Chronic kidney disease (CKD) is a common disease that affects millions across the US and the globe. Patients with CKD experience an increased risk of venous thrombosis. Here we use two longstanding robust murine models of nephropathies in conjunction with a reliable murine model of venous thrombosis to model venous thrombosis risk in CKD. We show that in the adenine diet-induced CKD, increased concentrations of adenine in the diet result in increased histological evidence of nephropathy and increased venous thrombosis risk assessed by Inferior Vena Cava ligation. Next, we demonstrate that in unilateral ureteric obstruction models, the duration of obstruction is proportional to the nephropathies developed by histological assessment. In both models, we relate nephropathy to venous thrombosis risk. When probed for aryl hydrocarbon receptor (AHR) activation, adenine diet-induced CKD mice show increased activation assessed by nuclear translocation of the receptor. This phenotype was confirmed in vitro when treating human telomerase immortalized human umbilical endothelial cells with uremic serum. Nuclear AHR was not observed in control conditions in vivo or in vitro. Pharmacologic AHR inhibition using a novel drug, BAY Compound, and a well-known AHR inhibitor were both able to abrogate uremic activation of AHR in vitro, which was then corroborated with in vivo studies. Tissue factor (TF) and plasminogen activator inhibitor 1 (PAI-1) are prothrombogenic proteins linked to AHR activation. TF and PAI-1 showed upregulation in CKD mice which were blocked when CKD mice were given AHR inhibitor BAY Compound. This work demonstrates a unique model of venous thrombosis in CKD and suggests that AHR inhibition may be able to limit the elevated risk of venous thrombosis associated with uremia. / 2026-03-08T00:00:00Z

During recent years, significant advances have been made in the field of molecular therapy in urologic oncology, mainly for advanced renal cell carcinoma. In this hitherto largely treatment-refractory disease, several agents have been developed targeting the von Hippel-Lindau metabolic pathway which is involved in carcinogenesis and progression of the majority of renal cell carcinomas. Although cure may not be expected, new drugs, such as the multikinase inhibitors sorafenib and sunitinib and the mammalian target of rapamycine inhibitor temsirolimus, frequently stabilize the disease course and may improve survival. Fewer data are available supporting molecular therapies in prostate, bladder, and testicular cancers. Preliminary data suggest a potential role of high-dose calcitriol and thalidomide in hormone-refractory prostate cancer, whereas targeted therapies in bladder and testicular cancers are still more or less limited to single-case experiences. The great theoretical potential and the multitude of possible targets and drug combinations, however, support further research into this exciting field of medical treatment of urologic malignancies. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

During recent years, significant advances have been made in the field of molecular therapy in urologic oncology, mainly for advanced renal cell carcinoma. In this hitherto largely treatment-refractory disease, several agents have been developed targeting the von Hippel-Lindau metabolic pathway which is involved in carcinogenesis and progression of the majority of renal cell carcinomas. Although cure may not be expected, new drugs, such as the multikinase inhibitors sorafenib and sunitinib and the mammalian target of rapamycine inhibitor temsirolimus, frequently stabilize the disease course and may improve survival. Fewer data are available supporting molecular therapies in prostate, bladder, and testicular cancers. Preliminary data suggest a potential role of high-dose calcitriol and thalidomide in hormone-refractory prostate cancer, whereas targeted therapies in bladder and testicular cancers are still more or less limited to single-case experiences. The great theoretical potential and the multitude of possible targets and drug combinations, however, support further research into this exciting field of medical treatment of urologic malignancies. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Die Verwendung von nukleinsäuretemplatgesteuerten Reaktionen stellt einen innovativen Ansatz zur Therapie von Krankheiten dar, deren Ursprung in einer genetischen Veränderung von Zellen liegt. Im Rahmen der hier vorliegenden Arbeit erfolgte eine Weiterentwicklung der RNA-templatgesteuerten Acyltransferreaktion nach Seitz et al. hinsichtlich des Aufbaus von aromatischen Amidbindungen, wie sie in vielen niedermolekularen Wirkstoffen vorkommen. Als Modellverbindungen dienten die Bcr-Abl-Tyrosinkinaseinhibitoren Nilotinib, Ponatinib und GZD824, die durch zentrale Benzanilidmotive charakterisiert sind und zur Therapie der chronischen myeloischen Leukämie eingesetzt werden. Das konzipierte Reaktionssystem beruht auf dem Mechanismus der nativen chemischen Ligation, weswegen die Bcr-Abl-Inhibitoren durch die Einführung einer Thiolgruppe modifiziert werden mussten. Es wurde gezeigt, dass diese Modifikation in den meisten Fällen nur zu einer geringen Beeinträchtigung der biologischen Aktivität führt. Der RNA-templatgesteuerte Aufbau der Benzanilidstrukturen konnte sowohl mit PNA- als auch mit DNA-verknüpften Inhibitorfragmenten basierend auf Ponatinib und GZD824 erzielt werden. In Gegenwart eines komplementären RNA-Templats erfolgte die benachbarte Hybridisierung der reaktiven Konjugate, infolgedessen ein Benzoyltransfer von einem thioestermodifizierten Donor auf ein ortho-Mercaptoanilinderivat als Akzeptor stattfand. Mit PNA/PNA-Reaktionssystemen wurde auch in Abwesenheit des RNA-Templats eine signifikante Produktbildung beobachtet, was auf hydrophobe Wechselwirkungen der Konjugate zurückgeführt wurde. Unter Verwendung von DNA/DNA- bzw. PNA/DNA-Konjugatpaaren blieb die templatunabhängige Produktbildung hingegen ausreichend gering. Die entsprechenden Reaktionssysteme wurden hinsichtlich der erzielten Produktausbeuten optimiert, wobei sowohl die Linkerlänge bzw. -struktur der reaktiven Konjugate als auch die Templatarchitektur variiert wurde. / The use of nucleic acid-templated reactions represents an innovative approach to the therapy of diseases that originate in genetic alterations of cells. In this work, the RNA-templated acyl transfer reaction invented by Seitz et al. was extended towards the formation of aromatic amide bonds which occur in a variety of small molecule drugs. The Bcr-Abl tyrosine kinase inhibitors nilotinib, ponatinib, and GZD824 were used as model compounds, as they are characterized by central benzanilide motifs and find application in the treatment of chronic myeloid leukemia. The designed reaction system is based on the mechanism of native chemical ligation which required the modification of the Bcr-Abl inhibitors by introducing a thiol group. It was shown that thiolation affected the biological activity only moderately. The RNA-templated formation of the benzanilide structures was achieved with both PNA- and DNA-linked inhibitor fragments of ponatinib and GZD824. The presence of a complementary RNA template enabled adjacent binding of the reactive conjugates, triggering a rapid benzoyl transfer from a thioester-linked donor to an ortho-mercaptoaniline derivative as an acceptor. With PNA/PNA reaction systems, significant product formation was observed in absence of the RNA template, which was attributed to hydrophobic interactions between the conjugates. However, the template-independent product formation remained low when DNA/DNA or PNA/DNA conjugate pairs were used. The product yields of the corresponding reaction systems were optimized by varying the linker length and structure of the conjugates as well as the template architecture.

<p dir="ltr">The eukaryotic genome is organized and packaged into DNA-protein complexes called chromatin. Nucleosomes, the repeating unit of chromatin, are composed of DNA in complex with histone octamers containing two of each of the four core histones, the H2A, H2B, H3, and H4. Accessibility of nucleosomal DNA by other DNA-binding proteins can be regulated, in-part, by the type and level of nucleosome-associated post-translational modifications (PTMs). PTMs, such as acetylation of lysine residues, including H3K9, H3K14, and H4K16, can neutralize their positive charge, thereby reducing the affinity of acetylated histones for the negatively charged DNA sugar phosphate backbone. This, in turn, promotes the formation of relaxed open chromatin which is crucial for the accessibility of DNA by the transcription machinery. Consequently, histone acetylation is associated with active gene expression, while deacetylation, which restores positive charges of lysine residues, is linked with condensed chromatin structure, and the associated decrease in gene expression. Other PTMs such as histone methylation on H3K9, which prevents H3K9 acetylation, promotes gene silencing via serving as a binding site for HP1, a structural component of silenced heterochromatin. Interestingly, this epigenetic control of gene expression, typically used to regulate endogenous genes, also influences ectopic gene expression in host cells. Transgenes delivered into target cells undergo host cell-mediated assembly into chromatin. As a result, transgenes assembled into hypoacetylated condensed chromatin experience a dramatic loss of expression shortly after delivery into target cells. As part of this thesis, we assessed the impact of "priming" plasmid-based transgenes to adopt accessible chromatin states on transgene expression. Nucleosome positioning elements were introduced at promoters of transgenes, or vectors were pre-assembled into nucleosomes containing either unmodified histones or histone mutants mimicking constitutively acetylated states at residues H3K9 and H3K14, or H4K16 prior to their introduction into human cells. Transgene expression was then monitored by epifluorescence microscopy and flow cytometry over time. We found that DNA sequences capable of positioning nucleosomes influenced the expression of adjacent transgenes in a distance-dependent manner, even in the absence of pre-assembly into chromatin. Intriguingly, pre-assembly of plasmids into chromatin facilitated prolonged transgene expression compared to plasmids that were not pre-packaged into chromatin. Interactions between pre-assembled chromatin states and nucleosome positioning effects on reporter gene expression were also assessed. Overall, nucleosome positioning played a more significant role in influencing gene expression than priming with hyperacetylated chromatin states. These findings have direct relevance to ongoing efforts to develop durable plasmid-based gene therapies for genetically-derived disorders such as cancer.</p><p dir="ltr">In this thesis, we also explored the roles of the tumor suppressor enzyme fumarate hydratase (FH) in cellular responses to DNA replication stress. In humans, biallelic loss of function mutations in FH predisposes individuals to hereditary leiomyomatosis and renal cell carcinoma (HLRCC). However, the role of fumarase in HLRCC is not fully understood. The eukaryotic genome experiences thousands of lesions per cell each day, with DNA double-strand breaks (DSBs) being among the most deleterious. If unrepaired or repaired incorrectly, DSBs can lead to various disorders, including cell death and cancer. Cellular processes such as metabolism, transcription, and DNA replication are among the major endogenous sources of DSBs. Impediments to DNA replication that result in persistent stalling of replication forks can lead to fork collapse, thereby exposing unprotected single-stranded DNA (ssDNA) to endonuclease attack and the formation of double-strand breaks (DSBs). DNA-protein crosslinks that form irreversible complexes, an imbalance or exhaustion of deoxynucleotides (dNTPs), as well as the presence of inherently difficult-to-replicate genomic regions such as common fragile sites (CFSs), are some of the many obstacles that can halt fork progression. Intrinsically, however, all organisms have evolved response mechanisms designed to sense, prevent, detect, and resolve the different sources of DNA replication stress. These response mechanisms are governed by the highly conserved DNA replication checkpoint (DRC), a part of the intra-S phase checkpoint. The main function of the DRC is to halt cell cycle progression and activate DNA damage responses, such as DNA repair and subsequent replication fork restart. The highly conserved tricarboxylic acid (TCA) cycle enzyme fumarase (FH in humans, Fum1p in yeast), which functions to convert fumarate to malate in the mitochondrial TCA cycle, has been implicated in DRC responses in the cell’s nucleus. Upon exposure of yeast model organism to hydroxyurea (HU), an inhibitor of ribonucleotide reductase (RNR) that results in the exhaustion of cellular dNTPs, the expression of Fum1p is upregulated and Fum1p is translocated to the nucleus. Fum1p’s metabolite fumarate suppresses sensitivity to HU in yeast in a manner independent of modulating cellular dNTP levels. Notwithstanding, our understanding of these extra-mitochondrial functions of fumarase remains incomplete. For example, the nature of the impediments to DNA replication that are affected by fumarase is presently unclear. In addition, across all eukaryotes, fumarase lacks a canonical nuclear localization signal, and the means of its nuclear translocation upon DNA replication stress remain a mystery. In this study, our immunofluorescence experiments revealed that, similar to yeast, exposure of human cells to HU promoted the nuclear translocation of fumarase. We also performed Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) using human cells exposed to DNA replication stress by HU to identify replication stress-dependent protein-protein interactions of FH. We observed that FH co-precipitated MUS81, a structure-specific endonuclease and a crucial component of cellular responses to DNA replication stress. MUS81 is localized to stalled replication forks during the S phase of the cell cycle, where it cleaves the three-way junctions created by stalled forks. MUS81 also functions to resolve recombination intermediates and Holliday junctions (HJs) during the S phase. MUS81 also localizes at common fragile sites (CFSs) during the G2/M phase. CFSs are genomic regions that are difficult-to-replicate, late-replicating, and tend to exit the S phase with under-replicated DNA. These CFSs are targeted by MUS81, cleaved, and replicated via Break-Induced Replication (BIR) that is dependent on POLD3 in a process called mitotic DNA synthesis (MiDAS). In our immunofluorescence studies, we observed that HLRCC-derived cancer cells expressing low levels of catalytically inactive fumarase exhibited bulky anaphase bridges. These observations are especially intriguing because the loss of MUS81 or inhibition of POLD3 is known to increase the frequency of bulky anaphase bridges, a phenotype associated with defects in MiDAS. Additionally, we observed that exposure of fumarase-deficient cells to aphidicolin (APH), an inhibitor of POLD3, dramatically increased the frequency of anaphase bridges. Furthermore, we found that upon exposure of human cells to APH, fumarase translocated to the nucleus. Whether fumarase suppresses the MiDAS defects observed in HLRCC cells is still under investigation. Taken together, the work described herein uncovers previously unknown roles of fumarase in DNA damage responses and provides direct links toward understanding how fumarase may function to safeguard genomic integrity.</p>