Virus phylogeography at the wild/domestic animal interface

With the recent advances in sequencing technology it is increasingly common to find freely available large genomic datasets composed of thousands of genetic samples of viral or bacterial origin. Because Bayesian approaches possess multiple advantages against more traditional phylogenetic methods, such methods are considered as a standard tool to study the evolution and circulation of fast-evolving pathogens such as viruses. With those Bayesian phylogenetic approaches, the evolutionary and transmission parameters of fast evolving infectious diseases can be estimated to inform their control of in both epidemic and endemic contexts. Zoonoses are diseases that have passed from a non-human animal to a human population. The emergence of such diseases in human populations can be caused by environmental changes bringing wild and domestic animals closer to each other facilitating the transmission to humans. Phylogenetic approaches can help us to understand how disease can be transmitted between wild and domestic animal populations. Using recently developed Bayesian phylogenetic methods the first aim of this thesis was to understand and study the transmission of infectious disease amongst wild and domestic animal populations. Therefore, I performed those epidemiological analysis in an endemic context, using both Eurasian avian influenza sequences and African foot-and-mouth disease virus (FMDV). The second aim was to develop a software capable of reducing potential sampling bias between multiple populations while analysing large genetic datasets in a short running time compared to currently available phylogenetic methods. I first studied the transmission and reassortment pattern of avian influenza within Europe and Asia using internal segments sequences (PB2) originated from wild and domestic birds. Using both a non-structured and structured coalescent approach I determined that the two continents constitute distinct demes that are sporadically connected. Most of the reassortment pattern observed occurred within western Europe and Eastern China. I also determined that while wild Anseriformes are responsible for most of the of the virus circulation in Europe, domestic Anseriformes birds are responsible for the virus movements in Asia. The circulation of the virus between Asia and Europe being mostly done by both domestic and wild Anseriformes birds. Secondly, to understand the patterns of FMDV, I compared the transmission patterns of four FMDV (FMDO, FMDA, FMD SAT1, FMD SAT2) serotypes and estimated the factors influencing the circulation of these viruses in Africa using a discrete and a continuous phylogeographic approach. One conclusion of this chapter is that FMDV strains currently circulating in African livestock were probably introduced in the early 18th century trough livestock movements for the serotype A/O and reintroduced from wild Buffalo population after the African rinderpest epidemic for the SAT serotypes. I also show that movements of domestic cattle were responsible of the FMDV propagation and circulation in Africa with a small role played by wild animal populations. Thirdly, using advanced Bayesian structured coalescent model approximations, I studied the role played by antelope in the transmission of FMDV SAT1 and SAT2 in Africa. I found that for both serotypes antelopes seem to act as an intermediate host between buffalo and cattle. In the last part of the thesis I present a new software “Epitree-sim” that allows the fast estimation of phylogenetic trees and transmission patterns between demes using a fast dating algorithm and repeated subsampling of the sequence analysed

Kiri tundmatule

Duchatel de Tanneguy, Charles Marie, 1803-1867, prantsuse riigitegelaneTänukir

Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data

When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies. </p

A review of the anti-tumor potential of current therapeutics targeting the mitochondrial protease ClpP in H3K27-altered, diffuse midline glioma

Diffuse midline gliomas (DMGs) are devastating pediatric brain tumors recognized as the leading cause of cancer-related death in children. DMGs are high-grade gliomas (HGGs) diagnosed along the brain's midline. Euchromatin is the hallmark feature of DMG, caused by global hypomethylation of H3K27 either through point mutations in histone H3 genes (H3K27M), or by overexpression of the enhancer of zeste homolog inhibitory protein (EZHIP). In a clinical trial for adults with progressive HGGs, a 22-year-old patient with a thalamic H3K27-altered DMG, showed remarkable clinical and radiological responses to dordaviprone (ONC201). This response in a H3K27-altered HGG patient, coupled with the lack of response of patients harboring wildtype-H3 tumors, has increased the clinical interest in dordaviprone for the treatment of DMG. Additional reports of clinical benefit have emerged, but research defining mechanisms of action (MOA) fall behind dordaviprone's clinical use, with biomarkers of response unresolved. Here, we summarize dordaviprone's safety, interrogate its preclinical MOA- identifying the mitochondrial protease 'ClpP' as a biomarker of response, and discuss other ClpP-agonists, expanding the arsenal of potential weapons in the fight against DMG. Finally, we discuss combination strategies including ClpP-agonists, and its immunomodulatory effects suggestive of a role for the tumor microenvironment in DMG patients' response

In Utero Development of the Fetal Gall Bladder in the Korean Population

OBJECTIVE: To provide reference ranges of the fetal gall bladder in the Korean population. MATERIALS AND METHODS: Fetal gall bladder development was evaluated in well-dated, non-anomalous fetuses in the Korean population between February and April 2003 and the visualization rate and reference values were determined from the obtained data. RESULTS: The visualization rate of the fetal gall bladder increased as gestation advanced to a plateau above 90%, which was maintained between 16 and 34 weeks. The measured parameters from the fetal gall bladder had a significant positive relationship with gestational age (p = 0.000 for all cases), and the correlation of length and area with the gestational age (r = 0.741 and r = 0.690, respectively) was better than the correlation of width, height, and volume with gestational age. The repeatability coefficients and coefficients of variation between the two operators were 5.56 mm and 12.9% for the length and 344.11 mm(2) and 33.52% for the area. The median length of the fetal gall bladder in the Korean population was not significantly different from the mean length of gall bladders in the Caucasian and African-American populations (p = 0.915). CONCLUSION: We have provided reference values for the fetal gall bladder throughout the gestation period in the Korean population

Shwachman-Bodian-Diamond syndrome (SBDS) protein is a direct inhibitor of protein phosphatase 2A (PP2A) activity and overexpressed in acute myeloid leukaemia.

Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase inactivated in many cancers including acute myeloid leukaemia (AML). Activation of PP2A is emerging as a therapeutic strategy, however the mechanisms underpinning PP2A inhibition are not well understood. Using myeloid progenitor cells harbouring oncogenic mutant c-KIT and characterised by PP2A inhibition, we have identified the ribosome biogenesis protein SBDS, as a target of the PP2A activating drugs FTY720 and AAL(S). We show SBDS binds to PP2A complexes comprised of the B55α regulatory subunit of PP2A. shRNA mediated knockdown of SBDS increased PP2A activity and induced apoptosis. At diagnosis, AML patients expressed significantly more SBDS mRNA than healthy controls, with relapsed patients expressing significantly more SBDS mRNA than both healthy controls and patients at diagnosis. Together, our data presents a role for SBDS in the dysregulation of PP2A in AML

Preclinical and clinical evaluation of German-sourced ONC201 for the treatment of H3K27M-mutant diffuse intrinsic pontine glioma

Background Diffuse intrinsic pontine glioma (DIPG) is a fatal childhood brainstem tumor for which radiation is the only treatment. Case studies report a clinical response to ONC201 for patients with H3K27M-mutant gliomas. Oncoceutics (ONC201) is only available in the United States and Japan; however, in Germany, DIPG patients can be prescribed and dispensed a locally produced compound-ONC201 German-sourced ONC201 (GsONC201). Pediatric oncologists face the dilemma of supporting the administration of GsONC201 as conjecture surrounds its authenticity. Therefore, we compared GsONC201 to original ONC201 manufactured by Oncoceutics Inc. Methods Authenticity of GsONC201 was determined by high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy. Biological activity was shown via assessment of on-target effects, in vitro growth, proliferation, and apoptosis analysis. Patient-derived xenograft mouse models were used to assess plasma and brain tissue pharmacokinetics, pharmacodynamics, and overall survival (OS). The clinical experience of 28 H3K27M+ mutant DIPG patients who received GsONC201 (2017-2020) was analyzed. Results GsONC201 harbored the authentic structure, however, was formulated as a free base rather than the dihydrochloride salt used in clinical trials. GsONC201 in vitro and in vivo efficacy and drug bioavailability studies showed no difference compared to Oncoceutics ONC201. Patients treated with GsONC201 (n = 28) showed a median OS of 18 months (P = .0007). GsONC201 patients who underwent reirradiation showed a median OS of 22 months compared to 12 months for GsONC201 patients who did not (P = .012). Conclusions This study confirms the biological activity of GsONC201 and documents the OS of patients who received the drug; however, GsONC201 was never used as a monotherapy

ONC201 in combination with paxalisib for the treatment of H3K27-altered diffuse midline glioma

Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPGs), are the most lethal of childhood cancers. Palliative radiotherapy is the only established treatment, with median patient survival of 9-11 months. ONC201 is a DRD2 antagonist and ClpP agonist that has shown preclinical and emerging clinical efficacy in DMG. However, further work is needed to identify the mechanisms of response of DIPGs to ONC201 treatment and to determine whether recurring genomic features influence response. Using a systems-biological approach, we showed that ONC201 elicits potent agonism of the mitochondrial protease ClpP to drive proteolysis of electron transport chain and tricarboxylic acid cycle proteins. DIPGs harboring PIK3CA-mutations showed increased sensitivity to ONC201, while those harboring TP53-mutations were more resistant. Metabolic adaptation and reduced sensitivity to ONC201 was promoted by redox-activated PI3K/Akt signaling, which could be counteracted using the brain penetrant PI3K/Akt inhibitor, paxalisib. Together, these discoveries coupled with the powerful anti-DIPG/DMG pharmacokinetic and pharmacodynamic properties of ONC201 and paxalisib have provided the rationale for the ongoing DIPG/DMG phase II combination clinical trial NCT05009992