Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions / 中华医学杂志(英文版)

Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.

Application of phylogenetic analysis in the molecular epidemiological study of infectious diseases / 中华流行病学杂志

The rapid development of sequencing technology brings the explosive growth of pathogen genetic data. The combination of genomic data and phylogenetic method is being used to elaborate the origin and evolution of pathogens, the time and space distribution and parameter changes in the prevalence process, and how phenotypes like antigen, virulence, and resistance change over time. This method is also being used to predict pathogen transmission trends. In this study, we described the aim of phylogeny and the process of the phylogenetic construction method. We elaborated the advantages and disadvantages and scope of application of tree-building methods including distance-based, maximum parsimony, maximum likelihood and bayesian methods. We have reviewed the application and the estimation methods of major epidemiological parameters of phylodynamics and phylogeography in domestic and foreign studies. We concluded that the time- and location-scaled phylogenetic trees are increasingly used for outbreak investigation and routine surveillance of infectious diseases.

Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

RNA Interference in Infectious Tropical Diseases

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.

RNA Interference in Infectious Tropical Diseases

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.

Immunogenetics and infectious diseases: special reference to the mayor histocompatibility complex

Many studies have tried to identify genetic markers for infectious diseases, some of them have focused on human leukocyte antigens (HLA). The products of HLA genes interact with surface-specific receptors of T lymphocytes, resulting in activation of the host's immune response. Association of bacterial, viral, parasitic and fungal infections with the host's HLA has been widely investigated. The type and strength of this association differs among distinct populations, as well as among racial and/or ethnic groups. The new molecular methods for the identification of the HLA alleles, and the resulting new nomenclature, have contributed to a better understanding of this system. Unfortunately, this information has not been adequately transmitted to clinicians, which hampers the understanding of the association between the HLA system and diseases. We revised relevant studies on the association of HLA genes with infectious diseases, demonstrating their importance in the pathogenic mechanisms, through increased susceptibility or protection against infections and their complications.

Genomas de microoganismos y diagnóstico molecular / Genome of microorganisms and molecular diagnosis

En este artículo se exponen los principales descubrimientos de la nueva ciencia denominada genómicas y sus principales repercusiones para el diagnóstico microbiológico, tales como la nueva tecnología de los ADN chips

Genoma microbiano en clínica / Microbial genome in clinics

El genoma microbiano comprende la secuencia completa de los genes de un microorganismo. Su conocimiento permite una mejor comprensión de la patogenia, con aplicaciones en la prevención, en el diagnóstico y en el tratamiento de las enfermedades infecciosas. Conocidas la dinámica de los mecanismos de invansión, producción de toxinas, capacidad de adaptación a ecosistemas adversos y otras múltiples posibilidades de variación, pueden diseñarse nuevas vacunas más específicas, así como establecer combinaciones interespecies, o utilizarse bacterias avirulentas de muy fácil cultivo para producir en forma industrial antígenos de gérmenes de crecimiento fastidioso. En el campo de los antibióticos, se abren perpectivas hacia líneas absolutamente distintas, con drogas capaces de bloquear determinados pasos en cadenas metabólicas vitales. Ya existen múltiples aplicaciones de la genética en diagnóstico microbiológico, con técnicas que indudablemente se irán simplificando y perfeccionando con el conocimiento de la entera secuencia del genoma bacteriano: hibridación, reacción de polimeras en cadena, etc. Por último, el conocimiento del genoma también permitirá la utilización benéfica, a escala industrial, de algunos microorganismo en la producción de hormonas, vitaminas, aminoácidos y antibióticos

Genetic epidemiology of infectious disease

The genetic mechanisms involved in the variability of the human response to the infection of some organisms are critically reviewed. For leprosy and leishmaniasis there seems to exist no simple and general mechanism. The Mitsuda reaction, however, seems to be the most important phenotype measuring the human response to M. leprae. Several genes are known to affect the resistance/susceptibility to malaria. Studies on this disease should take into account all of this variability and be particularly cautious regarding the natural history of the population under study in order to establish the relative importance of given genes on a given population subject to a give epidemic. The sole parasitic disease that did not show discrepancies among studies is schistosomiasis, indicating the importance of a single additive gene that, ultimately, acts on the individualïs capacity to build and efficient eosinophilia. Future studies should focus on general mechanisms as well as on explanations of the existent disparities between studies.