2024
Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA
Cheng J, Swarup N, Morselli M, Huang W, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong D. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Research 2024, 52: e50-e50. PMID: 38797520, PMCID: PMC11194076, DOI: 10.1093/nar/gkae276.Peer-Reviewed Original ResearchTranscription start siteMethylation profilesCell-free DNAWhole-genome bisulfite sequencingCytosine methylation changesLevels of DNA methylationSingle-base resolutionUpstream transcription start siteBS-seqStart siteBisulfite sequencingCpG islandsDNA fragmentationBisulfite conversionMethylation changesDNA methylationBisulfite treatmentLarge DNAsMethylation analysisDNANon-cancer samplesBisulfiteFragmentsHemopoietic cellsMethylationCirculating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors
Hu Y, Narayan A, Xu Y, Wolfe J, Vu D, Trinh T, Kantak C, Ivy S, Eder J, Deng Y, LoRusso P, Kim J, Patel A. Circulating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors. JCO Precision Oncology 2024, 8: e2300289. PMID: 38412387, PMCID: PMC10914240, DOI: 10.1200/po.23.00289.Peer-Reviewed Original ResearchConceptsCell-free circulating tumor DNANon-small-cell lung cancerSmall-cell lung cancerTriple-negative breast cancerPancreatic ductal adenocarcinomaAdvanced solid tumorsVariant allele fractionRadiographic responseOverall survivalCombination therapySolid tumorsCtDNA levelsLung cancerPretreated advanced solid tumorsDays of combination therapyMetastatic pancreatic ductal adenocarcinomaResponse to anticancer therapyAssociated with disease progressionProgression-free survivalPlasma samplesLead-inPoly(ADP-riboseInferior OSTumor DNASurvival outcomes
2023
Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer.
Batool SM, Hsia T, Beecroft A, Lewis B, Ekanayake E, Rosenfeld Y, Escobedo AK, Gamblin AS, Rawal S, Cote RJ, Watson M, Wong DTW, Patel AA, Skog J, Papadopoulos N, Bettegowda C, Castro CM, Lee H, Srivastava S, Carter BS, Balaj L. Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer. Cell Rep Med 2023, 4: 101196. PMID: 37725979, DOI: 10.1016/j.xcrm.2023.101196.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsThe Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring
Batool S, Yekula A, Khanna P, Hsia T, Gamblin A, Ekanayake E, Escobedo A, You D, Castro C, Im H, Kilic T, Garlin M, Skog J, Dinulescu D, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle D, Chia D, Elashoff D, Grognan T, Krysan K, Oh S, Strom C, Tu M, Wei F, Xian R, Skates S, Zhang D, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel S, Yang C, Shen C, Hochberg F, Wong D, Patel A, Papadopoulos N, Bettegowda C, Cote R, Srivastava S, Lee H, Carter B, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Reports Medicine 2023, 4: 101198. PMID: 37716353, PMCID: PMC10591039, DOI: 10.1016/j.xcrm.2023.101198.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsctDNA and Lung Cancer
Cheng J, Hu Y, Wong D, Patel A. ctDNA and Lung Cancer. Current Cancer Research 2023, 511-537. DOI: 10.1007/978-3-031-22903-9_20.ChaptersCell-free DNALung cancerNon-small cell lung cancerCell lung cancerMinimal residual diseaseResidual diseasePleural fluidImportant clinical applicationsClinical utilityTreatment selectionEarly cancer detectionPhysiologic underpinningsClinical modelTherapy monitoringClinical applicationCancerCancer detection
2022
Platelet-derived TLT-1 promotes tumor progression by suppressing CD8+ T cells
Tyagi T, Jain K, Yarovinsky TO, Chiorazzi M, Du J, Castro C, Griffin J, Korde A, Martin KA, Takyar SS, Flavell RA, Patel AA, Hwa J. Platelet-derived TLT-1 promotes tumor progression by suppressing CD8+ T cells. Journal Of Experimental Medicine 2022, 220: e20212218. PMID: 36305874, PMCID: PMC9814191, DOI: 10.1084/jem.20212218.Peer-Reviewed Original ResearchConceptsCD8 T cellsT cellsTLT-1Non-small cell lung cancer patientsCell lung cancer patientsTREM-like transcript-1Tumor immunosuppressive mechanismsT cell suppressionLung cancer patientsPatient T cellsNF-κB pathwayPatient-derived tumorsDistinct activation phenotypesNSCLC patientsImmunosuppressive mechanismsSyngeneic tumorsHumanized miceImmunoregulatory rolePrognostic significanceImmunocompetent miceCancer patientsCell suppressionActivation phenotypeReduced tumorTumor growthDirect capture and sequencing reveal ultra-short single-stranded DNA in biofluids
Cheng LY, Dai P, Wu LR, Patel AA, Zhang DY. Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids. IScience 2022, 25: 105046. PMID: 36147958, PMCID: PMC9486625, DOI: 10.1016/j.isci.2022.105046.Peer-Reviewed Original ResearchLimitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics
Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nature Biomedical Engineering 2022, 6: 232-245. PMID: 35102279, PMCID: PMC9336539, DOI: 10.1038/s41551-021-00837-3.Peer-Reviewed Original Research
2021
Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing
Song P, Chen SX, Yan YH, Pinto A, Cheng LY, Dai P, Patel AA, Zhang DY. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nature Biomedical Engineering 2021, 5: 690-701. PMID: 33941896, PMCID: PMC9631981, DOI: 10.1038/s41551-021-00713-0.Peer-Reviewed Original ResearchTumor DNA Mutations From Intraparenchymal Brain Metastases Are Detectable in CSF
Cheok SK, Narayan A, Arnal-Estape A, Gettinger S, Goldberg SB, Kluger HM, Nguyen D, Patel A, Chiang V. Tumor DNA Mutations From Intraparenchymal Brain Metastases Are Detectable in CSF. JCO Precision Oncology 2021, 5: 163-172. PMID: 34250381, PMCID: PMC8232069, DOI: 10.1200/po.20.00292.Peer-Reviewed Original ResearchConceptsIntraparenchymal brain metastasesBrain metastasesCell-free DNAExtracranial tumorsBrain metastasis tissuesProgressive brain metastasesThird of patientsNormal pressure hydrocephalusTumor DNA mutationsPrimary cancer typeAnalysis of CSFSamples of CSFLeptomeningeal diseaseEffective surrogate markerBrain biopsyPressure hydrocephalusLumbar punctureSurrogate markerCancer-associated genesMetastasis tissuesPatientsMetastasisDiscordant responsesRenal cellsGenomic profiling
2020
35. EVALUATING CSF CIRCULATING TUMOR DNA IN INTRAPARENCHYMAL BRAIN METASTASIS
Cheok S, Narayan A, Arnal-Estape A, Patel A, Nguyen D, Chiang V. 35. EVALUATING CSF CIRCULATING TUMOR DNA IN INTRAPARENCHYMAL BRAIN METASTASIS. Neuro-Oncology Advances 2020, 2: ii6-ii6. PMCID: PMC7401400, DOI: 10.1093/noajnl/vdaa073.023.Peer-Reviewed Original ResearchIntraparenchymal brain metastasesBrain metastasis tissuesNormal pressure hydrocephalusBrain metastasesCerebrospinal fluidLeptomeningeal diseaseCell-free DNACSF ctDNAMetastasis tissuesTumor DNASamples of CSFStudy 12 patientsPrimary cancer typeAnalysis of CSFIntraparenchymal diseaseFurther therapySystemic metastasesPlasma ctDNASixteen patientsIntraparenchymal tumorsPressure hydrocephalusColorectal cancerLumbar punctureDetection of novelCancer-associated genes
2019
Cerebrospinal Fluid Biomarkers of Brain Metastasis
Cheok S, Arnal-Estape A, Narayan A, Zakaria M, Goldberg S, Patel A, Nguyen D, Chiang V. Cerebrospinal Fluid Biomarkers of Brain Metastasis. Neurosurgery 2019, 66: 310-631. DOI: 10.1093/neuros/nyz310_631.Peer-Reviewed Original ResearchOverall survival is improved when DCIS accompanies invasive breast cancer
Kole AJ, Park HS, Johnson SB, Kelly JR, Moran MS, Patel AA. Overall survival is improved when DCIS accompanies invasive breast cancer. Scientific Reports 2019, 9: 9934. PMID: 31289308, PMCID: PMC6616329, DOI: 10.1038/s41598-019-46309-2.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingCarcinoma, LobularCombined Modality TherapyFemaleFollow-Up StudiesHumansMiddle AgedNeoplasm InvasivenessPrognosisReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneRetrospective StudiesSurvival RateConceptsInvasive ductal carcinomaOverall survivalDCIS componentDuctal carcinomaBreast cancerER/PR positivityPure invasive ductal carcinomasMultivariable Cox modelingReceipt of mastectomyNational Cancer DatabaseSuperior overall survivalNode-negative diseaseBetter overall survivalInvasive breast cancerFavorable clinical characteristicsTreatment-related variablesUseful prognostic factorBreast cancer patientsInvasive tumor sizeDifferent biological behaviorPR positivityClinical characteristicsNegative diseaseCox modelingPrognostic factors
2018
META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples
Narayan A, Johnkennedy R, Zakaria M, Lee V, Patel AA. META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples. Methods 2018, 152: 41-47. PMID: 30308315, PMCID: PMC6311137, DOI: 10.1016/j.ymeth.2018.09.012.Peer-Reviewed Original ResearchMonitoring immunotherapy outcomes with circulating tumor DNA
Goldberg SB, Patel AA. Monitoring immunotherapy outcomes with circulating tumor DNA. Immunotherapy 2018, 10: 1023-1025. PMID: 30185140, DOI: 10.2217/imt-2018-0084.Peer-Reviewed Original ResearchOligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors
Lopez Sambrooks C, Baro M, Quijano A, Narayan A, Cui W, Greninger P, Egan R, Patel A, Benes CH, Saltzman WM, Contessa JN. Oligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors. Cancer Research 2018, 78: canres.0505.2018. PMID: 30026325, PMCID: PMC6125176, DOI: 10.1158/0008-5472.can-18-0505.Peer-Reviewed Original ResearchConceptsMutant NSCLCMutant non-small cell lung cancerNon-small cell lung cancerSignificant tumor growth delayEGFR-TKI treatmentCell lung cancerTyrosine kinase inhibitor resistanceEGFR tyrosine kinase inhibitor resistanceLung cancer cell linesNGI-1Tumor growth delayEffective therapeutic targetCell linesKinase inhibitor resistanceTumor cell viabilityH1975 xenograftsCancer cell linesTKI treatmentComplex transmembrane proteinsEGFR-TKILung cancerTumor responseCell cycle arrestPreclinical modelsTherapeutic strategiesEarly Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA
Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger S, Wilson LD, Herbst RS, Patel AA. Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA. Clinical Cancer Research 2018, 24: 1872-1880. PMID: 29330207, PMCID: PMC5899677, DOI: 10.1158/1078-0432.ccr-17-1341.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerImmune checkpoint inhibitorsCtDNA responseCheckpoint inhibitorsCtDNA levelsMetastatic non-small cell lung cancerImmune checkpoint inhibitor therapySuperior progression-free survivalRadiographic tumor sizeCheckpoint inhibitor therapyProgression-free survivalSuperior overall survivalTumor DNA levelsCell lung cancerAllele fractionClin Cancer ResMultigene next-generation sequencingMutant allele fractionTumor cell deathInhibitor therapyOverall survivalRadiographic responseImmunotherapy efficacyImmunotherapy responseMedian timeA novel multiple biomarker panel for the early detection of high-grade serous ovarian carcinoma
Han C, Bellone S, Siegel ER, Altwerger G, Menderes G, Bonazzoli E, Egawa-Takata T, Pettinella F, Bianchi A, Riccio F, Zammataro L, Yadav G, Marto JA, Penet MF, Levine DA, Drapkin R, Patel A, Litkouhi B, Ratner E, Silasi DA, Huang GS, Azodi M, Schwartz PE, Santin AD. A novel multiple biomarker panel for the early detection of high-grade serous ovarian carcinoma. Gynecologic Oncology 2018, 149: 585-591. PMID: 29572027, PMCID: PMC5986604, DOI: 10.1016/j.ygyno.2018.03.050.Peer-Reviewed Original ResearchConceptsHigh-grade serous ovarian carcinomaSerous ovarian carcinomaIL-6Ovarian cancerOvarian carcinomaE-cadHigh-grade serous ovarian adenocarcinomaEarly-stage ovarian cancerROC analysisEarly detectionMajority of patientsLethal gynecologic malignancyStage ovarian cancerOvarian cancer patientsBenign gynecologic pathologyNon-cancer controlsSerous ovarian adenocarcinomaEffective cancer screeningSerous ovarian cancerMultiple biomarker panelsFour-marker panelHigh differential gene expressionGynecologic malignanciesCA 125IL-1ra
2017
Breast Cancer Survival is Improved When DCIS Accompanies Invasive Ductal Carcinoma
Kole A, Park H, Johnson S, Kelly J, Patel A. Breast Cancer Survival is Improved When DCIS Accompanies Invasive Ductal Carcinoma. International Journal Of Radiation Oncology • Biology • Physics 2017, 99: e25. DOI: 10.1016/j.ijrobp.2017.06.651.Peer-Reviewed Original ResearchMultiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification
Wu LR, Chen SX, Wu Y, Patel AA, Zhang DY. Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nature Biomedical Engineering 2017, 1: 714-723. PMID: 29805844, PMCID: PMC5969535, DOI: 10.1038/s41551-017-0126-5.Peer-Reviewed Original Research