Chengyang Liu
Visiting Student 2019/20, Halene LabAbout
Research
Publications
2026
Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes
Medina-Serpas M, Brusko M, Golden G, Campbell-Thompson M, Rogers T, Reardon S, Posgai A, Bacher R, Luning Prak E, Liu C, Kaestner K, Naji A, Betts M, McIntyre L, Atkinson M, Brusko T. Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes. Cell Reports 2026, 45: 117144. PMID: 41875135, DOI: 10.1016/j.celrep.2026.117144.Peer-Reviewed Original ResearchPancreatic lymph nodesType 1 diabetesDraining lymph node tissuesHistory of type 1 diabetesHuman type 1 diabetesInflammation-associated transcriptsNatural historyFollicular B cellsNatural history of type 1 diabetesLymph node tissueInsulitic lesionsChemokine signatureLymph nodesAutoantibody-positiveB cellsLymphoid folliclesReg family genesInflammatory responseSpatial transcriptomicsNode tissueT1D donorsTherapeutic interventionsT1DPancreasLTB expressionSEL1L-HRD1 ER-associated degradation facilitates prohormone convertase 2 maturation and glucagon production in islet α cells
Zhu W, Pan L, Cui X, Russo A, Ray R, Pederson B, Wei X, Lin L, Torres M, Hafner H, Gregg B, Shrestha N, Liu C, Naji A, Arvan P, Sandoval D, Lindberg I, Qi L, Reinert R. SEL1L-HRD1 ER-associated degradation facilitates prohormone convertase 2 maturation and glucagon production in islet α cells. Nature Communications 2026 PMID: 41741474, DOI: 10.1038/s41467-026-69928-6.Peer-Reviewed Original ResearchEndoplasmic reticulum (ER)-associated degradationProhormone convertase 2Proteolytic cleavageSel1L-Hrd1 ERADProtein quality control systemER-associated degradationIslet A cellsCleavage of proglucagonProglucagon-expressing cellsGlucagon productionMisfolded proteinsA cellsQuality control systemProPC2Regulatory mechanismsProteinCell functionProhormoneMouse modelGlucagon secretionGlucagon contentSEL1LPancreatic glucagon contentCellsIslets
2025
Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes
Abedi M, Rai P, Zhou Y, Liu C, Johnson I, Chandra A, Fasolino M, Rostami S, Wang W, Min Z, Li Y, Yu M, Jay A, Lian V, Silverman M, Kaestner K, Naji A, Faryabi R, Vahedi G. Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes. Science Immunology 2025, 10: eadz0472. PMID: 41270190, PMCID: PMC12766627, DOI: 10.1126/sciimmunol.adz0472.Peer-Reviewed Original ResearchConceptsPancreatic lymph nodesCD4 T cellsType 1 diabetesLymph nodesT cellsMouse modelHuman type 1 diabetesMouse model of T1DActive disease stageModel of T1DT1D onsetGene expressionImmune cellsB cellsAutoimmune diseasesComprehensive analysis of gene expressionChromatin accessibilityDisease stageProfile of gene expressionTherapeutic avenuesDisease-modifying interventionsT1DCD4Insulin-producing B-cellsAnalysis of gene expressionMolecular Mechanisms of Human Pancreatic Islet Dysfunction Under Overnutrition Metabolic Stress
Hu X, Guo L, Toledo M, Sanchez P, Xie G, Liu C, Naji A, Irianto J, Roper M, Wang Y. Molecular Mechanisms of Human Pancreatic Islet Dysfunction Under Overnutrition Metabolic Stress. Diabetes 2025, 74: 1825-1838. PMID: 40773375, PMCID: PMC12451085, DOI: 10.2337/db24-1038.Peer-Reviewed Original ResearchConceptsGene regulatory networksSingle-cell RNA sequencingH3K9 methyltransferase G9aMolecular mechanismsRegulatory networksCell type-specific impactRNA sequencingMethyltransferase G9aMetabolic stressIslet endocrine cell typesCell type-specific mannerLineage-specific transcription factorsType 2 diabetes genetic riskIslet endocrine cellsGene expression changesCell-cell communicationPathogenesis of type 2 diabetesCell-cell interactionsResponse to overnutritionTranscription factorsEndocrine cellsCellular stressEndocrine cell typesGlucolipotoxicityB cellsIntegrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals
D'Oliveira Albanus R, Zhang X, Zhao Z, Taylor H, Tang X, Han Y, Orchard P, Varshney A, Zhang T, Manickam N, Erdos M, Narisu N, Taylor L, Saavedra X, Liu X, Zhong A, Li B, Zhou T, Naji A, Liu C, Collins F, Parker S, Chen S. Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals. Cell Reports 2025, 44: 116065. PMID: 40737125, PMCID: PMC12477748, DOI: 10.1016/j.celrep.2025.116065.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesIsogenic human embryonic stem cellsGWAS signalsSingle nucleotide polymorphismsT1D risk allelesHuman pancreatic isletsRegulatory elementsRegulatory regionsCell type contextT1D-associated genesTransposase-accessible chromatinProfile of gene expressionSingle-cell multi-omicsCell typesB cell deathMulti-omics integrative analysisPancreatic isletsHuman embryonic stem cellsChromatin accessibilityRNA-seqAssociation studiesB-like cellsNucleotide polymorphismsRegulatory signalsRNA sequencingChemPerturb-seq screen identifies a small molecule cocktail enhancing human beta cell survival after subcutaneous transplantation
Vandana J, Zhu J, Giani A, Zhang T, Lacko L, Leng D, Taylor D, Lee B, Han Z, Jiao T, Huang Y, Zhao M, Liu X, Chong A, Xue D, Meng Z, Xiang J, Pan C, Wang W, Naji A, Evans T, Liu J, Collins F, Liu C, Chen S. ChemPerturb-seq screen identifies a small molecule cocktail enhancing human beta cell survival after subcutaneous transplantation. Cell Stem Cell 2025, 32: 1299-1307.e8. PMID: 40562034, PMCID: PMC12335368, DOI: 10.1016/j.stem.2025.06.002.Peer-Reviewed Original ResearchImmune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset
Golden G, Wu V, Hamilton J, Amses K, Shapiro M, Sada Japp A, Liu C, Pampena M, Kuri-Cervantes L, Knox J, Gardner J, Atkinson M, Brusko T, Luning Prak E, Kaestner K, Naji A, Betts M. Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset. Nature Communications 2025, 16: 4621. PMID: 40383826, PMCID: PMC12086209, DOI: 10.1038/s41467-025-59626-0.Peer-Reviewed Original ResearchConceptsPancreas-draining lymph nodesCD4+ TregsT cell expressionNon-diabetic controlsLymphatic tissueAutoimmune destructionExpression of activation markersType 1 diabetes onsetDestruction of pancreatic B-cellsT cell signatureStudies of immune cellsNK cell differentiationNaive T cellsT1D genetic riskType 1 diabetesIL7 receptorT1D onsetActivation markersImmune infiltrationPancreatic B-cellsT cellsLymph nodesImmune perturbationsImmune cellsImmune changes
2024
β-Cell Secretory Capacity Predicts Metabolic Outcomes Over 6 Years After Human Islet Transplantation.
Flatt A, Matus A, Gallop R, Markmann E, Dalton-Bakes C, Peleckis A, Liu C, Naji A, Rickels M. β-Cell Secretory Capacity Predicts Metabolic Outcomes Over 6 Years After Human Islet Transplantation. Diabetes 2024, 74: 749-759. PMID: 39630971, PMCID: PMC12015140, DOI: 10.2337/db24-0729.Peer-Reviewed Original ResearchPurified human pancreatic isletsB-cell massB-cell secretory capacityHuman pancreatic isletsSecretory capacityProinsulin secretory ratiosInsulin independenceBeta 2Pancreatic isletsMeasures of graft functionHormone metabolismSecretory ratioIntra-portal infusionOne-year post-transplantGlucose-potentiated arginineType 1 diabetesGraft functionPost-transplantB cellsIsletsMetabolic outcomesFasting glucagonHuman islet transplantationSustained insulin independenceHuman Peripancreatic Adipose Tissue Paracrine Signaling Impacts Insulin Secretion, Blood Flow, and Gene Transcription
Bergman B, Berry K, Garfield A, Keller A, Zarini S, Bowen S, McKenna C, Kahn D, Pavelka J, Macias E, Uhlson C, Johnson C, Russ H, Viesi C, Seldin M, Liu C, Doliba N, Schoen J, Rothchild K, Hazel K, Naji A. Human Peripancreatic Adipose Tissue Paracrine Signaling Impacts Insulin Secretion, Blood Flow, and Gene Transcription. The Journal Of Clinical Endocrinology & Metabolism 2024, 110: e2233-e2247. PMID: 39484843, DOI: 10.1210/clinem/dgae767.Peer-Reviewed Original ResearchConceptsPeripancreatic adipose tissueSubcutaneous adipose tissueHuman islet insulin secretionIslet insulin secretionInsulin secretionAdipose tissueB cell functionAssociated with obesityGene transcriptionPancreatic lipid accumulationSex-dependent mannerAdipose tissue accumulationSecretion of adipokinesAortic vasodilationInterferon-gB cellsMetabolic outcomesInflammatory eicosanoidsConditioned mediumMetabolic healthInsulin resistanceParacrine signalingRNA sequencing analysisHuman donorsBlood flowBiliary atresia susceptibility gene EFEMP1 regulates extrahepatic bile duct elastic fiber formation and mechanics
Gupta K, Llewellyn J, Roberts E, Liu C, Naji A, Assoian R, Wells R. Biliary atresia susceptibility gene EFEMP1 regulates extrahepatic bile duct elastic fiber formation and mechanics. JHEP Reports 2024, 7: 101215. PMID: 39717503, PMCID: PMC11663959, DOI: 10.1016/j.jhepr.2024.101215.Peer-Reviewed Original ResearchExtrahepatic bile ductNeonatal extrahepatic bile ductsBiliary atresiaSusceptibility genesBile ductFibulin-3Genome wide association studiesExtracellular matrix protein 1Pressure myographyGene EFEMP1Elastic fibersExtracellular matrix proteinsAssociation studiesHuman extrahepatic bile ductsExtracellular matrix componentsElastic fiber organizationMatrix protein 1Decreased elastic fibersBile duct structuresMatrix proteinsFormation of elastic fibersFunctional relevanceGenesFiber formationNormal ducts