Vitamin D is Associated with α4β7+ Immunophenotypes and Predicts Vedolizumab Therapy Failure in Patients with Inflammatory Bowel Disease.
Journal of Crohn's & colitis
Vitamin D downregulates the in vitro expression of the gut-tropic integrin α4β7 on immune cells. The clinical relevance of this finding in patients with inflammatory bowel disease (IBD) is unclear. We tested the hypothesis that vitamin D is associated with α4β7 immunophenotypes and risk of vedolizumab (anti- α4β7) failure in IBD.We performed single-cell immunophenotyping of peripheral and intestinal immune cells using mass cytometry (CyTOF) in vedolizumab-naïve patients with IBD (N=48). We analyzed whole-genome mucosal gene expression (GSE73661) from GEMINI I and GEMINI long-term safety (LTS) to determine the association between vitamin D receptor (VDR) and integrin alpha-4 (ITGA4) and beta-7 (ITGB7) genes. We estimated the odds of vedolizumab failure with low pre-treatment vitamin D in a combined retrospective and prospective IBD cohort (N= 252) with logistic regression.Immunophenotyping revealed that higher 25(OH)D was associated with decreased α4β7+ peripheral blood mononuclear cells (R = -0.400, P < 0.01) and α4β7+ intestinal leukocytes (R = -0.538, P= 0.03). Serum 25(OH)D was inversely associated with α4β7+ peripheral B cells and natural killer (NK) cells and α4β7+ intestinal B cells, NK cells, monocytes, and macrophages. Mucosal expression of VDR was inversely associated with ITGA4 and ITGB7 expression. In multivariate analysis, 25(OH)D < 25 ng/mL was associated with increased vedolizumab primary non-response during induction (OR 26.10, 95% CI 14.30-48.90, P<0.001) and failure at 1-year follow-up (OR 6.10, 95% CI 3.06-12.17, P<0.001).Low serum 25(OH)D is associated with α4β7+ immunophenotypes and predicts future vedolizumab failure in patients with IBD.
View details for DOI 10.1093/ecco-jcc/jjab114
View details for PubMedID 34180967
Engineering "Antimicrobial Peptides" and Other Peptides to Modulate Protein-Protein Interactions in Cancer.
Current topics in medicinal chemistry
Antimicrobial peptides (AMPs) are a class of peptides found across a wide array of organisms that play key roles in host defense. AMPs induce selective death in target cells and orchestrate specific or nonspecific immune responses. Many AMPs exhibit native anticancer activity in addition to antibacterial activity, and others have been engineered as antineoplastic agents. We discuss the use of AMPs in detection and treatment of cancer as well as mechanisms of AMPinduced cell death. We present key examples of cathelicidins and transferrins, which are major AMP families. Further, we discuss the critical roles of protein-protein interactions (PPIs) in cancer and how AMPs are well suited to target PPIs based on their unique druglike properties not exhibited by small molecules or antibodies. While peptides including AMPs can have limited stability and bioavailability, these issues can be overcome by peptide backbone cyclization or stapling and by the use of delivery systems such as cell-penetrating peptides (CPPs), respectively. We discuss approaches for optimizing drug properties of peptide and peptidomimetic leads, providing examples of promising techniques that may be applied to AMPs. These molecules represent an exciting resource as anticancer agents with unique therapeutic advantages that can target challenging mechanisms involving PPIs. Indeed, AMPs are suitable drug leads for further development of cancer therapeutics, and many studies to this end are underway.
View details for DOI 10.2174/1568026620666201021141401
View details for PubMedID 33087030
Effects of processing conditions on stability of immune analytes in human blood.
2020; 10 (1): 17328
Minimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual's baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range-10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for>20K genes)-with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.
View details for DOI 10.1038/s41598-020-74274-8
View details for PubMedID 33060628
- Peptide Therapeutics: Scientific Approaches, Current Development Trends, and Future Directions. Current topics in medicinal chemistry 2020; 20 (32): 2903
Clinical characteristics associated with COVID-19 severity in California.
Journal of clinical and translational science
2020; 5 (1): e3
Given the rapidly progressing coronavirus disease 2019 (COVID-19) pandemic, this report on a US cohort of 54 COVID-19 patients from Stanford Hospital and data regarding risk factors for severe disease obtained at initial clinical presentation is highly important and immediately clinically relevant. We identified low presenting oxygen saturation as predictive of severe disease outcomes, such as diagnosis of pneumonia, acute respiratory distress syndrome, and admission to the intensive care unit, and also replicated data from China suggesting an association between hypertension and disease severity. Clinicians will benefit by tools to rapidly risk stratify patients at presentation by likelihood of progression to severe disease.
View details for DOI 10.1017/cts.2020.40
View details for PubMedID 34192044
View details for PubMedCentralID PMC7274026
Safety of ACE-I and ARB medications in COVID-19: A retrospective cohort study of inpatients and outpatients in California
Journal of Clinical and Translational Science
View details for DOI 10.1017/cts.2020.489
Clinical characteristics associated with COVID-19 severity in California
Journal of Clinical and Translational Science
View details for DOI 10.1017/cts.2020.40
Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity.
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.
2019; 10 (1): 2686
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 2019; 15 (5): 303–15
B cell checkpoints in autoimmune rheumatic diseases.
Nature reviews. Rheumatology
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.)
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
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
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
2018; 18 (7): 525
View details for PubMedID 30014801
- Backbone-cyclized Peptides: A Critical Review CURRENT TOPICS IN MEDICINAL CHEMISTRY 2018; 18 (7): 526-555
- Conversion of Protein Active Regions into Peptidomimetic Therapeutic Leads Using Backbone Cyclization and Cycloscan - How to Do it Yourself! CURRENT TOPICS IN MEDICINAL CHEMISTRY 2018; 18 (7): 556-565
Gravity-Drawn Silicone Filaments: Production, Characterization, and Wormlike Chain Dynamics
ACS APPLIED MATERIALS & INTERFACES
2017; 9 (46): 39916–20
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
2017; 22 (2): 454-462
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
2016; 219 (5): 676-685
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
2016; 26 (3): 199-221
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
FEDERATION AMER SOC EXP BIOL. 2014
View details for Web of Science ID 000346651003133