Hongying Shen, PhD
Assistant Professor of Cellular and Molecular PhysiologyDownloadHi-Res Photo
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Cellular & Molecular Physiology
Primary
Contact Info
Cellular & Molecular Physiology
ISTC building Rm120, 850 West Campus Drive , Yale West Campus
West Haven, CT 06516
United States
About
Titles
Assistant Professor of Cellular and Molecular Physiology
Biography
Hongying (Hoy) Shen is an assistant professor at Cellular & Molecular Physiology at Yale School of Medicine and Systems Biology Institute at Yale West Campus from Jan 2020. Dr. Shen is interested to use multidisciplinary approaches ranging from biochemistry, cell biology, genetics, molecular evolution, and metabolomics to study cellular metabolism underlying human health and diseases, which would ultimately offer new directions for diagnostics and therapeutics. Specifically, we will focus on the “deorphanization” of hundreds of enzymes and transporters of unknown functions that are encoded in the human genome and are important to cellular and organismal physiology.
Dr. Shen received her B.S. in chemistry from Nanjing University in China in 2006 and her Ph.D. in Molecular Biophysics and Biochemistry (MB&B) at Yale University in 2013, where she studied membrane curvature formation and lipid metabolism in endocytic trafficking in the laboratory of Dr. Pietro De Camilli at the cell biology department. She then completed her postdoctoral training with Dr. Vamsi Mootha at Massachusetts General Hospital and Harvard Medical School to develop integrated metabolomics and CRISPR screen approaches to study mitochondrial metabolism.
Appointments
Cellular & Molecular Physiology
Assistant ProfessorPrimary
Other Departments & Organizations
- Cellular & Molecular Physiology
- Diabetes Research Center
- Interdepartmental Neuroscience Program
- Janeway Society
- Molecular Cell Biology, Genetics and Development
- Molecular Medicine, Pharmacology, and Physiology
- Neuroscience Track
- Wu Tsai Institute
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
Education & Training
- PhD
- Yale University, Molecular Biophysics and Biochemistry (2013)
- BS
- Nanjing University, China, Chemistry (2006)
Research
Overview
Medical Research Interests
Cell Biology; Mass Spectrometry; Metabolism
ORCID
0000-0002-2115-7037- View Lab Website
Shen lab
Research at a Glance
Yale Co-Authors
Frequent collaborators of Hongying Shen's published research.
Publications Timeline
A big-picture view of Hongying Shen's research output by year.
Pietro De Camilli, MD
James Duncan, PhD
Shawn Ferguson, PhD
TuKiet Lam, PhD, BS
Jesse Rinehart, PhD
Kariona Grabinska, PhD
25Publications
2,068Citations
Publications
Featured Publications
Systems biochemistry to “deorphanize” human mitochondrial proteome
Miros F, Liu R, Shen H. Systems biochemistry to “deorphanize” human mitochondrial proteome. Molecular Cell 2022, 82: 2735-2737. PMID: 35931038, DOI: 10.1016/j.molcel.2022.07.005.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsCombinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS
Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nature Communications 2022, 13: 2483. PMID: 35513392, PMCID: PMC9072411, DOI: 10.1038/s41467-022-30126-9.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsDe novo purine biosynthesisMitochondrial iron uptakeStructure-guided mutagenesisNovo purine biosynthesisMetabolic stateMitochondrial glutathione transportGlutathione importGenetic interactionsGenetic perturbationsDifferent metabolic environmentsFitness defectsLack of substrateGene interactionsMitochondrial OXPHOSMitochondrial membranePurine biosynthesisCarrier familyTransport assaysKO cellsIron uptakeGlutathione transportTransport activityIron homeostasisGlutathione homeostasisGenesThe Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
Shen H, Campanello GC, Flicker D, Grabarek Z, Hu J, Luo C, Banerjee R, Mootha VK. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell 2017, 171: 771-782.e11. PMID: 29056341, PMCID: PMC5827971, DOI: 10.1016/j.cell.2017.09.051.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMethylmalonyl-CoA mutaseCitramalyl-CoA lyaseAnti-microbial metabolitesCell-autonomous defectSubstrate analogue inhibitorsMammalian cellsStructural biologyPathway assignmentItaconyl-CoAMitochondrial enzymesCellular activitiesMetabolic pathwaysDependent methylmalonyl-CoA mutaseHomozygous lossConsistent phenotypeConsequence of exposureVertebratesCellsEnzymologyBiologyMutaseLyasePhenotypeEnzymePathwayPhylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.
Byrne, K.L.; Szeligowski, R.V.; Shen, H. Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters. Biomolecules 2023, 13, 1314.Peer-Reviewed Original Research
2023
Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis
Shi X, DeCiucis M, Grabinska K, Kanyo J, Liu A, Lam T, Shen H. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Molecular Cell 2023, 84: 802-810.e6. PMID: 38157846, PMCID: PMC10922821, DOI: 10.1016/j.molcel.2023.12.008.Peer-Reviewed Original ResearchCitationsAltmetricConceptsProtein quality controlMitochondrial protein quality controlDual regulationMetabolic compartmentalizationIron homeostasisMitochondrial iron-sulfur clustersIron-sulfur clustersMitochondrial transportersProtein regulationMammalian cellsCRISPR knockoutCysteine residuesTransporter regulationLoop 1SLC25A39Glutathione homeostasisMetabolic sensingGlutathione uptakeMature neuronsProtein levelsHomeostasisRegulationAFG3L2Biochemical featuresMitochondrial glutathione levelsSalvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions
Skinner O, Blanco-Fernández J, Goodman R, Kawakami A, Shen H, Kemény L, Joesch-Cohen L, Rees M, Roth J, Fisher D, Mootha V, Jourdain A. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nature Metabolism 2023, 5: 765-776. PMID: 37198474, PMCID: PMC10229423, DOI: 10.1038/s42255-023-00774-2.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsUpper glycolysisGenome-wide genetic screenNutrient-limited conditionsNon-oxidative branchGenetic screenCancer lineagesContext of diseaseRegulated stepGrowth of cellsATP productionGlyceraldehyde 3Cancer cell linesGlucose transportPrimary macrophagesGlycolysisCell linesComplete lossPyrimidine synthesisPathwayRNACarbon building blocksAlternative nutrientsRibose moietyUridineComplete absenceThe C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion
Onuchic L, Padovano V, Schena G, Rajendran V, Dong K, Shi X, Pandya R, Rai V, Gresko N, Ahmed O, Lam T, Wang W, Shen H, Somlo S, Caplan M. The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion. Nature Communications 2023, 14: 1790. PMID: 36997516, PMCID: PMC10063565, DOI: 10.1038/s41467-023-37449-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPolycystin-1Nicotinamide nucleotide transhydrogenaseTerminal tailCystic phenotypeAutosomal dominant polycystic kidney diseaseCyst cell proliferationC-terminal domainAmino acid residuesLethal monogenic disorderC-terminal cleavageNucleotide transhydrogenaseAcid residuesMitochondrial functionTransgenic expressionPKD1 geneRedox stateShort fragmentsCell proliferationMonogenic disordersDominant polycystic kidney diseasePolycystic kidney diseaseGene therapy strategiesProteinPhenotypeFragments
2022
Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine
Moen J, Mohler K, Rogulina S, Shi X, Shen H, Rinehart J. Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine. Nature Communications 2022, 13: 7226. PMID: 36433969, PMCID: PMC9700786, DOI: 10.1038/s41467-022-34980-5.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsUbiquitous post-translational modificationCo-translational insertionKinase activation mechanismProtein interaction platformOrthogonal translation systemProtein-protein interactionsPost-translational modificationsPhospho-amino acidsAminoacyl-tRNA synthetaseHuman phosphoproteomePhosphorylation eventsTRNA pairsFunctional assignmentCellular processesProtein phosphorylationUpstream kinasePhysiological functionsActivation mechanismTranslation systemKinasePhosphorylationInteraction platformPhosphoproteomePhosphothreoninePhospho
2021
VPS13D bridges the ER to mitochondria and peroxisomes via Miro
Guillén-Samander A, Leonzino M, Hanna MG, Tang N, Shen H, De Camilli P. VPS13D bridges the ER to mitochondria and peroxisomes via Miro. Journal Of Cell Biology 2021, 220: e202010004. PMID: 33891013, PMCID: PMC8077184, DOI: 10.1083/jcb.202010004.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsLipid transport proteinsHigher eukaryotesER-mitochondriaSecretory pathwayAccessory factorsMitochondrial dynamicsDisease pathogenesisTransport proteinsParkin substratesLipid transferSplice variantsParkinson's disease pathogenesisVps13Lipid supplyMitochondriaMiroVPS13DERMESYeastMost lipidsTransport domainEukaryotesGem1MetazoansER
2020
An IRON-clad Connection between Aging Organelles
Shen H. An IRON-clad Connection between Aging Organelles. Cell 2020, 180: 214-216. PMID: 31978339, DOI: 10.1016/j.cell.2019.12.037.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords
Academic Achievements & Community Involvement
honor Rita Allen Foundation Scholar
National AwardRita Allen FoundationDetails09/01/2023honor 1907 Foundation Trailblazer Award in mental health
National Award1907 FoundationDetails01/01/2022United Stateshonor Klingenstein-Simons Fellowship Award in Neurosciences
National AwardKlingenstein-Simons FoundationDetails07/01/2021United Stateshonor Lois E. and Franklin H. Top, Jr., Yale Scholar Award
Yale School of Medicine AwardYale School of MedicineDetails04/16/2021United Stateshonor Chan Zuckerberg Initiative Neurodegeneration Challenge Network Collaborative Pairs Pilot Project Awards
International AwardChan Zuckerberg InitiativeDetails12/01/2020United States
News
News
- September 19, 2023
Investigators Launch Study Aimed at Accelerating Understanding of Bipolar Disorder
- September 01, 2023Source: Yale West Campus
Hoy Shen Selected as Rita Allen Foundation Scholar
- May 11, 2022
The Molecular Machinery That Delivers Metabolites to Mitochondria
- June 22, 2021
Hoy Shen receives Klingenstein-Simons Fellowship Award in Neurosciences
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Cellular & Molecular Physiology
ISTC building Rm120, 850 West Campus Drive , Yale West Campus
West Haven, CT 06516
United States