Clinical Focus

  • Allergy and Immunology
  • Pediatric Allergy/Immun

Administrative Appointments

  • Assistant Professor, Pediatrics Immunology & Allergy (2009 - Present)

Honors & Awards

  • Fellow, American Academy of Pediatrics (2008-)
  • Scholar, SPARK (2010-11,11-13,14-15)
  • Award, Bio-X Interdisciplinary Award (2010)

Boards, Advisory Committees, Professional Organizations

  • Defense Sciences Study Group, US Department of Defense (2014 - Present)
  • Education Committee, Clinical Immunology Society (2014 - Present)
  • Annual Retreat Co-Chair, Stanford Immunology (2012 - 2013)

Professional Education

  • Medical Education:Warren Alpert Medical School Brown University (1996) RI
  • Fellowship:Children's Hospital Boston (2006) MA
  • Residency:Children's Hospital of Philadelphia (2003) PA
  • Board Certification: Pediatrics, American Board of Pediatrics (2004)
  • Ph.D., UCSF, Biophysics (2000)
  • M.D., Brown Univ. School of Medicine, Medicine (1996)
  • Sc.B., Brown University, Physics (1993)


  • Manish J Butte, Marc Amor Bruce, Jianwei Liu. "United States Patent US 13/307,882 Atomic force microscope manipulation of living cells", The Board Of Trustees Of The Leland Stanford Junior University, Nov 30, 2010
  • Manish J. BUTTE, John J. LeBlanc. "United States Patent US 13/317,180 Microfluidic Waveguide Detector", The Board Of Trustees Of The Leland Stanford Junior University, Oct 12, 2010
  • Arlene H. Sharpe, Manish J. Butte, Shinji Oyama. "United States Patent PCT/US2011/020046 Modulators of Immunoinhibitory Receptor PD-1, and Methods of Use Thereof", President And Fellows Of Harvard College, Jan 4, 2010
  • Meital Reches, Michael D. Dickey, Manish J. Butte, George M. Whitesides. "United States Patent PCT/US2009/038702 Cotton thread as a low-cost multi-assay diagnostic platform", President And Fellows Of Harvard College, Mar 27, 2008
  • George M. Whitesides, Scott T. PHILLIPS, Andreas W. Martinez, Manish J. BUTTE, Amy Wong, Samuel W. Thomas, Hayat Sindi, Sarah J. VELLA, Emanuel CARRILHO, Katherine A. MIRICA, Yanyan LIU,. "United States Patent US 13/730,028 Lateral flow and flow-through bioassay devices based on patterned porous media, methods of making same, and methods of using same", President And Fellows Of Harvard College, Oct 18, 2006

Research & Scholarship

Current Research and Scholarly Interests

Our laboratory's goal is to address fundamental and therapeutic questions in immunology using innovative nanotechnological and biophysical approaches to visualize and manipulate cells. Our primary focus is on understanding the molecular controls that balance T cell activation versus tolerance. The ultimate aim of our work is to manipulate T cell signaling pathways to control immunologically-mediated diseases.

Projects in the lab include:
1) Atomic force microscopy of T cells
2) Mechanobiology of biomaterials, cardiac cells, endothelial cells, and cancers
3) Discovery and characterization of new inhibitory pathways of T cells
4) High resolution visualization of receptor and ligands in the T cell immunological synapse
5) Manipulation of single-receptors on T cells to control activation versus tolerance
6) Development of diagnostic tools for immune monitoring and autoimmune diseases (such as Type 1 diabetes and multiple sclerosis)
7) Characterization of self-like antigens and their roles in autoimmunity (in multiple sclerosis and Type 1 diabetes)

Clinical Trials

  • Improving the Diagnosis of Common Variable Immune Deficiency Not Recruiting

    This is an observational, case--control study with a single blood draw among two cohorts, patients with CVID and healthy controls. Samples will be analyzed by cytometry (CyTOF) to simultaneously examine the major signaling pathways of all circulating innate and adaptive immune cell types as well as whole exome sequencing. The goal is to improve our general understanding of the human immune response to infections and the diagnosis of CVID.

    Stanford is currently not accepting patients for this trial. For more information, please contact Elisabeth Hoyte, 650-498-4039.

    View full details


2016-17 Courses

Stanford Advisees


All Publications

  • Fast Stiffness Mapping of Cells Using High-Bandwidth Atomic Force Microscopy ACS NANO Wang, A., Vijayraghavan, K., Solgaard, O., Butte, M. J. 2016; 10 (1): 257-264


    The cytoskeleton controls cellular morphology and mediates the mechanical interactions between a cell and its environment. Atomic force microscopy (AFM) has the unique capability to map cytoskeletal mechanics and structures with nanometer resolution. However, whole-cell cytomechanical imaging with conventional AFM techniques is limited by low imaging speed. Here, we present fast nanomechanical mapping of cells using high-bandwidth AFM (HB-AFM), where >10(6) nanoindentation measurements were acquired in ∼10 min-a task that would take weeks to finish using conventional AFM. High-bandwidth measurements enabled capture of the entire tip-sample interaction for each tap on cells, engendering a new measurement ("force phase") that exceeds the contrast of conventional tapping mode and enabling spectral visualization of >10 harmonics. The abundance of measurements allowed discovery of subtle cytomechanical features, including the stiffness of fibers of the cellular spectrin network in situ. This approach bridges HB-AFM and high-harmonic imaging and opens future opportunities for measuring the dynamic mechanical properties of living cells.

    View details for DOI 10.1021/acsnano.5b03959

    View details for Web of Science ID 000369115800025

    View details for PubMedID 26554581

  • Taking T cell priming down a Notch: signaling through Notch receptors enhances T cell sensitivity to antigen. Immunity Thauland, T. J., Butte, M. J. 2015; 42 (1): 6-8


    Notch receptors are widely expressed and have recognized functions in thymocytes and mature T cells. In this issue, Laky et al. (2015) show that Notch interactions with Delta-like ligand 4 (DLL4) amplify priming of naive T cells.

    View details for DOI 10.1016/j.immuni.2014.12.026

    View details for PubMedID 25607451

  • Compound heterozygous mutation of Rag1 leading to Omenn syndrome. PloS one Matthews, A. G., Briggs, C. E., Yamanaka, K., Small, T. N., Mooster, J. L., Bonilla, F. A., Oettinger, M. A., Butte, M. J. 2015; 10 (4)


    Omenn syndrome is a primary immunodeficiency disorder, featuring susceptibility to infections and autoreactive T cells and resulting from defective genomic rearrangement of genes for the T cell and B cell receptors. The most frequent etiologies are hypomorphic mutations in "non-core" regions of the Rag1 or Rag2 genes, the protein products of which are critical members of the cellular apparatus for V(D)J recombination. In this report, we describe an infant with Omenn syndrome with a previously unreported termination mutation (p.R142*) in Rag1 on one allele and a partially characterized substitution mutation (p.V779M) in a "core" region of the other Rag1 allele. Using a cellular recombination assay, we found that while the p.R142* mutation completely abolished V(D)J recombination activity, the p.V779M mutation conferred a severe, but not total, loss of V(D)J recombination activity. The recombination defect of the V779 mutant was not due to overall misfolding of Rag1, however, as this mutant supported wild-type levels of V(D)J cleavage. These findings provide insight into the role of this poorly understood region of Rag1 and support the role of Rag1 in a post-cleavage stage of recombination.

    View details for DOI 10.1371/journal.pone.0121489

    View details for PubMedID 25849362

  • Customized atomic force microscopy probe by focused-ion-beam-assisted tip transfer APPLIED PHYSICS LETTERS Wang, A., Butte, M. J. 2014; 105 (5)

    View details for DOI 10.1063/1.4892075

    View details for Web of Science ID 000341153000067

  • Use of bio-mimetic three-dimensional technology in therapeutics for heart disease. Bioengineered Serpooshan, V., Zhao, M., Metzler, S. A., Wei, K., Shah, P. B., Wang, A., Mahmoudi, M., Malkovskiy, A. V., Rajadas, J., Butte, M. J., Bernstein, D., Ruiz-Lozano, P. 2014; 5 (3): 193-197


    Due to the limited self-renewal capacity of cardiomyocytes, the mammalian heart exhibits impaired regeneration and insufficient ability to restore heart function after injury. Cardiovascular tissue engineering is currently considered as a promising alternative therapy to restore the structure and function of the failing heart. Recent evidences suggest that the epicardium may play critical roles in regulation of myocardial development and regeneration. One of the mechanisms has been proposed for the restorative effect of the epicardium is the specific physiomechanical cues that this layer provides to the cardiac cells. In this article we explore whether a new generation of epicardium-mimicking, acellular matrices can be utilized to enhance cardiac healing after injury. The matrix consists of a dense collagen scaffold, with optimized biomechanical properties approaching those of embryonic epicardium. Grafting the epicardial patch onto the ischemic myocardium, promptly post the incidence of infarct, resulted in preserved contractility, attenuated ventricular remodeling, diminished fibrosis, and vascularization within the injured tissue in the adult murine heart.

    View details for DOI 10.4161/bioe.27751

    View details for PubMedID 24637710

  • Spatiotemporally and mechanically controlled triggering of mast cells using atomic force microscopy IMMUNOLOGIC RESEARCH Hu, K. K., Bruce, M. A., Butte, M. J. 2014; 58 (2-3): 211-217


    Mast cells are thought to be sensitive to mechanical forces, for example, coughing in asthma or pressure in "physical urticarias." Conversion of mechanical forces to biochemical signals could potentially augment antigenic signaling. Studying the combined effects of mechanical and antigenic cues on mast cells and other hematopoietic cells has proven difficult. Here, we present an approach using a modified atomic force microscope cantilever to deliver antigenic signals to mast cells while simultaneously applying mechanical forces. We developed a strategy to concurrently record degranulation events by fluorescence microscopy during antigenic triggering. Finally, we also measured the mechanical forces generated by mast cells while antigen receptors are ligated. We showed that mast cells respond to antigen delivered by the atomic force microscopy cantilever with prompt degranulation and the generation of strong pushing and pulling forces. We did not discern any relationship between applied mechanical forces and the kinetics of degranulation. These experiments present a new method for dissecting the interactions of mechanical and biochemical cues in the signaling responses of immune cells.

    View details for DOI 10.1007/s12026-014-8510-7

    View details for Web of Science ID 000336333700006

  • Real-time GPU-based 3D Deconvolution OPTICS EXPRESS Bruce, M. A., Butte, M. J. 2013; 21 (4): 4766-4773


    Confocal microscopy is an oft-used technique in biology. Deconvolution of 3D images reduces blurring from out-of-focus light and enables quantitative analyses, but existing software for deconvolution is slow and expensive. We present a parallelized software method that runs within ImageJ and deconvolves 3D images ~100 times faster than conventional software (few seconds per image) by running on a low-cost graphics processor board (GPU). We demonstrate the utility of this software by analyzing microclusters of T cell receptors in the immunological synapse of a CD4 + T cell and dendritic cell. This software provides a low-cost and rapid way to improve the accuracy of 3D microscopic images obtained by any method.

    View details for DOI 10.1364/OE.21.004766

    View details for Web of Science ID 000315992600083

  • CD28 Costimulation Regulates Genome-Wide Effects on Alternative Splicing PLOS ONE Butte, M. J., Lee, S. J., Jesneck, J., Keir, M. E., Haining, W. N., Sharpe, A. H. 2012; 7 (6)


    CD28 is the major costimulatory receptor required for activation of naïve T cells, yet CD28 costimulation affects the expression level of surprisingly few genes over those altered by TCR stimulation alone. Alternate splicing of genes adds diversity to the proteome and contributes to tissue-specific regulation of genes. Here we demonstrate that CD28 costimulation leads to major changes in alternative splicing during activation of naïve T cells, beyond the effects of TCR alone. CD28 costimulation affected many more genes through modulation of alternate splicing than by modulation of transcription. Different families of biological processes are over-represented among genes alternatively spliced in response to CD28 costimulation compared to those genes whose transcription is altered, suggesting that alternative splicing regulates distinct biological effects. Moreover, genes dependent upon hnRNPLL, a global regulator of splicing in activated T cells, were enriched in T cells activated through TCR plus CD28 as compared to TCR alone. We show that hnRNPLL expression is dependent on CD28 signaling, providing a mechanism by which CD28 can regulate splicing in T cells and insight into how hnRNPLL can influence signal-induced alternative splicing in T cells. The effects of CD28 on alternative splicing provide a newly appreciated means by which CD28 can regulate T cell responses.

    View details for DOI 10.1371/journal.pone.0040032

    View details for Web of Science ID 000305892100181

    View details for PubMedID 22768209

  • Atomic Force Mechanobiology of Pluripotent Stem Cell-Derived Cardiomyocytes PLOS ONE Liu, J., Sun, N., Bruce, M. A., Wu, J. C., Butte, M. J. 2012; 7 (5)


    We describe a method using atomic force microscopy (AFM) to quantify the mechanobiological properties of pluripotent, stem cell-derived cardiomyocytes, including contraction force, rate, duration, and cellular elasticity. We measured beats from cardiomyocytes derived from induced pluripotent stem cells of healthy subjects and those with dilated cardiomyopathy, and from embryonic stem cell lines. We found that our AFM method could quantitate beat forces of single cells and clusters of cardiomyocytes. We demonstrate the dose-responsive, inotropic effect of norepinephrine and beta-adrenergic blockade of metoprolol. Cardiomyocytes derived from subjects with dilated cardiomyopathy showed decreased force and decreased cellular elasticity compared to controls. This AFM-based method can serve as a screening tool for the development of cardiac-active pharmacological agents, or as a platform for studying cardiomyocyte biology.

    View details for DOI 10.1371/journal.pone.0037559

    View details for Web of Science ID 000305343500135

    View details for PubMedID 22624048

  • Counting cells with a low-cost integrated microfluidics-waveguide sensor BIOMICROFLUIDICS Garcia, D., Ghansah, I., Leblanc, J., Butte, M. J. 2012; 6 (1)


    The capability to count cells from biofluids at low cost has important diagnostic implications in resource-poor settings. Many approaches have been developed to address this important need, and while most envision a low per-test cost, the detector instrument can be quite expensive. In this report, we present a novel device that enables low-cost and rapid counting of cells from a drop of blood. We demonstrate a shallow, buried, planar waveguide fabricated by ion exchange in glass that underlies a microfluidic structure for capturing cells. Laser light transmitted through the waveguide was attenuated by the number of metal nanoparticles tagged to the cells because of the interaction of the metal particles with the evanescent field of the waveguide. Calibration of the sensor using bead-tagged lymphocytes captured from human blood showed that the sensor could semi-quantitatively count as few as 100 cells/µL of blood. This technology enables the enumeration of specifically captured cells, allowing for a point-of-care, hand-held device for fast and affordable cell counting in screening, remote, or resource-poor settings.

    View details for DOI 10.1063/1.3689857

    View details for Web of Science ID 000302301000039

    View details for PubMedID 22454696

  • Optical planar waveguide for cell counting. Applied physics letters Leblanc, J., Mueller, A. J., Prinz, A., Butte, M. J. 2012; 100 (4): 43701-437015


    Low cost counting of cells has medical applications in screening, military medicine, disaster medicine, and rural healthcare. In this report, we present a shallow, buried, planar waveguide fabricated by potassium ion exchange in glass that enables low-cost and rapid counting of metal-tagged objects that lie in the evanescent field of the waveguide. Laser light transmitted through the waveguide was attenuated proportionately to the presence of metal-coated microstructures fabricated from photoresist. This technology enables the low-cost enumeration of cells from blood, urine, or other biofluids.

    View details for PubMedID 22331960

  • Single molecule labeling of an atomic force microscope cantilever tip. Applied physics letters Liu, J., Butte, M. J. 2012; 101 (16): 163705


    In this paper, we present a method to functionalize the very apex of an atomic force microscope cantilever with a single or a few molecules. In force spectroscopy or interaction mapping, the cantilever must be functionalized with only a few molecules to avoid noise or spurious measurements. Here, we covalently attached single molecules to the cantilever by touching it to a paper wetted with a solution of quantum dots. The paper competes with wicking up the hydrophilic surface of the tip. This method has broad applications in scanning probe microscopy where small numbers of molecules are needed on the tip.

    View details for PubMedID 23152642

  • Hyaluronan synthesis is necessary for autoreactive T-cell trafficking, activation, and Th1 polarization. Proceedings of the National Academy of Sciences of the United States of America Kuipers, H. F., Rieck, M., Gurevich, I., Nagy, N., Butte, M. J., Negrin, R. S., Wight, T. N., Steinman, L., Bollyky, P. L. 2016; 113 (5): 1339-1344


    The extracellular matrix polysaccharide hyaluronan (HA) accumulates at sites of autoimmune inflammation, including white matter lesions in multiple sclerosis (MS), but its functional importance in pathogenesis is unclear. We have evaluated the impact of 4-methylumbelliferone (4-MU), an oral inhibitor of HA synthesis, on disease progression in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. Treatment with 4-MU decreases the incidence of EAE, delays its onset, and reduces the severity of established disease. 4-MU inhibits the activation of autoreactive T cells and prevents their polarization toward a Th1 phenotype. Instead, 4-MU promotes polarization toward a Th2 phenotpye and induction of Foxp3(+) regulatory T cells. Further, 4-MU hastens trafficking of T cells through secondary lymphoid organs, impairs the infiltration of T cells into the CNS parenchyma, and limits astrogliosis. Together, these data suggest that HA synthesis is necessary for disease progression in EAE and that treatment with 4-MU may be a potential therapeutic strategy in CNS autoimmunity. Considering that 4-MU is already a therapeutic, called hymecromone, that is approved to treat biliary spasm in humans, we propose that it could be repurposed to treat MS.

    View details for DOI 10.1073/pnas.1525086113

    View details for PubMedID 26787861

  • Treatment with rituximab and brentuximab vedotin in a patient of common variable immune deficiency-associated classic Hodgkin lymphoma. Biomarker research Rael, E., Rakszawski, K., Koller, K., Bayerl, M., Butte, M., Zheng, H. 2016; 4: 7-?


    Patients with common variable immunodeficiency (CVID) have an increased risk of developing lymphoproliferative diseases, including non-Hodgkins lymphoma (Blood 116:1228-1234, 2010; Blood 119:1650-7, 2012). The incidence and prognosis of Hodgkin lymphoma in this population is not clear, with only a few case reports in the literature. Conventional cytotoxic chemotherapy, although highly efficacious in treating Hodgkin lymphoma in immune competent patients, is problematic in patients with CVID due to the increased risk of infectious complications (Ther Umsch 69:687-91, 2012; Pediatr Hematol Oncol 24:337-42, 2012). Rituximab and brentuximab vedotin are both targeted agents used to treat lymphomas that express CD20 and CD30, respectively. Compared to cytotoxic chemotherapy typically used in Hodgkin lymphoma, these agents are better tolerated with minimal side effects. This makes them an attractive option for treating lymphoma in patients who have significant co-morbidities, including those with immune deficiencies. Additionally, rituximab has been used safely to treat autoimmune cytopenias in patients with CVID5. However, the role of these targeted therapies in CVID-associated Hodgkin lymphoma has not been reported.Here we report the case of a 25 year old female diagnosed with CVID-associated classic Hodgkin lymphoma, who achieved a complete remission following treatment with rituximab followed by brentuximab vedotin.We demonstrate that rituximab and brentuximab are likely safe and effective in CVID-associated Hodgkin lymphoma, providing a feasible and potentially optimal treatment option for this patient population.

    View details for DOI 10.1186/s40364-016-0061-8

    View details for PubMedID 26966541

  • Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency JOURNAL OF CLINICAL INVESTIGATION Walter, J. E., Rosen, L. B., Csomos, K., Rosenberg, J. M., Mathew, D., Keszei, M., Ujhazi, B., Chen, K., Lee, Y. N., Tirosh, I., Dobbs, K., Al-Herz, W., Cowan, M. J., Puck, J., Bleesing, J. J., Grimley, M. S., Malech, H., De Ravin, S. S., Gennery, A. R., Abraham, R. S., Joshi, A. Y., Boyce, T. G., Butte, M. J., Nadeau, K. C., Balboni, I., Sullivan, K. E., Akhter, J., Adeli, M., El-Feky, R. A., El-Ghoneimy, D. H., Dbaibo, G., Wakim, R., Azzari, C., Palma, P., Cancrini, C., Capuder, K., Condino-Neto, A., Costa-Carvalho, B. T., Oliveira, J. B., Roifman, C., Buchbinder, D., Kumanovics, A., Luis Franco, J., Niehues, T., Schuetz, C., Kuijpers, T., Yee, C., Chou, J., Masaad, M. J., Geha, R., Uze, G., Gelman, R., Holland, S. M., Recher, M., Utz, P. J., Browne, S. K., Notarangelo, L. D. 2015; 125 (11): 4135-4148


    Patients with mutations of the recombination-activating genes (RAG) present with diverse clinical phenotypes, including severe combined immune deficiency (SCID), autoimmunity, and inflammation. However, the incidence and extent of immune dysregulation in RAG-dependent immunodeficiency have not been studied in detail. Here, we have demonstrated that patients with hypomorphic RAG mutations, especially those with delayed-onset combined immune deficiency and granulomatous/autoimmune manifestations (CID-G/AI), produce a broad spectrum of autoantibodies. Neutralizing anti-IFN-α or anti-IFN-ω antibodies were present at detectable levels in patients with CID-G/AI who had a history of severe viral infections. As this autoantibody profile is not observed in a wide range of other primary immunodeficiencies, we hypothesized that recurrent or chronic viral infections may precipitate or aggravate immune dysregulation in RAG-deficient hosts. We repeatedly challenged Rag1S723C/S723C mice, which serve as a model of leaky SCID, with agonists of the virus-recognizing receptors TLR3/MDA5, TLR7/-8, and TLR9 and found that this treatment elicits autoantibody production. Altogether, our data demonstrate that immune dysregulation is an integral aspect of RAG-associated immunodeficiency and indicate that environmental triggers may modulate the phenotypic expression of autoimmune manifestations.

    View details for DOI 10.1172/JCI80477

    View details for Web of Science ID 000364110000017

    View details for PubMedID 26457731

  • NKp46 clusters at the immune synapse and regulates NK cell polarization FRONTIERS IN IMMUNOLOGY Hadad, U., Thauland, T. J., Martinez, O. M., Butte, M. J., Porgador, A., Krams, S. M. 2015; 6
  • Epicardial FSTL1 reconstitution regenerates the adult mammalian heart. Nature Wei, K., Serpooshan, V., Hurtado, C., Diez-Cuñado, M., Zhao, M., Maruyama, S., Zhu, W., Fajardo, G., Noseda, M., Nakamura, K., Tian, X., Liu, Q., Wang, A., Matsuura, Y., Bushway, P., Cai, W., Savchenko, A., Mahmoudi, M., Schneider, M. D., van den Hoff, M. J., Butte, M. J., Yang, P. C., Walsh, K., Zhou, B., Bernstein, D., Mercola, M., Ruiz-Lozano, P. 2015; 525 (7570): 479-485


    The elucidation of factors that activate the regeneration of the adult mammalian heart is of major scientific and therapeutic importance. Here we found that epicardial cells contain a potent cardiogenic activity identified as follistatin-like 1 (Fstl1). Epicardial Fstl1 declines following myocardial infarction and is replaced by myocardial expression. Myocardial Fstl1 does not promote regeneration, either basally or upon transgenic overexpression. Application of the human Fstl1 protein (FSTL1) via an epicardial patch stimulates cell cycle entry and division of pre-existing cardiomyocytes, improving cardiac function and survival in mouse and swine models of myocardial infarction. The data suggest that the loss of epicardial FSTL1 is a maladaptive response to injury, and that its restoration would be an effective way to reverse myocardial death and remodelling following myocardial infarction in humans.

    View details for DOI 10.1038/nature15372

    View details for PubMedID 26375005

  • Epicardial FSTL1 reconstitution regenerates the adult mammalian heart NATURE Wei, K., Serpooshan, V., Hurtado, C., Diez-Cunado, M., Zhao, M., Maruyama, S., Zhu, W., Fajardo, G., Noseda, M., Nakamura, K., Tian, X., Liu, Q., Wang, A., Matsuura, Y., Bushway, P., Cai, W., Savchenko, A., Mahmoudi, M., Schneider, M. D., van den Hoff, M. J., Butte, M. J., Yang, P. C., Walsh, K., Zhou, B., Bernstein, D., Mercola, M., Ruiz-Lozano, P. 2015; 525 (7570): 479-?
  • PRKDC mutations associated with immunodeficiency, granuloma, and autoimmune regulator-dependent autoimmunity. journal of allergy and clinical immunology Mathieu, A., Verronese, E., Rice, G. I., Fouyssac, F., Bertrand, Y., Picard, C., Chansel, M., Walter, J. E., Notarangelo, L. D., Butte, M. J., Nadeau, K. C., Csomos, K., Chen, D. J., Chen, K., Delgado, A., Rigal, C., Bardin, C., Schuetz, C., Moshous, D., Reumaux, H., Plenat, F., Phan, A., Zabot, M., Balme, B., Viel, S., Bienvenu, J., Cochat, P., van der Burg, M., Caux, C., Kemp, E. H., Rouvet, I., Malcus, C., Méritet, J., Lim, A., Crow, Y. J., Fabien, N., Ménétrier-Caux, C., de Villartay, J., Walzer, T., Belot, A. 2015; 135 (6): 1578-88 e5


    PRKDC encodes for DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a kinase that forms part of a complex (DNA-dependent protein kinase [DNA-PK]) crucial for DNA double-strand break repair and V(D)J recombination. In mice DNA-PK also interacts with the transcription factor autoimmune regulator (AIRE) to promote central T-cell tolerance.We sought to understand the causes of an inflammatory disease with granuloma and autoimmunity associated with decreasing T- and B-cell counts over time that had been diagnosed in 2 unrelated patients.Genetic, molecular, and functional analyses were performed to characterize an inflammatory disease evocative of a combined immunodeficiency.We identified PRKDC mutations in both patients. These patients exhibited a defect in DNA double-strand break repair and V(D)J recombination. Whole-blood mRNA analysis revealed a strong interferon signature. On activation, memory T cells displayed a skewed cytokine response typical of TH2 and TH1 but not TH17. Moreover, mutated DNA-PKcs did not promote AIRE-dependent transcription of peripheral tissue antigens in vitro. The latter defect correlated in vivo with production of anti-calcium-sensing receptor autoantibodies, which are typically found in AIRE-deficient patients. In addition, 9 months after bone marrow transplantation, patient 1 had Hashimoto thyroiditis, suggesting that organ-specific autoimmunity might be linked to nonhematopoietic cells, such as AIRE-expressing thymic epithelial cells.Deficiency of DNA-PKcs, a key AIRE partner, can present as an inflammatory disease with organ-specific autoimmunity, suggesting a role for DNA-PKcs in regulating autoimmune responses and maintaining AIRE-dependent tolerance in human subjects.

    View details for DOI 10.1016/j.jaci.2015.01.040

    View details for PubMedID 25842288

  • PRKDC mutations associated with immunodeficiency, granuloma, and autoimmune regulator-dependent autoimmunity JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Mathieu, A., Verronese, E., Rice, G. I., Fouyssac, F., Bertrand, Y., Picard, C., Chansel, M., Walter, J. E., Notarangelo, L. D., Butte, M. J., Nadeau, K. C., Csomos, K., Chen, D. J., Chen, K., Delgado, A., Riga, C., Bardin, C., Schuetz, C., Moshous, D., Reumaux, H., Plenat, F., Phan, A., Zabot, M., Balme, B., Viel, S., Bienvenu, J., Cochat, P., van der Burg, M., Caux, C., Kemp, E. H., Rouvet, I., Malcus, C., Meritet, J., Lim, A., Crow, Y. J., Fabien, N., Menetrier-Caux, C., de Villartay, J., Walzer, T., Belot, A. 2015; 135 (6): 1578-U294
  • Compound Heterozygous Mutation of Rag1 Leading to Omenn Syndrome PLOS ONE Matthews, A. G., Briggs, C. E., Yamanaka, K., Small, T. N., Mooster, J. L., Bonilla, F. A., Oettinger, M. A., Butte, M. J. 2015; 10 (4)
  • Differential fates of biomolecules delivered to target cells via extracellular vesicles. Proceedings of the National Academy of Sciences of the United States of America Kanada, M., Bachmann, M. H., Hardy, J. W., Frimannson, D. O., Bronsart, L., Wang, A., Sylvester, M. D., Schmidt, T. L., Kaspar, R. L., Butte, M. J., Matin, A. C., Contag, C. H. 2015; 112 (12): E1433-42


    Extracellular vesicles (EVs), specifically exosomes and microvesicles (MVs), are presumed to play key roles in cell-cell communication via transfer of biomolecules between cells. The biogenesis of these two types of EVs differs as they originate from either the endosomal (exosomes) or plasma (MVs) membranes. To elucidate the primary means through which EVs mediate intercellular communication, we characterized their ability to encapsulate and deliver different types of macromolecules from transiently transfected cells. Both EV types encapsulated reporter proteins and mRNA but only MVs transferred the reporter function to recipient cells. De novo reporter protein expression in recipient cells resulted only from plasmid DNA (pDNA) after delivery via MVs. Reporter mRNA was delivered to recipient cells by both EV types, but was rapidly degraded without being translated. MVs also mediated delivery of functional pDNA encoding Cre recombinase in vivo to tissues in transgenic Cre-lox reporter mice. Within the parameters of this study, MVs delivered functional pDNA, but not RNA, whereas exosomes from the same source did not deliver functional nucleic acids. These results have significant implications for understanding the role of EVs in cellular communication and for development of EVs as delivery tools. Moreover, studies using EVs from transiently transfected cells may be confounded by a predominance of pDNA transfer.

    View details for DOI 10.1073/pnas.1418401112

    View details for PubMedID 25713383

  • Differential fates of biomolecules delivered to target cells via extracellular vesicles PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kanada, M., Bachmann, M. H., Hardy, J. W., Frimannson, D. O., Bronsart, L., Wang, A., Sylvester, M. D., Schmidt, T. L., Kaspar, R. L., Butte, M. J., Matin, A. C., Contag, C. H. 2015; 112 (12): E1433-E1442
  • Use of bio-mimetic three-dimensional technology in therapeutics for heart disease BIOENGINEERED Serpooshan, V., Zhao, M., Metzler, S. A., Wei, K., Shah, P. B., Wang, A., Mahmoudi, M., Malkovskiy, A. V., Rajadas, J., Butte, M. J., Bernstein, D., Ruiz-Lozano, P. 2014; 5 (3)

    View details for DOI 10.4161/bioe.27751

    View details for Web of Science ID 000338494200008

  • Multi-cellular interactions sustain long-term contractility of human pluripotent stem cell-derived cardiomyocytes AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH Burridge, P. W., Metzler, S. A., Nakayama, K. H., Abilez, O. J., Simmons, C. S., Bruce, M. A., Matsuura, Y., Kim, P., Wu, J. C., Butte, M., Huang, N. F., Yang, P. C. 2014; 6 (6): 724-735


    Therapeutic delivery of cardiomyocytes derived from human pluripotent stem cells (hPSC-CMs) represents a novel clinical approach to regenerate the injured myocardium. However, poor survival and contractility of these cells are a significant bottleneck to their clinical use. To better understand the role of cell-cell communication in enhancing the phenotype and contractile properties of hPSC-CMs, we developed a three-dimensional (3D) hydrogel composed of hPSC-CMs, human pluripotent stem cell-derived endothelial cells (hPSC-ECs), and/or human amniotic mesenchymal stem cells (hAMSCs). The objective of this study was to examine the role of multi-cellular interactions among hPSC-ECs and hAMSCs on the survival and long-term contractile phenotype of hPSC-CMs in a 3D hydrogel. Quantification of spontaneous contractility of hPSC-CMs in tri-culture demonstrated a 6-fold increase in the area of contractile motion after 6 weeks with characteristic rhythmic contraction frequency, when compared to hPSC-CMs alone (P < 0.05). This finding was supported by a statistically significant increase in cardiac troponin T protein expression in the tri-culture hydrogel construct at 6 weeks, when compared to hPSC-CMs alone (P < 0.001). The sustained hPSC-CM survival and contractility in tri-culture was associated with a significant upregulation in the gene expression of L-type Ca(2+) ion channel, Cav1.2, and the inward-rectifier potassium channel, Kir2.1 (P < 0.05), suggesting a role of ion channels in mediating these processes. These findings demonstrate that multi-cellular interactions modulate hPSC-CM phenotype, function, and survival, and they will have important implications in engineering cardiac tissues for treatment of cardiovascular diseases.

    View details for Web of Science ID 000348299700009

  • The effect of bioengineered acellular collagen patch on cardiac remodeling and ventricular function post myocardial infarction BIOMATERIALS Serpooshan, V., Zhao, M., Metzler, S. A., Wei, K., Shah, P. B., Wang, A., Mahmoudi, M., Malkovskiy, A. V., Rajadas, J., Butte, M. J., Bernstein, D., Ruiz-Lozano, P. 2013; 34 (36): 9048-9055


    Regeneration of the damaged myocardium is one of the most challenging fronts in the field of tissue engineering due to the limited capacity of adult heart tissue to heal and to the mechanical and structural constraints of the cardiac tissue. In this study we demonstrate that an engineered acellular scaffold comprising type I collagen, endowed with specific physiomechanical properties, improves cardiac function when used as a cardiac patch following myocardial infarction. Patches were grafted onto the infarcted myocardium in adult murine hearts immediately after ligation of left anterior descending artery and the physiological outcomes were monitored by echocardiography, and by hemodynamic and histological analyses four weeks post infarction. In comparison to infarcted hearts with no treatment, hearts bearing patches preserved contractility and significantly protected the cardiac tissue from injury at the anatomical and functional levels. This improvement was accompanied by attenuated left ventricular remodeling, diminished fibrosis, and formation of a network of interconnected blood vessels within the infarct. Histological and immunostaining confirmed integration of the patch with native cardiac cells including fibroblasts, smooth muscle cells, epicardial cells, and immature cardiomyocytes. In summary, an acellular biomaterial with specific biomechanical properties promotes the endogenous capacity of the infarcted myocardium to attenuate remodeling and improve heart function following myocardial infarction.

    View details for DOI 10.1016/j.biomaterials.2013.08.017

    View details for Web of Science ID 000326426500006

    View details for PubMedID 23992980

  • Polyvinylpyrrolidone microneedles enable delivery of intact proteins for diagnostic and therapeutic applications ACTA BIOMATERIALIA Sun, W., Araci, Z., Inayathullah, M., Manickam, S., Zhang, X., Bruce, M. A., Marinkovich, M. P., Lane, A. T., Milla, C., Rajadas, J., Butte, M. J. 2013; 9 (8): 7767-7774


    We present a method of fabricating microneedles from polyvinylpyrrolidone (PVP) that enables delivery of intact proteins (or peptides) to the dermal layers of the skin. PVP is known to self-assemble into branched hollow fibers in aqueous and alcoholic solutions; we utilized this property to develop dissolvable patches of microneedles. Proteins were dissolved in concentrated PVP solution in both alcohol and water, poured into polydimethylsiloxane templates shaped as microneedles and, upon evaporation of solvent, formed into concentric, fibrous, layered structures. This approach of making PVP microneedles overcomes problems in dosage, uniform delivery and stability of protein formulation as compared to protein-coated metallic microneedles or photopolymerized PVP microneedles. Here we characterize the PVP microneedles and measure the delivery of proteins into skin. We show that our method of fabrication preserves the protein conformation. These microneedles can serve as a broadly useful platform for delivering protein antigens and therapeutic proteins to the skin, for example for allergen skin testing or immunotherapy.

    View details for DOI 10.1016/j.actbio.2013.04.045

    View details for Web of Science ID 000322207700017

  • High-Bandwidth AFM Probes for Imaging in Air and Fluid JOURNAL OF MICROELECTROMECHANICAL SYSTEMS Vijayraghavan, K., Gellineau, A. A., Wang, A., Butte, M. J., Melosh, N. A., Solgaard, O. 2013; 22 (3): 603-612
  • Measurement of elastic properties in fluid using high bandwidth atomic force microscope probes APPLIED PHYSICS LETTERS Vijayraghavan, K., Wang, A., Solgaard, O., Butte, M. J., Melosh, N. A. 2013; 102 (10)

    View details for DOI 10.1063/1.4795598

    View details for Web of Science ID 000316501200074

  • Single molecule labeling of an atomic force microscope cantilever tip APPLIED PHYSICS LETTERS Liu, J., Butte, M. J. 2012; 101 (16)

    View details for DOI 10.1063/1.4760283

    View details for Web of Science ID 000310669300073

  • Human amniotic mesenchymal stem cell-derived induced pluripotent stem cells may generate a universal source of cardiac cells. Stem cells and development Ge, X., Wang, I. E., Toma, I., Sebastiano, V., Liu, J., Butte, M. J., Reijo Pera, R. A., Yang, P. C. 2012; 21 (15): 2798-2808


    Human amniotic mesenchymal stem cells (hAMSCs) demonstrated partially pluripotent characteristics with a strong expression of Oct4 and Nanog genes and immunomodulatory properties characterized by the absence of HLA-DR and the presence of HLA-G and CD59. The hAMSCs were reprogrammed into induced pluripotent stem cells (iPSCs) that generate a promising source of universal cardiac cells. The hAMSC-derived iPSCs (MiPSCs) successfully underwent robust cardiac differentiation to generate cardiomyocytes. This study investigated 3 key properties of the hAMSCs and MiPSCs: (1) the reprogramming efficiency of the partially pluripotent hAMSCs to generate MiPSCs; (2) immunomodulatory properties of the hAMSCs and MiPSCs; and (3) the cardiac differentiation potential of the MiPSCs. The characteristic iPSC colony formation was observed within 10 days after the transduction of the hAMSCs with a single integration polycistronic vector containing 4 Yamanaka factors. Immunohistology and reverse transcription-polymerase chain reaction assays revealed that the MiPSCs expressed stem cell surface markers and pluripotency-specific genes. Furthermore, the hAMSCs and MiPSCs demonstrated immunomodulatory properties enabling successful engraftment in the SVJ mice. Finally, the cardiac differentiation of MiPSCs exhibited robust spontaneous contractility, characteristic calcium transience across the membrane, a high expression of cardiac genes and mature cardiac phenotypes, and a contractile force comparable to cardiomyocytes. Our results demonstrated that the hAMSCs are reprogrammed with a high efficiency into MiPSCs, which possess pluripotent, immunomodulatory, and precardiac properties. The MiPSC-derived cardiac cells express a c-kit cell surface marker, which may be employed to purify the cardiac cell population and enable allogeneic cardiac stem cell therapy.

    View details for DOI 10.1089/scd.2011.0435

    View details for PubMedID 22530853

  • Apelin Enhances Directed Cardiac Differentiation of Mouse and Human Embryonic Stem Cells PLOS ONE Wang, I. E., Wang, X., Ge, X., Anderson, J., Ho, M., Ashley, E., Liu, J., Butte, M. J., Yazawa, M., Dolmetsch, R. E., Quertermous, T., Yang, P. C. 2012; 7 (6)


    Apelin is a peptide ligand for an orphan G-protein coupled receptor (APJ receptor) and serves as a critical gradient for migration of mesodermal cells fated to contribute to the myocardial lineage. The present study was designed to establish a robust cardiac differentiation protocol, specifically, to evaluate the effect of apelin on directed differentiation of mouse and human embryonic stem cells (mESCs and hESCs) into cardiac lineage. Different concentrations of apelin (50, 100, 500 nM) were evaluated to determine its differentiation potential. The optimized dose of apelin was then combined with mesodermal differentiation factors, including BMP-4, activin-A, and bFGF, in a developmentally specific temporal sequence to examine the synergistic effects on cardiac differentiation. Cellular, molecular, and physiologic characteristics of the apelin-induced contractile embryoid bodies (EBs) were analyzed. It was found that 100 nM apelin resulted in highest percentage of contractile EB for mESCs while 500 nM had the highest effects on hESCs. Functionally, the contractile frequency of mESCs-derived EBs (mEBs) responded appropriately to increasing concentration of isoprenaline and diltiazem. Positive phenotype of cardiac specific markers was confirmed in the apelin-treated groups. The protocol, consisting of apelin and mesodermal differentiation factors, induced contractility in significantly higher percentage of hESC-derived EBs (hEBs), up-regulated cardiac-specific genes and cell surface markers, and increased the contractile force. In conclusion, we have demonstrated that the treatment of apelin enhanced cardiac differentiation of mouse and human ESCs and exhibited synergistic effects with mesodermal differentiation factors.

    View details for DOI 10.1371/journal.pone.0038328

    View details for Web of Science ID 000305339900024

    View details for PubMedID 22675543

  • Patient-Specific Induced Pluripotent Stem Cells as a Model for Familial Dilated Cardiomyopathy SCIENCE TRANSLATIONAL MEDICINE Sun, N., Yazawa, M., Liu, J., Han, L., Sanchez-Freire, V., Abilez, O. J., Navarrete, E. G., Hu, S., Wang, L., Lee, A., Pavlovic, A., Lin, S., Chen, R., Hajjar, R. J., Snyder, M. P., Dolmetsch, R. E., Butte, M. J., Ashley, E. A., Longaker, M. T., Robbins, R. C., Wu, J. C. 2012; 4 (130)


    Characterized by ventricular dilatation, systolic dysfunction, and progressive heart failure, dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy in patients. DCM is the most common diagnosis leading to heart transplantation and places a significant burden on healthcare worldwide. The advent of induced pluripotent stem cells (iPSCs) offers an exceptional opportunity for creating disease-specific cellular models, investigating underlying mechanisms, and optimizing therapy. Here, we generated cardiomyocytes from iPSCs derived from patients in a DCM family carrying a point mutation (R173W) in the gene encoding sarcomeric protein cardiac troponin T. Compared to control healthy individuals in the same family cohort, cardiomyocytes derived from iPSCs from DCM patients exhibited altered regulation of calcium ion (Ca(2+)), decreased contractility, and abnormal distribution of sarcomeric ?-actinin. When stimulated with a ?-adrenergic agonist, DCM iPSC-derived cardiomyocytes showed characteristics of cellular stress such as reduced beating rates, compromised contraction, and a greater number of cells with abnormal sarcomeric ?-actinin distribution. Treatment with ?-adrenergic blockers or overexpression of sarcoplasmic reticulum Ca(2+) adenosine triphosphatase (Serca2a) improved the function of iPSC-derived cardiomyocytes from DCM patients. Thus, iPSC-derived cardiomyocytes from DCM patients recapitulate to some extent the morphological and functional phenotypes of DCM and may serve as a useful platform for exploring disease mechanisms and for drug screening.

    View details for DOI 10.1126/scitranslmed.3003552

    View details for Web of Science ID 000303045900004

    View details for PubMedID 22517884

  • Optical planar waveguide for cell counting APPLIED PHYSICS LETTERS Leblanc, J., Mueller, A. J., Prinz, A., Butte, M. J. 2012; 100 (4)

    View details for DOI 10.1063/1.3678339

    View details for Web of Science ID 000300064500079

  • Dependence of Avidity on Linker Length for a Bivalent Ligand-Bivalent Receptor Model System JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mack, E. T., Snyder, P. W., Perez-Castillejos, R., Bilgicer, B., Moustakas, D. T., Butte, M. J., Whitesides, G. M. 2012; 134 (1): 333-345


    This paper describes a synthetic dimer of carbonic anhydrase, and a series of bivalent sulfonamide ligands with different lengths (25 to 69 Å between the ends of the fully extended ligands), as a model system to use in examining the binding of bivalent antibodies to antigens. Assays based on analytical ultracentrifugation and fluorescence binding indicate that this system forms cyclic, noncovalent complexes with a stoichiometry of one bivalent ligand to one dimer. This dimer binds the series of bivalent ligands with low picomolar avidities (K(d)(avidity) = 3-40 pM). A structurally analogous monovalent ligand binds to one active site of the dimer with K(d)(mono) = 16 nM. The bivalent association is thus significantly stronger (K(d)(mono)/K(d)(avidity) ranging from ~500 to 5000 unitless) than the monovalent association. We infer from these results, and by comparison of these results to previous studies, that bivalency in antibodies can lead to associations much tighter than monovalent associations (although the observed bivalent association is much weaker than predicted from the simplest level of theory: predicted K(d)(avidity) of ~0.002 pM and K(d)(mono)/K(d)(avidity) ~ 8 × 10(6) unitless).

    View details for DOI 10.1021/ja2073033

    View details for Web of Science ID 000301084200068

    View details for PubMedID 22088143

  • Patient-Specific Induced Pluripotent Stem Cell as a Model for Familial Dilated Cardiomyopathy Sun, N., Yazawa, M., Liu, J., Han, L., Sanchez-Freire, V., Hu, S., Ricardo, D., Butte, M., Ashley, E., Longaker, M., Robbins, R., Wu, J. LIPPINCOTT WILLIAMS & WILKINS. 2011
  • Thread as a Matrix for Biomedical Assays ACS APPLIED MATERIALS & INTERFACES Reches, M., Mirica, K. A., Dasgupta, R., Dickey, M. D., Butte, M. J., Whitesides, G. M. 2010; 2 (6): 1722-1728


    This paper describes the use of thread as a matrix for the fabrication of diagnostic assay systems. The kinds of thread used for this study are inexpensive, broadly available, and lightweight; some of them are already familiar materials in healthcare. Fluids wick along these threads by capillary action; no external power source is necessary for pumping. This paper demonstrates three designs for diagnostic assays that use different characteristics of the thread. The first two designs-the "woven array" and the "branching design"-take advantage of the ease with which thread can be woven on a loom to generate fluidic pathways that enable multiple assays to be performed in parallel. The third design-the "sewn array"-takes advantage of the ease with which thread can be sewn through a hydrophobic polymer sheet to incorporate assays into bandages, diapers and similar systems. These designs lead to microfluidic devices that may be useful in performing simple colorimetric assays that require qualitative results. We demonstrate the function of thread-based microfluidic devices in the context of five different colorimetric assays: detection of ketones, nitrite, protein, and glucose in artificial urine, and detection of alkaline phosphatase in artificial plasma.

    View details for DOI 10.1021/am1002266

    View details for Web of Science ID 000278963600027

    View details for PubMedID 20496913

  • Interaction of human PD-L1 and B7-1 MOLECULAR IMMUNOLOGY Butte, M. J., Pena-Cruz, V., Kim, M., Freeman, G. J., Sharpe, A. H. 2008; 45 (13): 3567-3572


    Numerous studies have pointed to the role of programmed death-1 ligand 1 (PD-L1) in regulating tolerance, chronic infection, and tumor immunity. Recently, we have identified murine B7-1 as a new binding partner for murine PD-L1. Human and mouse B7-1 share only 46% identity, leading us to question whether human B7-1 and PD-L1 can participate in a similar interaction. Here we show that human B7-1 can interact with human PD-L1 with affinity greater than that of B7-1 with CD28, but less than that of B7-1 with CTLA-4 or of PD-L1 with PD-1. We characterize a series of anti-human PD-L1 monoclonal antibodies and identify antibodies that can block interactions of PD-L1 with B7-1, PD-1, or both. Since PD-L1 and CD28 on T cells may compete for B7-1 as a binding partner and CD8 T cells may express high or low levels of CD28, we examined when PD-L1 and CD28 are co-expressed on CD8 T cells. We compared the time-course and extent of PD-L1 induction on CD8 CD28high versus CD28low T cells following stimulation with anti-CD3. We show that PD-L1 is induced to a higher level on CD28high T cells than on CD28low T cells upon activation. These results suggest that PD-L1 may play an important and undervalued role on human T cells.

    View details for DOI 10.1016/j.molimm.2008.05.014

    View details for Web of Science ID 000259473500008

    View details for PubMedID 18585785

  • Cell Encapsulation in Sub-mm Sized Gel Modules Using Replica Molding PLOS ONE McGuigan, A. P., Bruzewicz, D. A., Glavan, A., Butte, M., Whitesides, G. M. 2008; 3 (5)


    For many types of cells, behavior in two-dimensional (2D) culture differs from that in three-dimensional (3D) culture. Among biologists, 2D culture on treated plastic surfaces is currently the most popular method for cell culture. In 3D, no analogous standard method--one that is similarly convenient, flexible, and reproducible--exists. This paper describes a soft-lithographic method to encapsulate cells in 3D gel objects (modules) in a variety of simple shapes (cylinders, crosses, rectangular prisms) with lateral dimensions between 40 and 1000 microm, cell densities of 10(5)-10(8) cells/cm(3), and total volumes between 1x10(-7) and 8x10(-4) cm(3). By varying (i) the initial density of cells at seeding, and (ii) the dimensions of the modules, the number of cells per module ranged from 1 to 2500 cells. Modules were formed from a range of standard biopolymers, including collagen, Matrigel, and agarose, without the complex equipment often used in encapsulation. The small dimensions of the modules allowed rapid transport of nutrients by diffusion to cells at any location in the module, and therefore allowed generation of modules with cell densities near to those of dense tissues (10(8)-10(9) cells/cm(3)). This modular method is based on soft lithography and requires little special equipment; the method is therefore accessible, flexible, and well suited to (i) understanding the behavior of cells in 3D environments at high densities of cells, as in dense tissues, and (ii) developing applications in tissue engineering.

    View details for DOI 10.1371/journal.pone.0002258

    View details for Web of Science ID 000262258700058

    View details for PubMedID 18493609

  • PD-1 and its ligands in tolerance and immunity ANNUAL REVIEW OF IMMUNOLOGY Keir, M. E., Butte, M. J., Freeman, G. J., Sharpel, A. H. 2008; 26: 677-704


    Programmed death 1 (PD-1) and its ligands, PD-L1 and PD-L2, deliver inhibitory signals that regulate the balance between T cell activation, tolerance, and immunopathology. Immune responses to foreign and self-antigens require specific and balanced responses to clear pathogens and tumors and yet maintain tolerance. Induction and maintenance of T cell tolerance requires PD-1, and its ligand PD-L1 on nonhematopoietic cells can limit effector T cell responses and protect tissues from immune-mediated tissue damage. The PD-1:PD-L pathway also has been usurped by microorganisms and tumors to attenuate antimicrobial or tumor immunity and facilitate chronic infection and tumor survival. The identification of B7-1 as an additional binding partner for PD-L1, together with the discovery of an inhibitory bidirectional interaction between PD-L1 and B7-1, reveals new ways the B7:CD28 family regulates T cell activation and tolerance. In this review, we discuss current understanding of the immunoregulatory functions of PD-1 and its ligands and their therapeutic potential.

    View details for DOI 10.1146/annurev.immunol.26.021607.090331

    View details for Web of Science ID 000255349300022

    View details for PubMedID 18173375

  • TIM-1 and TIM-4 glycoproteins bind phosphatidylserine and mediate uptake of apoptotic cells IMMUNITY Kobayashi, N., Karisola, P., Pena-Cruz, V., Dorfman, D. M., Jinushi, M., Umetsu, S. E., Butte, M. J., Nagumo, H., Chernova, I., Zhu, B., Sharpe, A. H., Ito, S., Dranoff, G., Kaplan, G. G., Casasnovas, J. M., Umetsu, D. T., DeKruyff, R. H., Freeman, G. J. 2007; 27 (6): 927-940


    The T cell immunoglobulin mucin (TIM) proteins regulate T cell activation and tolerance. Here we showed that TIM-4 is expressed on human and mouse macrophages and dendritic cells, and both TIM-4 and TIM-1 specifically bound phosphatidylserine (PS) on the surface of apoptotic cells but not any other phospholipid tested. TIM-4(+) peritoneal macrophages, TIM-1(+) kidney cells, and TIM-4- or TIM-1-transfected cells efficiently phagocytosed apoptotic cells, and phagocytosis could be blocked by TIM-4 or TIM-1 monoclonal antibodies. Mutations in the unique cavity of TIM-4 eliminated PS binding and phagocytosis. TIM-4 mAbs that blocked PS binding and phagocytosis mapped to epitopes in this binding cavity. These results show that TIM-4 and TIM-1 are immunologically restricted members of the group of receptors whose recognition of PS is critical for the efficient clearance of apoptotic cells and prevention of autoimmunity.

    View details for DOI 10.1016/j.immuni.2007.11.011

    View details for Web of Science ID 000251907300012

    View details for PubMedID 18082433

  • IL-7 receptor deficient SCID with a unique intronic mutation and post-transplant autoimmunity due to chronic GVHD CLINICAL IMMUNOLOGY Butte, M. J., Haines, C., Bonilla, F. A., Puck, J. 2007; 125 (2): 159-164


    Severe combined immunodeficiency (SCID) may result from a variety of genetic defects that impair the development of T cells. Signaling mediated by the cytokine interleukin-7 is essential for the differentiation of T cells from lymphoid progenitors, and mutations of either the interleukin-7 receptor alpha chain (IL-7Ralpha) or its associated cytokine receptor chain, the common gamma chain (gammac), result in SCID. Here we report a case of SCID due to heterozygous mutations of the IL7R gene encoding IL-7Ralpha. A previously unrecognized mutation found within intron 3 created a new exon between exons 3 and 4 in the mRNA transcribed from this allele, producing a truncated, unstable mRNA. This mutation illustrates the necessity of evaluating both coding and non-coding regions of genes when searching for pathogenic mutations. Following hematopoietic stem cell transplantation of our patient, immune reconstitution was accompanied by two unusual complications, immune-mediated myositis and myasthenia gravis.

    View details for DOI 10.1016/j.clim.2007.06.007

    View details for Web of Science ID 000250466900007

    View details for PubMedID 17827065

  • Endothelial programmed death-1 ligand 1 (PD-L1) regulates CD8(+) T-cell-mediated injury in the heart CIRCULATION Grabie, N., Gotsman, I., DaCosta, R., Pang, H., Stavrakis, G., Butte, M. J., Keir, M. E., Freeman, G. J., Sharpe, A. H., Lichtman, A. H. 2007; 116 (18): 2062-2071


    PD-L1 and PD-L2 are ligands for the inhibitory receptor programmed death-1 (PD-1), which is an important regulator of immune responses. PD-L1 is induced on cardiac endothelial cells under inflammatory conditions, but little is known about its role in regulating immune injury in the heart.Cytotoxic T-lymphocyte-mediated myocarditis was induced in mice, and the influence of PD-L1 signaling was studied with PD-L1/L2-deficient mice and blocking antibodies. During cytotoxic T-lymphocyte-induced myocarditis, the upregulation of PD-L1 on cardiac endothelia was dependent on T-cell-derived interferon-gamma, and blocking of interferon-gamma signaling worsened disease. Genetic deletion of both PD-1 ligands [PD-L1/2(-/-)], as well as treatment with PD-L1 blocking antibody, transformed transient myocarditis to lethal disease, in association with widespread polymorphonuclear leukocyte-rich microabscesses but without change in cytotoxic T-lymphocyte recruitment. PD-L1/2(-/-) mice reconstituted with bone marrow from wild-type mice remained susceptible to severe disease, which demonstrates that PD-L1 on non-bone marrow-derived cells confers the protective effect. Finally, depletion of polymorphonuclear leukocytes reversed the enhanced susceptibility to lethal myocarditis attributable to PD-L1 deficiency.Myocardial PD-L1, mainly localized on endothelium, is critical for control of immune-mediated cardiac injury and polymorphonuclear leukocyte inflammation.

    View details for DOI 10.1161/CIRCULATIONAHA.107.709360

    View details for Web of Science ID 000250518000010

    View details for PubMedID 17938288

  • Programmed death-1 ligand 1 interacts specifically with the B7-1 costimulatory molecule to inhibit T cell responses IMMUNITY Butte, M. J., Keir, M. E., Phamduy, T. B., Sharpe, A. H., Freeman, G. J. 2007; 27 (1): 111-122


    Pathways in the B7:CD28 family of costimulatory molecules regulate T cell activation and tolerance. B7-dependent responses in Cd28(-/-)Ctla4(-/-) T cells together with reports of stimulatory and inhibitory functions for Programmed Death-1 Ligand 1 or 2 molecules (PD-L1 or PD-L2) have suggested additional receptors for these B7 family members. We show that B7-1 and PD-L1 interacted with affinity intermediate to that of B7-1:CD28 and B7-1:CTLA-4. The PD-L1:B7-1 interface overlapped with the B7-1:CTLA-4 and PD-L1:PD-1 (Programmed Death-1) interfaces. T cell activation and cytokine production were inhibited by the interaction of B7-1 with PD-L1. The responses of PD-1-deficient versus PD-1,B7-1 double-deficient T cells to PD-L1 and of CD28,CTLA-4 double-deficient versus CD28,CTLA-4,PD-L1 triple-deficient T cells to B7-1 demonstrated that PD-L1 and B7-1 interact specifically to inhibit T cell activation. Our findings point to a substantial bidirectional inhibitory interaction between B7-1 and PD-L1 and add an additional dimension to immunoregulatory functions of the B7:CD28 family.

    View details for DOI 10.1016/j.immuni.2007.05.016

    View details for Web of Science ID 000248398100013

    View details for PubMedID 17629517

  • Patterned paper as a platform for inexpensive, low-volume, portable bioassays ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Martinez, A. W., Phillips, S. T., Butte, M. J., Whitesides, G. M. 2007; 46 (8): 1318-1320

    View details for DOI 10.1002/anie.200603817

    View details for Web of Science ID 000244382200027

    View details for PubMedID 17211899

  • Pentobarbital desensitization in a 3-month-old child ALLERGY AND ASTHMA PROCEEDINGS Butte, M. J., Dodson, B., Dioun, A. 2004; 25 (4): 225-227


    Barbiturates, a class of medications commonly used as antiepileptics and sedatives, are known to cause adverse reaction, with the most commonly reported immune-mediated reactions being anticonvulsant hypersensitivity syndrome. Other types of allergic reactions such as immediate hypersensitivity reactions also can occur. We present a 3-month-old child with refractory generalized convulsive status epilepticus who required pentobarbital therapy in the context of phenobarbital sensitivity because of progressive generalized seizures unresponsive to other aggressive therapies. Skin tests to pentobarbital and phenobarbital were negative. In the intensive care unit setting, intravenous pentobarbital desensitization was performed without reaction. To our knowledge, this is the first reported protocol for pentobarbital desensitization.

    View details for Web of Science ID 000223899700002

    View details for PubMedID 15510580

  • Neurotrophic factor structures reveal clues to evolution, binding, specificity, and receptor activation CELLULAR AND MOLECULAR LIFE SCIENCES Butte, M. J. 2001; 58 (8): 1003-1013


    The neutrophin family, the glial-derived neurotrophic factor family, and the ciliary neurotrophic factor are the best described growth factors specific for developing neurons and neutral crest cells. As might be expected for regulatory molecules of the complex central and peripheral nervous system, these factors show considerable receptor specificity and cross-talk. Thanks to a decade of intense research by numerous laboratories, the structures of many of these factors are now available. This review discusses the structural bases of receptor binding, specificity, and activation in each of these systems. Using structure-based sequence alignments, the evolutionary implications of these molecules and their receptors are discussed, followed by suggestions for further directions for research on the structure and function of these neurotrophic factors.

    View details for Web of Science ID 000170535200002

    View details for PubMedID 11529493

  • Functional studies of the BTB domain in the Drosophila GAGA and Mod(mdg4) proteins NUCLEIC ACIDS RESEARCH Read, D., Butte, M. J., Dernburg, A. F., Frasch, M., Kornberg, T. B. 2000; 28 (20): 3864-3870


    The BTB/POZ (BTB) domain is an approximately 120 residue sequence that is conserved at the N-terminus of many proteins in both vertebrates and invertebrates. We found that the protein encoded by a lethal allele of the Drosophila modifier of mdg4 [mod(mdg4)] gene has two mutated residues in its BTB domain. The identities of the residues at the positions of these mutations are highly conserved in the BTB domain family of proteins, and when the corresponding mutations were engineered into the BTB domain-containing GAGA protein, the activity of GAGA as a transcription activator in a transient transfection assay was severely reduced. The functional equivalence of the BTB domains was established by showing that the BTB domain of the mod(mdg4) protein can effectively substitute for that of GAGA.

    View details for Web of Science ID 000089954300004

    View details for PubMedID 11024164

  • Pediatric myocardial infarction after racemic epinephrine administration PEDIATRICS Butte, M. J., Nguyen, B. X., Hutchison, T. J., Wiggins, J. W., Ziegler, J. W. 1999; 104 (1)


    Myocardial infarction is a previously unreported complication of treatment with racemic epinephrine that is used commonly in the emergency department for severe respiratory distress in bronchiolitis or croup syndrome. We describe a pediatric patient who presented with the croup syndrome and severe respiratory distress that required multiple doses of nebulized racemic epinephrine in the emergency department. The patient developed ventricular tachycardia and mild chest discomfort during one treatment, which resolved spontaneously on discontinuation of the nebulization. Persistently abnormal electrocardiograms and elevated creatine phosphokinase MB isoenzyme (CPK-MB) levels suggested a myocardial infarction had occurred. Subsequent echocardiography, cardiac catheterization, and angiography revealed an anatomically normal heart with normal coronary circulation; however, a stress nuclear study showed a small myocardial infarct. The significance of this previously unreported complication of racemic epinephrine is discussed, along with recommendations for proper use in the emergency department.

    View details for Web of Science ID 000081258700024

    View details for PubMedID 10390295

  • Crystal structure of neurotrophin-3 homodimer shows distinct regions are used to bind its receptors BIOCHEMISTRY Butte, M. J., Hwang, P. K., Mobley, W. C., Fletterick, R. J. 1998; 37 (48): 16846-16852


    Neurotrophin-3 (NT-3) is a cystine knot growth factor that promotes the survival, proliferation, and differentiation of developing neurons and is a potential therapeutic for neurodegenerative diseases. To clarify the structural basis of receptor specificity and the role of neurotrophin dimerization in receptor activation, the structure of the NT-3 homodimer was determined using X-ray crystallography. The orthorhombic crystals diffract to 2.4 A, with dimer symmetry occurring about a crystallographic 2-fold axis. The overall structure of NT-3 resembles that of the other neurotrophins, NGF and BDNF; each protomer forms a twisted four-stranded beta sheet, with three intertwined disulfide bonds. There are notable differences, however, between NT-3 and NGF in the surface loops and in three functionally important regions, shown in previous mutagenesis studies to be critical for binding. One such difference implies that NT-3's binding affinity and specificity depend on a novel hydrogen bond between Gln 83, a residue important for binding specificity with TrkC, and Arg 103, a residue crucial for binding affinity with TrkC. NT-3's extensive dimer interface buries much of the otherwise solvent-accessible hydrophobic surface area and suggests that the dimeric state is stabilized through the formation of this hydrophobic core. A comparison of the dimer interface between the NT-3 homodimer and the BDNF/NT-3 heterodimer reveals similar patterns of hydrogen bonds and nonpolar contacts, which reinforces the notion that the evolutionarily conserved neurotrophin interface resulted from the need for receptor dimerization in signal initiation.

    View details for Web of Science ID 000077339600002

    View details for PubMedID 9836577



    We describe a classification scheme for bursting oscillations which encompasses many of those found in the literature on bursting in excitable media. This is an extension of the scheme of Rinzel (in Mathematical Topics in Population Biology, Springer, Berlin, 1987), put in the context of a sequence of horizontal cuts through a two-parameter bifurcation diagram. We use this to describe the phenomenological character of different types of bursting, addressing the issue of how well the bursting can be characterized given the limited amount of information often available in experimental settings.

    View details for Web of Science ID A1995QM41500003

    View details for PubMedID 7728115