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Rene Maehr PhD

TitleAssociate Professor
InstitutionUMass Chan Medical School
DepartmentProgram in Molecular Medicine
AddressUMass Chan Medical School
368 Plantation Street AS7.2057
Worcester MA 01605
Phone508-856-3037
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionT.H. Chan School of Medicine
    DepartmentRNA Therapeutics Institute

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program


    Collapse Biography 
    Collapse education and training
    Vrije Universiteit, Amsterdam, , NetherlandsPHDPathology
    Harvard University, Cambridge, USAPostdocwith Doug Melton
    Harvard Medical School, Boston, USAVisiting Studentwith Hidde Ploegh
    Albert Ludwig University of Freiburg, Freiburg, GermanyDiplom
    Collapse awards and honors
    2015The Glass Charitable Foundation Term Chair in Diabetes
    2014 - 2016Charles H Hood Foundation Child Health Research Award for junior faculty
    2005Naomi Berrie Diabetes Research Fellow
    2001 - 2004Boehringer Ingelheim Fonds Pre-doctoral Fellowship

    Collapse Overview 
    Collapse overview

    The focus of our research program is to delineate the molecular pathways that govern immune system development and function. We combine of variety experimental approaches, including human pluripotent stem cell differentiation, CRISPR-based (epi-)genome engineering, single cell RNAseq, computational biology and functional genomics, as well as various disease models to elucidate the molecular bases of human immune syndromes. The long-term goal is to recapitulate the disease in a patient-specific manner and to identify novel treatment strategies.


    Collapse Rotation Projects
    A rotation project is available
    Collapse Post Docs
    A postdoctoral position is available


    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods. 2021 09; 18(9):1046-1055. PMID: 34480151.
      Citations: 11     Fields:    Translation:HumansCells
    2. Reis M, Willis GR, Fernandez-Gonzalez A, Yeung V, Taglauer E, Magaletta M, Parsons T, Derr A, Liu X, Maehr R, Kourembanas S, Mitsialis SA. Mesenchymal Stromal Cell-Derived Extracellular Vesicles Restore Thymic Architecture and T Cell Function Disrupted by Neonatal Hyperoxia. Front Immunol. 2021; 12:640595. PMID: 33936055.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    3. Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Mol Cell. 2020 05 07; 78(3):554-565.e7. PMID: 32213324.
      Citations: 97     Fields:    Translation:HumansAnimalsCells
    4. Han L, Choudhury S, Mich-Basso JD, Ammanamanchi N, Ganapathy B, Suresh S, Khaladkar M, Singh J, Maehr R, Zuppo DA, Kim J, Eberwine JH, Wyman SK, Wu YL, Kühn B. Lamin B2 Levels Regulate Polyploidization of Cardiomyocyte Nuclei and Myocardial Regeneration. Dev Cell. 2020 04 06; 53(1):42-59.e11. PMID: 32109383.
      Citations: 25     Fields:    Translation:AnimalsCells
    5. Magaletta ME, Siller R, Maehr R. Differentiation of human pluripotent stem cells toward pharyngeal endoderm derivatives: Current status and potential. Curr Top Dev Biol. 2020; 138:175-208. PMID: 32220297.
      Citations: 1     Fields:    Translation:HumansCells
    6. Stanney W, Ladam F, Donaldson IJ, Parsons TJ, Maehr R, Bobola N, Sagerström CG. Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish. Dev Biol. 2020 03 15; 459(2):161-180. PMID: 31862379.
      Citations: 3     Fields:    Translation:AnimalsCells
    7. Phillips HM, Stothard CA, Shaikh Qureshi WM, Kousa AI, Briones-Leon JA, Khasawneh RR, O'Loughlin C, Sanders R, Mazzotta S, Dodds R, Seidel K, Bates T, Nakatomi M, Cockell SJ, Schneider JE, Mohun TJ, Maehr R, Kist R, Peters H, Bamforth SD. Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis. Development. 2019 09 23; 146(18). PMID: 31444215.
      Citations: 12     Fields:    Translation:AnimalsCells
    8. Min SY, Desai A, Yang Z, Sharma A, DeSouza T, Genga RMJ, Kucukural A, Lifshitz LM, Nielsen S, Scheele C, Maehr R, Garber M, Corvera S. Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells. Proc Natl Acad Sci U S A. 2019 09 03; 116(36):17970-17979. PMID: 31420514.
      Citations: 41     Fields:    Translation:HumansCells
    9. Genga RMJ, Kernfeld EM, Parsi KM, Parsons TJ, Ziller MJ, Maehr R. Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development. Cell Rep. 2019 04 16; 27(3):708-718.e10. PMID: 30995470.
      Citations: 27     Fields:    Translation:HumansCells
    10. Fischer DS, Fiedler AK, Kernfeld EM, Genga RMJ, Bastidas-Ponce A, Bakhti M, Lickert H, Hasenauer J, Maehr R, Theis FJ. Inferring population dynamics from single-cell RNA-sequencing time series data. Nat Biotechnol. 2019 04; 37(4):461-468. PMID: 30936567.
      Citations: 33     Fields:    Translation:AnimalsCells
    11. Kernfeld EM, Genga RMJ, Neherin K, Magaletta ME, Xu P, Maehr R. A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation. Immunity. 2018 06 19; 48(6):1258-1270.e6. PMID: 29884461.
      Citations: 68     Fields:    Translation:HumansAnimalsCells
    12. Fischer DS, Fiedler AK, Kernfeld E, Genga RMJ, Hasenauer J, Maehr R, Theis FJ. Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series. bioRxiv 219188. . 2017.
    13. Parsi KM, Hennessy E, Kearns N, Maehr R. Using an Inducible CRISPR-dCas9-KRAB Effector System to Dissect Transcriptional Regulation in Human Embryonic Stem Cells. Methods Mol Biol. 2017; 1507:221-233. PMID: 27832543.
      Citations: 13     Fields:    Translation:HumansCells
    14. Babon JA, DeNicola ME, Blodgett DM, Crèvecoeur I, Buttrick TS, Maehr R, Bottino R, Naji A, Kaddis J, Elyaman W, James EA, Haliyur R, Brissova M, Overbergh L, Mathieu C, Delong T, Haskins K, Pugliese A, Campbell-Thompson M, Mathews C, Atkinson MA, Powers AC, Harlan DM, Kent SC. Analysis of self-antigen specificity of islet-infiltrating T cells from human donors with type 1 diabetes. Nat Med. 2016 12; 22(12):1482-1487. PMID: 27798614.
      Citations: 138     Fields:    Translation:HumansCells
    15. Pham H, Kearns NA, Maehr R. Transcriptional Regulation with CRISPR/Cas9 Effectors in Mammalian Cells. Methods Mol Biol. 2016; 1358:43-57. PMID: 26463376.
      Citations: 15     Fields:    Translation:AnimalsCells
    16. Genga RM, Kearns NA, Maehr R. Controlling transcription in human pluripotent stem cells using CRISPR-effectors. Methods. 2016 05 15; 101:36-42. PMID: 26525193.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    17. Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods. 2015 May; 12(5):401-403. PMID: 25775043.
      Citations: 253     Fields:    Translation:AnimalsCells
    18. Blum B, Roose AN, Barrandon O, Maehr R, Arvanites AC, Davidow LS, Davis JC, Peterson QP, Rubin LL, Melton DA. Reversal of ? cell de-differentiation by a small molecule inhibitor of the TGF? pathway. Elife. 2014 Sep 16; 3:e02809. PMID: 25233132.
      Citations: 61     Fields:    Translation:HumansAnimalsCells
    19. Chen YJ, Finkbeiner SR, Weinblatt D, Emmett MJ, Tameire F, Yousefi M, Yang C, Maehr R, Zhou Q, Shemer R, Dor Y, Li C, Spence JR, Stanger BZ. De novo formation of insulin-producing "neo-? cell islets" from intestinal crypts. Cell Rep. 2014 Mar 27; 6(6):1046-1058. PMID: 24613355.
      Citations: 72     Fields:    Translation:HumansAnimalsCells
    20. Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan; 141(1):219-23. PMID: 24346702.
      Citations: 132     Fields:    Translation:HumansCells
    21. Tajonar A, Maehr R, Hu G, Sneddon JB, Rivera-Feliciano J, Cohen DE, Elledge SJ, Melton DA. Brief report: VGLL4 is a novel regulator of survival in human embryonic stem cells. Stem Cells. 2013 Dec; 31(12):2833-41. PMID: 23765749.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    22. Kearns NA, Genga RM, Ziller M, Kapinas K, Peters H, Brehm MA, Meissner A, Maehr R. Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules. Stem Cell Res. 2013 Nov; 11(3):1003-12. PMID: 23917481.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    23. Sherwood RI, Maehr R, Mazzoni EO, Melton DA. Wnt signaling specifies and patterns intestinal endoderm. Mech Dev. 2011 Sep-Dec; 128(7-10):387-400. PMID: 21854845.
      Citations: 55     Fields:    Translation:AnimalsCells
    24. Maehr R. iPS cells in type 1 diabetes research and treatment. Clin Pharmacol Ther. 2011 May; 89(5):750-3. PMID: 21430661.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    25. Greer PL, Hanayama R, Bloodgood BL, Mardinly AR, Lipton DM, Flavell SW, Kim TK, Griffith EC, Waldon Z, Maehr R, Ploegh HL, Chowdhury S, Worley PF, Steen J, Greenberg ME. The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc. Cell. 2010 Mar 05; 140(5):704-16. PMID: 20211139.
      Citations: 289     Fields:    Translation:HumansAnimalsCells
    26. Niakan KK, Ji H, Maehr R, Vokes SA, Rodolfa KT, Sherwood RI, Yamaki M, Dimos JT, Chen AE, Melton DA, McMahon AP, Eggan K. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev. 2010 Feb 01; 24(3):312-26. PMID: 20123909.
      Citations: 134     Fields:    Translation:AnimalsCells
    27. Maehr R, Chen S, Snitow M, Ludwig T, Yagasaki L, Goland R, Leibel RL, Melton DA. Generation of pluripotent stem cells from patients with type 1 diabetes. Proc Natl Acad Sci U S A. 2009 Sep 15; 106(37):15768-73. PMID: 19720998.
      Citations: 247     Fields:    Translation:HumansCells
    28. Borowiak M, Maehr R, Chen S, Chen AE, Tang W, Fox JL, Schreiber SL, Melton DA. Small molecules efficiently direct endodermal differentiation of mouse and human embryonic stem cells. Cell Stem Cell. 2009 Apr 03; 4(4):348-58. PMID: 19341624.
      Citations: 188     Fields:    Translation:HumansAnimalsCells
    29. Chen S, Borowiak M, Fox JL, Maehr R, Osafune K, Davidow L, Lam K, Peng LF, Schreiber SL, Rubin LL, Melton D. A small molecule that directs differentiation of human ESCs into the pancreatic lineage. Nat Chem Biol. 2009 Apr; 5(4):258-65. PMID: 19287398.
      Citations: 199     Fields:    Translation:HumansAnimalsCells
    30. Huangfu D, Osafune K, Maehr R, Guo W, Eijkelenboom A, Chen S, Muhlestein W, Melton DA. Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol. 2008 Nov; 26(11):1269-75. PMID: 18849973.
      Citations: 539     Fields:    Translation:HumansAnimalsCells
    31. Gounaris E, Tung CH, Restaino C, Maehr R, Kohler R, Joyce JA, Ploegh HL, Plough HL, Barrett TA, Weissleder R, Khazaie K. Live imaging of cysteine-cathepsin activity reveals dynamics of focal inflammation, angiogenesis, and polyp growth. PLoS One. 2008 Aug 13; 3(8):e2916. PMID: 18698347.
      Citations: 66     Fields:    Translation:AnimalsCells
    32. Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, Melton DA. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol. 2008 Jul; 26(7):795-7. PMID: 18568017.
      Citations: 650     Fields:    Translation:AnimalsCells
    33. Westbrook TF, Hu G, Ang XL, Mulligan P, Pavlova NN, Liang A, Leng Y, Maehr R, Shi Y, Harper JW, Elledge SJ. SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature. 2008 Mar 20; 452(7185):370-4. PMID: 18354483.
      Citations: 171     Fields:    Translation:HumansAnimalsCells
    34. Ryu KY, Maehr R, Gilchrist CA, Long MA, Bouley DM, Mueller B, Ploegh HL, Kopito RR. The mouse polyubiquitin gene UbC is essential for fetal liver development, cell-cycle progression and stress tolerance. EMBO J. 2007 Jun 06; 26(11):2693-706. PMID: 17491588.
      Citations: 73     Fields:    Translation:AnimalsCells
    35. Kumazaki K, Tirosh B, Maehr R, Boes M, Honjo T, Ploegh HL. AID-/-mus-/- mice are agammaglobulinemic and fail to maintain B220-CD138+ plasma cells. J Immunol. 2007 Feb 15; 178(4):2192-203. PMID: 17277124.
      Citations: 21     Fields:    Translation:AnimalsCells
    36. Hang HC, Loureiro J, Spooner E, van der Velden AW, Kim YM, Pollington AM, Maehr R, Starnbach MN, Ploegh HL. Mechanism-based probe for the analysis of cathepsin cysteine proteases in living cells. ACS Chem Biol. 2006 Dec 20; 1(11):713-23. PMID: 17184136.
      Citations: 28     Fields:    Translation:AnimalsCells
    37. Koch KS, Son KH, Maehr R, Pellicciotta I, Ploegh HL, Zanetti M, Sell S, Leffert HL. Immune-privileged embryonic Swiss mouse STO and STO cell-derived progenitor cells: major histocompatibility complex and cell differentiation antigen expression patterns resemble those of human embryonic stem cell lines. Immunology. 2006 Sep; 119(1):98-115. PMID: 16836618.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    38. Maehr R, Mintern JD, Herman AE, Lennon-Duménil AM, Mathis D, Benoist C, Ploegh HL. Cathepsin L is essential for onset of autoimmune diabetes in NOD mice. J Clin Invest. 2005 Oct; 115(10):2934-43. PMID: 16184198.
      Citations: 38     Fields:    Translation:AnimalsCells
    39. Maehr R, Hang HC, Mintern JD, Kim YM, Cuvillier A, Nishimura M, Yamada K, Shirahama-Noda K, Hara-Nishimura I, Ploegh HL. Asparagine endopeptidase is not essential for class II MHC antigen presentation but is required for processing of cathepsin L in mice. J Immunol. 2005 Jun 01; 174(11):7066-74. PMID: 15905550.
      Citations: 38     Fields:    Translation:AnimalsCells
    40. Maehr R, Kraus M, Ploegh HL. Mice deficient in invariant-chain and MHC class II exhibit a normal mature B2 cell compartment. Eur J Immunol. 2004 Aug; 34(8):2230-6. PMID: 15259020.
      Citations: 8     Fields:    Translation:AnimalsCells
    41. van Swieten PF, Maehr R, van den Nieuwendijk AM, Kessler BM, Reich M, Wong CS, Kalbacher H, Leeuwenburgh MA, Driessen C, van der Marel GA, Ploegh HL, Overkleeft HS. Development of an isotope-coded activity-based probe for the quantitative profiling of cysteine proteases. Bioorg Med Chem Lett. 2004 Jun 21; 14(12):3131-4. PMID: 15149659.
      Citations: 3     Fields:    
    42. Schmidt-Supprian M, Tian J, Grant EP, Pasparakis M, Maehr R, Ovaa H, Ploegh HL, Coyle AJ, Rajewsky K. Differential dependence of CD4+CD25+ regulatory and natural killer-like T cells on signals leading to NF-kappaB activation. Proc Natl Acad Sci U S A. 2004 Mar 30; 101(13):4566-71. PMID: 15070758.
      Citations: 112     Fields:    Translation:AnimalsCells
    43. Kocks C, Maehr R, Overkleeft HS, Wang EW, Iyer LK, Lennon-Dumenil AM, Ploegh HL, Kessler BM. Functional proteomics of the active cysteine protease content in Drosophila S2 cells. Mol Cell Proteomics. 2003 Nov; 2(11):1188-97. PMID: 13130081.
      Citations: 14     Fields:    Translation:AnimalsCells
    44. Fiebiger E, Maehr R, Villadangos J, Weber E, Erickson A, Bikoff E, Ploegh HL, Lennon-Duménil AM. Invariant chain controls the activity of extracellular cathepsin L. J Exp Med. 2002 Nov 04; 196(9):1263-9. PMID: 12417635.
      Citations: 24     Fields:    Translation:AnimalsCells
    45. Vugmeyster Y, Borodovsky A, Maurice MM, Maehr R, Furman MH, Ploegh HL. The ubiquitin-proteasome pathway in thymocyte apoptosis: caspase-dependent processing of the deubiquitinating enzyme USP7 (HAUSP). Mol Immunol. 2002 Nov; 39(7-8):431-41. PMID: 12413694.
      Citations: 9     Fields:    Translation:AnimalsCells
    46. Lennon-Duménil AM, Bakker AH, Maehr R, Fiebiger E, Overkleeft HS, Rosemblatt M, Ploegh HL, Lagaudrière-Gesbert C. Analysis of protease activity in live antigen-presenting cells shows regulation of the phagosomal proteolytic contents during dendritic cell activation. J Exp Med. 2002 Aug 19; 196(4):529-40. PMID: 12186844.
      Citations: 73     Fields:    Translation:AnimalsCells
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