Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outcome of such studies regarding common responses and toxicity pathways is currently lacking. We developed an R-scripted computational pipeline to perform reanalysis and functional analysis of relevant transcriptomic data sets using a common approach, independent from the ENM type, and across different organisms, including Arabidopsis thaliana, Caenorhabditis elegans, and Danio rerio. Using the pipeline that can semiautomatically process data from different microarray technologies, we were able to determine the most common molecular mechanisins of nanotoxicity across extremely variable data sets. As expected, we found known mechanisms, such as interference with energy generation, oxidative stress, disruption of DNA synthesis, and activation of DNA-repair but also discovered that some less-described molecular responses to ENMs, such as DNA/RNA methylation, protein folding, and interference with neurological functions, are present across the different studies. Results were visualized in radar charts to assess toxicological response patterns allowing the comparison of different organisms and ENM types. This can be helpful to retrieve ENM-related hazard information and thus fill knowledge gaps in a comprehensive way in regard to the molecular underpinnings and mechanistic understanding of nanotoxicity.

Toward a mechanistic understanding of variable chromatin modules

Gerard Llimos Aubach

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is almost identical between organisms of the same species (>99.9% in humans), however it varies in a small percentage due to some nucleotides being different at specific positions of the genome. This variation in the DNA will therefore influence our traits and affect our susceptibility to a certain condition. Thus, their study is highly relevant in genetics and biomedicine since they allow not only to predict the predisposition to a disease, such as cancer, but also to understand the molecular and cellular mechanism behind a certain phenotype. The effect of a genetic variant on a phenotype is given by their capacity to modulate the expression of a gene, either by directly impacting its sequence and thus changing the protein, or by regulating its expression levels. Interestingly, more than 88% of the disease-associated genetic variants present in humans are located outside genes, on the so-called non-coding part of the genome. This poses a challenge to identify what gene the genetic variant affects and to understand how it does so. Genetic variants do not only influence gene expression but they also affect the epigenetics state of the DNA (i.e. DNA methylation, histone marks, transcription factor (TF) binding...) and its 3D conformation, consequently modifying the activity of gene regulatory elements like promoters and enhancers. Previously, it has been shown that some of these regulatory regions located in the same locus exhibit a high level of molecular coordination and interindividual variation, mostly affected by genetic variation or environmental effects. These regions were termed variable chromatin modules (VCMs) or cis-regulatory domains (CRDs) and are thought to be the manifestation of fine-grained regulatory units of the genome. Understanding how a VCM is formed and the molecular basis behind the cooperativity between regulatory elements is an outstanding question in the field. In this work, we aim at resolving part of this puzzle by mechanistically dissecting one VCM that is influenced by a non-coding germline variant in B cells. Using a set of tools such as genetic engineering, TF binding assays and chromosome conformation studies, we demonstrate that this variant creates a de novo binding site for the TF MEF2, which acts as a pioneering factor for dozens of other collaborating TFs. In turn, this actuates a cluster of enhancers spanning a region over 150 kilobases (kb) that regulates AXIN2 gene expression, and is associated with a global compaction of the chromatin. In addition, in line with the known tumor-suppressor properties of AXIN2, we found that this variant influences chronic lymphocytic leukemia (CLL) progression and predisposition. Together, the characterization of the AXIN2 VCM provides an unique example to the community of how a germline variant is able to switch on an entire genomic locus with high degree of cooperativity between regulatory elements, since it captures both the formation and transition behavior of a VCM. Furthermore, given the link with CLL, this focal variant could have translational potential by serving as a patient-stratifying or treatment diagnostic.

EPFL2021

Endocrine disruption in soil invertebrates

Sophie Campiche

In the past years, it has been observed that some compounds present in our environment can disturb the reproduction and development of animals like fishes, birds, or reptiles by interfering with their endocrine system. Indeed, these endocrine disrupting compounds (EDC) can mimic or antagonize the effects of hormones, alter the pattern of synthesis and metabolism of hormones or modify hormone receptor levels. These substances represent a risk for wildlife, and possibly for humans. Up to now, endocrine disruption was mainly evaluated for vertebrates and aquatic organisms and for oestrogeniclike substances. However, soil invertebrates, which play an important role in soil functioning, have rarely been considered. Moreover, as their endocrine system differs substantially from those of vertebrates (estrogens do not seem to regulate endocrine functions in invertebrates), other substances than can mimic invertebrate hormones should be taken into account. In this sense, insect growth regulators (IGR), which are third generation insecticides specially developed to interfere with insect endocrine system, are interesting compounds. These substances are supposed to have a high specificity for insect pest and a low toxicity for non-target organisms. In the first part of this study, the sublethal effects of six IGR (methoprene, fenoxycarb, precocene II, tebufenozide, hexaflumuron and teflubenzuron) were evaluated on the non-target soil arthropod Folsomia candida. The collembola F. candida represents an integral and beneficial part of the soil ecosystem. It is an euedaphic (subsurface) species which plays an important role in soil respiration and decomposition processes and is therefore vulnerable to the effects of soil contamination. This ecologically relevant organism is one of the most appropriate invertebrate test species for the assessment of environmental quality. It is recommended as test organism by the international standard ISO 11267. The 28-days reproduction tests conducted according to this protocol show that F. candida is affected by the chosen IGR. The most toxic compounds were the two chitin synthesis inhibitors, teflubenzuron and hexaflumuron, with an EC50 of 0.05 mg/kg (dw) for teflubenzuron and an EC50 of 0.6 mg/kg for hexaflumuron. These concentrations are probably environmentally relevant (toxicity/exposure ratios

EPFL2006

Human and eco-toxicological impacts of organometallic halide perovskites

Ryma Iness Benmessaoud

Solar radiation currently represents the most important source of renewable energy. Existing technologies to collect and distribute solar energy are expensive, difficult to manufacture, non-recyclable and not very cost-effective. Recent advances in physics and materials engineering have pointed to photovoltaic (PV) perovskites (or CH3NH3MI3, where M=Pb, Sn) as the future solution for sustainable energy because of their simple fabrication procedure, low price, and high efficiency. Several companies are already building perovskites-based PV devices for commercialization in the near future. Nevertheless, perovskites contain heavy metals, and safety concerns during PV fabrication and transportation have not yet been addressed, not to mention recycling, and environmental hazards in case of any failure of large-area solar panels. This dissertation documents my investigation of the potential health and environmental effects of perovskites. I have performed a "zoom-in approach" on human cells to study gene expression and biochemical changes, and a "zoom-out approach" in vivo to investigate toxicity at an organism level. The time frame during which living cells can be manipulated on the same substrate is short, therefore we selected concentrations in the range of 50 to 200 µg /ml (from 80 to 400 µM)) to observe a measurable effect in vitro. These concentrations may seem relatively high, however, an accidental exposure scenario with such concentrations may occur during material fabrication if safety measures are not taken properly. In the in vitro study using human cells, I have discovered not only a dose- and time-dependent response to perovskites exposure, but also a cell-type dependent effect. Within 24 hours following perovskites exposure, neuronal cells died whereas lung cells became giant and polynucleated. Complementary assays showed that mitochondria were heavily damaged, with an increase in their activity when compared to untreated cells. Furthermore, genome profile studies showed many differences in gene expression levels. Extra analysis identified the co-regulated gene networks rather than individual coding genes, which indicated that some pathways critical to basic cellular functions were heavily affected by perovskite exposure (such as regulation of the metabolism, cell division, cell signaling etc.). To understand more thoroughly, I applied the Scanning Fourier Transform Infrared Microspecrometry (S-FTIRM) to study cell toxicity. This has never been done before. I investigated the biochemical changes displayed on infrared absorption spectra. The results are complementary to other techniques, which makes the use of S-FTIRMS applicable to real-time toxicity studies because of its submolecular sensitivity and high-resolution. I also explored the eco-toxic effects of photovoltaic perovskites on small model organisms: fruit flies (Drosophila melanogaster) and nematodes (Caenorhabditis elegans). In both models, life span and organism development were reduced by the exposure. Moreover, the fertility of young adults was drastically affected. My in vitro and in vivo studies showed that CH3NH3PbI3 and CH3NH3SnI3 are acutely and chronically toxic compounds. The obtained results are conclusive, and encourage the scientific community not only to conduct further tests on more complex organisms, but to first search for novel solutions with non-toxic properties.

EPFL2017