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1.
Cell ; 179(2): 417-431.e19, 2019 Oct 03.
Article in English | MEDLINE | ID: mdl-31585081

ABSTRACT

Severe asthma patients with low type 2 inflammation derive less clinical benefit from therapies targeting type 2 cytokines and represent an unmet need. We show that mast cell tryptase is elevated in severe asthma patients independent of type 2 biomarker status. Active ß-tryptase allele count correlates with blood tryptase levels, and asthma patients carrying more active alleles benefit less from anti-IgE treatment. We generated a noncompetitive inhibitory antibody against human ß-tryptase, which dissociates active tetramers into inactive monomers. A 2.15 Å crystal structure of a ß-tryptase/antibody complex coupled with biochemical studies reveal the molecular basis for allosteric destabilization of small and large interfaces required for tetramerization. This anti-tryptase antibody potently blocks tryptase enzymatic activity in a humanized mouse model, reducing IgE-mediated systemic anaphylaxis, and inhibits airway tryptase in Ascaris-sensitized cynomolgus monkeys with favorable pharmacokinetics. These data provide a foundation for developing anti-tryptase as a clinical therapy for severe asthma.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Asthma/therapy , Mast Cells/enzymology , Mast Cells/immunology , Tryptases/antagonists & inhibitors , Tryptases/immunology , Adolescent , Allosteric Regulation/immunology , Animals , Cell Line , Female , Humans , Macaca fascicularis , Male , Mice , Mice, Inbred BALB C , Mice, Inbred NOD , Mice, SCID , Rabbits
2.
Nat Immunol ; 20(4): 471-481, 2019 04.
Article in English | MEDLINE | ID: mdl-30778241

ABSTRACT

Foxp3+ regulatory T cells (Treg cells) are crucial for the maintenance of immune homeostasis both in lymphoid tissues and in non-lymphoid tissues. Here we demonstrate that the ability of intestinal Treg cells to constrain microbiota-dependent interleukin (IL)-17-producing helper T cell (TH17 cell) and immunoglobulin A responses critically required expression of the transcription factor c-Maf. The terminal differentiation and function of several intestinal Treg cell populations, including RORγt+ Treg cells and follicular regulatory T cells, were c-Maf dependent. c-Maf controlled Treg cell-derived IL-10 production and prevented excessive signaling via the kinases PI(3)K (phosphatidylinositol-3-OH kinase) and Akt and the metabolic checkpoint kinase complex mTORC1 (mammalian target of rapamycin) and expression of inflammatory cytokines in intestinal Treg cells. c-Maf deficiency in Treg cells led to profound dysbiosis of the intestinal microbiota, which when transferred to germ-free mice was sufficient to induce exacerbated intestinal TH17 responses, even in a c-Maf-competent environment. Thus, c-Maf acts to preserve the identity and function of intestinal Treg cells, which is essential for the establishment of host-microbe symbiosis.


Subject(s)
Immunoglobulin A/biosynthesis , Intestines/immunology , Microbiota , Proto-Oncogene Proteins c-maf/physiology , T-Lymphocytes, Regulatory/immunology , Th17 Cells/immunology , Animals , Cells, Cultured , Colitis/immunology , Cytokines/metabolism , Dysbiosis , Gene Expression Regulation , Homeostasis , Interleukin-10/biosynthesis , Mice, Inbred C57BL , Proto-Oncogene Proteins c-maf/genetics , Proto-Oncogene Proteins c-maf/metabolism , T-Lymphocytes, Regulatory/enzymology
4.
Nat Immunol ; 19(3): 246-254, 2018 03.
Article in English | MEDLINE | ID: mdl-29358708

ABSTRACT

Defective autophagy is linked to diseases such as rheumatoid arthritis, lupus and inflammatory bowel disease (IBD). However, the mechanisms by which autophagy limits inflammation remain poorly understood. Here we found that loss of the autophagy-related gene Atg16l1 promoted accumulation of the adaptor TRIF and downstream signaling in macrophages. Multiplex proteomic profiling identified SQSTM1 and Tax1BP1 as selective autophagy-related receptors that mediated the turnover of TRIF. Knockdown of Tax1bp1 increased production of the cytokines IFN-ß and IL-1ß. Mice lacking Atg16l1 in myeloid cells succumbed to lipopolysaccharide-mediated sepsis but enhanced their clearance of intestinal Salmonella typhimurium in an interferon receptor-dependent manner. Human macrophages with the Crohn's disease-associated Atg16l1 variant T300A exhibited more production of IFN-ß and IL-1ß. An elevated interferon-response gene signature was observed in patients with IBD who were resistant to treatment with an antibody to the cytokine TNF. These findings identify selective autophagy as a key regulator of signaling via the innate immune system.


Subject(s)
Adaptor Proteins, Vesicular Transport/immunology , Autophagy/immunology , Immunity, Innate/immunology , Inflammation/immunology , Animals , Autophagy-Related Proteins/genetics , Autophagy-Related Proteins/immunology , Crohn Disease/immunology , Female , Humans , Macrophages/immunology , Male , Mice , Mice, Transgenic , Signal Transduction/immunology
6.
Nat Immunol ; 18(6): 633-641, 2017 06.
Article in English | MEDLINE | ID: mdl-28459434

ABSTRACT

Microglia and other tissue-resident macrophages within the central nervous system (CNS) have essential roles in neural development, inflammation and homeostasis. However, the molecular pathways underlying their development and function remain poorly understood. Here we report that mice deficient in NRROS, a myeloid-expressed transmembrane protein in the endoplasmic reticulum, develop spontaneous neurological disorders. NRROS-deficient (Nrros-/-) mice show defects in motor functions and die before 6 months of age. Nrros-/- mice display astrogliosis and lack normal CD11bhiCD45lo microglia, but they show no detectable demyelination or neuronal loss. Instead, perivascular macrophage-like myeloid cells populate the Nrros-/- CNS. Cx3cr1-driven deletion of Nrros shows its crucial role in microglial establishment during early embryonic stages. NRROS is required for normal expression of Sall1 and other microglial genes that are important for microglial development and function. Our study reveals a NRROS-mediated pathway that controls CNS-resident macrophage development and affects neurological function.


Subject(s)
Astrocytes/metabolism , Central Nervous System/embryology , Gene Expression Regulation, Developmental , Microglia/metabolism , Myeloid Cells/metabolism , Nervous System Diseases/genetics , Proteins/genetics , Animals , Astrocytes/cytology , Blotting, Western , Central Nervous System/cytology , Flow Cytometry , Immunohistochemistry , Lameness, Animal/genetics , Latent TGF-beta Binding Proteins , Locomotion , Macrophages/cytology , Macrophages/metabolism , Membrane Proteins , Mice , Mice, Knockout , Microglia/cytology , Myeloid Cells/cytology , Posture , Transcription Factors/genetics , Urinary Incontinence/genetics , Urinary Retention/genetics
7.
Nat Immunol ; 15(2): 161-7, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24362890

ABSTRACT

CD11b(+) dendritic cells (DCs) seem to be specialized for presenting antigens via major histocompatibility (MHC) class II complexes to stimulate helper T cells, but the genetic and regulatory basis for this is not established. Conditional deletion of Irf4 resulted in loss of CD11b(+) DCs, impaired formation of peptide-MHC class II complexes and defective priming of helper T cells but not of cytotoxic T lymphocyte (CTL) responses. Gene expression and chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analyses delineated an IRF4-dependent regulatory module that programs enhanced MHC class II antigen presentation. Expression of the transcription factor IRF4 but not of IRF8 restored the ability of IRF4-deficient DCs to efficiently process and present antigen to MHC class II-restricted T cells and promote helper T cell responses. We propose that the evolutionary divergence of IRF4 and IRF8 facilitated the specialization of DC subsets for distinct modes of antigen presentation and priming of helper T cell versus CTL responses.


Subject(s)
Antigen Presentation/genetics , Dendritic Cells/immunology , Histocompatibility Antigens Class II/immunology , Interferon Regulatory Factors/metabolism , T-Lymphocytes, Cytotoxic/immunology , T-Lymphocytes, Helper-Inducer/immunology , Animals , Cell Differentiation/genetics , Cell Differentiation/immunology , Cells, Cultured , Gene Expression Profiling , Gene Expression Regulation/genetics , Gene Expression Regulation/immunology , Histocompatibility Antigens Class II/genetics , Interferon Regulatory Factors/genetics , Lymphocyte Activation/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , Protein Binding/genetics , Transgenes/genetics
8.
Nat Immunol ; 12(12): 1238-45, 2011 Oct 16.
Article in English | MEDLINE | ID: mdl-22001828

ABSTRACT

Interleukin 22 (IL-22), which is produced by cells of the T(H)17 subset of helper T cells and other leukocytes, not only enhances proinflammatory innate defense mechanisms in epithelial cells but also provides crucial protection to tissues from damage caused by inflammation and infection. In T(H)17 cells, transforming growth factor-ß (TGF-ß) regulates IL-22 and IL-17 differently. IL-6 alone induces T cells to produce only IL-22, whereas the combination of IL-6 and high concentrations of TGF-ß results in the production of IL-17 but not IL-22 by T cells. Here we identify the transcription factor c-Maf, which is induced by TGF-ß, as a downstream repressor of Il22. We found that c-Maf bound to the Il22 promoter and was both necessary and sufficient for the TGF-ß-dependent suppression of IL-22 production in T(H)17 cells.


Subject(s)
Interleukins/biosynthesis , Proto-Oncogene Proteins c-maf/metabolism , Th17 Cells/immunology , Transforming Growth Factor beta/pharmacology , Animals , Base Sequence , Basic-Leucine Zipper Transcription Factors/genetics , Basic-Leucine Zipper Transcription Factors/metabolism , Binding Sites/genetics , Cells, Cultured , Gene Expression Profiling , Gene Expression Regulation/drug effects , HEK293 Cells , Humans , Interleukins/genetics , Mice , Mice, Inbred BALB C , Nuclear Receptor Subfamily 1, Group F, Member 3/genetics , Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism , Nucleotide Motifs , Promoter Regions, Genetic , Proto-Oncogene Proteins c-maf/genetics , Receptors, Aryl Hydrocarbon/genetics , Receptors, Aryl Hydrocarbon/metabolism , Th17 Cells/drug effects , Transcription, Genetic , Interleukin-22
9.
Nat Immunol ; 12(12): 1159-66, 2011 Oct 12.
Article in English | MEDLINE | ID: mdl-21993848

ABSTRACT

Interleukin 17C (IL-17C) is a member of the IL-17 family that is selectively induced in epithelia by bacterial challenge and inflammatory stimuli. Here we show that IL-17C functioned in a unique autocrine manner, binding to a receptor complex consisting of the receptors IL-17RA and IL-17RE, which was preferentially expressed on tissue epithelial cells. IL-17C stimulated epithelial inflammatory responses, including the expression of proinflammatory cytokines, chemokines and antimicrobial peptides, which were similar to those induced by IL-17A and IL-17F. However, IL-17C was produced by distinct cellular sources, such as epithelial cells, in contrast to IL-17A, which was produced mainly by leukocytes, especially those of the T(H)17 subset of helper T cells. Whereas IL-17C promoted inflammation in an imiquimod-induced skin-inflammation model, it exerted protective functions in dextran sodium sulfate-induced colitis. Thus, IL-17C is an essential autocrine cytokine that regulates innate epithelial immune responses.


Subject(s)
Autocrine Communication , Epithelial Cells/immunology , Immunity, Innate/immunology , Interleukin-17/metabolism , Animals , Cell Line , Colitis/chemically induced , Colitis/metabolism , Colitis/pathology , Epithelial Cells/metabolism , Gene Expression Profiling , HEK293 Cells , Humans , Inflammation/immunology , Inflammation/microbiology , Intestinal Mucosa/immunology , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Leukocytes/immunology , Leukocytes/metabolism , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Knockout , Phenotype , Protein Binding , Receptors, Interleukin-17/metabolism , Respiratory Mucosa/immunology , Respiratory Mucosa/metabolism , Respiratory Mucosa/microbiology , Signal Transduction , Skin/immunology , Skin/metabolism , Skin/pathology
10.
J Immunol ; 207(9): 2245-2254, 2021 11 01.
Article in English | MEDLINE | ID: mdl-34561227

ABSTRACT

Targeting interactions between α4ß7 integrin and endothelial adhesion molecule MAdCAM-1 to inhibit lymphocyte migration to the gastrointestinal tract is an effective therapy in inflammatory bowel disease (IBD). Following lymphocyte entry into the mucosa, a subset of these cells expresses αEß7 integrin, which is expressed on proinflammatory lymphocytes, to increase cell retention. The factors governing lymphocyte migration into the intestinal mucosa and αE integrin expression in healthy subjects and IBD patients remain incompletely understood. We evaluated changes in factors involved in lymphocyte migration and differentiation within tissues. Both ileal and colonic tissue from active IBD patients showed upregulation of ICAM-1, VCAM-1, and MAdCAM-1 at the gene and protein levels compared with healthy subjects and/or inactive IBD patients. ß1 and ß7 integrin expression on circulating lymphocytes was similar across groups. TGF-ß1 treatment induced expression of αE on both ß7+ and ß7- T cells, suggesting that cells entering the mucosa independently of MAdCAM-1/α4ß7 can become αEß7+ ITGAE gene polymorphisms did not alter protein induction following TGF-ß1 stimulation. Increased phospho-SMAD3, which is directly downstream of TGF-ß, and increased TGF-ß-responsive gene expression were observed in the colonic mucosa of IBD patients. Finally, in vitro stimulation experiments showed that baseline ß7 expression had little effect on cytokine, chemokine, transcription factor, and effector molecule gene expression in αE+ and αE- T cells. These findings suggest cell migration to the gut mucosa may be altered in IBD and α4ß7-, and α4ß7+ T cells may upregulate αEß7 in response to TGF-ß once within the gut mucosa.


Subject(s)
Antigens, CD/metabolism , Inflammatory Bowel Diseases/immunology , Integrin alpha Chains/metabolism , Integrin beta Chains/metabolism , Intestinal Mucosa/immunology , Receptors, Lymphocyte Homing/metabolism , T-Lymphocytes/immunology , Adult , Aged , Cell Movement , Female , Humans , Integrin beta Chains/genetics , Male , Middle Aged , Signal Transduction , Smad3 Protein/metabolism , Transforming Growth Factor beta1/metabolism
11.
J Immunol ; 202(7): 1935-1941, 2019 04 01.
Article in English | MEDLINE | ID: mdl-30770417

ABSTRACT

IL-17 family cytokines are critical to host defense responses at cutaneous and mucosal surfaces. Whereas IL-17A, IL-17F, and IL-17C induce overlapping inflammatory cascades to promote neutrophil-mediated immunity, IL-17E/IL-25 drives type 2 immune pathways and eosinophil activity. Genetic and pharmacological studies reveal the significant contribution these cytokines play in antimicrobial and autoimmune mechanisms. However, little is known about the related family member, IL-17B, with contrasting reports of both pro- and anti-inflammatory function in rodents. We demonstrate that in the human immune system, IL-17B is functionally similar to IL-25 and elicits type 2 cytokine secretion from innate type 2 lymphocytes, NKT, and CD4+ CRTH2+ Th2 cells. Like IL-25, this activity is dependent on the IL-17RA and IL-17RB receptor subunits. Furthermore, IL-17B can augment IL-33-driven type 2 responses. These data position IL-17B as a novel component in the regulation of human type 2 immunity.


Subject(s)
Immunity, Innate/immunology , Interleukin-17/immunology , Receptors, Interleukin-17/immunology , T-Lymphocyte Subsets/immunology , Humans , Inflammation/immunology
12.
J Immunol ; 202(4): 1069-1078, 2019 02 15.
Article in English | MEDLINE | ID: mdl-30659109

ABSTRACT

Genetic variants in C5orf30 have been associated with development of the autoimmune conditions primary biliary cirrhosis and rheumatoid arthritis. In rheumatoid arthritis, C5orf30 expression is cell-specific, with highest expression found in macrophages and synovial fibroblasts. C5orf30 is highly expressed in inflamed joints and is a negative regulator of tissue damage in a mouse model of inflammatory arthritis. Transcriptomic analysis from ultrasound-guided synovial biopsy of inflamed joints in a well characterized clinical cohort of newly diagnosed, disease-modifying antirheumatic drugs-naive rheumatoid arthritis patients was used to determine the clinical association of C5orf30 expression with disease activity. A combined molecular and computational biology approach was used to elucidate C5orf30 function in macrophages both in vitro and in vivo. Synovial expression of C5orf30 is inversely correlated with both clinical measures of rheumatoid arthritis disease activity and with synovial TNF mRNA expression. C5orf30 plays a role in regulating macrophage phenotype and is differentially turned over in inflammatory and anti-inflammatory macrophages. Inhibition of C5orf30 reduces wound healing/repair-associated functions of macrophages, reduces signaling required for resolution of inflammation, and decreases secretion of anti-inflammatory mediators. In an animal model of wound healing (zebrafish), C5orf30 inhibition increases the recruitment of macrophages to the wound site. Finally, we demonstrate that C5orf30 skews macrophage immunometabolism, demonstrating a mechanism for C5orf30-mediated immune regulation.


Subject(s)
Arthritis, Rheumatoid/immunology , Carrier Proteins/genetics , Inflammation/immunology , Macrophages/immunology , Animals , Antirheumatic Agents/pharmacology , Arthritis, Rheumatoid/diagnosis , Arthritis, Rheumatoid/drug therapy , Carrier Proteins/antagonists & inhibitors , Cells, Cultured , Cohort Studies , Humans , Inflammation/diagnosis , Inflammation/drug therapy , Inflammation/genetics , Macrophages/drug effects , Phosphoproteins , Wound Healing/drug effects , Wound Healing/immunology , Zebrafish
13.
Int J Mol Sci ; 22(15)2021 Jul 30.
Article in English | MEDLINE | ID: mdl-34360971

ABSTRACT

Interleukin-22 (IL-22) plays a role in epithelial barrier function and repair, and may provide benefits in conditions like inflammatory bowel disease. However, limited human data are available to assess the clinical effect of IL-22 administration. This study used a human intestinal cell line to identify an IL-22-dependent gene signature that could serve as a pharmacodynamic biomarker for IL-22 therapy. The response to IL-22Fc (UTTR1147A, an Fc-stabilized version of IL-22) was assessed in HT-29 cells by microarray, and the selected responsive genes were confirmed by qPCR. HT-29 cells demonstrated dose-dependent increases in STAT3 phosphorylation and multiple gene expression changes in response to UTTR1147A. Genes were selected that were upregulated by UTTR1147A, but to a lesser extent by IL-6, which also signals via STAT3. IL-1R1 was highly upregulated by UTTR1147A, and differential gene expression patterns were observed in response to IL-22Fc in the presence of IL-1ß. An IL-22-dependent gene signature was identified that could serve as a pharmacodynamic biomarker in intestinal biopsies to support the clinical development of an IL-22 therapeutic. The differential gene expression pattern in the presence of IL-1ß suggests that an inflammatory cytokine milieu in the disease setting could influence the clinical responses to IL-22.


Subject(s)
Anti-Inflammatory Agents/pharmacology , Immunoglobulin G/genetics , Inflammatory Bowel Diseases/metabolism , Interleukins/genetics , Transcriptome/drug effects , Biomarkers/metabolism , HT29 Cells , Humans , Immunoglobulin G/metabolism , Interleukins/metabolism , Receptors, Interleukin-1/genetics , Receptors, Interleukin-1/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/pharmacology , STAT3 Transcription Factor/metabolism , Interleukin-22
14.
Nature ; 509(7499): 235-9, 2014 May 08.
Article in English | MEDLINE | ID: mdl-24739962

ABSTRACT

Reactive oxygen species (ROS) produced by phagocytes are essential for host defence against bacterial and fungal infections. Individuals with defective ROS production machinery develop chronic granulomatous disease. Conversely, excessive ROS can cause collateral tissue damage during inflammatory processes and therefore needs to be tightly regulated. Here we describe a protein, we termed negative regulator of ROS (NRROS), which limits ROS generation by phagocytes during inflammatory responses. NRROS expression in phagocytes can be repressed by inflammatory signals. NRROS-deficient phagocytes produce increased ROS upon inflammatory challenges, and mice lacking NRROS in their phagocytes show enhanced bactericidal activity against Escherichia coli and Listeria monocytogenes. Conversely, these mice develop severe experimental autoimmune encephalomyelitis owing to oxidative tissue damage in the central nervous system. Mechanistically, NRROS is localized to the endoplasmic reticulum, where it directly interacts with nascent NOX2 (also known as gp91(phox) and encoded by Cybb) monomer, one of the membrane-bound subunits of the NADPH oxidase complex, and facilitates the degradation of NOX2 through the endoplasmic-reticulum-associated degradation pathway. Thus, NRROS provides a hitherto undefined mechanism for regulating ROS production--one that enables phagocytes to produce higher amounts of ROS, if required to control invading pathogens, while minimizing unwanted collateral tissue damage.


Subject(s)
Encephalomyelitis, Autoimmune, Experimental/immunology , Encephalomyelitis, Autoimmune, Experimental/metabolism , Escherichia coli/immunology , Listeria monocytogenes/immunology , Proteins/metabolism , Reactive Oxygen Species/antagonists & inhibitors , Animals , Autoimmunity/genetics , Bone Marrow Cells/cytology , Central Nervous System/metabolism , Central Nervous System/pathology , Encephalomyelitis, Autoimmune, Experimental/pathology , Endoplasmic Reticulum/enzymology , Endoplasmic Reticulum/metabolism , Female , Inflammation/immunology , Inflammation/metabolism , Inflammation/pathology , Latent TGF-beta Binding Proteins , Macrophages/cytology , Macrophages/enzymology , Macrophages/immunology , Macrophages/metabolism , Male , Membrane Proteins , Mice , NADPH Oxidases/metabolism , Oxidation-Reduction , Oxidative Stress , Phagocytes/cytology , Phagocytes/immunology , Phagocytes/metabolism , Proteins/genetics , Reactive Oxygen Species/metabolism
15.
Ann Rheum Dis ; 78(12): 1642-1652, 2019 12.
Article in English | MEDLINE | ID: mdl-31582377

ABSTRACT

OBJECTIVE: To establish whether synovial pathobiology improves current clinical classification and prognostic algorithms in early inflammatory arthritis and identify predictors of subsequent biological therapy requirement. METHODS: 200 treatment-naïve patients with early arthritis were classified as fulfilling RA1987 American College of Rheumatology (ACR) criteria (RA1987) or as undifferentiated arthritis (UA) and patients with UA further classified into those fulfilling RA2010 ACR/European League Against Rheumatism (EULAR) criteria. Treatment requirements at 12 months (Conventional Synthetic Disease Modifying Antirheumatic Drugs (csDMARDs) vs biologics vs no-csDMARDs treatment) were determined. Synovial tissue was retrieved by minimally invasive, ultrasound-guided biopsy and underwent processing for immunohistochemical (IHC) and molecular characterisation. Samples were analysed for macrophage, plasma-cell and B-cells and T-cells markers, pathotype classification (lympho-myeloid, diffuse-myeloid or pauci-immune) by IHC and gene expression profiling by Nanostring. RESULTS: 128/200 patients were classified as RA1987, 25 as RA2010 and 47 as UA. Patients classified as RA1987 criteria had significantly higher levels of disease activity, histological synovitis, degree of immune cell infiltration and differential upregulation of genes involved in B and T cell activation/function compared with RA2010 or UA, which shared similar clinical and pathobiological features. At 12-month follow-up, a significantly higher proportion of patients classified as lympho-myeloid pathotype required biological therapy. Performance of a clinical prediction model for biological therapy requirement was improved by the integration of synovial pathobiological markers from 78.8% to 89%-90%. CONCLUSION: The capacity to refine early clinical classification criteria through synovial pathobiological markers offers the potential to predict disease outcome and stratify therapeutic intervention to patients most in need.


Subject(s)
Algorithms , Arthritis, Rheumatoid/therapy , Biological Therapy/methods , Synovial Membrane/diagnostic imaging , Antirheumatic Agents/therapeutic use , Arthritis, Rheumatoid/classification , Arthritis, Rheumatoid/diagnosis , Disease Progression , Female , Humans , Image-Guided Biopsy , Male , Middle Aged , Prognosis , Prospective Studies , Severity of Illness Index , Synovial Membrane/metabolism , Ultrasonography
16.
Ann Rheum Dis ; 78(6): 761-772, 2019 06.
Article in English | MEDLINE | ID: mdl-30878974

ABSTRACT

OBJECTIVES: To unravel the hierarchy of cellular/molecular pathways in the disease tissue of early, treatment-naïve rheumatoid arthritis (RA) patients and determine their relationship with clinical phenotypes and treatment response/outcomes longitudinally. METHODS: 144 consecutive treatment-naïve early RA patients (<12 months symptoms duration) underwent ultrasound-guided synovial biopsy before and 6 months after disease-modifying antirheumatic drug (DMARD) initiation. Synovial biopsies were analysed for cellular (immunohistology) and molecular (NanoString) characteristics and results compared with clinical and imaging outcomes. Differential gene expression analysis and logistic regression were applied to define variables correlating with treatment response and predicting radiographic progression. RESULTS: Cellular and molecular analyses of synovial tissue demonstrated for the first time in early RA the presence of three pathology groups: (1) lympho-myeloid dominated by the presence of B cells in addition to myeloid cells; (2) diffuse-myeloid with myeloid lineage predominance but poor in B cells nd (3) pauci-immune characterised by scanty immune cells and prevalent stromal cells. Longitudinal correlation of molecular signatures demonstrated that elevation of myeloid- and lymphoid-associated gene expression strongly correlated with disease activity, acute phase reactants and DMARD response at 6 months. Furthermore, elevation of synovial lymphoid-associated genes correlated with autoantibody positivity and elevation of osteoclast-targeting genes predicting radiographic joint damage progression at 12 months. Patients with predominant pauci-immune pathology showed less severe disease activity and radiographic progression. CONCLUSIONS: We demonstrate at disease presentation, prior to pathology modulation by therapy, the presence of specific cellular/molecular synovial signatures that delineate disease severity/progression and therapeutic response and may pave the way to more precise definition of RA taxonomy, therapeutic targeting and improved outcomes.


Subject(s)
Antirheumatic Agents/therapeutic use , Arthritis, Rheumatoid/drug therapy , Synovial Membrane/pathology , Adult , Aged , Arthritis, Rheumatoid/diagnostic imaging , Arthritis, Rheumatoid/metabolism , Arthritis, Rheumatoid/pathology , Biomarkers/blood , Biopsy , Disease Progression , Female , Gene Expression Regulation , Humans , Longitudinal Studies , Male , Middle Aged , Phenotype , Prognosis , Radiography , Severity of Illness Index , Synovial Membrane/metabolism , Synovial Membrane/physiopathology , Transcriptome , Ultrasonography, Interventional/methods
17.
Gastroenterology ; 150(2): 477-87.e9, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26522261

ABSTRACT

BACKGROUND & AIMS: Etrolizumab is a humanized monoclonal antibody against the ß7 integrin subunit that has shown efficacy vs placebo in patients with moderate to severely active ulcerative colitis (UC). Patients with colon tissues that expressed high levels of the integrin αE gene (ITGAE) appeared to have the best response. We compared differences in colonic expression of ITGAE and other genes between patients who achieved clinical remission with etrolizumab vs those who did. METHODS: We performed a retrospective analysis of data collected from 110 patients with UC who participated in a phase 2 placebo-controlled trial of etrolizumab, as well as from 21 patients with UC or without inflammatory bowel disease (controls) enrolled in an observational study at a separate site. Colon biopsies were collected from patients in both studies and analyzed by immunohistochemistry and gene expression profiling. Mononuclear cells were isolated and analyzed by flow cytometry. We identified biomarkers associated with response to etrolizumab. In the placebo-controlled trial, clinical remission was defined as total Mayo Clinic Score ≤2, with no individual subscore >1, and mucosal healing was defined as endoscopic score ≤1. RESULTS: Colon tissues collected at baseline from patients who had a clinical response to etrolizumab expressed higher levels of T-cell-associated genes than patients who did not respond (P < .05). Colonic CD4(+) integrin αE(+) cells from patients with UC expressed higher levels of granzyme A messenger RNA (GZMA mRNA) than CD4(+) αE(-) cells (P < .0001); granzyme A and integrin αE protein were detected in the same cells. Of patients receiving 100 mg etrolizumab, a higher proportion of those with high levels of GZMA mRNA (41%) or ITGAE mRNA (38%) than those with low levels of GZMA (6%) or ITGAE mRNA (13%) achieved clinical remission (P < .05) and mucosal healing (41% GZMA(high) vs 19% GZMA(low) and 44% ITGAE(high) vs 19% ITGAE(low)). Compared with ITGAE(low) and GZMA(low) patients, patients with ITGAE(high) and GZMA(high) had higher baseline numbers of epithelial crypt-associated integrin αE(+) cells (P < .01 for both), but a smaller number of crypt-associated integrin αE(+) cells after etrolizumab treatment (P < .05 for both). After 10 weeks of etrolizumab treatment, expression of genes associated with T-cell activation and genes encoding inflammatory cytokines decreased by 40%-80% from baseline (P < .05) in patients with colon tissues expressing high levels of GZMA at baseline. CONCLUSIONS: Levels of GZMA and ITGAE mRNAs in colon tissues can identify patients with UC who are most likely to benefit from etrolizumab; expression levels decrease with etrolizumab administration in biomarker(high) patients. Larger, prospective studies of markers are needed to assess their clinical value.


Subject(s)
Anti-Inflammatory Agents/therapeutic use , Antibodies, Monoclonal, Humanized/therapeutic use , Antigens, CD/metabolism , Colitis, Ulcerative/drug therapy , Colon/drug effects , Gastrointestinal Agents/therapeutic use , Granzymes/metabolism , Integrin alpha Chains/metabolism , Antigens, CD/genetics , Biopsy , Clinical Trials, Phase II as Topic , Colitis, Ulcerative/diagnosis , Colitis, Ulcerative/enzymology , Colitis, Ulcerative/genetics , Colon/enzymology , Colon/pathology , Gene Expression Profiling/methods , Granzymes/genetics , Humans , Immunohistochemistry , Integrin alpha Chains/genetics , Predictive Value of Tests , RNA, Messenger/metabolism , Randomized Controlled Trials as Topic , Remission Induction , Retrospective Studies , Time Factors , Treatment Outcome , Wound Healing/drug effects
18.
Bioinformatics ; 29(24): 3220-1, 2013 Dec 15.
Article in English | MEDLINE | ID: mdl-24078713

ABSTRACT

UNLABELLED: It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. AVAILABILITY: The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.


Subject(s)
Computational Biology , Gene Expression Profiling/methods , Genomics/methods , High-Throughput Nucleotide Sequencing , Software , Algorithms , Databases, Factual
19.
PLoS One ; 19(2): e0291947, 2024.
Article in English | MEDLINE | ID: mdl-38335181

ABSTRACT

Tryptase, the most abundant mast cell granule protein, is elevated in severe asthma patients independent of type 2 inflammation status. Higher active ß tryptase allele counts are associated with higher levels of peripheral tryptase and lower clinical benefit from anti-IgE therapies. Tryptase is a therapeutic target of interest in severe asthma and chronic spontaneous urticaria. Active and inactive allele counts may enable stratification to assess response to therapies in asthmatic patient subpopulations. Tryptase gene loci TPSAB1 and TPSB2 have high levels of sequence identity, which makes genotyping a challenging task. Here, we report a targeted next-generation sequencing (NGS) assay and downstream bioinformatics analysis for determining polymorphisms at tryptase TPSAB1 and TPSB2 loci. Machine learning modeling using multiple polymorphisms in the tryptase loci was used to improve the accuracy of genotyping calls. The assay was tested and qualified on DNA extracted from whole blood of healthy donors and asthma patients, achieving accuracy of 96%, 96% and 94% for estimation of inactive α and ßΙΙΙFS tryptase alleles and α duplication on TPSAB1, respectively. The reported NGS assay is a cost-effective method that is more efficient than Sanger sequencing and provides coverage to evaluate known as well as unreported tryptase polymorphisms.


Subject(s)
Asthma , Mast Cells , Humans , Tryptases/genetics , Tryptases/metabolism , Mast Cells/metabolism , Genotype , Asthma/drug therapy , Asthma/genetics , High-Throughput Nucleotide Sequencing
20.
Proteomics Clin Appl ; : e2300075, 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38552248

ABSTRACT

PURPOSE: Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), is characterized by chronic gastrointestinal inflammation. A high unmet need exists for noninvasive biomarkers in IBD to monitor changes in disease activity and guide treatment decisions. Stool is an easily accessed, disease proximal matrix in IBD, however the composition of the IBD fecal proteome remains poorly characterized. EXPERIMENTAL DESIGN: A data-independent acquisition LC-MS/MS approach was used to profile the human fecal proteome in two independent cohorts (Cohort 1: healthy n = 5, UC n = 5, CD n = 5, Cohort 2: healthy n = 20, UC n = 10, and CD n = 10) to identify noninvasive biomarkers reflective of disease activity. RESULTS: 688 human proteins were quantified, with 523 measured in both cohorts. In UC stool 96 proteins were differentially abundant and in CD stool 126 proteins were differentially abundant compared to healthy stool (absolute log2 fold change > 1, p-value < 0.05). Many of these fecal proteins are associated with infiltrating immune cells and ulceration/rectal bleeding, which are hallmarks of IBD pathobiology. Mapping the identified fecal proteins to a whole blood single-cell RNA sequencing data set revealed the involvement of various immune cell subsets to the IBD fecal proteome. CONCLUSIONS AND CLINICAL RELEVANCE: Findings from this study not only confirmed the presence of established fecal biomarkers for IBD, such as calprotectin and lactoferrin, but also revealed new fecal proteins from multiple pathways known to be dysregulated in IBD. These novel proteins could serve as potential noninvasive biomarkers to monitor specific aspects of IBD disease activity which could expedite clinical development of novel therapeutic targets.

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