2022
Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nature Biomedical Engineering 2022, 6: 257-266. PMID: 35301450, PMCID: PMC9089460, DOI: 10.1038/s41551-022-00855-9.Peer-Reviewed Original ResearchConceptsLow-frequency mutationsDuplex SequencingNumber of lociLow-frequency allelesWhole-genome sequencingHuman cell linesSingle nucleotide polymorphismsGenomic DNAWhole-exome sequencingMutation enrichmentParallel enrichmentBreast tumor samplesSequencingLociMutationsDistinct mutationsCell linesDNADetection of mutationsReads
2016
Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer
Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Jin Huh S, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Peluffo G, Brown J, D’Santos C, Krop I, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao P, Duarte M, Wu S, Chiang C, Anders L, Young R, Winer E, Letai A, Barry W, Carroll J, Long H, Brown M, Shirley Liu X, Meyer C, Bradner J, Polyak K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature 2016, 529: 413-417. PMID: 26735014, PMCID: PMC4854653, DOI: 10.1038/nature16508.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAzepinesBinding, CompetitiveCasein Kinase IICell Cycle ProteinsCell Line, TumorCell ProliferationChromatinDrug Resistance, NeoplasmEpigenesis, GeneticFemaleGene Expression Regulation, NeoplasticGenome, HumanHumansMediator Complex Subunit 1MiceNuclear ProteinsPhosphorylationPhosphoserineProtein BindingProtein Phosphatase 2Protein Structure, TertiaryProteomicsTranscription FactorsTranscription, GeneticTriazolesTriple Negative Breast NeoplasmsXenograft Model Antitumor Assays
2011
P1-06-23: Changes in Gene Expression after One Dose of Trastuzumab (T) in HER2+ Breast Cancer Cell Lines Predict Novel Pathways of Response in HER2 Positive Early Stage Breast Cancer.
Sprecher E, Lezon-Geyda K, Sarkar S, Bossuyt V, Narayaan M, Kumar A, Krop I, Winer E, Tuck D, Kleinstein S, Harris L. P1-06-23: Changes in Gene Expression after One Dose of Trastuzumab (T) in HER2+ Breast Cancer Cell Lines Predict Novel Pathways of Response in HER2 Positive Early Stage Breast Cancer. Cancer Research 2011, 71: p1-06-23-p1-06-23. DOI: 10.1158/0008-5472.sabcs11-p1-06-23.Peer-Reviewed Original ResearchPathologic complete responseBreast cancer patientsBreast cancer cell linesSensitive cell linesCancer cell linesCancer patientsSingle doseBreast cancerHER2-positive early-stage breast cancerPositive early-stage breast cancerCell linesBreast tumorsEarly breast cancer patientsEarly-stage breast cancerDose of trastuzumabEarly-stage HER2Early breast cancerResistant breast tumorsStage breast cancerTumor core biopsiesPathway analysisMechanism of actionResistant HER2RECIST criteriaClinical responseAssociation between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors
Sprecher E, Sarkar S, Kleinstein S, Narayan M, Winer E, Tuck D, Lezon-Geyda K, Krop I, Harris L. Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors. 2011, 446-450. DOI: 10.1145/2147805.2147867.Peer-Reviewed Original ResearchEarly-stage HER2Breast cancer patientsBreast tumorsTrastuzumab treatmentCancer patientsCell linesHuman epidermal growth factor receptor 2Epidermal growth factor receptor 2Breast cancer settingGrowth factor receptor 2Resistant breast tumorsTrastuzumab-resistant HER2Breast cancer cell linesClinical treatment decisionsFactor receptor 2Trastuzumab exposureCancer cell linesGene expression signaturesResponsive patientsTrastuzumab resistanceSingle doseTargeted therapyBreast cancerCancer settingTreatment decisionsRibavirin Treatment Effects on Breast Cancers Overexpressing eIF4E, a Biomarker with Prognostic Specificity for Luminal B-Type Breast Cancer
Pettersson F, Yau C, Dobocan MC, Culjkovic-Kraljacic B, Retrouvay H, Puckett R, Flores LM, Krop IE, Rousseau C, Cocolakis E, Borden KL, Benz CC, Miller WH. Ribavirin Treatment Effects on Breast Cancers Overexpressing eIF4E, a Biomarker with Prognostic Specificity for Luminal B-Type Breast Cancer. Clinical Cancer Research 2011, 17: 2874-2884. PMID: 21415224, PMCID: PMC3086959, DOI: 10.1158/1078-0432.ccr-10-2334.Peer-Reviewed Original ResearchMeSH KeywordsAntimetabolites, AntineoplasticBiomarkers, TumorBreast NeoplasmsCarcinomaCell Line, TumorCells, CulturedEukaryotic Initiation Factor-4EFemaleGene Expression Regulation, NeoplasticGene Knockdown TechniquesHumansMammary Glands, HumanOrgan SpecificityPrognosisRibavirinRNA, Small InterferingUp-RegulationConceptsDistant metastasis-free survivalBreast cancer cell linesBreast cancerCancer cell linesLuminal B type breast cancerNode-negative breast cancerIntrinsic breast cancer subtypesPoor outcome groupMetastasis-free survivalLuminal B casesSpecific molecular subtypesCell proliferationBreast cancer subtypesCell linesBreast cancer cellsSpecific molecular profilePrognostic specificityMetastatic diseasePrognostic valuePrimary tumorCancer therapeutic strategiesOutcome groupSkin biopsiesMolecular subtypesPatient tumors
2002
Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression)
Seth P, Krop I, Porter D, Polyak K. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression). Oncogene 2002, 21: 836-843. PMID: 11850811, DOI: 10.1038/sj.onc.1205113.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBreast NeoplasmsDioxygenasesEstrogen AntagonistsEstrogensFemaleGene Expression ProfilingHypoxia-Inducible Factor-Proline DioxygenasesIn Situ HybridizationMolecular Sequence DataNuclear ProteinsOligonucleotide Array Sequence AnalysisPhylogenyProcollagen-Proline DioxygenaseReceptors, EstrogenRNA, NeoplasmSequence Homology, Amino AcidTamoxifenTranscriptional ActivationTumor Cells, CulturedConceptsNovel nuclear proteinLigand-dependent transcription factorsDirect transcriptional targetGene expression profilesImmediate early genesTranscriptional targetsTranscription factorsEstrogen-dependent breast cancer cell linesNuclear proteinsSAGE technologyExpression profilesConstitutive expressionHuman breast cancer cellsBreast cancer cellsGenesBreast cancer cell linesCell growthCancer cell linesInitial characterizationNew memberColony growthCancer cellsCell linesNovel estrogenEstrogen receptor
2001
HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells
Krop I, Sgroi D, Porter D, Lunetta K, LeVangie R, Seth P, Kaelin C, Rhei E, Bosenberg M, Schnitt S, Marks J, Pagon Z, Belina D, Razumovic J, Polyak K. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 9796-9801. PMID: 11481438, PMCID: PMC55532, DOI: 10.1073/pnas.171138398.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBlotting, NorthernBlotting, WesternBreastBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingCarcinoma, LobularCell DivisionCells, CulturedChlorocebus aethiopsCHO CellsCOS CellsCricetinaeCricetulusCytokinesDNA MethylationEpithelial CellsFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticGene LibraryGene SilencingGenes, Tumor SuppressorGrowth InhibitorsHumansMolecular Sequence DataNeoplasm ProteinsPromoter Regions, GeneticRecombinant Fusion ProteinsRNA, MessengerRNA, NeoplasmSequence AlignmentSequence Homology, Amino AcidTransfectionTumor Cells, CulturedTumor Suppressor ProteinsConceptsHIN-1 expressionHIN-1Mammary epithelial cellsPutative cytokineEpithelial cellsBreast cancer cell linesHuman breast carcinomaCancerous mammary epithelial cellsBreast cancer cellsCancer cell linesDuctal carcinomaLobular carcinomaPrimary tumorPreinvasive lesionsBreast carcinomaCandidate tumor suppressor geneMolecular alterationsTumor suppressor geneCarcinomaCancer cellsGene expression profilesCell linesCytokinesSuppressor geneCell growth