Featured Publications
HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART
Farhadian SF, Lindenbaum O, Zhao J, Corley MJ, Im Y, Walsh H, Vecchio A, Garcia-Milian R, Chiarella J, Chintanaphol M, Calvi R, Wang G, Ndhlovu LC, Yoon J, Trotta D, Ma S, Kluger Y, Spudich S. HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART. JCI Insight 2022, 7: e160267. PMID: 35801589, PMCID: PMC9310520, DOI: 10.1172/jci.insight.160267.Peer-Reviewed Original ResearchConceptsCerebrospinal fluidHIV infectionHIV-1-infected cellsCNS viral persistenceCentral memory CD4T-cell abnormalitiesHIV-1 RNAMicroglia-like cellsT cell activationSystemic viral suppressionAbnormal CD8HIV neuropathogenesisViral suppressionMemory CD4CNS reservoirsImmune perturbationsExperience elevated ratesNeuroimmune effectsPeripheral bloodNeurological impairmentViral persistenceT cellsCell abnormalitiesUninfected controlsCell activationBorrelia miyamotoi Meningoencephalitis in an Immunocompetent Patient
Gandhi S, Narasimhan S, Workineh A, Mamula M, Yoon J, Krause PJ, Farhadian SF. Borrelia miyamotoi Meningoencephalitis in an Immunocompetent Patient. Open Forum Infectious Diseases 2022, 9: ofac295. PMID: 35873293, PMCID: PMC9301576, DOI: 10.1093/ofid/ofac295.Peer-Reviewed Original ResearchEmerging Single-cell Approaches to Understand HIV in the Central Nervous System
Corley MJ, Farhadian SF. Emerging Single-cell Approaches to Understand HIV in the Central Nervous System. Current HIV/AIDS Reports 2021, 19: 113-120. PMID: 34822063, PMCID: PMC8613726, DOI: 10.1007/s11904-021-00586-7.Peer-Reviewed Original ResearchConceptsCentral nervous systemSingle-cell sequencing methodsSingle-cell approachesStudy of genomesSingle-cell technologiesSingle-cell analysisSingle-cell levelSingle-cell studiesNervous systemMolecular identitySequencing methodsRare infected cellsViral establishmentCentral nervous system tissueInfected cellsNervous system tissueAutopsy brainsCNS reservoirsCSF cellsHIV StudyHIVTranslational studiesCNS perturbationsCNS studiesTissue compartmentsDivergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Reports Medicine 2021, 2: 100288. PMID: 33969321, PMCID: PMC8091032, DOI: 10.1016/j.xcrm.2021.100288.Peer-Reviewed Original ResearchNeurological symptomsImmune responseCerebrospinal fluidAnti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodiesCOVID-19Self-reactive immune responsesSARS-CoV-2 antibodiesCompartmentalized immune responseCSF immunoglobulin GRole of autoimmunityCOVID-19 patientsB cell responsesCoronavirus disease 2019Immune surveyNeurologic sequelaePulmonary infectionBrain infectionSerum antibodiesDisease 2019Monoclonal antibody targetsAnimal modelsTarget epitopesCell activationCell responsesSingle-cell RNA sequencingNeurologic Complications of Babesiosis, United States, 2011–2021 - Volume 29, Number 6—June 2023 - Emerging Infectious Diseases journal - CDC
Locke S, O’Bryan J, Zubair A, Rethana M, Moffarah A, Krause P, Farhadian S. Neurologic Complications of Babesiosis, United States, 2011–2021 - Volume 29, Number 6—June 2023 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2023, 29: 1127-1135. PMID: 37209667, PMCID: PMC10202888, DOI: 10.3201/eid2906.221890.Peer-Reviewed Original ResearchConceptsNeurologic complicationsNeurologic symptomsRisk factorsYale-New Haven HospitalInfectious Diseases journal - CDCHigh-grade parasitemiaNeurologic risk factorsRange of symptomsAdult patientsRenal failureDiabetes mellitusFrequent symptomsHospital admissionImpaired consciousnessMedical recordsEndemic areasParasitic infectionsPatientsSymptomsIntraerythrocytic protozoaComplicationsBabesiosisNew HavenDeliriumMellitusSingle-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV
Farhadian SF, Mehta SS, Zografou C, Robertson K, Price RW, Pappalardo J, Chiarella J, Hafler DA, Spudich SS. Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV. JCI Insight 2018, 3: e121718. PMID: 30232286, PMCID: PMC6237230, DOI: 10.1172/jci.insight.121718.Peer-Reviewed Original ResearchConceptsCerebrospinal fluidHIV infectionImmune activationAntiretroviral therapyNeuronal injuryCentral nervous system immune activationLong-term suppressive antiretroviral therapySingle-cell RNA sequencingCNS immune activationDisease-associated microgliaSuppressive antiretroviral therapyImmune cell subsetsMicroglia-like cellsGene expression signaturesNeuronal damageNeuroinflammatory diseasesRNA sequencingCell subsetsCNS cellsNeurological conditionsRare subsetNeurocognitive impairmentMyeloid cellsCellular subsetsInfectionHIV and Age Do Not Synergistically Affect Age-Related T-Cell Markers
Farhadian S, Jalbert E, Deng Y, Goetz MB, Park LS, Justice A, Dubrow R, Emu B. HIV and Age Do Not Synergistically Affect Age-Related T-Cell Markers. JAIDS Journal Of Acquired Immune Deficiency Syndromes 2018, 77: 337-344. PMID: 29140874, PMCID: PMC5807137, DOI: 10.1097/qai.0000000000001595.Peer-Reviewed Original ResearchConceptsCD8 T cellsT-cell markersCD4 T cellsHIV infectionT cellsAntiretroviral therapyEffector memory CD4 T cellsImmune systemVeterans Aging Cohort StudyMemory CD4 T cellsNaive CD4 T cellsAging Cohort StudyT cell subsetsT-cell phenotypeCopies/mLCross-sectional studyRace/ethnicityChronic HIVUninfected subjectsUninfected menCohort studyHIV diseaseHigher proportionHIV serostatusHIV status
2024
Epigenetic Changes in Cerebrospinal Fluid and Blood of People with Neurosyphilis
Mostaghimi D, Mehta S, Yoon J, Kosana P, Marra C, Corley M, Farhadian S. Epigenetic Changes in Cerebrospinal Fluid and Blood of People with Neurosyphilis. The Journal Of Infectious Diseases 2024, jiae476. PMID: 39356164, DOI: 10.1093/infdis/jiae476.Peer-Reviewed Original ResearchPeripheral blood mononuclear cellsCerebrospinal fluidRNA expression changesEpigenetic changesExpression changesBlood mononuclear cellsDifferentially methylated sitesDNA methylation profilesInsulin-responsive pathwaysAntibiotic treatmentImmune cellsB cellsMononuclear cellsMethylation changesDNA methylationMethylation profilesMatched controlsBacterial infectionsNon-NENeurosyphilisBlood of peopleInfectionRNANSRetinal integrity in human babesiosis: a pilot study
Dionne E, Adelman R, Cekic O, Golden M, Moffarah A, Krause P, Farhadian S. Retinal integrity in human babesiosis: a pilot study. BMC Ophthalmology 2024, 24: 310. PMID: 39048971, PMCID: PMC11267664, DOI: 10.1186/s12886-024-03568-6.Peer-Reviewed Original ResearchConceptsEvidence of retinopathyNo study patientRetina of patientsCohort of patientsAbnormal vessel formationComplication of babesiosisRetinal tearsRetinal inflammationRetinal eye examResultsTen patientsRetinal integrityRetinal examinationRetinal bleedingIndirect ophthalmoscopeRetinal abnormalitiesStudy patientsChart reviewCase reportEye examPilot studyPatientsAnimal studiesSmall studyClinical informationHuman babesiosisA single item screen for clinically significant insomnia symptoms in community‐living older adults
Webster L, Hobbs J, Farhadian S, Gill T, Miner B. A single item screen for clinically significant insomnia symptoms in community‐living older adults. Journal Of The American Geriatrics Society 2024, 72: 3604-3606. PMID: 39007457, PMCID: PMC11560724, DOI: 10.1111/jgs.19086.Peer-Reviewed Original ResearchTranscobalamin receptor antibodies in autoimmune vitamin B12 central deficiency
Pluvinage J, Ngo T, Fouassier C, McDonagh M, Holmes B, Bartley C, Kondapavulur S, Hurabielle C, Bodansky A, Pai V, Hinman S, Aslanpour A, Alvarenga B, Zorn K, Zamecnik C, McCann A, Asencor A, Huynh T, Browne W, Tubati A, Haney M, Douglas V, Louine M, Cree B, Hauser S, Seeley W, Baranzini S, Wells J, Spudich S, Farhadian S, Ramachandran P, Gillum L, Hales C, Zikherman J, Anderson M, Yazdany J, Smith B, Nath A, Suh G, Flanagan E, Green A, Green R, Gelfand J, DeRisi J, Pleasure S, Wilson M. Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency. Science Translational Medicine 2024, 16: eadl3758. PMID: 38924428, PMCID: PMC11520464, DOI: 10.1126/scitranslmed.adl3758.Peer-Reviewed Original ResearchConceptsBlood-brain barrierCerebrospinal fluidNeurological deficitsAutoimmune neurological conditionsCohort of patientsCellular uptake of cobalaminVitamin B12B12 transportCerebrospinal fluid samplesMeasurement of vitamin B12Low-density lipoprotein receptorProgrammable phage displayImmunosuppressive treatmentIn vitro modelNeuropsychiatric lupusImmunomodulatory treatmentReceptor antibodiesClinical improvementUptake of cobalaminB12 deficiencyUnknown etiologyHematopoietic cellsTranscobalamin receptorCentral deficiencyB12 supplementationClimate Change and Meningoencephalitis in the Americas: A Brewing Storm
Dionne E, Machiavello Roman F, Farhadian S. Climate Change and Meningoencephalitis in the Americas: A Brewing Storm. Current Infectious Disease Reports 2024, 26: 189-196. DOI: 10.1007/s11908-024-00843-x.Peer-Reviewed Original ResearchGeographical distributionImpacts of climate changeEcological interactionsGeographical distribution of vectorsLa Crosse virusVirus infectionVector-borne infectionsNorthward expansionPrecipitation seasonalityClimate changeWest Nile virusPowassan virus infectionCase of meningoencephalitisWarmer wintersPathogensSeasonHuman populationNile virusIncreased incidenceClimate modelsPrecipitation patternsVirusEpidemiological changesMeningoencephalitisDistribution of vectorsFocal White Matter Damage in Individuals with Cognitive Impairment After COVID-19 (P11-13.004)
McAlpine L, Nelson A, Chiarella J, Lacadie C, Farhadian S, Constable T, Spudich S. Focal White Matter Damage in Individuals with Cognitive Impairment After COVID-19 (P11-13.004). Neurology 2024, 102 DOI: 10.1212/wnl.0000000000204666.Peer-Reviewed Original ResearchHIV-1–infected T cell clones are shared across cerebrospinal fluid and blood during ART
Wang M, Yoon J, Reisert H, Das B, Orlinick B, Chiarella J, Halvas E, Mellors J, Pang A, Barakat L, Fikrig M, Cyktor J, Kluger Y, Spudich S, Corley M, Farhadian S. HIV-1–infected T cell clones are shared across cerebrospinal fluid and blood during ART. JCI Insight 2024, 9: e176208. PMID: 38587074, PMCID: PMC11128194, DOI: 10.1172/jci.insight.176208.Peer-Reviewed Original ResearchConceptsT cell clonesT cell receptorCerebrospinal fluidT cellsHIV-1Infected T-cell clonesCentral memory T cellsCD4 T-cell clonesDetectable HIV RNAMemory T cellsHIV-1 RNAInfected T cellsCNS reservoirsHIV persistenceHIV reservoirHIV RNAHIV cureReservoir cellsPWHTissue compartmentsBloodCNSUninfected controlsCD4Infected cellsNeurosyphilis is characterized by a compartmentalized and robust neuroimmune response but not by neuronal injury
Catalano A, Yoon J, Fertuzinhos S, Reisert H, Walsh H, Kosana P, Wilson M, Gisslen M, Zetterberg H, Marra C, Farhadian S. Neurosyphilis is characterized by a compartmentalized and robust neuroimmune response but not by neuronal injury. Med 2024, 5: 321-334.e3. PMID: 38513660, PMCID: PMC11216317, DOI: 10.1016/j.medj.2024.02.005.Peer-Reviewed Original ResearchMarker of neuronal injuryNeuronal injuryNeurological symptomsWhite blood cell count <Immune responsePresence of neurological symptomsNeuroinflammatory diseasesCell count <CSF-VDRL testPlasma reagin titerCNS immune responsesCNS-specific immune responseImmune cell activationCSF inflammatory responseCSF cellsNeurosyphilis casesAsymptomatic neurosyphilisCSF neopterinImmune profileNeuroimmune responseHIV statusNational Institutes of HealthNeurosyphilisCell activationInflammatory response
2023
Polypharmacy Is Associated With Slow Gait Speed and Recurrent Falls in Older People With HIV
Kosana P, Wu K, Tassiopoulos K, Letendre S, Ma Q, Paul R, Ellis R, Erlandson K, Farhadian S. Polypharmacy Is Associated With Slow Gait Speed and Recurrent Falls in Older People With HIV. Clinical Infectious Diseases 2023, 78: 1608-1616. PMID: 38147306, PMCID: PMC11175684, DOI: 10.1093/cid/ciad782.Peer-Reviewed Original Research1494. Impact of Polypharmacy on Gait Speed and Falls in Older People Living with HIV.
Kosana P, Wu K, Tassiopoulos K, Letendre S, Ma Q, Erlandson K, Farhadian S. 1494. Impact of Polypharmacy on Gait Speed and Falls in Older People Living with HIV. Open Forum Infectious Diseases 2023, 10: ofad500.1329. PMCID: PMC10677239, DOI: 10.1093/ofid/ofad500.1329.Peer-Reviewed Original ResearchSlow gait speedGait speedPrescription medicationsLogistic regression modelsStudy participantsMedical comorbiditiesRecurrent fallsOlder PWHIncreased oddsClinical informationOlder peopleAntiretroviral drug useImpact of polypharmacyManagement of polypharmacyHigher CD4 countsNumber of comorbiditiesPlasma viral loadPercent of participantsCross-sectional analysisSelf-reported raceGeriatric outcomesLow CD4Medication burdenCD4 countCD8 ratioSelf-Reported Neuropsychiatric Post–COVID-19 Condition and CSF Markers of Neuroinflammation
Farhadian S, Reisert H, McAlpine L, Chiarella J, Kosana P, Yoon J, Spudich S. Self-Reported Neuropsychiatric Post–COVID-19 Condition and CSF Markers of Neuroinflammation. JAMA Network Open 2023, 6: e2342741. PMID: 37948085, PMCID: PMC10638645, DOI: 10.1001/jamanetworkopen.2023.42741.Peer-Reviewed Original ResearchAn AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model
Charkoftaki G, Aalizadeh R, Santos-Neto A, Tan W, Davidson E, Nikolopoulou V, Wang Y, Thompson B, Furnary T, Chen Y, Wunder E, Coppi A, Schulz W, Iwasaki A, Pierce R, Cruz C, Desir G, Kaminski N, Farhadian S, Veselkov K, Datta R, Campbell M, Thomaidis N, Ko A, Thompson D, Vasiliou V. An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model. Human Genomics 2023, 17: 80. PMID: 37641126, PMCID: PMC10463861, DOI: 10.1186/s40246-023-00521-4.Peer-Reviewed Original ResearchConceptsCOVID-19 patientsDisease severityViral outbreaksFuture viral outbreaksLength of hospitalizationIntensive care unitWorse disease prognosisLife-threatening illnessEffective medical interventionsCOVID-19Clinical decision treeGlucuronic acid metabolitesNew potential biomarkersHospitalization lengthCare unitComorbidity dataSerotonin levelsDisease progressionHealthy controlsPatient outcomesDisease prognosisPatient transferPatientsHealthcare resourcesPotential biomarkersSleep deficiency among people living with human immunodeficiency virus: A growing challenge
Reisert H, Miner B, Farhadian S. Sleep deficiency among people living with human immunodeficiency virus: A growing challenge. HIV Medicine 2023, 25: 5-15. PMID: 37485570, PMCID: PMC10803648, DOI: 10.1111/hiv.13526.Peer-Reviewed Original ResearchConceptsHuman immunodeficiency virusSleep qualitySleep deficiencyImmunodeficiency virusSleep durationHIV-specific factorsSelf-reported sleep qualitySleep timingAntiretroviral therapy drugsObjective sleep qualityAntiretroviral therapyEpidemiological correlatesHigh-quality researchSociodemographic factorsClinical implicationsNarrative reviewTherapy drugsMental healthMore high-quality researchPLWHLongitudinal studyDeficiencyObjective measuresDurationVirus