Graduate School of Life Sciences
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Background: Integrase strand transfer inhibitors (INSTIs) are the latest addition to the array of antiretroviral compounds used to treat an infection with Human Immunodeficiency Virus (HIV). Due to their high efficacy and increased tolerability, INSTIs have become an integral part of first-line therapy in most high-income countries over the past years. However, little is known about HIV-1’s genetic inter- and intra-subtype diversity on the Integrase (IN)-gene and its impact on the emergence of INSTI-resistance. In the absence of a functional cure, long-term efficacy of first-line compounds remains paramount for reducing virological failure and curbing on-going HIV transmissions. South Africa, harbouring more than 20% of the global HIV burden (7.7 / 37.9 million people), requires international attention in order to globally pursue UNAIDS’ (Joint United Nations Programme on HIV/AIDS) 90-90-90 goals and the road to ending the HIV/AIDS (Acquired immunodeficiency syndrome) pandemic by 2030.
Methods: In this study, the prevalence of INSTI-resistance associated mutations (RAM) was investigated in a cohort of 169 archived drug-naïve blood samples from multiple collection sites around Cape Town, South Africa. Viral RNA was isolated from plasma samples, the integrase fragment amplified by RT-PCR and subsequently sequenced by Sanger-sequencing. Additionally, all publicly available drug-naïve, South African IN sequences, isolated before the availability of the first INSTIs in 2007, were retrieved from the Los Alamos HIV sequence database (n=284). All sequences were analysed for RAMs using the Stanford HIV Drug resistance database. The identification of polymorphism in the South African subtype C IN consensus sequence allowed for comparative analyses with global subtype B, as well as subtype C sequences, from countries other than South Africa.
Results: The IN gene could be amplified and sequenced in 95/169 samples (56%). Phylogenetic inference revealed close homology between three sequence-pairs, warranting the exclusion of 3/95 sequences from further analyses. Of the 92 samples used for mutational analyses, 86/92 (93.5%) belonged to subtype C, 5/92 (5.4%) to subtype B and 1/92 (1.1%) to subtype A. The prevalence of major and accessory INSTI RAMs was 0/92 (0%) and 1/91 (1.1%), respectively, similar to the observed rates of 8/284 (2.8%) and 8/284 (2.8%) in the database sequences (p = 0.2076 and p = 0.6944, Fisher’s exact test). Compared to subtype B IN sequences, 15 polymorphisms were significantly enriched in South African subtype C sequences (corrected p<0.0015. Fisher’s exact test, Bonferroni post-hoc procedure).
Compared to subtype C IN sequences isolated outside South Africa, four polymorphisms were significantly enriched in this study cohort (corrected p<0.0014, Fisher’s exact test, Bonferroni post-hoc procedure). The highest prevalence margin was observed for the polymorphism Met50Ile being present in 60.1% of South African subtype C sequences, compared to 37% in non-South African subtype C sequences.
Conclusions: The low prevalence of major and minor RAMs in all South African Integrase sequences predicts a high susceptibility to INSTIs, however, the presence of natural polymorphisms, in particular Met50Ile, in the majority of sequences warrants further monitoring under therapeutic pressure, as their role in mutational pathways leading to INSTI- resistance is yet to be determined. Additionally, this study revealed the presence of substantial inter- and intra-subtype diversity within the HIV-1 Subtype C IN-gene. These results implicate the need for more research on a regional, potentially patient-specific level, as mutational insights from other diverse backgrounds may not accurately represent the South African context. The implementation of a national pre-treatment INSTI-resistance screening program may provide necessary insights into the development of mutational pathways leading to INSTI-resistance under therapeutic pressure for the South African context and thereby bring South Africa one step closer to achieving UNAIDS 90-90-90 goals and ending the AIDS epidemic by 2030.
Modulation CD4+ humaner Treg- und Tconv-Zellen durch Inhibition der sauren Sphingomyelinase in vitro
(2020)
Die saure Sphingomyelinase (ASM) stellt durch die Umwandlung von Sphingomyelin in Ceramid und Phosphorylcholin ein zentrales, fein reguliertes Enzym im Sphingolipidmetabolismus dar. Dadurch nimmt es Einfluss auf verschiedene zelluläre Mechanismen wie Signalvermittlung, Endo- und Exozytose und Zellaktivierung. Dementsprechend weitreichend ist auch die Bedeutung der ASM bei verschiedenen Krankheiten wie Arteriosklerose, Depression oder Neoplasien. Auch auf das Immunsystem, insbesondere auf die Signalvermittlung durch T-Zellen innerhalb des adaptiven Immunsystems, nimmt die saure Sphingomyelinase Einfluss. Aufbauend auf früheren Forschungsarbeiten zur pharmakologischen und genetischen Hemmung der ASM im Mausmodell untersuchten wir, welche Auswirkungen die Hemmung dieses Enzyms in humanen Zellkulturen auf die Population regulatorischer und konventioneller T-Zellen haben. Hierzu verwendeten wir die beiden selektiven Serotonin-Wiederaufnahmehemmer Sertralin und Citalopram; zwei antidepressiv wirksame Medikamente, die durch eine Verdrängung der ASM von der lysosomalen Membran eine hemmende Wirkung ausüben. Wir konnten zeigen, dass diese beiden Substanzen sowohl in Maus-T-Zellen, als auch in humanen T-Zellen, in der Lage sind, die Aktivität der sauren Sphingomyelinase zu inhibieren. Durch Kultivierung von Immunzellen der Maus zusammen mit den Inhibitoren konnte darüber hinaus eine Erhöhung der Treg-Zellfrequenz erreicht werden. Verschiedene Zellkulturexperimente mit humanen PBMCs zeigten weiterhin, dass unter gewissen Umständen so auch eine Vermehrung regulatorischer T-Zellen im Menschen möglich ist, und dass dies mutmaßlich durch Einbindung der ASM im CD3/CD28-Signalweg bedingt ist. In mit AntiCD3-Antikörper stimulierten experimentellen Ansätzen kam es jedoch nur bei einzelnen Individuen, die als Responder identifiziert werden konnten, zu einer Treg-Zellvermehrung. Umgekehrt kam es durch externe Zugabe von C6-Ceramid zu einer Verringerung des Anteils an regulatorischen T-Zellen. Des Weiteren wurden verschiedene Veränderungen im Expressionsverhalten von Treg- und Tconv-Zellen bezüglich CD25, CD69 und CTLA-4 in Anwesenheit der ASMInhibitoren beobachtet. Weiterhin bestätigte sich, dass die pharmakologische Hemmung der sauren Sphingomyelinase auch Auswirkungen auf die Effektorfunktion von T-Zellen hat. Während die Proliferation der Zellen weitgehend unbeeinträchtigt blieb, kam es zu einer verringerten Sekretion der Zytokine IFN-gamma, TNF, IL-5 und IL-10. In ihrer Gesamtheit sprechen diese Ergebnisse dafür, dass Inhibitoren der sauren Sphingomyelinase begünstigend auf Krankheitsgeschehen mit überschießender oder dysregulierter Aktivität des Immunsystems einwirken könnten. Immunmodulatorischen Wirkungen durch Inhibition der ASM erklären möglicherweise auch Einflüsse auf das Immunsystem, die für verschiedene Antidepressiva beschrieben wurden. Insgesamt ist die Bedeutung der sauren Sphingomyelinase innerhalb der Regulation des adaptiven Immunsystems jedoch noch ein weitgehend ungeklärtes Thema mit vielen offenen Fragen. Daher ist auch in Zukunft weitere klinische und experimentelle Forschung erforderlich, um zu klären, welchen Einfluss dieses Enzyms auf Immunzellen hat und wie sich dieser auch klinisch anwenden lässt.
Genome-wide association studies revealed CLEC16A as a candidate gene for Type 1 Diabetes and multiple other autoimmune disorders. The function of CLEC16A remains unknown. However, previous work showed that the CLEC16A ortholog ema and the murine Clec16a were both implicated in autophagy, a process partially required for MHC class II loading and antigen presentation. Furthermore, studies could show that autophagy was required in thymic epithelial cells for antigen presentation during T cell selection, suggesting a possible role of CLEC16A in T cell selection in the thymus. Additionally, it was postulated that CLEC16A may function as an expression quantitative trait locus for its neighboring genes and that Clec16a KD was involved in pancreatic islet function and impaired insulin secretion and glucose homeostasis. Prior to this work, Schuster et al. had created a Clec16a KD NOD mouse, which was protected from spontaneous autoimmune diabetes.
For this work it was hypothesized that CLEC16A variation serves as a Type 1 Diabetes risk gene by affecting autophagy in thymic epithelial cells, which modulates antigen presentation and shapes the T cell repertoire. To expand and complement previous findings by Schuster et al., this thesis aimed to investigate how CLEC16A modifies the function of thymic epithelial cells. For this purpose, CLEC16A KD was induced in human cells via RNA interference and autophagy was studied through immunoblotting. Additionally, inflammation of pancreatic tissue in Clec16a KD NOD mice was scored using H.E. stained pancreatic sections. Thymic transplantation experiments were conducted to test whether the effects of Clec16a KD were T cell intrinsic. Also, intraperitoneal glucose tolerance tests were performed to study glucose homeostasis in Clec16a KD NOD animals. Finally, using qPCR, gene expression levels of neighboring genes such as Dexi and Socs1 were measured to study Clec16a as an expression quantitative trait locus.
In combination with the findings of Schuster et al., this thesis demonstrates that Clec16a KD reduces the severity of insulitis and protects from onset of spontaneous diabetes in the NOD mouse. Disease protection is conveyed by impaired autophagy in TEC, which leads to altered T cell selection and hyporeactive CD4+ T cells. The effects of Clec16a KD in the NOD mouse are thymus intrinsic. Glucose homeostasis remains unchanged in the Clec16a KD NOD mouse and plays no role in disease protection. Clec16a and Dexi presented similar expression levels, but further studies are required to investigate a clear link between these two genes. Finally, impaired autophagy could be replicated in human CLEC16A KD cells, which demonstrates a conserved function of CLEC16A and suggests a possible link between CLEC16A variation and risk of autoimmune disease in human.