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26
Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
27
Yoon SO, Shin S, Liu Y, Ballif BA, Woo MS, Gygi SP, Blenis J. Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Mol Cell 2023;83:4190. [PMID: 37980093 DOI: 10.1016/j.molcel.2023.10.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
28
Zhang T, Liu X, Rossio V, Dawson SL, Gygi SP, Paulo JA. Enhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics. J Proteome Res 2023:10.1021/acs.jproteome.3c00492. [PMID: 37962907 PMCID: PMC11090996 DOI: 10.1021/acs.jproteome.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
29
Hu Z, Zhang M, Fan J, Hu J, Lin G, Piao S, Liu P, Liu J, Fu S, Sun W, Gygi SP, Zhang J, Zhou C. High-Level Secretion of Pregnancy Zone Protein Is a Novel Biomarker of DNA Damage-Induced Senescence and Promotes Spontaneous Senescence. J Proteome Res 2023;22:3570-3579. [PMID: 37831546 DOI: 10.1021/acs.jproteome.3c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
30
Adhikary U, Paulo JA, Godes M, Roychoudhury S, Prew MS, Ben-Nun Y, Yu EW, Budhraja A, Opferman JT, Chowdhury D, Gygi SP, Walensky LD. Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction. Cell Rep 2023;42:113176. [PMID: 37773750 PMCID: PMC10787359 DOI: 10.1016/j.celrep.2023.113176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]  Open
31
Patil A, Strom AR, Paulo JA, Collings CK, Ruff KM, Shinn MK, Sankar A, Cervantes KS, Wauer T, St Laurent JD, Xu G, Becker LA, Gygi SP, Pappu RV, Brangwynne CP, Kadoch C. A disordered region controls cBAF activity via condensation and partner recruitment. Cell 2023;186:4936-4955.e26. [PMID: 37788668 PMCID: PMC10792396 DOI: 10.1016/j.cell.2023.08.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023]
32
Shuken SR, McAlister GC, Barshop WD, Canterbury JD, Bergen D, Huang J, Huguet R, Paulo JA, Zabrouskov V, Gygi SP, Yu Q. Deep Proteomic Compound Profiling with the Orbitrap Ascend Tribrid Mass Spectrometer Using Tandem Mass Tags and Real-Time Search. Anal Chem 2023;95:15180-15188. [PMID: 37811788 PMCID: PMC10785648 DOI: 10.1021/acs.analchem.3c01701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
33
Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
34
Chi B, Öztürk MM, Paraggio CL, Leonard CE, Sanita ME, Dastpak M, O’Connell JD, Coady JA, Zhang J, Gygi SP, Lopez-Gonzalez R, Yin S, Reed R. Causal ALS genes impact the MHC class II antigen presentation pathway. Proc Natl Acad Sci U S A 2023;120:e2305756120. [PMID: 37722062 PMCID: PMC10523463 DOI: 10.1073/pnas.2305756120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023]  Open
35
Kurmi K, Liang D, van de Ven R, Georgiev P, Gassaway BM, Han S, Notarangelo G, Harris IS, Yao CH, Park JS, Hu SH, Peng J, Drijvers JM, Boswell S, Sokolov A, Dougan SK, Sorger PK, Gygi SP, Sharpe AH, Haigis MC. Metabolic modulation of mitochondrial mass during CD4+ T cell activation. Cell Chem Biol 2023;30:1064-1075.e8. [PMID: 37716347 PMCID: PMC10604707 DOI: 10.1016/j.chembiol.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 06/28/2023] [Accepted: 08/21/2023] [Indexed: 09/18/2023]
36
Yin TC, Van Vranken JG, Srivastava D, Mittal A, Buscaglia P, Moore AE, Verdinez JA, Graham AE, Walsh SA, Acevedo MA, Kerns RJ, Artemyev NO, Gygi SP, Sebag JA. Insulin sensitization by small molecules enhancing GLUT4 translocation. Cell Chem Biol 2023;30:933-942.e6. [PMID: 37453421 DOI: 10.1016/j.chembiol.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
37
Wang N, Shibata Y, Paulo JA, Gygi SP, Rapoport TA. A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast. Nat Commun 2023;14:4765. [PMID: 37553386 PMCID: PMC10409813 DOI: 10.1038/s41467-023-40530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023]  Open
38
Sohn JH, Mutlu B, Latorre-Muro P, Liang J, Bennett CF, Sharabi K, Kantorovich N, Jedrychowski M, Gygi SP, Banks AS, Puigserver P. Liver mitochondrial cristae organizing protein MIC19 promotes energy expenditure and pedestrian locomotion by altering nucleotide metabolism. Cell Metab 2023;35:1356-1372.e5. [PMID: 37473754 PMCID: PMC10528355 DOI: 10.1016/j.cmet.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
39
Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC. The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. Nat Chem Biol 2023;19:1013-1021. [PMID: 37081311 PMCID: PMC10530065 DOI: 10.1038/s41589-023-01321-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
40
Keele GR, Zhang JG, Szpyt J, Korstanje R, Gygi SP, Churchill GA, Schweppe DK. Global and tissue-specific aging effects on murine proteomes. Cell Rep 2023;42:112715. [PMID: 37405913 PMCID: PMC10588767 DOI: 10.1016/j.celrep.2023.112715] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/06/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023]  Open
41
Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol 2023;41:845-857. [PMID: 36593396 PMCID: PMC11069389 DOI: 10.1038/s41587-022-01539-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/30/2022] [Indexed: 01/03/2023]
42
A M, Wales TE, Zhou H, Draga-Coletă SV, Gorgulla C, Blackmore KA, Mittenbühler MJ, Kim CR, Bogoslavski D, Zhang Q, Wang ZF, Jedrychowski MP, Seo HS, Song K, Xu AZ, Sebastian L, Gygi SP, Arthanari H, Dhe-Paganon S, Griffin PR, Engen JR, Spiegelman BM. Irisin acts through its integrin receptor in a two-step process involving extracellular Hsp90α. Mol Cell 2023;83:1903-1920.e12. [PMID: 37267907 PMCID: PMC10984146 DOI: 10.1016/j.molcel.2023.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/19/2023] [Accepted: 05/05/2023] [Indexed: 06/04/2023]
43
Yeo AT, Shah R, Aliazis K, Pal R, Xu T, Zhang P, Rawal S, Rose CM, Varn FS, Appleman VA, Yoon J, Varma H, Gygi SP, Verhaak RG, Boussiotis VA, Charest A. Driver Mutations Dictate the Immunologic Landscape and Response to Checkpoint Immunotherapy of Glioblastoma. Cancer Immunol Res 2023;11:629-645. [PMID: 36881002 PMCID: PMC10155040 DOI: 10.1158/2326-6066.cir-22-0655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/20/2022] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
44
Cullati SN, Zhang E, Shan Y, Guillen RX, Chen JS, Navarrete-Perea J, Elmore ZC, Ren L, Gygi SP, Gould KL. Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538600. [PMID: 37162912 PMCID: PMC10168346 DOI: 10.1101/2023.04.27.538600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
45
Zhou H, Feng W, Yu J, Shafiq TA, Paulo JA, Zhang J, Luo Z, Gygi SP, Moazed D. SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions. Cell Rep 2023;42:112339. [PMID: 37014752 PMCID: PMC10777863 DOI: 10.1016/j.celrep.2023.112339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/14/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023]  Open
46
Gao X, Wu Y, Chick JM, Abbott A, Jiang B, Wang DJ, Comte-Walters S, Johnson RH, Oberholtzer N, Nishimura MI, Gygi SP, Mehta A, Guttridge DC, Ball L, Mehrotra S, Sicinski P, Yu XZ, Wang H. Targeting protein tyrosine phosphatases for CDK6-induced immunotherapy resistance. Cell Rep 2023;42:112314. [PMID: 37000627 PMCID: PMC10544673 DOI: 10.1016/j.celrep.2023.112314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 12/20/2022] [Accepted: 03/14/2023] [Indexed: 04/01/2023]  Open
47
Shinde SR, Mick DU, Aoki E, Rodrigues RB, Gygi SP, Nachury MV. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. Dev Cell 2023;58:677-693.e9. [PMID: 37019113 PMCID: PMC10133032 DOI: 10.1016/j.devcel.2023.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
48
Naulé L, Mancini A, Pereira SA, Gassaway BM, Lydeard JR, Magnotto JC, Kim HK, Liang J, Matos C, Gygi SP, Merkle FT, Carroll RS, Abreu AP, Kaiser UB. MKRN3 inhibits puberty onset via interaction with IGF2BP1 and regulation of hypothalamic plasticity. JCI Insight 2023;8:e164178. [PMID: 37092553 PMCID: PMC10243807 DOI: 10.1172/jci.insight.164178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/24/2023] [Indexed: 04/25/2023]  Open
49
Bohmer MJ, Wang J, Istvan ES, Luth MR, Collins JE, Huttlin EL, Wang L, Mittal N, Hao M, Kwiatkowski NP, Gygi SP, Chakrabarti R, Deng X, Goldberg DE, Winzeler EA, Gray NS, Chakrabarti D. Human Polo-like Kinase Inhibitors as Antiplasmodials. ACS Infect Dis 2023;9:1004-1021. [PMID: 36919909 PMCID: PMC10106425 DOI: 10.1021/acsinfecdis.3c00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
50
Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC. Genetic dissection of the pluripotent proteome through multi-omics data integration. CELL GENOMICS 2023;3:100283. [PMID: 37082146 PMCID: PMC10112288 DOI: 10.1016/j.xgen.2023.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
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