All Publications


  • Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity. Immunity Fenton, T. M., Jørgensen, P. B., Niss, K., Rubin, S. J., Mörbe, U. M., Riis, L. B., Da Silva, C., Plumb, A., Vandamme, J., Jakobsen, H. L., Brunak, S., Habtezion, A., Nielsen, O. H., Johansson-Lindbom, B., Agace, W. W. 2020

    Abstract

    The intestine contains some of the most diverse and complex immune compartments in the body. Here we describe a method for isolating human gut-associated lymphoid tissues (GALTs) that allows unprecedented profiling of the adaptive immune system in submucosal and mucosal isolated lymphoid follicles (SM-ILFs and M-ILFs, respectively) as well as in GALT-free intestinal lamina propria (LP). SM-ILF and M-ILF showed distinct patterns of distribution along the length of the intestine, were linked to the systemic circulation through MAdCAM-1+ high endothelial venules and efferent lymphatics, and had immune profiles consistent with immune-inductive sites. IgA sequencing analysis indicated that human ILFs are sites where intestinal adaptive immune responses are initiated in an anatomically restricted manner. Our findings position ILFs as key inductive hubs for regional immunity in the human intestine, and the methods presented will allow future assessment of these compartments in health and disease.

    View details for DOI 10.1016/j.immuni.2020.02.001

    View details for PubMedID 32160523

  • Mass cytometry reveals systemic and local immune signatures that distinguish inflammatory bowel diseases. Nature communications Rubin, S. J., Bai, L., Haileselassie, Y., Garay, G., Yun, C., Becker, L., Streett, S. E., Sinha, S. R., Habtezion, A. 2019; 10 (1): 2686

    Abstract

    Inflammatory bowel disease (IBD) includes Crohn's disease and ulcerative colitis. Each disease is characterized by a diverse set of potential manifestations, which determine patients' disease phenotype. Current understanding of phenotype determinants is limited, despite increasing prevalence and healthcare costs. Diagnosis and monitoring of disease requires invasive procedures, such as endoscopy and tissue biopsy. Here we report signatures of heterogeneity between disease diagnoses and phenotypes. Using mass cytometry, we analyze leukocyte subsets, characterize their function(s), and examine gut-homing molecule expression in blood and intestinal tissue from healthy and/or IBD subjects. Some signatures persist in IBD despite remission, and many signatures are highly represented by leukocytes that express gut trafficking molecules. Moreover, distinct systemic and local immune signatures suggest patterns of cell localization in disease. Our findings highlight the importance of gut tropic leukocytes in circulation and reveal that blood-based immune signatures differentiate clinically relevant subsets of IBD.

    View details for DOI 10.1038/s41467-019-10387-7

    View details for PubMedID 31217423

  • B cell checkpoints in autoimmune rheumatic diseases NATURE REVIEWS RHEUMATOLOGY Rubin, S. S., Bloom, M. S., Robinson, W. H. 2019; 15 (5): 303–15
  • B cell checkpoints in autoimmune rheumatic diseases. Nature reviews. Rheumatology Rubin, S. J., Bloom, M. S., Robinson, W. H. 2019

    Abstract

    B cells have important functions in the pathogenesis of autoimmune diseases, including autoimmune rheumatic diseases. In addition to producing autoantibodies, B cells contribute to autoimmunity by serving as professional antigen-presenting cells (APCs), producing cytokines, and through additional mechanisms. B cell activation and effector functions are regulated byimmune checkpoints, including both activating and inhibitory checkpoint receptors that contribute to the regulation of B cell tolerance, activation, antigen presentation, T cell help, classswitching, antibody production and cytokine production. The various activating checkpoint receptors include B cell activating receptors that engage with cognate receptors on T cells or other cells, as well as Toll-like receptors that can provide dual stimulation to B cells via co-engagement with the B cell receptor. Furthermore, various inhibitory checkpoint receptors, including B cell inhibitory receptors, have important functions in regulating B cell development, activation and effector functions. Therapeutically targeting B cell checkpoints represents a promising strategy for the treatment of a variety of autoimmune rheumatic diseases.

    View details for PubMedID 30967621

  • Immunomodulatory receptors are differentially expressed in B and T cell subsets relevant to autoimmune disease. Clinical immunology (Orlando, Fla.) Murphy, K. A., Bhamidiphati, K., Rubin, S. J., Kipp, L., Robinson, W. H., Lanz, T. V. 2019: 108276

    Abstract

    Inhibitory cell-surface receptors on lymphocytes, often called immune checkpoints, are powerful targets for cancer therapy. Despite their direct involvement in autoimmune pathology, they are currently not exploited therapeutically for autoimmune diseases. Understanding the receptors' expression patterns in health and disease is essential for targeted drug design. Here, we designed three 23-colour flow cytometry panels for peripheral-blood T cells, including 15 lineage-defining markers and 21 immunomodulatory cell-surface receptors, and a 22-marker panel for B cells. Blood samples from healthy individuals, multiple sclerosis (MS), and lupus (SLE) patients were included in the study. Several receptors show differential expression on regulatory T cells (Treg) compared to T helper (Th) 1 and Th17 cells, and functional relevance of this difference could be shown for BTLA and CD5. Unbiased multiparametric analysis revealed a subset of activated CD8+ T cells and a subset of unswitched memory B cells that are diminished in MS and SLE, respectively.

    View details for DOI 10.1016/j.clim.2019.108276

    View details for PubMedID 31669582

  • Backbone-Cyclized Peptides: a Critical Review. Current topics in medicinal chemistry Rubin, S. J., Qvit, N. 2018

    Abstract

    Backbone-cyclized peptides and peptidomimetics integrate the biological activity and pharmacological features necessary for successful research tools and therapeutics. In general, these structures demonstrate improved maintenance of bioactive conformation, stability and cell permeability compared to their linear counterparts, while maintaining support for a variety of side chain chemistries. We explain how backbone cyclization and cycloscan techniques allow scientists to cyclize linear peptides with retained or enhanced biological activity and improved drug-like features. We discuss head-to-tail (C-terminus to N-terminus), building unit-to-tail, building unit-to-side chain, building unit-to-building unit, and building unit-to-head backbone cyclization, with examples of building blocks, such as Nalpha-(omega-thioalkylene), Nalpha-(omega-aminoalkylene) and Nalpha-(omega-carboxyalkylene) units. We also present several methods for recombinant expression of backbone-cyclized peptides, including backbone cyclic peptide synthesis using recombinant elements (bcPURE), phage display and induced peptidyl-tRNA drop-off. Moreover, natural backbone-cyclized peptides are also produced by cyanobacteria, plants and other organisms; several of these compounds have been developed and commercialized for therapeutic applications, which we review. Backbone-cyclized peptides and peptidomimetics comprise a growing share of the pharmaceutical industry and will be applied to additional problems in the near future.

    View details for PubMedID 29773062

  • Conversion of Protein Active Regions into Peptidomimetic Therapeutic Leads using Backbone Cyclization and Cycloscan - How to Do It Yourself. Current topics in medicinal chemistry Rubin, S. J., Tal-Gan, Y., Gilon, C., Qvit, N. 2018

    Abstract

    Protein-protein interactions (PPIs) are particularly important for controlling both physiologic and pathologic biological processes but are difficult to target due to their large and/or shallow interaction surfaces unsuitable for small molecules. Linear peptides found in nature interact with some PPIs, and protein active regions can be used to design synthetic peptide compounds for inhibition of PPIs. However, linear peptides are limited therapeutically by poor metabolic and conformational stability, which can compromise their bioactivity and half-life. Cyclic peptidomimetics (modified peptides) can be used to overcome these challenges because they are more resistant to metabolic degradation and can be engineered to adopt desired conformations. Backbone cyclization is a strategy that we developed to improve drug-like properties of linear peptide leads without jeopardizing the integrity of functionally relevant side-chains. Here, we provide the first description of an entire approach for developing backbone cyclized peptide compounds, based upon two straightforward 'ABC' and 'DEF' processes. We present practical examples throughout our discussion of revealing active regions important for PPIs and identifying critical pharmacophores, as well as developing backbone cyclized peptide libraries and screening them using cycloscan. Finally, we review the impact of these advances and provide a summary of current ongoing work in the field.

    View details for PubMedID 29773063

  • Cyclic Peptides for Protein-Protein Interaction Targets CURRENT TOPICS IN MEDICINAL CHEMISTRY Qvit, N., Rubin, S. S. 2018; 18 (7): 525

    View details for PubMedID 30014801

  • Gravity-Drawn Silicone Filaments: Production, Characterization, and Wormlike Chain Dynamics ACS APPLIED MATERIALS & INTERFACES Kiessling, R., Rubin, S. S., Zehner, J., Barraugh, C., Snell, K., Fukushima, C., Mulligan, M., Keckley, M., Bosshardt, A., Cook, W., Sanii, B. 2017; 9 (46): 39916–20

    Abstract

    We introduce a method to produce continuous polydimethylsiloxane (PDMS) silicone filaments on the order of 0.5 m long and 100 μm in diameter. The approach overcomes traditional limitations in silicone drawing by partially precuring the polymer and drawing through a tube furnace. We characterize the filaments' mechanical properties, and their ability to switch hydrophobicity by UV-ozone and corona discharge patterning. The flexible filaments' dynamic properties were evaluated by way of athermal acoustic excitation at the air-water interface, revealing conformational reconfigurability consistent with a wormlike chain model. We envision applications in rapid prototyping and as a platform for model foldamer studies.

    View details for DOI 10.1021/acsami.7b11972

    View details for Web of Science ID 000416614600006

    View details for PubMedID 29111635

  • Peptidomimetic therapeutics: scientific approaches and opportunities. Drug discovery today Qvit, N., Rubin, S. J., Urban, T. J., Mochly-Rosen, D., Gross, E. R. 2017; 22 (2): 454-462

    Abstract

    Natural endogenously occurring peptides exhibit desirable medicinal properties, but are often limited in application by rapid proteolysis and inadequate membrane permeability. However, editing naturally occurring peptide sequences to develop peptidomimetic analogs created a promising class of therapeutics that can augment or inhibit molecular interactions. Here, we discuss a variety of chemical modifications, including l to d isomerization, cyclization, and unnatural amino acid substitution, as well as design strategies, such as attachment to cell-penetrating peptides, which are used to develop peptidomimetics. We also provide examples of approved peptidomimetics and discuss several compounds in clinical trials.

    View details for DOI 10.1016/j.drudis.2016.11.003

    View details for PubMedID 27856346

  • Exceptional running and turning performance in a mite JOURNAL OF EXPERIMENTAL BIOLOGY Rubin, S., Young, M. H., Wright, J. C., Whitaker, D. L., Ahn, A. N. 2016; 219 (5): 676-685

    Abstract

    The Southern California endemic mite Paratarsotomus macropalpis was filmed in the field on a concrete substrate and in the lab to analyze stride frequency, gait and running speed under different temperature conditions and during turning. At ground temperatures ranging from 45 to 60 °C, mites ran at a mean relative speed of 192.4 ± 2.1 body lengths (BL) s(-1), exceeding the highest previously documented value for a land animal by 12.5%. Stride frequencies were also exceptionally high (up to 135 Hz), and increased with substrate temperature. Juveniles exhibited higher relative speeds than adults and possess proportionally longer legs, which allow for greater relative stride lengths. Although mites accelerated and decelerated rapidly during straight running (7.2 ± 1.2 and -10.1 ± 2.1 m s(-2), respectively), the forces involved were comparable to those found in other animals. Paratarsotomus macropalpis employs an alternating tetrapod gait during steady running. Shallow turns were accomplished by a simple asymmetry in stride length. During tight turns, mites pivoted around the tarsus of the inside third leg (L3), which thus behaved like a grappling hook. Pivot turns were characterized by a 42% decrease in turning radius and a 40% increase in angular velocity compared with non-pivot turns. The joint angle amplitudes of the inner L2 and L3 were negligible during a pivot turn. While exceptional, running speeds in P. macropalpis approximate values predicted from inter-specific scaling relationships.

    View details for DOI 10.1242/jeb.128652

    View details for Web of Science ID 000371134700016

    View details for PubMedID 26787481

  • Cyclic Peptides for Protein-Protein Interaction Targets: Applications to Human Disease CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION Rubin, S., Qvit, N. 2016; 26 (3): 199-221

    Abstract

    Protein-protein interactions (PPIs) represent a significant portion of functionally relevant biological interactions, and therefore potential therapeutic targets. Small molecules were traditionally used to target PPIs. However, many PPI surfaces lack binding pockets due to their large and flat structures. Antibodies can also be used to modulate PPIs, but they are expensive and not cell permeable. Linear peptides are less expensive to produce than antibodies and are generally more selective than small molecules, but they are limited by decreased stability and poor permeability. Modified peptides (peptidomimetics, e.g., cyclic peptides) can overcome these obstacles. Advantages of using cyclic peptidomimetics to modulate PPIs derive from their conformational constraint, which supports target specificity, cell permeability, and metabolic stability. Methods for rational design coupled with high-throughput techniques continue to support advances in the field. Further development of cyclic peptidomimetics to modulate PPIs will improve treatment of human diseases, such as cancer, infection, neurodegeneration, and autoimmunity. Here we describe several cyclic peptidomimetics that are currently used as drugs and many potential cyclic peptides PPI inhibitors in different stages of pre-clinical and clinical development. Further development of cyclic peptidomimetics to modulate PPIs will continue to improve treatment of human diseases, such as cancer, infection, neurodegeneration, and autoimmunity.

    View details for DOI 10.1615/CritRevEukaryotGeneExpr.2016016525

    View details for Web of Science ID 000385947400002

    View details for PubMedID 27650985

  • Exceptional locomotory performance in Paratarsotomus macropalpis mites Rubin, S., Wright, J., Young, M., Whitaker, D., Ahn, A. FEDERATION AMER SOC EXP BIOL. 2014