Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency

<p>Abstract</p> <p>Background</p> <p>To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes involved in mitochondrial biology, cell cycle regulation, signal transduction and apoptosis. Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F₁F_oATP synthase deficiency consisting of 2 patients with mt9205ΔTA microdeletion and a genetically heterogeneous group of 11 patients with not yet characterized nuclear defects. Analysing gene expression profiles, we attempted to classify patients into expected defect specific subgroups, and subsequently reveal group specific compensatory changes, identify potential phenotype causing pathways and define candidate disease causing genes.</p> <p>Results</p> <p>Molecular studies, in combination with unsupervised clustering methods, defined three subgroups of patient cell lines – M group with mtDNA mutation and N1 and N2 groups with nuclear defect. Comparison of expression profiles and functional annotation, gene enrichment and pathway analyses of differentially expressed genes revealed in the M group a transcription profile suggestive of synchronized suppression of mitochondrial biogenesis and G1/S arrest. The N1 group showed elevated expression of complex I and reduced expression of complexes III, V, and V-type ATP synthase subunit genes, reduced expression of genes involved in phosphorylation dependent signaling along MAPK, Jak-STAT, JNK, and p38 MAP kinase pathways, signs of activated apoptosis and oxidative stress resembling phenotype of premature senescent fibroblasts. No specific functionally meaningful changes, except of signs of activated apoptosis, were detected in the N2 group. Evaluation of individual gene expression profiles confirmed already known <it>ATP6/ATP8 </it>defect in patients from the M group and indicated several candidate disease causing genes for nuclear defects.</p> <p>Conclusion</p> <p>Our analysis showed that deficiency in the ATP synthase protein complex amount is generally accompanied by only minor changes in expression of ATP synthase related genes. It also suggested that the site (mtDNA vs nuclear DNA) and the severity (ATP synthase content) of the underlying defect have diverse effects on cellular gene expression phenotypes, which warrants further investigation of cell cycle regulatory and signal transduction pathways in other OXPHOS disorders and related pharmacological models.</p

Characterization of Mitochondrial Respiratory Chain Defects Using DNA Microarrays

A mitochondrion is a organelle under nuclear and mitochondrial genetic control and its maintence requires a nucleo-mitochnodrial cross-talk. Better understanding of mitochondrial pahologies using various gene expression techniques. This thesis presents the implementation and application of microarray technology for identification of disease causing genes in respiratory chain disorders, expecially in patients with ATP synthase deficiency of nuclear origin. The introduction to this thesis provides an overview of mitochondrial structure and biogenesis, respiratory chain complexes and their disorders as well as different types of microarrays. A study of mitochondrial ATP synthase deficiency represents the major experimental part of this thesis and is accordingly that were used in further studies centered on characterization of inherited metabolic disorders. This is documented in positional cloning of patientes with lysosomal storage disorders - mucopolysaccharidosis IIIC

Design and Optimization of the Mitochondrial Chip

Katedra genetiky a mikrobiologieDepartment of Genetics and MicrobiologyFaculty of SciencePřírodovědecká fakult

Studium regulace a poruch mitochondriálních funkcí pomoci DNA čipu

Poruchy respiračního řetězce jsou zpravidla způsobeny ztrátou aktivity jednoho případně několika specifických enzymů nebo poruchou transportu proteinů. Tyto poruchy představují širokou skupinu onemocnění s rozsáhlým spektrem patologických stavů, které se liší věkem nástupu onemocnění, závažností a klinickým fenotypem. Jejich diagnostika musí být komplexní a vyžaduje využití nových genetických a genomických technik, které tento proces urychlují a zefektivňují. Jedním z těchto genomickcých nástrojů pro kvalitativní a kvantitativní analýzu nukleových kyselin je technologie DNA čipů. Tato technologie je nyní využívána nejen v základním výkumu, ale také v klinické diagnostice a to v několika modifikacích, jako je analýza genové exprese, detekce polymorfismů, komparativní genomová hybridizace nebo detekce mutací. Tato dizertační práce se zabývá vývojem a následnou aplikací čipové technologie ve studiích zaměřených na identifikaci a charakterizaci genů způsobujících závažná onemocnění. Realizované projekty byly zaměřeny především na porozumění mitochondriálním dědičným poruchám jaderného původu (poruchy ATP syntázy), an charakterizaci změn v mitochondriální giogenezi v ledvinných nádorových buňkách a na molekulární charakterizaci mukopolysacharidózy IIIC. Všechny výsledky dokumentují významnost čipové technologie...A mitochondrion is a organelle under nuclear and mitochondrial genetic control and its maintence requires a nucleo-mitochnodrial cross-talk. Better understanding of mitochondrial pahologies using various gene expression techniques. This thesis presents the implementation and application of microarray technology for identification of disease causing genes in respiratory chain disorders, expecially in patients with ATP synthase deficiency of nuclear origin. The introduction to this thesis provides an overview of mitochondrial structure and biogenesis, respiratory chain complexes and their disorders as well as different types of microarrays. A study of mitochondrial ATP synthase deficiency represents the major experimental part of this thesis and is accordingly that were used in further studies centered on characterization of inherited metabolic disorders. This is documented in positional cloning of patientes with lysosomal storage disorders - mucopolysaccharidosis IIIC.Institute of Inherited Metabolic Disorders First Faculty of Medicine Charles University in PragueÚstav dědičných metabolických poruch 1.LF a VFN v PrazeFirst Faculty of Medicine1. lékařská fakult

Investigating the effects of radiation, T cell depletion, and bone marrow transplantation on murine gut microbiota

Microbiome research has gained much attention in recent years as the importance of gut microbiota in regulating host health becomes increasingly evident. However, the impact of radiation on the microbiota in the murine bone marrow transplantation model is still poorly understood. In this paper, we present key findings from our study on how radiation, followed by bone marrow transplantation with or without T cell depletion, impacts the microbiota in the ileum and caecum. Our findings show that radiation has different effects on the microbiota of the two intestinal regions, with the caecum showing increased interindividual variation, suggesting an impaired ability of the host to regulate microbial symbionts, consistent with the Anna Karenina principle. Additionally, we observed changes in the ileum composition, including an increase in bacterial taxa that are important modulators of host health, such as Akkermansia and Faecalibaculum. In contrast, radiation in the caecum was associated with an increased abundance of several common commensal taxa in the gut, including Lachnospiraceae and Bacteroides. Finally, we found that high doses of radiation had more substantial effects on the caecal microbiota of the T-cell-depleted group than that of the non-T-cell-depleted group. Overall, our results contribute to a better understanding of the complex relationship between radiation and the gut microbiota in the context of bone marrow transplantation and highlight the importance of considering different intestinal regions when studying microbiome responses to environmental stressors

In Vitro Model of Human Trophoblast in Early Placentation

The complex process of placental implantation and development affects trophoblast progenitors and uterine cells through the regulation of transcription factors, cytokines, adhesion receptors and their ligands. Differentiation of trophoblast precursors in the trophectoderm of early ontogenesis, caused by the transcription factors, such as CDX2, TEAD4, Eomes and GATA3, leads to the formation of cytotrophoblast and syncytiotrophoblast populations. The molecular mechanisms involved in placental formation inside the human body along with the specification and differentiation of trophoblast cell lines are, mostly due to the lack of suitable cell models, not sufficiently elucidated. This review is an evaluation of current technologies, which are used to study the behavior of human trophoblasts and other placental cells, as well as their ability to represent physiological conditions both in vivo and in vitro. An in vitro 3D model with a characteristic phenotype is of great benefit for the study of placental physiology. At the same time, it provides great support for future modeling of placental disease

Investigating the effects of radiation, T cell depletion, and bone marrow transplantation on murine gut microbiota.

Microbiome research has gained much attention in recent years as the importance of gut microbiota in regulating host health becomes increasingly evident. However, the impact of radiation on the microbiota in the murine bone marrow transplantation model is still poorly understood. In this paper, we present key findings from our study on how radiation, followed by bone marrow transplantation with or without T cell depletion, impacts the microbiota in the ileum and caecum. Our findings show that radiation has different effects on the microbiota of the two intestinal regions, with the caecum showing increased interindividual variation, suggesting an impaired ability of the host to regulate microbial symbionts, consistent with the Anna Karenina principle. Additionally, we observed changes in the ileum composition, including an increase in bacterial taxa that are important modulators of host health, such as Akkermansia and Faecalibaculum. In contrast, radiation in the caecum was associated with an increased abundance of several common commensal taxa in the gut, including Lachnospiraceae and Bacteroides. Finally, we found that high doses of radiation had more substantial effects on the caecal microbiota of the T-cell-depleted group than that of the non-T-cell-depleted group. Overall, our results contribute to a better understanding of the complex relationship between radiation and the gut microbiota in the context of bone marrow transplantation and highlight the importance of considering different intestinal regions when studying microbiome responses to environmental stressors