Tissue- and site-specific effects of PPARγ activation and its role in chronic inflammation

Developmental programming, metabolism, immune function and tissue homeostasis in multicellular organisms are regulated by a plethora of stimuli. Transcription factors (TFs) convert incoming signals to appropriate transcriptional responses of the genome. Nuclear receptors (NRs), a particular family of TFs, are especially well suited for this task given their capacity to influence gene regulation in multiple tissues and conditions. In this work, I addressed how environmental cues affect the expression of NRs and how gene regulation is mediated in different tissues. My thesis comprises a set of four separate manuscripts of which the first paper established how an important environmental factor, the gut microbiome, modulates NRs, including the peroxisome proliferator-activated receptor gamma (PPARγ), in vivo. The ligand-activated TF PPARγ is a key regulator of adipogenesis and glucose homeostasis, and possesses profound anti-inflammatory properties. In the subsequent manuscripts (paper II-IV), I have used PPARγ as a model to gain insights into the mechanisms that guide tissue-specific activity of NRs on a genome-wide level. To this end I have identified PPARγ binding sites in a genomewide manner using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq) in adipocytes, macrophages and intestinal epithelium. These data were superimposed with information from gene-expression profiling to facilitate identification of direct PPARγ target genes. Specifically, our comprehensive genomic analysis of PPARγ binding during adipogenesis confirmed the role of PPARγ as key regulator of this process and, potentially, revealed novel adipogenic target genes of PPARγ (paper II). In addition, an inter-species comparison of PPARγ binding sites in human and mouse macrophages identified a core set of conserved PPARγ targets. In this study we also identified PU.1 as a co-factor necessary for PPARγ function in macrophages (paper III). In the final manuscript, I mapped the genomic landscape of PPARγ-DNA interactions in intestinal epithelial cells (paper IV). These studies revealed that PPARγ antagonizes the WNT/TCF4 signaling pathways potentially identifying a mechanism by which activation of PPARγ affects cell fate of intestinal epithelial cells. My PhD work yielded important novel insights into general mechanisms related to PPARγ-dependent gene regulation. While in the tissues studied, PPARγ activation seemed to always induce a core set of lipid metabolic genes, tissue-specific utilization of PPARγ binding sites appeared to be dependent on cell type restricted transcription factors which may determine binding site accessibility at the chromatin level. My studies further suggest that the regulation of lipid metabolism is the evolutionary most conserved function of PPARγ and additional functions might have developed later, representing adaptations to changing metabolic needs and environmental challenges. While not studied in depth, our data on tissue-specific mechanisms of TF binding might also have implications for the interpretation of population-wide genetic studies. In conclusion, my work has revealed common principles that guide PPARγ activation in a tissue-dependent and -independent manner and has laid the fundament for further detailed molecular studies of NRs in general and PPARγ in particular

Evidence of a discontinuous disk structure around the Herbig Ae star HD 139 614

A new class of pre-main sequence objects has been recently identified as pre-transitional disks. They present near-infrared excess coupled to a flux deficit at about 10 microns and a rising mid-infrared and far-infrared spectrum. These features suggest a disk structure with inner and outer dust components, separated by a dust-depleted region (or gap). We here report on the first interferometric observations of the disk around the Herbig Ae star HD 139614. Its infrared spectrum suggests a flared disk, and presents pre-transitional features,namely a substantial near-infrared excess accompanied by a dip around 6 microns and a rising mid-infrared part. In this framework, we performed a study of the spectral energy distribution (SED) and the mid-infrared VLTI/MIDI interferometric data to constrain thespatial structure of the inner dust disk region and assess its possibly multi-component structure. We based our work on a temperature-gradient disk model that includes dust opacity. While we could not reproduce the SED and interferometric visibilities with a one-component disk, a better agreement was obtained with a two-component disk model composed of an optically thin inner disk extending from 0.22 to 2.3 au, a gap, and an outer temperature-gradient disk starting at 5.6 au. Therefore, our modeling favors an extended and optically thin inner dust component and in principle rules out the possibility that the near-infrared excess originates only from a spatially confined region. Moreover, the outer disk is characterized by a very steep temperature profile and a temperature higher than 300 K at its inner edge. This suggests the existence of a warm component corresponding to a scenario where the inner edge of the outer disk is directly illuminated by the central star. This is an expected consequence of the presence of a gap, thus indicative of a pre-transitional structure.Comment: 14 pages, 6 figure

A diversity of dusty AGN tori: Data release for the VLTI/MIDI AGN Large Program and first results for 23 galaxies

The AGN-heated dust distribution (the "torus") is increasingly recognized not only as the absorber required in unifying models, but as a tracer for the reservoir that feeds the nuclear Super-Massive Black Hole. Yet, even its most basic structural properties (such as its extent, geometry and elongation) are unknown for all but a few archetypal objects. Since most AGNs are unresolved in the mid-infrared, we utilize the MID-infrared interferometric Instrument (MIDI) at the Very Large Telescope Interferometer (VLTI) that is sensitive to structures as small as a few milli-arcseconds (mas). We present here an extensive amount of new interferometric observations from the MIDI AGN Large Program (2009 - 2011) and add data from the archive to give a complete view of the existing MIDI observations of AGNs. Additionally, we have obtained high-quality mid-infrared spectra from VLT/VISIR. We present correlated and total flux spectra for 23 AGNs and derive flux and size estimates at 12 micron using simple axisymmetric geometrical models. Perhaps the most surprising result is the relatively high level of unresolved flux and its large scatter: The median "point source fraction" is 70 % for type 1 and 47 % for type 2 AGNs meaning that a large part of the flux is concentrated on scales smaller than about 5 mas (0.1 - 10 pc). Among sources observed with similar spatial resolution, it varies from 20 % - 100 %. For 18 of the sources, two nuclear components can be distinguished in the radial fits. While these models provide good fits to all but the brightest sources, significant elongations are detected in eight sources. The half-light radii of the fainter sources are smaller than expected from the size ~ L^0.5 scaling of the bright sources and show a large scatter, especially when compared to the relatively tight size--luminosity relation in the near-infrared.Comment: A&A in press; 93 pages, 63 figures, 39 tables; data available only via CD

HD139614: the interferometric case for a group-Ib pre-transitional young disk

The Herbig Ae star HD 139614 is a group-Ib object, which featureless SED indicates disk flaring and a possible pre-transitional evolutionary stage. We present mid- and near-IR interferometric results collected with MIDI, AMBER and PIONIER with the aim of constraining the spatial structure of the 0.1-10 AU disk region and assess its possible multi-component structure. A two-component disk model composed of an optically thin 2-AU wide inner disk and an outer temperature-gradient disk starting at 5.6 AU reproduces well the observations. This is an additional argument to the idea that group-I HAeBe inner disks could be already in the disk-clearing transient stage. HD 139614 will become a prime target for mid-IR interferometric imaging with the second-generation instrument MATISSE of the VLTI.Comment: SPIE Astronomical Telescopes and Instrumentation conference, June 2014, 11 pages, 7 Figure

GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets

Help, my Signal has bad Device! Breaking the Signal Messenger’s Post-CompromiseSecurity through a Malicious Device

In response to ongoing discussions about data usage by companies and governments, and its implications for privacy, there is a growing demand for secure communication techniques. While during their advent, most messenger apps focused on features rather than security, this has changed in the recent years: Since then, many have adapted end-to-end encryption as a standard feature. One of the most popular solutions is the Signal messenger, which aims to guarantee forward secrecy (i.e. security of previous communications in case of leakage of long-term secrets) and future secrecy (i.e. security of future communications in case of leakage of short-term secrets). If every user uses exactly one device, it is known that Signal achieves forward secrecy and even post-compromise security (i.e. security of future communications in case of leakage of long-term secrets). But the Signal protocol also allows for the use of multiple devices via the Sesame protocol. This multi-device setting is typically ignored in the security analysis of Signal. In this work, we discuss the security of the Signal messenger in this multi-device setting. We show that the current implementation of the device registration allows an attacker to register an own, malicious device, which gives them unrestricted access to all future communication of their victim, and even allows full impersonation. This directly shows that the current Signal implementation does not guarantee post-compromise security. We discuss several countermeasures, both simple ones aiming to increase detectability of our attack, as well as a broader approach that seeks to solve the root issue, namely the weak device registration flow

ASAP: Algorithm Substitution Attacks on Cryptographic Protocols

The security of digital communication relies on few cryptographic protocols that are used to protect internet traffic, from web sessions to instant messaging. These protocols and the cryptographic primitives they rely on have been extensively studied and are considered secure. Yet, sophisticated attackers are often able to bypass rather than break security mechanisms. Kleptography or algorithm substitution attacks (ASA) describe techniques to place backdoors right into cryptographic primitives. While highly relevant as a building block, we show that the real danger of ASAs is their use in cryptographic protocols. In fact, we show that highly desirable security properties of these protocols - forward secrecy and post-compromise security - imply the applicability of ASAs. We then analyze the application of ASAs in three widely used protocols: TLS, WireGuard, and Signal. We show that these protocols can be easily subverted by carefully placing ASAs. Our analysis shows that careful design of ASAs makes detection unlikely while leaking long-term secrets within a few messages in the case of TLS and WireGuard, allowing impersonation attacks. In contrast,Signal\u27s double-ratchet protocol shows higher immunity to ASAs, as the leakage requires much more messages

A dust-parallax distance of 19 megaparsecs to the supermassive black hole in NGC 4151

The active galaxy NGC 4151 has a crucial role as one of only two active galactic nuclei for which black hole mass measurements based on emission line reverberation mapping can be calibrated against other dynamical methods. Unfortunately, effective calibration requires an accurate distance to NGC 4151, which is currently not available. Recently reported distances range from 4 to 29 megaparsecs (Mpc). Strong peculiar motions make a redshift-based distance very uncertain, and the geometry of the galaxy and its nucleus prohibit accurate measurements using other techniques. Here we report a dust-parallax distance to NGC 4151 of $D_A = 19.0^{+2.4}_{-2.6}$ Mpc. The measurement is based on an adaptation of a geometric method proposed previously using the emission line regions of active galaxies. Since this region is too small for current imaging capabilities, we use instead the ratio of the physical-to-angular sizes of the more extended hot dust emission as determined from time-delays and infrared interferometry. This new distance leads to an approximately 1.4-fold increase in the dynamical black hole mass, implying a corresponding correction to emission line reverberation masses of black holes if they are calibrated against the two objects with additional dynamical masses.Comment: Authors' version of a letter published in Nature (27 November 2014); 8 pages, 5 figures, 1 tabl

Ribonucleotide reductase regulatory subunit M2 drives glioblastoma TMZ resistance through modulation of dNTP production

During therapy, adaptations driven by cellular plasticity are partly responsible for driving the inevitable recurrence of glioblastoma (GBM). To investigate plasticity-induced adaptation during standard-of-care chemotherapy temozolomide (TMZ), we performed in vivo single-cell RNA sequencing in patient-derived xenograft (PDX) tumors of GBM before, during, and after therapy. Comparing single-cell transcriptomic patterns identified distinct cellular populations present during TMZ therapy. Of interest was the increased expression of ribonucleotide reductase regulatory subunit M2 (RRM2), which we found to regulate dGTP and dCTP production vital for DNA damage response during TMZ therapy. Furthermore, multidimensional modeling of spatially resolved transcriptomic and metabolomic analysis in patients’ tissues revealed strong correlations between RRM2 and dGTP. This supports our data that RRM2 regulates the demand for specific dNTPs during therapy. In addition, treatment with the RRM2 inhibitor 3-AP (Triapine) enhances the efficacy of TMZ therapy in PDX models. We present a previously unidentified understanding of chemoresistance through critical RRM2-mediated nucleotide production