2025
Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution
Loft A, Emont M, Weinstock A, Divoux A, Ghosh A, Wagner A, Hertzel A, Maniyadath B, Deplancke B, Liu B, Scheele C, Lumeng C, Ding C, Ma C, Wolfrum C, Strieder-Barboza C, Li C, Truong D, Bernlohr D, Stener-Victorin E, Kershaw E, Yeger-Lotem E, Shamsi F, Hui H, Camara H, Zhong J, Kalucka J, Ludwig J, Semon J, Jalkanen J, Whytock K, Dumont K, Sparks L, Muir L, Fang L, Massier L, Saraiva L, Beyer M, Jeschke M, Mori M, Boroni M, Walsh M, Patti M, Lynes M, Blüher M, Rydén M, Hamda N, Solimini N, Mejhert N, Gao P, Gupta R, Murphy R, Pirouzpanah S, Corvera S, Tang S, Das S, Schmidt S, Zhang T, Nelson T, O’Sullivan T, Efthymiou V, Wang W, Tong Y, Tseng Y, Mandrup S, Rosen E. Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution. Nature Metabolism 2025, 7: 875-894. PMID: 40360756, DOI: 10.1038/s42255-025-01296-9.Peer-Reviewed Original ResearchConceptsCell annotationSingle-cell dataRegulation of metabolic homeostasisSingle-cell resolutionSingle-cell atlasMouse adipose tissueAdipose tissueMetabolic homeostasisSpecialized cellsPrimary repositoryAnnotationCellsExcess caloriesBionetworkProportion of adipocytesConnective tissueMiceTissueComplex connective tissueAdipocytesHomeostasis
2024
Single-cell multi-cohort dissection of the schizophrenia transcriptome
Ruzicka W, Mohammadi S, Fullard J, Davila-Velderrain J, Subburaju S, Tso D, Hourihan M, Jiang S, Lee H, Bendl J, Voloudakis G, Haroutunian V, Hoffman G, Roussos P, Kellis M, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Berretta S, Bharadwaj R, Bhattacharya A, Bicks L, Brennand K, Capauto D, Champagne F, Chatterjee T, Chatzinakos C, Chen Y, Chen H, Cheng Y, Cheng L, Chess A, Chien J, Chu Z, Clarke D, Clement A, Collado-Torres L, Cooper G, Crawford G, Dai R, Daskalakis N, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duan Z, Duong D, Dursun C, Eagles N, Edelstein J, Emani P, Galani K, Galeev T, Gandal M, Gaynor S, Gerstein M, Geschwind D, Girdhar K, Goes F, Greenleaf W, Grundman J, Guo H, Guo Q, Gupta C, Hadas Y, Hallmayer J, Han X, Hawken N, He C, Henry E, Hicks S, Ho M, Ho L, Huang Y, Huuki-Myers L, Hwang A, Hyde T, Iatrou A, Inoue F, Jajoo A, Jensen M, Jiang L, Jin P, Jin T, Jops C, Jourdon A, Kawaguchi R, Kleinman J, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Lee C, Lee D, Li J, Li M, Lin X, Liu S, Liu J, Liu J, Liu C, Liu S, Lou S, Loupe J, Lu D, Ma S, Ma L, Margolis M, Mariani J, Martinowich K, Maynard K, Mazariegos S, Meng R, Myers R, Micallef C, Mikhailova T, Ming G, Monte E, Montgomery K, Moore J, Moran J, Mukamel E, Nairn A, Nemeroff C, Ni P, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Peters M, Phalke N, Pinto D, Pjanic M, Pochareddy S, Pollard K, Pollen A, Pratt H, Przytycki P, Purmann C, Qin Z, Qu P, Quintero D, Raj T, Rajagopalan A, Reach S, Reimonn T, Ressler K, Ross D, Rozowsky J, Ruth M, Sanders S, Schneider J, Scuderi S, Sebra R, Sestan N, Seyfried N, Shao Z, Shedd N, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Stein J, Steyert M, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Vo D, Wamsley B, Wang T, Wang S, Wang D, Wang Y, Warrell J, Wei Y, Weimer A, Weinberger D, Wen C, Weng Z, Whalen S, White K, Willsey A, Won H, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Xu S, Yap C, Zeng B, Zhang P, Zhang C, Zhang B, Zhang J, Zhang Y, Zhou X, Ziffra R, Zeier Z, Zintel T. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science 2024, 384: eadg5136. PMID: 38781388, DOI: 10.1126/science.adg5136.Peer-Reviewed Original ResearchConceptsGenetic risk factorsRisk factorsTranscriptional changesHeterogeneity of schizophreniaNeuronal cell statesSchizophrenia pathophysiologySingle-cell dissectionExcitatory neuronsEffective therapySchizophrenia transcriptomicsCortical cytoarchitectureSingle-cell atlasGenomic variantsCell groupsHuman prefrontal cortexMolecular pathwaysSchizophreniaTranscriptional alterationsTranscriptomic changesPrefrontal cortexCell statesAlterationsTherapyPathophysiologyDissectionFatty acid binding protein 5 suppression attenuates obesity-induced hepatocellular carcinoma by promoting ferroptosis and intratumoral immune rewiring
Sun J, Esplugues E, Bort A, Cardelo M, Ruz-Maldonado I, Fernández-Tussy P, Wong C, Wang H, Ojima I, Kaczocha M, Perry R, Suárez Y, Fernández-Hernando C. Fatty acid binding protein 5 suppression attenuates obesity-induced hepatocellular carcinoma by promoting ferroptosis and intratumoral immune rewiring. Nature Metabolism 2024, 6: 741-763. PMID: 38664583, PMCID: PMC12355809, DOI: 10.1038/s42255-024-01019-6.Peer-Reviewed Original ResearchConceptsFatty acid binding protein 5Tumor-associated macrophagesHepatocellular carcinomaImmunosuppressive phenotype of tumor-associated macrophagesIncreased CD8+ T cell activationCD8+ T cell activationPhenotype of tumor-associated macrophagesPro-inflammatory tumor microenvironmentCo-stimulatory molecules CD80T cell activationHepatocellular carcinoma burdenTransformation of hepatocytesBinding protein 5Potential therapeutic approachImmunosuppressive phenotypeTumor microenvironmentFerroptosis-induced cell deathMale miceEnhanced ferroptosisTherapeutic approachesPharmacological inhibitionGenetic ablationIncreased expressionSingle-cell atlasAnalysis of transformed cellsSingle-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells
Gu W, Eke C, Santiago E, Olaloye O, Konnikova L. Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells. Mucosal Immunology 2024, 17: 599-617. PMID: 38555026, PMCID: PMC11384551, DOI: 10.1016/j.mucimm.2024.03.011.Peer-Reviewed Original ResearchImmune cellsDevelopment of mucosal immunityComplex immune landscapeFetal immune cellsSevere intestinal complicationsComplications of prematurityMemory T cellsAdaptive immune cellsMucosal immune cellsSmall intestineT cell statesMemory T cell statesStem-like propertiesNecrotizing enterocolitisNeonatal samplesMyeloid populationsImmune landscapeFetal samplesT cellsExpression of activationPostnatal samplesMucosal diseaseMucosal immunitySingle-cell RNA sequencingSingle-cell atlas
2023
TMIC-20. A SPATIALLY RESOLVED HUMAN GLIOBLASTOMA ATLAS REVEALS DISTINCT CELLULAR AND MOLECULAR PATTERNS OF ANATOMICAL NICHES
Shah N, Park H, Sonpatki P, Han K, Yu H, Kim S, Chowdhury T, Byun Y, Kang H, Lee J, Lee S, Won J, Kim T, Choi S, Shin Y, Ku J, Lee S, Yun H, Park S, Park C, Park W. TMIC-20. A SPATIALLY RESOLVED HUMAN GLIOBLASTOMA ATLAS REVEALS DISTINCT CELLULAR AND MOLECULAR PATTERNS OF ANATOMICAL NICHES. Neuro-Oncology 2023, 25: v282-v282. PMCID: PMC10639919, DOI: 10.1093/neuonc/noad179.1086.Peer-Reviewed Original ResearchCellular componentsBulk RNA-seq dataAnatomical nichesSingle-cell atlasSingle-cell RNARNA-seq dataMulti-omics profilingDifferent cellular componentsInteraction networksSpatial transcriptomeCellular heterogeneitySpatial interaction networkDistinct cellularMolecular patternsCellular architectureNicheUnrecognized subtypesSpatial organizationAbstract GlioblastomaValuable resourceGlioma samplesStromal cellsEffective combinatorial therapiesComprehensive insightGlioblastomaSingle-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis
Egozi A, Olaloye O, Werner L, Silva T, McCourt B, Pierce R, An X, Wang F, Chen K, Pober J, Shouval D, Itzkovitz S, Konnikova L. Single-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis. PLOS Biology 2023, 21: e3002124. PMID: 37205711, PMCID: PMC10234541, DOI: 10.1371/journal.pbio.3002124.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingSingle-cell atlasEpithelial cellsCell identityRNA sequencingBulk transcriptomicsCellular dysregulationAberrant interactionsNeonatal small intestinePotential targetCellular changesBiomarker discoveryGastrointestinal complicationsPremature infantsProinflammatory macrophagesProinflammatory genesClonal expansionT cellsEndothelial cellsImmune interactionsIntestinal tissueCellsSmall intestineComprehensive viewNEC
2022
Correction: Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Khaliq A, Erdogan C, Kurt Z, Turgut S, Grunvald M, Rand T, Khare S, Borgia J, Hayden D, Pappas S, Govekar H, Kam A, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel M, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel T, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen A, Masood A. Correction: Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biology 2022, 23: 156. PMID: 35831907, PMCID: PMC9277898, DOI: 10.1186/s13059-022-02724-9.Peer-Reviewed Original ResearchSingle-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric CancerSingle-Cell Atlas of Gastric Cancer Subtypes
Kumar V, Ramnarayanan K, Sundar R, Padmanabhan N, Srivastava S, Koiwa M, Yasuda T, Koh V, Huang K, Tay S, Ho S, Tan A, Ishimoto T, Kim G, Shabbir A, Chen Q, Zhang B, Xu S, Lam K, Lum H, Teh M, Yong W, So J, Tan P. Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric CancerSingle-Cell Atlas of Gastric Cancer Subtypes. Cancer Discovery 2022, 12: 670-691. PMID: 34642171, PMCID: PMC9394383, DOI: 10.1158/2159-8290.cd-21-0683.Peer-Reviewed Original ResearchConceptsPatient-derived organoidsPlasma cell proportionsGastric cancer subtypesLineage statePredictors of poor clinical prognosisCancer subtypesSingle-cell atlasCell proportionCancer-associated fibroblasts' subtypesCell populationsDiffuse-type tumorsPoor clinical prognosisIn vivo modelsComprehensive single-cell atlasPrimary tumorHistological subtypesRNA-sequencing cohortsTumor microenvironmentClinical stageClinical prognosisGastric malignancyTumor ecosystemGastric cancerCancer heterogeneityTumor
2021
Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis
Nakahara Y, Hashimoto N, Sakamoto K, Enomoto A, Adams TS, Yokoi T, Omote N, Poli S, Ando A, Wakahara K, Suzuki A, Inoue M, Hara A, Mizutani Y, Imaizumi K, Kawabe T, Rosas IO, Takahashi M, Kaminski N, Hasegawa Y. Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis. European Respiratory Journal 2021, 58: 2003397. PMID: 34049947, DOI: 10.1183/13993003.03397-2020.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPulmonary fibrosisAnti-fibrotic propertiesRole of fibroblastsFibroblastic fociPathogenesis of IPFLung fibrosis modelSenescence-associated secretory phenotypeNormal lung samplesMesenchymal stromal cellsIPF patientsIPF lungsDense fibrosisPathological hallmark lesionsFibrosis modelFibrotic lungsHallmark lesionsSingle-cell atlasActive fibrogenesisElderly individualsLung samplesFibrosisSingle-cell RNA sequencingFibrotic regionsSecretory phenotypeIntegrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.Peer-Reviewed Original ResearchConceptsDifferential expression analysisPrimary lung endothelial cellsLung endothelial cellsCell typesMarker genesExpression analysisSingle-cell RNA sequencing dataCross-species analysisVenous endothelial cellsEndothelial marker genesSingle-cell atlasMarker gene setsRNA sequencing dataEndothelial cellsSubsequent differential expression analysisDifferent lung cell typesResident cell typesLung cell typesCellular diversityEndothelial cell typesCapillary endothelial cellsHuman lung endothelial cellsPhenotypic diversityEndothelial diversityIndistinguishable populations
2020
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis
Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Science Advances 2020, 6: eaba1983. PMID: 32832599, PMCID: PMC7439502, DOI: 10.1126/sciadv.aba1983.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisVascular endothelial cellsIPF lungsPulmonary fibrosisChronic obstructive pulmonary disease (COPD) lungsFatal interstitial lung diseaseEndothelial cellsInterstitial lung diseaseCell populationsIPF myofibroblastsMyofibroblast fociNonsmoker controlsLung diseaseCOPD lungsBasaloid cellsSingle-cell atlasInvasive fibroblastsMacrophage populationsLungStromal cellsEpithelial cellsFibrosisCellular populationsDevelopmental markersSingle-cell RNA-seq
2019
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, Verma R, Abdala-Valencia H, Nam K, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Watanabe S, Williams KJN, Flozak AS, Nicholson TT, Morgan VK, Winter DR, Hinchcliff M, Hrusch CL, Guzy RD, Bonham CA, Sperling AI, Bag R, Hamanaka RB, Mutlu GM, Yeldandi AV, Marshall SA, Shilatifard A, Amaral LAN, Perlman H, Sznajder JI, Argento AC, Gillespie CT, Dematte J, Jain M, Singer BD, Ridge KM, Lam AP, Bharat A, Bhorade SM, Gottardi CJ, Budinger GRS, Misharin AV. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2019, 199: 1517-1536. PMID: 30554520, PMCID: PMC6580683, DOI: 10.1164/rccm.201712-2410oc.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingRNA sequencingPulmonary fibrosisAlveolar macrophagesLung tissueSingle-cell transcriptomic analysisEpithelial cellsCell populationsNext-generation sequencing technologiesSingle-cell atlasHuman lungDiverse cell populationsExpression of genesRare cell populationsPulmonary fibrosis pathogenesisIdiopathic pulmonary fibrosisAirway stem cellsIndividual cell populationsTranscriptomic analysisSequencing technologiesWnt secretionRNA hybridizationSenescent cellsTransplant donorsDiscovery-based approachA Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer
Wagner J, Rapsomaniki M, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal S, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes K, Martínez M, Weber W, Bodenmiller B. A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell 2019, 177: 1330-1345.e18. PMID: 30982598, PMCID: PMC6526772, DOI: 10.1016/j.cell.2019.03.005.Peer-Reviewed Original ResearchConceptsBreast cancerBreast cancer ecosystemsTumor-associated macrophagesResponse to therapyHuman breast tumorsTumor cell compositionHuman breast cancerNon-tumor tissue samplesPrecision medicine approachT cellsBreast tumorsImmune cellsPoor prognosisAntibody panelTumor cellsTumor ecosystemHeterogeneous diseaseClinical dataDisease progressionTumorSingle-cell atlasMass cytometryPhenotypic abnormalitiesMedicine approachImmune ecosystem
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply