Hidden diversity of moss mites (Acari: Oribatida) unveiled with ecological and genetic approach

Moss mites (Acari: Oribatida) are microscopic (0.1–1 mm) soil-dwelling arachnids that function as soil decomposers. The oribatids are among the most numerous soil animals with abundances reaching up to 200,000 specimens and 50 species per one square meter of soil. Despite their ubiquitous and abundant existence, they are classified as a poorly known animal group, both in Finland and elsewhere. In this thesis I study the diversity of oribatids in a previously undocumented microhabitat, red wood ant nest mounds (of the Formica rufa group), and the special characteristics of that habitat. In addition, I study whether forest clear felling detrimentally affects the physical properties of ant nests and the oribatid fauna inhabiting those nests. Using DNA-based methods, I also investigate species richness, phylogeny, and species boundaries within the genus Phthiracarus Perty 1841. First, I compared the community composition of oribatids between ant (Formica polyctena) nest mounds and the surrounding soil. The study revealed that equally abundant fauna inhabited the two habitats, but the community composition differed; these two habitats were predominantly inhabited by different species. Second, I compared the community composition of oribatids between the parts of an ant mound. I found that, as was presumed, the oribatids predominantly inhabited the surface layer of mounds, which was also observed to host the highest moisture. This study revealed that the distribution of oribatids is moisture-related within ant mounds. These results revealed that ants and their nest mounds providing optimal conditions for decomposer fauna are important factors in maintaining oribatid diversity in the forest landscape. The next study investigated how the physical properties of ant nests (those of F. aquilonia) change due to forest clear felling by comparing mounds located in mature spruce forest and its clear fells. The study showed that the surface layer of mounds was significantly drier in clear fells than in undisturbed forest, and due to the dryness, the mounds were also relatively cooler as they lose thermal capacity on clear fells. Next, I studied whether these carry-over effects have an impact on the oribatid communities inhabiting the ant nests. The study revealed that the species richness was lower in clear fell mounds, but there were no clear changes in the total abundance or community composition of oribatids. Morphology-based identification of these minute animals is difficult due to the phenotypic variation of species. Therefore, using molecular systematic methods I investigated the species delineation of the genus Phthiracarus among nine species. Despite the challenges in obtaining DNA sequences, the DNA-based analysis (using markers COI, 28S D3, ITSS) showed that five species formed clear entities (clades), while the other four species were split into two haplotypes, indicating cryptic diversity. These results highlight that the actual species diversity may be higher than previously known. Hence, the results reveal a need to develop further the DNA-based taxonomic methods for oribatids. This thesis provides novel information about the diversity, ecology, and habitat selection of oribatid mites in a distinct habitat: wood ant nest mounds. Using systematic sampling and a species-specific approach I showed that ant mounds are central factors in maintaining the oribatid diversity in forests. Moreover, the ant mounds are inhabited by a large variety of other invertebrates, and hence these microhabitats form diversity hotspots in the forest landscape. Thus, the red wood ant colonies should be taken into consideration when making conservation decisions. The red wood ant species are still viable (to use the IUCN category) in the boreal forest of Finland, but in many other European countries they are classified as near-threatened species. Hence, conservation of these distinct habitats is of great value. Appropriate identification of organisms (taxonomy, systematics) is a cornerstone in the studies focusing on biodiversity research. For this purpose, DNA taxonomy may provide a fast and precise tool in characterizing species, especially in the case of microscopic organisms that are otherwise challenging to identify. This thesis provided the first DNA reference library for the genus Phthiracarus, revealing possible cryptic diversity, but also highlighting the need for developing new laboratory protocols for the future studies of this poorly known animal group

Absence of Francisella tularensis in Finnish Ixodes ricinus and Ixodes persulcatus ticks

Francisella tularensis subsp. holarctica is the causative agent of tularaemia in Europe. Finland is a high-incidence region for tularaemia, with mosquito bites as the most common sources of infection. However, in Central and Western Europe, ticks (Acari: Ixodidae) have been suggested as the main vectors. Indeed, several studies have reported the pathogen from the locally most common human-biting tick species, Ixodes ricinus. In Finland, the occurrence of the pathogen in ticks has started receiving attention only recently. Here, we collate previous tick screening data from Finland regarding F. tularensis as well as present the results from a novel screening of roughly 15 000 I. ricinus and I. persulcatus collected from across the country. In total, 14 878 ticks collected between 2015 and 2020 were screened for F. tularensis using a TaqMan-based qPCR assay targeting the 23 KDa gene. The combined screening efforts of the current and previous studies, encompassing roughly 20 000 ticks, did not find any positive ticks. Given the negative results despite the considerable sample size, it appears that the pathogen is not circulating in local tick populations in Finland. We discuss some possible reasons for the lack of the bacterium in ticks in this high-incidence region of tularaemia

High intratumoral dihydrotestosterone is associated with antiandrogen resistance in VCaP prostate cancer xenografts in castrated mice

Antiandrogen treatment resistance is a major clinical concern in castration-resistant prostate cancer (CRPC) treatment. Using xenografts of VCaP cells we showed that growth of antiandrogen resistant CRPC tumors were characterized by a higher intratumor dihydrotestosterone (DHT) concentration than that of treatment responsive tumors. Furthermore, the slow tumor growth after adrenalectomy was associated with a low intratumor DHT concentration. Reactivation of androgen signaling in enzalutamide-resistant tumors was further shown by the expression of several androgen-dependent genes. The data indicate that intratumor DHT concentration and expression of several androgen-dependent genes in CRPC lesions is an indication of enzalutamide treatment resistance and an indication of the need for further androgen blockade. The presence of an androgen synthesis, independent of CYP17A1 activity, has been shown to exist in prostate cancer cells, and thus, novel androgen synthesis inhibitors are needed for the treatment of enzalutamide-resistant CRPC tumors that do not respond to abiraterone.Peer reviewe

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data

BackgroundDetection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is known about the applicability of the developed algorithms to ultra-low-coverage (0.0005–0.8×) data that is used in various research and clinical applications, such as digital karyotyping and single-cell CNV detection.ResultHere, the performance of six popular read-depth based CNV detection algorithms (BIC-seq2, Canvas, CNVnator, FREEC, HMMcopy, and QDNAseq) was studied using ultra-low-coverage WGS data. Real-world array- and karyotyping kit-based validation were used as a benchmark in the evaluation. Additionally, ultra-low-coverage WGS data was simulated to investigate the ability of the algorithms to identify CNVs in the sex chromosomes and the theoretical minimum coverage at which these tools can accurately function. Our results suggest that while all the methods were able to detect large CNVs, many methods were susceptible to producing false positives when smaller CNVs (< 2 Mbp) were detected. There was also significant variability in their ability to identify CNVs in the sex chromosomes. Overall, BIC-seq2 was found to be the best method in terms of statistical performance. However, its significant drawback was by far the slowest runtime among the methods (> 3 h) compared with FREEC (~ 3 min), which we considered the second-best method.ConclusionsOur comparative analysis demonstrates that CNV detection from ultra-low-coverage WGS data can be a highly accurate method for the detection of large copy number variations when their length is in millions of base pairs. These findings facilitate applications that utilize ultra-low-coverage CNV detection.</div

The L1TD1 Protein Interactome Reveals the Importance of Post-transcriptional Regulation in Human Pluripotency

Peer reviewe

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

Aims/hypothesis Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. Methods Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4(+) T cell, CD8(+) T cell and CD4(-)CD8(-) cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. Results We identified 79, 56 and 45 differentially methylated regions in CD4(+) T cells, CD8(+) T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4(+) T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4(+) T cells. Conclusions/interpretation These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.Peer reviewe

Adrenals Contribute to Growth of Castration-Resistant VCaP Prostate Cancer Xenografts

The role of adrenal androgens as drivers for castration-resistant prostate cancer (CRPC) growth in humans is generally accepted; however, the value of preclinical mouse models of CRPC is debatable, because mouse adrenals do not produce steroids activating the androgen receptor. In this study, we confirmed the expression of enzymes essential for de novo synthesis of androgens in mouse adrenals, with high intratissue concentration of progesterone (P-4) and moderate levels of androgens, such as androstenedione, testosterone, and dihydrotestosterone, in the adrenal glands of both intact and orchectomized (ORX) mice. ORX alone had no effect on serum P-4 concentration, whereas orchectomized and adrenalectomized (ORX + ADX) resulted in a significant decrease in serum P-4 and in a further reduction in the Low levels of serum androgens (androstenedione, testosterone, and dihydrotestosterone), measured by mass spectrometry. In line with this, the serum prostate-specific antigen and growth of VCaP xenografts in mice after ORX + ADX were markedly reduced compared with ORX alone, and the growth difference was not abolished by a glucocorticoid treatment. Moreover, ORX + ADX altered the androgen-dependent gene expression in the tumors, similar to that recently shown for the enzalutamide treatment. These data indicate that in contrast to the current view, and similar to humans, mouse adrenals synthesize significant amounts of steroids that contribute to the androgen receptor dependent growth of CRPC.Peer reviewe

Umbilical cord blood DNA methylation in children who later develop type 1 diabetes

Aims/hypothesis Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim was to determine whether perinatal DNA methylation is associated with later progression to type 1 diabetes. Methods Reduced representation bisulphite sequencing (RRBS) analysis was performed on umbilical cord blood samples collected within the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) Study. Children later diagnosed with type 1 diabetes and/or who tested positive for multiple islet autoantibodies (n = 43) were compared with control individuals (n = 79) who remained autoantibody-negative throughout the DIPP follow-up until 15 years of age. Potential confounding factors related to the pregnancy and the mother were included in the analysis. Results No differences in the umbilical cord blood methylation patterns were observed between the cases and controls at a false discovery rate Conclusions/interpretation Based on our results, differences between children who progress to type 1 diabetes and those who remain healthy throughout childhood are not yet present in the perinatal DNA methylome. However, we cannot exclude the possibility that such differences would be found in a larger dataset.Peer reviewe

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

Aims/hypothesis Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies.Methods Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4(+) T cell, CD8(+) T cell and CD4(-)CD8(-) cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing.Results We identified 79, 56 and 45 differentially methylated regions in CD4(+) T cells, CD8(+) T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4(+) T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4(+) T cells.Conclusions/interpretation These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.</p

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease

Background Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. Results Comparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p valuePeer reviewe