MicroRNAs in parasite-host interaction: Cooperative effect and biomedical applications

Abstract

Ixodes ricinus, the European castor bean tick, is a hard-bodied parasitiform mite that relies on blood feeding for survival and reproduction. It is widely distributed across Europe and Northern Africa and is responsible for transmitting several pathogens, including Borrelia burgdorferi, the causative agent of Lyme borreliosis. The increasing prevalence of tick-borne diseases in recent years, exacerbated by climate change and habitat modifications, poses significant public health and economic concerns. The ability of ticks to successfully parasitize their hosts is largely attributed to their saliva, which contains bioactive molecules capable of manipulating different host defense mechanisms, including the immune system, wound healing processes, and blood coagulation. Recent studies propose non-coding RNAs (ncRNAs) present in saliva, such as microRNAs (miRNAs), as potential modulators of the tick-host interface. miRNAs are highly conserved non-coding genes present in virtually all metazoans. Their functional product consists of small RNA molecules (21–23 bp) that regulate gene expression negatively and post-transcriptionally. Their importance in cellular homeostasis has been extensively demonstrated through functional assays and is also evident in the apparent causal involvement of miRNAs in various pathologies. Recent findings suggest that miRNAs can function cooperatively, enhancing their regulatory effects. Long non-coding RNAs (lncRNAs), in turn, have been proposed to act as miRNA sponges, possessing the ability to sequester miRNAs via target regions on the lncRNAs themselves, adding another layer of complexity to the process of gene regulation. This thesis aims to determine the functional importance of miRNAs and lncRNAs in the parasitism and blood-feeding processes carried out by I. ricinus. To achieve this, we comprehensively analyzed the transcriptomic dynamics of I. ricinus during active parasitism, assessing the role of gene products, miRNAs, and lncRNAs in the tick-host interface through an extensive bioinformatics approach. The ultimate goal is to establish a foundation for the development of novel clinical and pest control strategies. During the course of this thesis, we collaborated on the generation of a new reference genome assembly for I. ricinus. The use of this new reference genome, along with multiple datasets from various tissues, such as salivary glands, midgut, saliva, and even the whole tick body, allowed us to improve the annotation of miRNAs and lncRNAs. To analyze the potential functional impact of tick miRNAs on the host, we designed a new computational workflow that integrates miRNA target site prediction and the functional characterization of regulated genes. Target prediction incorporates target sequence conservation profiles based on position and recent findings on the importance of the TNRC6 protein in the synergistic cooperation of miRNAs in gene silencing. By applying the aforementioned workflow, we could demonstrate that integrating target sequence conservation into miRNA target prediction drastically reduces the number of predicted targets. We found that conserved predicted target genes were functionally enriched in pathways highly relevant to host defense. In addition to this, we successfully detected cooperative target regions for tick salivary miRNAs in host genes that were abundant in skin cells of the host and involved in key processes at the tick-host interface, such as immunity, wound healing, nociception, and mechanosensation. We also demonstrated that these tick miRNAs are present and protected in extracellular vesicles, which increases their potential to interact with host cells. To study how lncRNAs can influence the parasitism of I. ricinus, we generated a de novo assembled reference transcriptome from tick salivary gland and midgut samples. These samples were collected at different time points from sister ticks that were either unfed, fed on naïve hosts, or fed on hosts that had been previously exposed to ticks and, therefore, sensitized to tick parasitism. The specific samples allowed us to analyze the transcriptional dynamics occurring under these different conditions over time in non-coding RNAs and, additionally, in coding RNAs. By means of this analysis, we observed significant differences between the specific groups of ticks and found that genes differentially expressed over time are involved in key biological processes, including glycosylation and protein folding, which play crucial roles in tick adaptation to parasitism and in the evasion of the host immune response. Several lncRNAs were identified as potential host miRNA sponges, with the capability to inhibit the action of host miRNAs involved in critical processes against parasitism. One of these lncRNAs emerges as the most promising candidate, as it was detected in extracellular vesicles and it has the capability to impair glycosylation processes in hosts, which are essential for host immunity, and signaling processes of extracellular matrix receptors. Overall, this thesis aims to establish a foundation for future research and clinical advancements, such as the development of therapeutic miRNAs and antimiRs. Continued investigation, particularly in biological validation and host response analysis, will be crucial to complement the bioinformatically driven results presented in this thesis. This knowledge will be essential in ultimately reducing the public health and economic impact of I. ricinus on our society.