranscription kineticsSplicing factorsChIP-seqEpigenetic regulatorsEpigenetic changesEpigenetic therapyMutant allelesEditing approachesFactor mutationsK562 cell lineDownstream effectsCell linesMyeloid disordersClonal myeloid disordersHDAC pathwayMutations
2020
Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.Peer-Reviewed Original ResearchTriple-negative breast cancer cellsCancer cellsBreast cancer cellsStress response genesMulti-omics landscapeCell population compositionDrug-induced cell deathMulti-omics investigationsCell linesBCL2 family inhibitorsSingle-cell analysisChromatin accessibilityGenome structureMDA-MB-231 triple-negative breast cancer cellsChromatin structureMethylation stateResponse genesFamily inhibitorsCell deathTNBC cell linesNumber variationsDefense mechanismsResistance mechanismsNew therapeutic strategiesGenes
2013
Primary Marrow-Derived Stromal Cells: Isolation and Manipulation
Ramakrishnan A, Torok-Storb B, Pillai M. Primary Marrow-Derived Stromal Cells: Isolation and Manipulation. Methods In Molecular Biology 2013, 1035: 75-101. PMID: 23959984, PMCID: PMC3748384, DOI: 10.1007/978-1-62703-508-8_8.Peer-Reviewed Original ResearchConceptsMarrow stromal cellsStem cellsMSC populationsPrimary marrow stromal cellsMultipotent stem cellsImmortalized cell linesStromal cellsPrimary marrowMesenchymal lineagesCellular heterogeneityMesenchymal stem cellsHematopoietic cellsCell linesRare cellsCellsBone marrow mononuclear cellsMarrow mononuclear cellsBone marrow harvestLineagesBone marrowMarrow biopsyMononuclear cellsClinical transplantationMarrow harvestPopulation
2010
High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-193a as a Regulator of Jagged1 In Marrow Stromal Cells.
Balakrishnan I, Yang X, Torok-Storb B, Hesselberth J, Pillai M. High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-193a as a Regulator of Jagged1 In Marrow Stromal Cells. Blood 2010, 116: 3847. DOI: 10.1182/blood.v116.21.3847.3847.Peer-Reviewed Original ResearchHigh-throughput sequencingStem cell nicheStromal cell lineArgonaute proteinsHITS-CLIPMiR-193aThroughput sequencingMRNA interactionsCell nicheCell linesSmall non-coding RNAsMarrow microenvironmentRNA-protein complexesMiRNA-based regulationMarrow stromal cell lineCross-link RNAPost-transcriptional regulationHematopoietic stem cell nicheHS27a cellsMajority of mRNAsMiRNA-mRNA interactionsUCSC Genome BrowserDirect interactionNon-coding RNAsLong-term culture
2009
Mir-886-3p Contributes to the Regulation of the hematopoietic microenvironment by down-Regulating SDF-1α (CXCL12).
Pillai M, Yang X, Iwata M, Bemis L, Torok-Storb B. Mir-886-3p Contributes to the Regulation of the hematopoietic microenvironment by down-Regulating SDF-1α (CXCL12). Blood 2009, 114: 561. DOI: 10.1182/blood.v114.22.561.561.Peer-Reviewed Original ResearchStem cell nicheCell nicheVivo cell-cell interactionsGene expressionExpression profilesQuantitative RT-PCRHematopoietic stem cell nicheHS27a cellsLong-term cultureStromal cellsCell-cell interactionsMiR‑886‑3pCell linesPrimary marrow stromal cellsStromal cell lineMiRNA expression profilesImmortalized cell linesSDF-1αGene productsMarrow stromal cellsRT-PCRUndifferentiated stateTranscript levelsMiRNA transfectionHematopoietic stem