The immune system and gene expression microarrays--new answers to old questions

Transcriptomic studies in tolerance: Lessons learned and the path forward

Immunosuppression after solid organ transplantation is a delicate balance of the immune response and is a complex phenomenon with many factors involved. Despite advances in the care of patients receiving organ transplants the adverse effects associated with immunosuppressive agents and the risks of long-term immunosuppression present a series of challenges and the need to weigh the risks and benefits of either over or under-immunosuppression. Ideally, if all transplant recipients could develop donor-specific immunological tolerance, it could drastically improve long-term graft survival without the need for immunosuppressive agents. In the absence of this ideal situation, the next best approach would be to develop tools to determine the adequacy of immunosuppression in each patient, in a manner that would individualize or personalize therapy. Despite current genomics-based studies of tolerance biomarkers in transplantation there are currently, no clinically validated tools to safely increase or decrease the level of IS that is beneficial to the patient. However, the successful identification of biomarkers and/or mechanisms of tolerance that have implications on long-term graft survival and outcomes depend on proper integration of study design, experimental protocols, and data-driven hypotheses. The objective of this article is to first, discuss the progress made on genomic biomarkers of immunological tolerance and the future avenues for the development of such biomarkers specifically in kidney transplantation. Secondly, we provide a set of guiding principles and identify the pitfalls, advantages, and drawbacks of studies that generate genomic data aimed at understanding transplant tolerance that is applicable to all solid transplants.

Toxicological investigation of acute and chronic treatment with Gnidia stenophylla Gilg root extract on some blood parameters and histopathology of spleen, liver and kidney in mice

Background

In southeast Ethiopia, people locally use the roots of Gnidia stenophylla Gilg (Thymelaeaceae) to cure malaria and other diseases with no literature evidence substantiating its safety. The aim of this study was, therefore, to investigate the safety of the aqueous root extract of G. stenophylla after acute (single dose) and repeated sub chronic oral administration in mice.

Results

A single oral administration of the extract at 500, 1000, 2000 and 4000 mg/kg body weight did not induce any behavioral change and mortality in both sexes. The oral LD₅₀ of the extract was found to be above 6000 mg/kg body weight in mice. Chronic treatment with the extract for 13 weeks did not induce any sign of illness and/or death and had no adverse effect on the body weight. Dose-related elevations of erythrocytes, hematocrit, hemoglobin, platelets and neutrophils differential and significant decrease in the number of lymphocyte were observed. Liver sections of mice treated with 800 mg/kg body weight, revealed mild inflammations around the portal triads and central veins; whereas the spleen and kidneys appeared normal with no detectable gross morphological and histopathological alteration at both doses.

Conclusions

The results of this study revealed that aqueous root extract of G. stenophylla Gilg at antimalarial dose is safe even when taken for a longer period. At a higher dose, the extract may have a potential to increase some hematological indices but may induce mild hepatotoxicity as a side effect.

Electronic supplementary material

The online version of this article (10.1186/s13104-017-2964-3) contains supplementary material, which is available to authorized users.

Gene Expression and Antimicrobial Activity of Bovine Macrophages in Response to Mycobacterium avium subsp. paratuberculosis

We evaluated gene expression and antimicrobial responses of bovine monocyte—derived macrophages incubated with Mycobacterium avium subsp. paratuberculosis (M. a. ptb), the causative agent of Johne's disease. Gene expression was evaluated by the use of human noncompetitive high-density oligonucleotide microarrays. Bovine messenger RNA hybridized with 14.2–18.2% of the 12,600 oligonucleotide probe sets. When macrophages incubated with M. a. ptb were compared with nonactivated control macrophages, macrophages activated by addition of interferon-γ and lipopolysaccharide, and macrophages incubated with Mycobacterium avium subspecies avium (M. a. a), 47, 79, and 27 genes, respectively, were differentially expressed. Differential expression of six of these genes was confirmed using reverse transcriptase polymerase chain reaction. Several functional assays were performed to evaluate the potential relevance of differentially expressed genes to host defense. Macrophages phagocytizing M. a. a had a greater capacity to kill the organisms and to acidify phagosomes and a greater degree of apoptosis than did macrophages incubated with M. a. ptb. The results of these studies indicate that multiple genes and metabolic pathways are differentially expressed by macrophages ingesting mycobacterial organisms. Although the intracellular fate of mycobacterial organisms appears to be dependent on a complex interaction between macrophage and organism, phagosome acidification and apoptosis may play central roles in organism survival.

Computational vaccinology and epitope vaccine design by immunoinformatics

Human immune system includes variety of different cells and molecules correlating with other body systems. These instances complicate the analysis of the system; particularly in postgenomic era by introducing more amount of data, the complexity is increased and necessity of using computational approaches to process and interpret them is more tangible.Immunoinformatics as a subset of bioinformatics is a new approach with variety of tools and databases that facilitate analysis of enormous amount of immunologic data obtained from experimental researches. In addition to directing the insight regarding experiment selections, it helps new thesis design which was not feasible with conventional methods due to the complexity of data. Considering this features immunoinformatics appears to be one of the fields that accelerate the immunological research progression.In this study we discuss advances in genomics and vaccine design and their relevance to the development of effective vaccines furthermore several division of this field and available tools in each item are introduced.

Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers

The field of biomarker discovery made a significant leap over the past few decades. As we enter the Era of the Human Genome, thousands of biomarkers can be identified in a relatively high-throughput fashion. While such magnitude and diversity of biomarkers can be seen as a challenge by itself, the field is being moved forward by new advances in bioinformatics and Systems Biology. Because of the life and death nature of end stage organ failure that transplantation treats, the severe donor organ shortage, and the powerful and toxic drug therapies required for the lifetimes of transplant patients, we envision a future for biomarkers as tools to diagnose disease in its early stages, predict prognosis, suggest treatment options and then assist in the implementation of therapies. By harnessing the power of multiple technologies in parallel makes it possible to discover and then validate the next generation of biomarkers for transplantation. We see the road ahead diverge into two paths: one from biomarkers to diagnosis and therapy and the other to a new level of insight into the complex molecular networks that determine when a healthy state becomes diseased and dysfunctional.

Toxicogenomics in the assessment of immunotoxicity

Microarray analysis is used for simultaneous measurement of expression of thousands of genes in a given sample and as such extends and deepens our understanding of biological processes. Application of the technique in toxicology is referred to as toxicogenomics. The examples of assessment of immunotoxicity by gene expression profiling presented and discussed here, show that microarray analysis is able to detect known and novel effects of a wide range of immunomodulating agents. Besides the elucidation of mechanisms of action, toxicogenomics is also applied to predict consequences of exposing biological systems to toxic agents. Successful attempts to classify compounds using signature gene expression profiles have been reported. These did, however, not specifically focus on immunotoxicity. Databases containing expression profiles can facilitate the applications of toxicogenomics. Platforms and methodologies for gene expression profiling may vary, however, hampering data compiling across different laboratories. Therefore, attention is paid to standardization of the generation, reporting, and management of microarray data. Obtained gene expression profiles should be anchored to pathological and functional endpoints for correct interpretation of results. These issues are also important when using toxicogenomics in risk assessment. The application of toxicogenomics in evaluation of immunotoxicity is thus not yet without challenges. It already contributes to the understanding of immunotoxic processes and the development of in vitro screening assays, though, and is therefore expected to be of value for mechanistic insight into immunotoxicity and hazard identification of existing and novel compounds.

Chipping into the human genome: novel insights for transplantation

High throughput, high density platforms for transcriptional, proteomic, and metabonomic analyses are opening new doors for improving our understanding of the complexity and redundancy of the immune system in the interplay of the innate and allo-immune responses in organ transplantation. New insights are being obtained into the possible discrepancies between the gold standard of tissue pathological diagnosis and clinical graft outcomes, as new transcriptional categories of transplant rejection evolve. The bystander effects of chronic immunosuppression underlying the complexities of graft dysfunction are beginning to be understood. Non-invasive mechanisms to monitor transplants, by following 'footprints' of biomarker sets that reflect the disease phenotype, are being pursued for their clinical application for direct patient care. Utilization of these same biomarker sets may also offer a unique means to titrate immunosuppression and predict specific graft dysfunction events prior to clinical decline, thus bringing in the potential to reduce patient morbidity from infection and malignancy, preserve graft integrity, and limit the progression of chronic graft injury. Bioinformatics support is integral to the unraveling of the mysteries of the human genome, proteome, and metabolome in disease and in health.

Development of a functional cDNA array for evaluation of the Th1/Th2 balance

The immune balance controlled by CD4(+) helper T cell subsets (T helper 1 (Th1) and T helper 2 (Th2)) is crucial for immunoregulation and its imbalance causes various immune diseases including infections, allergic disorders and autoimmune diseases. Therefore, it is of great importance to develop a system of diagnosing Th1/Th2 imbalances for curing immune diseases. Here we developed a functional cDNA array filter useful for assessing the Th1/Th2 balance in mice. To overcome the disadvantages of conventional microarrays carrying thousands of genes, we prepared an array filter containing 40 Th1-specific and 32 Th2-specific genes, which were selected from over 8700 genes based on (i) the specificity of expression in Th1 or Th2 cells and (ii) an expression level which is high enough for detection using a DNA array. This array filter provided a prompt and precise evaluation for the skewing of the Th1/Th2 balance combined with our calculation algorithm. The bias toward Th1 or Th2 was evaluated visually at a glance by aligning the genes on the filter. Moreover, we succeeded in evaluating the skewing of the Th1/Th2 balance in vivo during acute graft versus host disease (GVHD). Thus, this array filter will provide a novel tool for evaluation of the Th1/Th2 balance in a variety of immune diseases.

Sequential patterns of gene expression by bovine monocyte-derived macrophages associated with ingestion of mycobacterial organisms

We investigated mechanisms involved in killing of mycobacterial organisms by comparing the response of bovine monocyte-derived macrophages to ingestion of Mycobacterium avium subsp. paratuberculosis or M. avium subsp. avium organisms. Previous studies have shown that bovine macrophages have the capacity to kill M. avium subsp. avium organisms in vitro but cannot kill M. avium subsp. paratuberculosis organisms. We used bovine cDNA microarray technology to investigate sequential gene expression by bovine monocyte-derived macrophages and function assays to correlate gene expression with biological activity. Results of the gene expression studies indicated substantial differences between macrophages phagocytizing the two organisms. At 2, 6, and 24h after infection, 12, 53, and 19 genes, respectively, were differentially expressed. Over all time periods, approximately twice as many genes had lower expression in M. avium subsp. paratuberculosis-infected macrophages than had greater expression. Differentially regulated genes of most interest to antimicrobial responses included inflammatory molecules (transforming growth factor-beta, thrombospondin 1, monocyte chemokine, and cathepsin K), phagosome-lysosome-related genes (H(+) ATPases, lysosomal-associated membrane protein 2, vesicle trafficking protein, and solute carrier protein), and apoptosis-related genes (tumor necrosis factor receptor-associated factor 2, and tumor protein p(53) binding protein). Function assays indicated that M. avium subsp. avium-infected macrophages had a greater capacity to acidify phagosomes and a greater percentage of apoptotic cells. In conclusion, these results suggest that a complex interaction between macrophages and mycobacterial organisms is involved in determining the fate of the organism. Although multiple genes and metabolic pathways are involved, the capacity of cells to acidify phagosomes and induce apoptosis appears to play a prominent role.

Tracking gene expression in primary immunodeficiencies

PURPOSE OF REVIEW

Extensive research on molecular genetics in recent decades has provided a wealth of information about the mechanisms of primary immunodeficiency diseases. Microarray technology enables the survey of the expression of thousands of genes simultaneously. This review focuses on the commonly used arrays and initial applications in the study of primary immunodeficiency diseases. The application of this technology has been found to accelerate the discovery rate of gene expression disturbances in primary immunodeficiency diseases and provide potential molecular diagnostic tools.

RECENT FINDINGS

The important role of microarray technology in functional genomic study has been demonstrated by the exponential growth in the number of scientific publications in the last few years. Microarray analysis has been used to study gene expression in several immunodeficiency diseases with known gene mutations as well as those with unknown causes. It has provided snapshots of gene expression and has presented the molecular phenotypes in the cells at defined times and under certain stimulation conditions. Studies comparing differential gene expression in patients and normal controls have allowed us to better understand the immunodeficiencies at the molecular level.

SUMMARY

Application of microarray technology in immunodeficiency study has facilitated tracking the expression of thousands of genes simultaneously. The molecular phenotypes obtained from microarray results can be used in diagnosis of diseases, supplemental to clinical phenotypes. It is a powerful survey tool that can detect disturbed gene expression in immunodeficiency diseases, which will provide clues for disease gene discovery and potential targets for drug development.

The plant virus Tomato Spotted Wilt Tospovirus activates the immune system of its main insect vector, Frankliniella occidentalis

Tospoviruses have the ability to infect plants and their insect vectors. Tomato spotted wilt virus (TSWV), the type species in the Tospovirus genus, infects its most important insect vector, Frankliniella occidentalis, the western flower thrips (WFT). However, no detrimental effects on the life cycle or cytopathological changes have been reported in the WFT after TSWV infection, and relatively few viral particles can be observed even several days after infection. We hypothesized that TSWV infection triggers an immune response in the WFT. Using subtractive cDNA libraries to probe WFT DNA macroarrays, we found that the WFT's immune system is activated by TSWV infection. The activated genes included (i) those encoding antimicrobial peptides, such as defensin and cecropin; (ii) genes involved in pathogen recognition, such as those encoding lectins; (iii) those encoding receptors that activate the innate immune response, such as Toll-3; and (iv) those encoding members of signal transduction pathways activated by Toll-like receptors, such as JNK kinase. Transcriptional upregulation of these genes after TSWV infection was confirmed by Northern analysis, and the kinetics of the immune response was measured over time. Several of the detected genes were activated at the same time that viral replication was first detected by reverse transcription-PCR. To our knowledge, this is the first report of the activation of an insect vector immune response by a plant virus. The results may lead to a better understanding of insects' immune responses against viruses and may help in the future development of novel control strategies against plant viruses, as well as human and animal viruses transmitted by insect vectors.

Chips with everything: DNA microarrays in infectious diseases

Two developments are set to revolutionise research in and clinical management of infectious diseases. First, the completion of the human genome project together with the sequencing of many pathogen genomes, and second, the development of microarray technology. This review explains the principles underlying DNA microarrays and highlights the uses to which they are being put to investigate the molecular basis of infectious diseases. Pathogen studies enable identification of both known and novel organisms, understanding of genetic evolution, and investigation of determinants of pathogenicity. Host studies show the complexities of development and activation of both innate and adaptive immunity. Host-pathogen studies allow global analysis of gene expression during pathogenesis. Microarray technology will accelerate our understanding of the complex genetic processes underlying the interaction between microorganisms and the host, with consequent improvements in the diagnosis, treatment, and prevention of infectious diseases.

A determination of tumor necrosis factor expression in TMJ inflammation with the use of microarray analysis

Many different factors can lead to inflammatory changes within temporomandibular joint tissues. This investigation examined if the expression of TNF-alpha and its receptors was altered in TMJ tissues during inflammation. Adult male rats were injected bilaterally with complete Freund's adjuvant (CFA) into the TMJ or served as uninjected controls and were killed two days after CFA treatment. TMJ tissues were removed, and expression of TNF-alpha and its receptors was examined via gene microarray analysis, RT-PCR, Western blot, and ELISA. Gene microarray analysis provided evidence for changes in gene expression, notably that TNF-alpha and TNF-R1, but not TNF-R2, were significantly elevated in CFA-treated TMJ tissues. However, protein levels of TNF-alpha, TNF-R1, and TNF-R2 were all significantly increased in CFA-treated TMJ tissues. These results indicate that the pro-inflammatory cytokine TNF-alpha may play a significant role in the onset of inflammatory conditions associated with adjuvant-induced arthritis of the TMJ.

Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.

Microarray-based expression profiling of normal and malignant immune cells

Recent advances in gene microarray technology have facilitated global analyses of gene expression profiles in normal and malignant immune cells. Great strides have been made in our understanding of molecular differences among various types of immune cells, the process of T and B cell activation, and the genomic changes that convert normal cells to malignant ones. Genomic analysis has become a crucial aspect of cancer classification, diagnosis, therapy, and prognosis. This technology has the potential to reveal the comprehensive transcriptional alterations that dictate fundamental biological processes such as signal transduction in response to specific stimuli, cell growth, differentiation, and apoptosis. While reaping the benefits of genomic analyses, it is important to realize its limitations with respect to accuracy of interpretation, reproducibility, and signal detection. It is crucial to optimize signals for individual probe-target pairs and to develop a uniform set of criteria for data analyses. The development of a public-access database of results from individual laboratories will pave the way for identifying discrepancies and advancing scientific breakthroughs.