Textbook of autoinflammation

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Preface Contents Part I: Introduction 1: Autoinflammation: Past, Present, and Future 1.1 ‘Ancient’ History 1.1.1 First Discoveries: The Birth of Autoinflammation 1.2 The ‘Eureka’ Decade 1.2.1 Expanding the Discovery of Diseases Caused by Genetic Mutations 1.2.2 Early Thoughts on Pathophysiologic Mechanisms 1.3 Horror Autoinflammaticus: The Golden Age of Autoinflammation 1.3.1 New Discoveries of Rare Mongenic Autoinflammatory Diseases 1.3.2 Expanded Understanding of Disease Pathophysiology Related to the Innate Immune System and Novel Genetic Mechanisms 1.3.3 Expansion of Autoinflammation to Non-monogenic and Common Diseases 1.4 Nomenclature of the Autoinflammatory Diseases 1.5 Quō vādis? Autoinflammation and the Human Condition 1.6 Questions for the Next Decade References Part II: Basic Science and Biology of Autoinflammation 2: Genetic Aspects of Investigating and Understanding Autoinflammation 2.1 Introduction 2.2 Autoinflammatory Diseases: Approaches to Gene Identification 2.2.1 Experimental Methods Used in the Pre-NGS Era 2.2.2 DNA Sequencing: The Sanger Method 2.2.3 DNA Sequencing: The NGS Method 2.2.4 NGS-Based Techniques for New Gene Discovery 2.3 Autoinflammatory Diseases: Approaches to Molecular Genetic Diagnosis 2.3.1 NGS-Based Gene Panels 2.3.2 Other Approaches Employed in Patients with Autoinflammatory Disorders 2.3.2.1 Array-Comparative Genomic Hybridization (aCGH) 2.3.2.2 Real-Time Polymerase Chain Reaction (PCR) 2.3.2.3 Gene Expression in Autoinflammatory Disease 2.4 Gene Mosaicism 2.4.1 Germline and Post-zygotic Mutations 2.4.2 Tissue Distribution of Gene Mosaicism 2.4.3 State of the Art in Monogenic Autoinflammatory Diseases 2.4.3.1 Somatic NLRP3 Mosaicism in Cryopyrin-Associated Periodic Syndromes (CAPS) Myeloid-Restricted Somatic NLRP3 Mosaicism Localization of Post-zygotic Mutations in the NLRP3 Gene 2.4.3.2 Somatic Mosaicism in Other Monogenic Autoinflammatory Diseases 2.4.3.3 Gonadal and Gonosomal Gene Mosaicism 2.4.4 Conclusions on Genetic Mosaicism References 3: Epigenetics in Autoinflammation 3.1 Introduction 3.2 Epigenetic Control in Immune Cells 3.2.1 DNA Methylation and Histone Modifications 3.2.2 Epigenetic Control of Differentiation of Hematopoietic Stem Cells 3.3 Epigenetic Control in Inflammation 3.4 Perspectives on Autoinflammatory Diseases 3.4.1 Cryopyrin-Associated Periodic Syndromes (CAPS) 3.4.2 Familial Mediterranean Fever (FMF) 3.4.3 Mevalonate Kinase Deficiency (MKD) 3.4.4 Behçet Disease 3.4.5 Chronic Non-bacterial Osteomyelitis (CNO) 3.4.6 Crohn Disease 3.5 Conclusions References 4: Pattern Recognition Receptors in Autoinflammation 4.1 Introduction: Molecular Patterns and Processes 4.1.1 Pathogen-Associated Molecular Patterns (PAMPs) 4.1.2 Damage- or Danger-Associated Molecular Patterns (DAMPs) 4.1.3 Homeostasis-Altering Molecular Processes (HAMPs) 4.2 Toll Like Receptors (TLRs) 4.2.1 TLRs 1, 2, 6, 10 4.2.2 TLR4 4.2.3 TLR5 4.2.4 TLR3 4.2.5 TLRs 7, 8, 9 4.3 NOD-Like Receptors (NLRs) 4.3.1 NOD1 4.3.2 NOD2 4.4 Other Pattern Recognition Receptors (PRRs) 4.4.1 RIG-I Like Receptors (RLRs) 4.4.2 C-Type Lectin Receptors (CLRs) 4.4.3 Absent in Melanoma 2 (AIM2) 4.4.4 cGAMP Synthase (cGAS) and Stimulator of Interferon Genes (STING) 4.4.5 Non-canonical Inflammasome 4.5 Conclusion References 5: Inflammasomes and Autoinflammation 5.1 Introduction 5.2 The Inflammasome 5.2.1 Assembly of the Inflammasome 5.2.1.1 Apoptosis-Associated Speck-Like Protein with a CARD (ASC) 5.2.1.2 Caspase-1 Caspase-1 in Cytokine Release Caspase-1 in Pyroptosis Additional Roles for Caspase-1 5.2.1.3 Inflammasomes as DAMPs 5.2.1.4 Inflammasome Triggers: An Overview 5.2.1.5 Inflammasome Regulation 5.2.1.6 Non-canonical Inflammasomes 5.3 Individual Inflammasomes 5.3.1 NLRP1 5.3.1.1 Regulation of NLRP1 5.3.1.2 Activators of NLRP1 5.3.1.3 NLRP1 in Autoinflammatory Disease 5.3.2 NLRP3 5.3.2.1 Regulation of NLRP3 5.3.2.2 Activators of NLRP3 5.3.2.3 NLRP3 in Autoinflammatory Disease 5.3.3 Pyrin 5.3.3.1 Activation of Pyrin 5.3.3.2 Regulation of Pyrin 5.3.3.3 Pyrin in Autoinflammatory Disease 5.3.4 NLRC4 5.3.4.1 NLRC4 in Disease 5.4 Other Inflammasomes 5.4.1 NLRP6 5.4.1.1 NLRP6 in Autoinflammatory Disease 5.4.2 NLRP7 5.4.2.1 Regulation of NLRP7 5.4.2.2 NLRP7 Triggers 5.4.2.3 NLRP7 in Disease 5.4.3 NLRP12 5.4.3.1 NLRP12 in Disease 5.4.4 Absent in Melanoma 2 (AIM2) 5.4.4.1 AIM2 in Disease 5.5 Summary References 6: Cytokines in Autoinflammation 6.1 Introduction 6.2 The Interleukin (IL)-1 Family 6.2.1 Processing of IL-1F Cytokines: Canonical and Non-canonical Inflammasome Activation 6.2.1.1 Canonical Inflammasomes 6.2.1.2 Non-canonical Inflammasome 6.2.2 Secretion of IL-1F Cytokines 6.2.2.1 Secretory Mechanisms for IL-1β (and IL-18) Vesicle Mediated Secretion Direct Transport Across the Plasma Membrane 6.2.2.2 IL-1α and IL-33 Extracellular Release 6.2.3 IL-1F Member-Linked Autoinflammatory Diseases 6.2.3.1 IL-1-Mediated Autoinflammatory Diseases Cryopyrin-Associated Periodic Syndromes (CAPS) Deficiency of IL-1Ra (DIRA) IL-1α in Autoinflammatory Diseases 6.2.3.2 IL-18 in Autoinflammatory Diseases 6.2.3.3 Deficiency of IL-36 Receptor Antagonist (DITRA) 6.2.4 Role of Stress in Autoinflammatory Diseases Mediated by IL-1F Members 6.3 Type I Interferons 6.3.1 Diseases Associated with Elevated Type I Interferons References 7: Proteasomes in Autoinflammation 7.1 Concept of Protein Homeostasis and Its Importance in Preserving Cell Function and Integrity 7.1.1 The Ubiquitin-Proteasome System 7.1.2 Structure of the Proteasome 7.1.3 Proteasome Assembly 7.1.4 Alternative Proteasomes 7.1.5 Further Sources of Proteasome Substrates 7.2 Protein Homeostasis Perturbations 7.2.1 Physiological Perturbations 7.2.2 Pathological Protein Homeostasis Perturbations 7.3 Cellular Responses to Unbalanced Protein Homeostasis 7.3.1 The Unfolded Protein Response 7.3.2 Cellular Responses to Proteasome Inhibition References 8: Disruption of Protein Homeostasis and Activation of Cellular Stress Pathways in Autoinflammation 8.1 Cellular Mechanisms Maintaining Protein Homeostasis and Links to Inflammation Biology 8.1.1 The Proteasome 8.1.2 Autophagy 8.2 Protein Homeostasis in the Pathogenesis and Regulation of Monogenic Autoinflammatory Diseases 8.2.1 Degradation of Inflammasomes Through Autophagy (Fig. 8.2) 8.2.2 Regulation of Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthetase (cGAS) and Stimulator of Interferon Genes-(STING) Pathway by Autophagy 8.2.3 Accumulation of Misfolded Mutated Proteins 8.3 Alteration in Protein Homeostasis Mechanisms and Triggering of Inflammatory Responses by Misfolded Proteins in Complex Diseases 8.3.1 Defects in the Autophagy Pathway 8.3.2 Accumulation of Intracellular Misfolded Proteins (Fig. 8.2) 8.3.3 Accumulation of Extracellular Misfolded Proteins 8.4 Targeting Protein Homeostasis for the Therapy of Autoinflammatory Diseases: Future Perspectives References 9: S100 Proteins in Autoinflammation 9.1 Functions of Phagocyte-Specific S100 Proteins 9.1.1 Intracellular Functions 9.1.2 Release from Phagocytes 9.1.3 Extracellular Functions 9.1.4 Function as Danger Associated Molecular Pattern (DAMP) 9.2 S100 Proteins in Autoinflammatory Diseases 9.2.1 Monogenic Autoinflammatory Syndromes 9.2.1.1 Familial Mediterranean Fever (FMF) 9.2.1.2 PSTPIP1 Associated Inflammatory Diseases (PAID) 9.2.1.3 Cryopyrin-Associated Periodic Syndromes (CAPS) 9.2.2 Polygenic Autoinflammatory Diseases 9.2.2.1 Systemic Juvenile Idiopathic Arthritis (SJIA) 9.2.2.2 Periodic Fever, Aphthous Stomatitis, Pharyngitis, Cervical Adenitis (PFAPA) Syndrome 9.3 S100 Proteins in Clinical Practice 9.3.1 Use as Biomarkers 9.3.2 Differential Diagnosis of Fever of Unknown Origin (FUO) 9.3.3 Monitoring Therapies 9.3.4 Prediction of Relapses References Part III: General Approach to Autoinflammatory Diseases 10: Classification of Genetically Defined Autoinflammatory Diseases 10.1 Introduction 10.2 Clinical Classification of Autoinflammatory Diseases 10.2.1 Group 1. Recurrent/Episodic Fever and Abdominal Pain with Absence or Sporadic Presence of Maculopapular Rashes (Hereditary Periodic Fever Syndromes) 10.2.1.1 Recurrent Fever Attacks of Short Duration (Typically ≤7 days) Familial Mediterranean Fever (FMF) Hyperimmunoglobulinemia D with Periodic Fever Syndrome (HIDS)/Mevalonate Kinase Deficiency (MKD) 10.2.1.2 Recurrent Fever Attacks with Longer Duration (Typically >7 days) TNF Receptor-Associated Periodic Syndrome (TRAPS) 10.2.2 Group 2. Syndromes Presenting with Neutrophilic Urticaria (e.g. Cryopyrin-Associated Periodic Syndrome—CAPS) 10.2.2.1 Recurrent Fever Attacks of Short Duration (Typically