Design principles of adaptive immune systems

Both jawless vertebrates, such as lampreys and hagfish, and jawed vertebrates (encompassing species as diverse as sharks and humans) have an adaptive immune system that is based on somatically diversified and clonally expressed antigen receptors. Although the molecular nature of the antigen receptors and the mechanisms of their assembly are different, recent findings suggest that the general design principles underlying the two adaptive immune systems are surprisingly similar. The identification of such commonalities promises to further our understanding of the mammalian immune system and to inspire the development of new strategies for medical interventions targeting the consequences of faulty immune functions.     

The evolution of adaptive immune systems

A clonally diverse anticipatory repertoire in which each lymphocyte bears a unique antigen receptor is the central feature of the adaptive immune system that evolved in our vertebrate ancestors. The survival advantage gained through adding this type of adaptive immune system to a pre-existing innate immune system led to the evolution of alternative ways for lymphocytes to generate diverse antigen receptors for use in recognizing and repelling pathogen invaders. All jawed vertebrates assemble their antigen-receptor genes through recombinatorial rearrangement of different immunoglobulin or T cell receptor gene segments. The surviving jawless vertebrates, lampreys and hagfish, instead solved the receptor diversification problem by the recombinatorial assembly of leucine-rich-repeat genetic modules to encode variable lymphocyte receptors. The convergent evolution of these remarkably different adaptive immune systems involved innovative genetic modification of innate-immune-system components.     

Memory in the innate and adaptive immune systems

Specific memory is a hallmark of the vertebrate adaptive immune system. However, recent experiments indicate that specific memory might also exist in the innate immune systems of invertebrates. At present, the underlying mechanisms are unknown; yet such phenomenological evidence is relevant for understanding the principles and evolution of immune defence.     

CRISPR-Cas adaptive immune systems in Sulfolobales: genetic studies and molecular mechanisms

CRISPR-Cas systems provide the small RNA-based adaptive immunity to defend against invasive genetic elements in archaea and bacteria. Organisms of Sulfolobales, an order of thermophilic acidophiles belonging to the Crenarchaeotal Phylum, usually contain both type I and type Ⅲ CRISPR-Cas systems. Two species, Saccharolobus solfataricus and Sulfolobus islandicus, have been important models for CRISPR study in archaea, and knowledge obtained from these studies has greatly expanded our understanding of molecular mechanisms of antiviral defense in all three steps: adaptation, expression and crRNA processing, and interference. Four subtypes of CRISPR-Cas systems are common in these organisms, including I-A, I-D, Ⅲ-B, and Ⅲ-D. These cas genes form functional modules, e.g., all genes required for adaptation and for interference in the I-A immune system are clustered together to form aCas and i Cas modules. Genetic assays have been developed to study mechanisms of adaptation and interference by different CRISPR-Cas systems in these model archaea, and these methodologies are useful in demonstration of the protospacer-adjacent motif(PAM)-dependent DNA interference by I-A interference modules and multiple interference activities by Ⅲ-B Cmr systems. Ribonucleoprotein effector complexes have been isolated for Sulfolobales Ⅲ-B and Ⅲ-D systems, and their biochemical characterization has greatly enriched the knowledge of molecular mechanisms of these novel antiviral immune responses.     

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein–binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap.     

Collectin surfactant protein D binds antibodies and interlinks innate and adaptive immune systems

Innate immune collectins, such as surfactant protein D (SP-D), contain fibrillar collagen-like regions and globular carbohydrate-recognition domains (CRDs). SP-D recognizes carbohydrate arrays present on microbial surfaces via its CRDs, agglutinates microbes and enhances their phagocytosis. In contrast, adaptive immune proteins such as immunoglobulins (Igs) recognize pathogens via binding to specific antigens. Here we show that: SP-D binds various classes of immunoglobins, including IgG, IgM, IgE and secretory IgA, but not serum IgA; the globular domains of SP-D bind both the Fab and Fc domains of IgG; SP-D recognizes IgG via calcium-dependent protein-protein interactions, aggregates IgG-coated beads and enhances their phagocytosis by murine macrophage RAW 264.7 cells. Therefore, we propose that SP-D effectively interlinks innate and adaptive immune systems.     

Origins and evolutionary relationships between the innate and adaptive arms of immune systems

Long before vertebrates first appeared, protists, plants andanimals had evolved diverse, effective systems of innate immunity.Ancestors of the vertebrates utilized components of the complementsystem, protease-inhibitors, metal-binding proteins, carbohydrate-bindingproteins and other plasma-born molecules as humoral agents ofdefense. In these same animals, immunocytes endowed with a repertoireof defensive behaviors expressed Toll-like receptors. They madeNADPH oxidase, superoxide dismutase and other respiratory burstenzymes to produce toxic oxygen radicals, and nitric oxide synthaseto produce nitric oxide. Antimicrobial peptides and lytic enzymeswere in their armory. Immune responses were orchestrated bycytokines. Furthermore, genes within the immunoglobulin superfamilywere expressed to meet a variety of needs possibly includingdefense. However, recombination activating genes played no role.With the acquisition of one or more transposases and the resultingcapacity to generate diverse receptors from immunoglobulin genefragments, the adaptive (lymphoid) arm of the immune systemwas born. This may have coincided with the elaboration of theneural crest. Naturally, the role of the adaptive arm was initiallysubservient to the defensive functions of the pre-existing innatearm. The strong selective advantages that stemmed from having"sharp-shooters" (cells making antigen-specific receptors) onthe defense team ensured their retention. Refined through evolution,adaptive immunity, even in mammals, remains dependent upon cellsof the innate series (e.g., dendritic cells) for signals drivingtheir functional maturation. This paper calls for some freshthinking leading to a clearer vision of the origins and co-evolutionof the two arms of modern immune systems, and suggests a possibleneural origin for the adaptive immune system.     

计算机辅助CRISPR向导RNA设计

基于CRISPR/Cas9系统的基因编辑已被成功应用于多种细胞类型中。计算机辅助的向导RNA(Guide RNA)设计是使用CRISPR系统成功进行基因编辑的关键步骤之一。目前的计算工作主要致力于利用计算模型来提高sgRNA的打靶效率并降低其脱靶。文中对于目前存在的sgRNA设计工具进行综述,并且说明可以通过建立高效的计算模型,对当前的异质基因编辑数据进行整合挖掘,以获得无偏差的sgRNA设计规则,并预测影响sgRNA设计的关键特征。笔者认为,对于sgRNA打靶和脱靶效果的系统总结和评价,将有助于使用CRISPR系统进行更加精准的基因编辑和基因治疗。     

CRISPR-based point-of-care plant disease diagnostics

The coupling of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas RNA-programmable nucleases with nucleic acid detection platforms has brought radical changes to the field of disease diagnosis. Recently, Sánchez et al. developed a simple, rapid, highly sensitive, precise, and in-field deployable point-of-care (POC) and point-of-need (PON) molecular disease detection tool that can be used in diverse agricultural applications.     

Secretory IgA N- and O-glycans provide a link between the innate and adaptive immune systems

Secretory IgA (SIgA) is a multi-polypeptide complex consisting of a secretory component (SC) covalently attached to dimeric IgA containing one joining (J) chain. We present the analysis of both the N- and O-glycans on the individual peptides from this complex. Based on these data, we have constructed a molecular model of SIgA1 with all its glycans, in which the Fab arms form a T shape and the SC is wrapped around the heavy chains. The O-glycan regions on the heavy (H) chains and the SC N-glycans have adhesin-binding glycan epitopes including galactose-linked beta1-4 and beta1-3 to GlcNAc, fucose-linked alpha1-3 and alpha1-4 to GlcNAc and alpha1-2 to galactose, and alpha2-3 and alpha2-6-linked sialic acids. These glycan epitopes provide SIgA with further bacteria-binding sites in addition to the four Fab-binding sites, thus enabling SIgA to participate in both innate and adaptive immunity. We also show that the N-glycans on the H chains of both SIgA1 and SIgA2 present terminal GlcNAc and mannose residues that are normally masked by SC, but that can be unmasked and recognized by mannose-binding lectin, by disrupting the SC-H chain noncovalent interactions.     

Modeling adaptive biological systems

During the evolution of many systems found in nature, both the system composition and the interactions between components will vary. Equating the dimension with the number of different components, a system which adds or deletes components belongs to a class of dynamical systems with a finite dimensional phase space of variable dimension. We present two models of biochemical systems with a variable phase space, a model of autocatalytic reaction networks in the prebiotic soup and a model of the idiotypic network of the immune system. Each model contains characteristic meta-dynamical rules for constructing equations of motion from component properties. The simulation of each model occurs on two levels. On one level, the equations of motion are integrated to determine the state of each component. On a second level, algorithms which approximate physical processes in the real system are employed to change the equations of motion. Models with meta-dynamical rules possess several advantages for the study of evolving systems. First, there are no explicit fitness functions to determine how the components of the model rank in terms of survivability. The success of any component is a function of its relationship to the rest of the system. A second advantage is that since the phase space representation of the system is always finite but continually changing, we can explore a potentially infinite phase space which would otherwise be inaccessible with finite computer resources. Third, the enlarged capacity of systems with meta-dynamics for variation allows us to conduct true evolution experiments. The modeling methods presented here can be applied to many real biological systems. In the two studies we present, we are investigating two apparent properties of adaptive networks. With the simulation of the prebiotic soup, we are most interested in how a chemical reaction network might emerge from an initial state of relative disorder. With the study of the immune system, we study the self-regulation of the network including its ability to distinguish between species which are part of the network and those which are not.     

基于CRISPR的快速灵敏便捷分子检测

快速灵敏检测技术对疾病防控必不可少。特别是新冠疫情暴发以来,人们深刻认识到快速灵敏检测技术的重要性。近年来,以CRISPR/Cas为代表的基因编辑技术带来了生物技术革命性的进步。CRISPR的核酸检测技术因其快速、准确、灵敏、经济等特点,正在引发分子诊断革新,并已被成功应用于传染病、遗传病、肿瘤基因突变诊断,以及食品安全等领域。本文归纳了基于CRISPR的多种核酸检测体系及应用,并对未来CRISPR核酸检测发展趋势及结合人工智能的智能化检测进行了展望。