Kien Pham, PhD
Research Scientist in PathologyCards
About
Research
Publications
2025
Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US
Chen N, Pham K, Chaguza C, Lopes R, Klaassen F, Kalinich C, Initiative Y, Kerantzas N, Pandya S, Ferguson D, Schulz W, Weinberger D, Pitzer V, Warren J, Grubaugh N, Hahn A. Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US. Viruses 2025, 17: 1020. PMID: 40733636, PMCID: PMC12299087, DOI: 10.3390/v17071020.Peer-Reviewed Original ResearchConceptsDominant lineageHost-pathogen dynamicsGenomic surveillance programsResponse to previous infectionsSequence dataVariant fitnessLineage replacementCopy numberDynamic fitness landscapesLineagesSARS-CoV-2Integrated analysisViral copy numberFitness landscapeReplacement dynamicsReproductive rateOmicron lineagesGrowth rateImmune escapeAntigen exposureVariant emergenceViral sheddingPrevious infectionEpidemiological dataInfectionEarly Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC
Pham K, Chaguza C, Lopes R, Cohen T, Taylor-Salmon E, Wilkinson M, Katebi V, Grubaugh N, Hill V. Early Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2025, 31: s45-s56. PMID: 40359081, PMCID: PMC12078544, DOI: 10.3201/eid3113.240981.Peer-Reviewed Original ResearchExploring Glypican-3 targeted CAR-NK treatment and potential therapy resistance in hepatocellular carcinoma
Yang L, Pham K, Xi Y, Wu Q, Liu D, Robertson K, Liu C. Exploring Glypican-3 targeted CAR-NK treatment and potential therapy resistance in hepatocellular carcinoma. PLOS ONE 2025, 20: e0317401. PMID: 39841705, PMCID: PMC11753693, DOI: 10.1371/journal.pone.0317401.Peer-Reviewed Original ResearchConceptsGlypican-3Hepatocellular carcinomaCAR-NKNatural killerCell linesCAR-NK therapyCAR-NK cellsTreatment of hepatocellular carcinomaNK cell lineAnti-tumor effectsCancer-related mortalitySuppressed tumor growthPrimary liver cancerInfluence therapeutic outcomesCells in vitroHepatocellular carcinoma treatmentHepG2 cells in vitroNK92MI cellsImmunotherapy strategiesNSG miceImmunotherapy targetOncofetal glycoproteinTherapy resistanceImprove patient outcomesPoor prognosis
2024
Acyl-CoA Synthetase Medium-Chain Family Member 5–Mediated Fatty Acid Metabolism Dysregulation Promotes the Progression of Hepatocellular Carcinoma
Yang L, Pham K, Xi Y, Jiang S, Robertson K, Liu C. Acyl-CoA Synthetase Medium-Chain Family Member 5–Mediated Fatty Acid Metabolism Dysregulation Promotes the Progression of Hepatocellular Carcinoma. American Journal Of Pathology 2024, 194: 1951-1966. PMID: 39069168, PMCID: PMC11423759, DOI: 10.1016/j.ajpath.2024.07.002.Peer-Reviewed Original ResearchConceptsDNA methyltransferase 1Fatty acid metabolismAcyl-CoADown-regulationAcid metabolismDecreased STAT3 phosphorylationCell linesPromoter region methylationHepatocellular carcinoma cell lineHepatocellular carcinoma patient samplesDNA methylationFatty acid accumulationDysregulated fatty acid metabolismSTAT3 phosphorylationDecreased cell proliferationHepatocellular carcinomaHepatocellular carcinoma tumor tissuesMethyltransferase 1Region methylationRegulatory mechanismsACSM5Molecular mechanismsMetabolic dysregulationProgression of hepatocellular carcinomaAcid accumulationEpigenetic heterogeneity hotspots in human liver disease progression
Hlady R, Zhao X, Khoury L, Wagner R, Luna A, Pham K, Pyrosopoulos N, Jain D, Wang L, Liu C, Robertson K. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology 2024, 81: 1197-1210. PMID: 39028883, PMCID: PMC11742070, DOI: 10.1097/hep.0000000000001023.Peer-Reviewed Original ResearchEpigenetic heterogeneityGenome-wide profiling of DNA methylationProfiling of DNA methylationDNA methylation landscapeGenome-wide profilingGene expression heterogeneityCopy number variationsMethylation landscapeOnset of liver cancerDNA methylationLiver disease developmentPhenotypic effectsNumber variationsGenetic heterogeneityTranscriptional heterogeneityFunctional screeningLiver disease progressionCopy numberExpression heterogeneityGene expressionTumor suppressorHuman diseasesGenesPathological phenotypesKey pathwaysCombining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
Lopes R, Pham K, Klaassen F, Chitwood M, Hahn A, Redmond S, Swartwood N, Salomon J, Menzies N, Cohen T, Grubaugh N. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Reports 2024, 43: 114451. PMID: 38970788, DOI: 10.1016/j.celrep.2024.114451.Peer-Reviewed Original Research
2023
Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants
Moriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.Peer-Reviewed Original ResearchConceptsMHC-I expressionBreakthrough infectionsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variantsMajor histocompatibility complex class I expressionCell-mediated immunityInfluenza virus infectionSARS-CoV-2 VOCsMHC-I upregulationClass I expressionSARS-CoV-2T cell recognitionVirus infectionMHC II expressionSpike proteinEnhanced inhibitionInfectionCell recognitionCommon mutationsReinfectionE proteinAntibodiesViral genesSubvariantsExpressionAge-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose
Filardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.Peer-Reviewed Original ResearchConceptsBooster doseAntibody responseNeutralization titersVirus-specific IgG titersOlder adultsAntiviral humoral immunityPlasma antibody responsesHigh-risk populationSARS-CoV-2 spikeYears of ageAge-dependent impairmentHeterologous regimensBooster dosesBooster vaccineCoronaVac vaccineIgG titersProtective immunityHumoral immunityHumoral responseCoronaVacOmicron waveBooster strategyAge groupsEarly controlVaccineAccelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.Peer-Reviewed Original ResearchConceptsChronic infectionEvolutionary ratesGenetic diversityIntrahost evolutionDistinct genotypesHigher viral genome copiesVirus evolutionary ratesSARS-CoV-2 evolutionUntreated chronic infectionAdvantageous mutationsNucleotide substitutionsViral genome copiesDivergent variantsInfection hypothesisVariant emergenceViral populationsInfectious virusInfectionHallmark changesGenome copiesDifferent genotypesDiversityGenotypesTemporal dynamicsEvolution
2022
Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic
Paulino-Ramírez R, Pham K, Breban M, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh N, Hahn A. Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic. Microbiology Resource Announcements 2022, 12: e01113-22. PMID: 36448812, PMCID: PMC9872639, DOI: 10.1128/mra.01113-22.Peer-Reviewed Original Research
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