Photo of Tom Kirchhausen,  PhD

Tom Kirchhausen, PhD

Harvard Medical School

Harvard Medical School
Phone: (617) 713-8888
Fax: (617) 713-8898

Tom Kirchhausen, PhD

Harvard Medical School


  • Professor, Cell Biology, Harvard Medical School
  • Professor, Pediatrics, Harvard Medical School
  • Director, HMS-Portugal Program, Harvard Medical School


Research Abstract

Our research focuses on the processes that mediate and regulate the movement of membrane proteins throughout cells. In particular we study the molecular mechanisms that underlie the cell's sorting machineries responsible for receptor-mediated endocytosis and for secretion, and how they are high jacked by toxins, viruses and bacterial pathogens to enter cells. We also study how during cell division, cells control their size and organelle architecture.

These studies led to the first structure determination at atomic resolution of clathrin. By using X-ray crystallography, we determined the structure of its amino-terminal portion, a region critical for interactions controlling coat assembly and cargo sorting. We continued with this structural approach and determined the mode of interaction of ß-arrestins and adaptors with clathrin. We also used cryo-electronmicroscopy to visualize a complete clathrin coat at 8 Å resolution and thereby unveiled the basic structure of the triskelion leg and established the way triskelions pack when they form the clathrin coat, and how auxilin and Hsc70 mediate the ATP-dependent uncoating step. Current high-resolution studies focus on the uncoating step and on the linkage between the clathrin machinery and the non-canonical Wnt-signaling pathway.

Recent developments in fluorescent live-cell imaging techniques geared for single-molecule detection, used in combination with object-identification algorithms, now allow sufficient temporal and spatial resolution to follow the life of a single clathrin coated pit. To use this powerful approach, we have developed and implemented over the past years light-microscopic techniques to analyze the clathrin pathway in living cells. We have shown that it is possible to gather in real time, quantitative, "single-object" data from hundreds of uniquely identified clathrin coated pits and coated vesicles, tracked while they are assembling, recruiting cargo and uncoating, using as probes clathrin, AP-2, auxilin, dynamin and other molecules fused to fluorescent proteins such as EGFP, and fluorescently tagged cargo such as transferrin, LDL, viruses and bacteria.

With these type of dynamic studies we expect to integrate molecular snapshots obtained at high resolution with live-cell processes, in an effort to generate ‘molecular movies' to allow us to obtain new frameworks for analyzing some of the molecular contacts and switches that participate in the regulation, availability, and intracellular traffic of the many molecules involved in signal transduction, immune responsiveness, lipid homeostasis, cell-cell recognition and organelle biogenesis. Such biological phenomena have importance for our understanding of such diseases as cancer, viral infection and pathogen invasion, Alzheimer's, as well as other neurological diseases.

Publications from Harvard Catalyst Profiles

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  • Chou YY, Upadhyayula S, Houser J, He K, Skillern W, Scanavachi G, Dang S, Sanyal A, Ohashi KG, Di Caprio G, Kreutzberger AJB, Vadakkan TJ, Kirchhausen T. Inherited nuclear pore substructures template post-mitotic pore assembly. Dev Cell 2021. PubMed
  • Chen YC, Dinavahi SS, Feng Q, Gowda R, Ramisetti S, Xia X, LaPenna KB, Chirasani VR, Cho SH, Hafenstein SL, Battu MB, Berg A, Sharma AK, Kirchhausen T, Dokholyan NV, Amin S, He P, Robertson GP. Activating sphingosine-1-phospahte signaling in endothelial cells increases myosin light chain phosphorylation to decrease endothelial permeability thereby inhibiting cancer metastasis. Cancer Lett 2021. PubMed
  • He K, Song E, Upadhyayula S, Dang S, Gaudin R, Skillern W, Bu K, Capraro BR, Rapoport I, Kusters I, Ma M, Kirchhausen T. Dynamics of Auxilin 1 and GAK in clathrin-mediated traffic. J Cell Biol 2020. PubMed
  • Magupalli VG, Negro R, Tian Y, Hauenstein AV, Di Caprio G, Skillern W, Deng Q, Orning P, Alam HB, Maliga Z, Sharif H, Hu JJ, Evavold CL, Kagan JC, Schmidt FI, Fitzgerald KA, Kirchhausen T, Li Y, Wu H. HDAC6 mediates an aggresome-like mechanism for NLRP3 and pyrin inflammasome activation. Science 2020. PubMed
  • Salman MM, Marsh G, Kusters I, Delincé M, Di Caprio G, Upadhyayula S, de Nola G, Hunt R, Ohashi KG, Gray T, Shimizu F, Sano Y, Kanda T, Obermeier B, Kirchhausen T. Design and Validation of a Human Brain Endothelial Microvessel-on-a-Chip Open Microfluidic Model Enabling Advanced Optical Imaging. Front Bioeng Biotechnol 2020; 8:573775. PubMed
  • Pascolutti R, Algisi V, Conte A, Raimondi A, Pasham M, Upadhyayula S, Gaudin R, Maritzen T, Barbieri E, Caldieri G, Tordonato C, Confalonieri S, Freddi S, Malabarba MG, Maspero E, Polo S, Tacchetti C, Haucke V, Kirchhausen T, Di Fiore PP, Sigismund S. Molecularly Distinct Clathrin-Coated Pits Differentially Impact EGFR Fate and Signaling. Cell Rep 2019; 27:3049-3061.e6. PubMed
  • Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 2018. PubMed
  • Böcking T, Upadhyayula S, Rapoport I, Capraro BR, Kirchhausen T. Reconstitution of Clathrin Coat Disassembly for Fluorescence Microscopy and Single-Molecule Analysis. Methods Mol Biol 2018; 1847:121-146. PubMed
  • He K, Marsland Iii R, Upadhyayula S, Song E, Dang S, Capraro BR, Wang W, Skillern W, Gaudin R, Ma M, Kirchhausen T. Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic. Nature 2017; 552:410-414. PubMed
  • Schuler MH, Lewandowska A, Di Caprio G, Skillern W, Upadhyayula S, Kirchhausen T, Shaw JM, Cunniff B. Miro1-mediated mitochondrial positioning shapes intracellular energy gradients required for cell migration. Mol Biol Cell 2017. PubMed
  • Hu Y, Kim JH, He K, Wan Q, Kim J, Flach M, Kirchhausen T, Vortkamp A, Winau F. Scramblase TMEM16F terminates T cell receptor signaling to restrict T cell exhaustion. J Exp Med 2016; 213:2759-2772. PubMed
  • Antonny B, Burd C, De Camilli P, Chen E, Daumke O, Faelber K, Ford M, Frolov VA, Frost A, Hinshaw JE, Kirchhausen T, Kozlov MM, Lenz M, Low HH, McMahon H, Merrifield C, Pollard TD, Robinson PJ, Roux A, Schmid S. Membrane fission by dynamin: what we know and what we need to know. EMBO J 2016. PubMed
  • Aguet F, Upadhyayula S, Gaudin R, Chou YY, Cocucci E, He K, Chen BC, Mosaliganti K, Pasham M, Skillern W, Legant WR, Liu TL, Findlay G, Marino E, Danuser G, Megason S, Betzig E, Kirchhausen T. Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy. Mol Biol Cell 2016. PubMed
  • Chou YY, Cuevas C, Carocci M, Stubbs SH, Ma M, Cureton DK, Chao L, Evesson F, He K, Yang PL, Whelan SP, Ross SR, Kirchhausen T, Gaudin R. Identification and characterization of a novel broad spectrum virus entry inhibitor. J Virol 2016. PubMed
  • Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun 2016; 7:10882. PubMed
  • Reeves PM, Kang YL, Kirchhausen T. Endocytosis of ligand activated sphingosine 1-phosphate receptor 1 mediated by the clathrin-pathway. Traffic 2015. PubMed
  • Wittrup A, Ai A, Liu X, Hamar P, Trifonova R, Charisse K, Manoharan M, Kirchhausen T, Lieberman J. Visualizing lipid-formulated siRNA release from endosomes and target gene knockdown. Nat Biotechnol 2015; 33:870-6. PubMed
  • Kural C, Akatay AA, Gaudin R, Chen BC, Legant WR, Betzig E, Kirchhausen T. Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells. Mol Biol Cell 2015. PubMed
  • Ishikawa Y, Maeda M, Pasham M, Aguet F, Tacheva-Grigorova SK, Masuda T, Yi H, Lee SU, Xu J, Teruya-Feldstein J, Ericsson M, Mullally A, Heuser J, Kirchhausen T, Maeda T. Role of the clathrin adaptor PICALM in normal hematopoiesis and polycythemia vera pathophysiology. Haematologica 2015. PubMed
  • Cocucci E, Gaudin R, Kirchhausen T. Dynamin recruitment and membrane scission at the neck of a clathrin-coated pit. Mol Biol Cell 2014. PubMed
  • Böcking T, Aguet F, Rapoport I, Banzhaf M, Yu A, Zeeh JC, Kirchhausen T. Key interactions for clathrin coat stability. Structure 2014; 22:819-29. PubMed
  • Carmo-Fonseca M, Kirchhausen T. The timing of pre-mRNA splicing visualized in real-time. Nucleus 2014; 5:11-4. PubMed
  • Piccinotti S, Kirchhausen T, Whelan SP. Uptake of rabies virus into epithelial cells by clathrin-mediated endocytosis depends upon actin. J Virol 2013; 87:11637-47. PubMed
  • Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep 2013; 4:1144-55. PubMed
  • Heesters BA, Chatterjee P, Kim YA, Gonzalez SF, Kuligowski MP, Kirchhausen T, Carroll MC. Endocytosis and recycling of immune complexes by follicular dendritic cells enhances B cell antigen binding and activation. Immunity 2013; 38:1164-75. PubMed
  • Martinelli R, Kamei M, Sage PT, Massol R, Varghese L, Sciuto T, Toporsian M, Dvorak AM, Kirchhausen T, Springer TA, Carman CV. Release of cellular tension signals self-restorative ventral lamellipodia to heal barrier micro-wounds. J Cell Biol 2013; 201:449-65. PubMed
  • Hori K, Sen A, Kirchhausen T, Artavanis-Tsakonas S. Regulation of ligand-independent Notch signal through intracellular trafficking. Commun Integr Biol 2012; 5:374-6. PubMed
  • Böcking T, Aguet F, Harrison SC, Kirchhausen T. Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating. Nat Struct Mol Biol 2011; 18:295-301. PubMed
  • Yu A, Xing Y, Harrison SC, Kirchhausen T. Structural analysis of the interaction between Dishevelled2 and clathrin AP-2 adaptor, a critical step in noncanonical Wnt signaling. Structure 2010; 18:1311-20. PubMed
  • Guan R, Han D, Harrison SC, Kirchhausen T. Structure of the PTEN-like region of auxilin, a detector of clathrin-coated vesicle budding. Structure 2010; 18:1191-8. PubMed
  • Harrison SC, Kirchhausen T. Structural biology: Conservation in vesicle coats. Nature 2010; 466:1048-9. PubMed
  • Anitei M, Stange C, Parshina I, Baust T, Schenck A, Raposo G, Kirchhausen T, Hoflack B. Protein complexes containing CYFIP/Sra/PIR121 coordinate Arf1 and Rac1 signalling during clathrin-AP-1-coated carrier biogenesis at the TGN. Nat Cell Biol 2010; 12:330-40. PubMed
  • Thiery J, Keefe D, Saffarian S, Martinvalet D, Walch M, Boucrot E, Kirchhausen T, Lieberman J. Perforin activates clathrin- and dynamin-dependent endocytosis, which is required for plasma membrane repair and delivery of granzyme B for granzyme-mediated apoptosis. Blood 2010; 115:1582-93. PubMed
  • Xing Y, Böcking T, Wolf M, Grigorieff N, Kirchhausen T, Harrison SC. Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly. EMBO J 2010; 29:655-65. PubMed
  • Boucrot E, Saffarian S, Zhang R, Kirchhausen T. Roles of AP-2 in clathrin-mediated endocytosis. PLoS ONE 2010; 5:e10597. PubMed
  • Utskarpen A, Massol R, van Deurs B, Lauvrak SU, Kirchhausen T, Sandvig K. Shiga toxin increases formation of clathrin-coated pits through Syk kinase. PLoS ONE 2010; 5:e10944. PubMed
  • Saffarian S, Cocucci E, Kirchhausen T. Distinct dynamics of endocytic clathrin-coated pits and coated plaques. PLoS Biol. 2009; 7:e1000191. PubMed
  • Cureton DK,Massol RH,Saffarian S,Kirchhausen TL,Whelan SP. Vesicular stomatitis virus enters cells through vesicles incompletely coated with clathrin that depend upon actin for internalization. PLoS Pathog 2009; 5:e1000394. PubMed
  • Saffarian S, Kirchhausen T. Differential evanescence nanometry: live-cell fluorescence measurements with 10-nm axial resolution on the plasma membrane. Biophys J 2008; 94:2333-42. PubMed
  • Nieland TJ, Shaw JT, Jaipuri FA, Duffner JL, Koehler AN, Banakos S, Zannis VI, Kirchhausen T, Krieger M. Identification of the molecular target of small molecule inhibitors of HDL receptor SR-BI activity. Biochemistry 2008; 47:460-72. PubMed
  • Boucrot E, Kirchhausen T. Mammalian Cells Change Volume during Mitosis. PLoS ONE 2008; 3:e1477. PubMed
  • Kirchhausen T, Macia E, Pelish HE. Use of dynasore, the small molecule inhibitor of dynamin, in the regulation of endocytosis. Methods Enzymol 2008; 438:77-93. PubMed
  • Rapoport I, Boll W, Yu A, Bocking T, Kirchhausen T. A motif in the clathrin heavy chain required for the hsc70/auxilin uncoating reaction. Mol Biol Cell 2008; 19:405-13. PubMed
  • Veiga E, Guttman JA, Bonazzi M, Boucrot E, Toledo-Arana A, Lin AE, Enninga J, Pizarro-Cerda J, Finlay BB, Kirchhausen T, Cossart P. Invasive and adherent bacterial pathogens co-Opt host clathrin for infection. Cell Host Microbe 2007; 2:340-51. PubMed
  • Jiang S, Zhou X, Kirchhausen T, Wong ST. Tracking molecular particles in live cells using fuzzy rule-based system. Cytometry A 2007; 71:576-84. PubMed
  • Li J, Peters PJ, Bai M, Dai J, Bos E, Kirchhausen T, Kandror KV, Hsu VW. An ACAP1-containing clathrin coat complex for endocytic recycling. J Cell Biol 2007; 178:453-64. PubMed
  • Wang J, Sun HQ, Macia E, Kirchhausen T, Watson H, Bonifacino JS, Yin HL. PI4P promotes the recruitment of the GGA adaptor proteins to the trans-Golgi network and regulates their recognition of the ubiquitin sorting signal. Mol Biol Cell 2007; 18:2646-55. PubMed
  • Kirchhausen T. Making COPII coats. Cell 2007; 129:1251-2. PubMed
  • Yu A, Rual JF, Tamai K, Harada Y, Vidal M, He X, Kirchhausen T. Association of Dishevelled with the clathrin AP-2 adaptor is required for Frizzled endocytosis and planar cell polarity signaling. Dev Cell 2007; 12:129-41. PubMed