Detecting cell-of-origin and cancer-specific features of cell-free DNA with Nanopore sequencing

DNA methylation (5mC) is a promising biomarker for detecting circulating tumor DNA (ctDNA), providing information on a cell's genomic regulation, developmental lineage, and molecular age. Sequencing assays for detecting ctDNA methylation involve pre-processing steps such as immunoprecipitation, enzymatic treatment, or the most common method, sodium bisulfite treatment. These steps add complexity and time that pose a challenge for clinical labs, and bisulfite treatment in particular degrades input DNA and can result in loss of informative ctDNA fragmentation patterns. In this feasibility study, we demonstrate that whole genome sequencing of circulating cell-free DNA using conventional Oxford Nanopore Technologies (ONT) sequencing can accurately detect cell-of-origin and cancer-specific 5mC changes while preserving important fragmentomic information. The simplicity of this approach makes it attractive as a liquid biopsy assay for cancer as well as non-cancer applications in emergency medicine.

Cell scientist to watch – Verena Ruprecht

ABSTRACT Verena Ruprecht received her PhD in Biophysics from the Johannes Kepler University in 2010 for her work on developing single-molecule super-resolution imaging tools in the lab of Gerhard Schütz. Following a research visit in Didier Marguet's lab at the Centre d'Immunologie de Marseille-Luminy (CIML) in France, she moved to the Institute of Science and Technology (IST) in Austria for a postdoc, working jointly with Carl-Philipp Heisenberg and Michael Sixt. There, she discovered a unique amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Verena started her independent laboratory at the Centre for Genomic Regulation (CRG) in Barcelona, Spain, in September 2016. Her group combines genetic and biophysical methods with multi-scale imaging and mathematical modelling to study cellular dynamics in embryo development. In 2020, Verena was selected as an EMBO Young Investigator and in the same year awarded an HFSP Young Investigator Grant for a collaborative project to study the biophysics of zebrafish fertilization.

Transcriptional and Genomic Regulation of Pituitary Function by Thyroid Hormone Receptor Beta

Background : The pituitary is a key target for thyroid hormone but underlying transcriptional mechanisms are poorly understood. Thyroid hormone modifies expression of hormones, including growth hormone (GH) and thyroid-stimulating hormone (TSH, thyrotropin). Wider transcriptome responses are undefined. Thyroid hormone receptor beta (TRb) encoded by THRB are expressed in the anterior pituitary and THRB mutations cause human resistance to thyroid hormone. Method: To investigate genomic genomic regulation by TRb, we derived Thrb-HAB knockin mice that express TRb protein with a tag that is biotinylated in vivo in presence of an R26-BirA allele. Specific, sensitive streptavidin pull-down facilitated Chromatin-Affinity-Purification-sequencing (ChAPseq) to identify genomic TRβ binding sites in pituitary of male mice. Hypo- and hyperthyroidism were produced using methimazole (MMI) in drinking water for 4 weeks with/without added thyroid hormone (T3) for the 4th week. Pituitaries from wild type and Thrb-KO mice were also isolated for RNA-sequencing (RNA-seq). Selected expression changes were confirmed by quantitative PCR. Epigenetic changes were determined by ChIPseq for histone acetylation and methylation and open chromatin analysis (ATAC-seq). Results: Transcriptome analysis revealed genes with statistically different expression induced by T3, including known response genes such as Tshb, Hr and Gh. Responses were impaired in Thrb-KO mice. T3 induced recruitment of TRb binding, chromatin opening and specific histone acetylation marks. Conclusion: Most T3 response genes in pituitary depend to some extent upon TRb. T3-dependent chromatin modifications indicate properties of TRb-dependent enhancer regions and a critical role for TRb in transcriptional regulation of pituitary function.

Distal mediator-enriched, placental transcriptome-wide analyses illustrate the Developmental Origins of Health and Disease

ABSTRACTAs the master regulator of the intrauterine environment, the placenta is core to the Developmental Origins of Health and Disease (DOHaD) but is understudied in relation to tissue-specific gene and trait regulation. We performed distal mediator-enriched transcriptome-wide association studies (TWAS) for 40 health traits across 5 physiological categories, using gene expression models trained with multi-omic data from the Extremely Low Gestational Age Newborn Study (N = 272). At P < 2.5 × 10−6, we detected 248 gene-trait associations (GTAs) across 176 genes, mostly for metabolic and neonatal traits and enriched for cell growth and immunological pathways. Of these GTAs, 89 showed significant mediation through genetic variants distal to the gene, identifying potential targets for functional validation. Functional validation of a mediator gene (EPS15) in human placenta-derived JEG-3 trophoblasts resulted in increased expression of its predicted targets, SPATA13 and FAM214A, both associated with the trait of waist-hip ratio in TWAS. These results illustrate the profound health impacts of placental genetic and genomic regulation in developmental programming across the life course.

Bodies of the Anthropocene: On the interactive plasticity of earth systems and biological organisms

The Anthropocene literature has brought attention to the plasticity and porosity of Earth systems under the dramatic impact of human activities. Moving across scales of analysis, this paper focuses attention on anthropogenic effects at the micro-scale of genomic regulation, neuronal functioning and cellular activity. Building on expanding dialogues at the interface of Anthropocene science, biogeography, microbiology and ecotoxicology, we mobilize epigenetic findings to show increasing evidence of anthropogenic changes in plants, animals and human bodies. Treating human-induced changes at the macro-global and micro-biological scales as part of an intertwined process has implications for how these problems are conceptualised and addressed. While we are sceptics about major geo-bio-social syntheses, we believe that agile social-scientific tools can facilitate interaction across disciplines without denying unevenness, and differences. If rightly contextualized in broad anthropological and social science frameworks, biosocial work on epigenetics offers a compelling avenue to make detectable the ‘slow violence’ of everyday pollution, racism, inequalities and the disproportionate impact of the Anthropocene on the poor and vulnerable. Consolidating work at the Anthropocene/biology interface has potential to offer a richer and more complete picture of the present crisis at the macro and micro-scale alike.

The evolution of feathers

&lt;p&gt;Feathers are a diagnostic character of birds, and yet new fossils show they likely originated more than 100 million years before the first birds. In fact, feathers probably occurred in all dinosaur groups, and in their cousins, the pterosaurs, as we showed in 2019. This finding confirms current knowledge of the genomic regulation of feather development. Our work stems from ten years of collaboration with Chinese colleagues, during which we set ourselves the task of understanding fossil feathers. Our first discovery was to answer the question, &amp;#8216;Will we ever know the colour of dinosaurs?&amp;#8217;. In 2010, we were able to announce the first objective evidence for colour in a dinosaur. Using ultrastructural studies of fossil feathers, we identified melanosomes for the first time in dinosaur feathers, and these demonstrated that Sinosauropteryx had ginger and white rings down its tail. Studies of other dinosaurs identified patterns of black, white, grey, brown, and ginger. This is part of a new wave in Palaeobiology where we apply objective approaches to provide testable hypotheses, once thought impossible in the historical sciences.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Benton, M.J., Dhouailly, D., Jiang, B.Y., and McNamara, M. 2019. The early origin of feathers.&amp;#160;Trends in Ecology &amp; Evolution&amp;#160;34, 856-869 (doi: 10.1016/j.tree.2019.04.018).&lt;/p&gt;&lt;p&gt;https://dinocolour.blogs.bristol.ac.uk/&lt;/p&gt;&lt;p&gt;https://dinosaurs.blogs.bristol.ac.uk/&lt;/p&gt;

A Wolf in Another Wolf’s Clothing: Post-Genomic Regulation Dictates Venom Profiles of Medically-Important Cryptic Kraits in India

The Common Krait (Bungarus caeruleus) shares a distribution range with many other ‘phenotypically-similar’ kraits across the Indian subcontinent. Despite several reports of fatal envenomings by other Bungarus species, commercial Indian antivenoms are only manufactured against B. caeruleus. It is, therefore, imperative to understand the distribution of genetically distinct lineages of kraits, the compositional differences in their venoms, and the consequent impact of venom variation on the (pre)clinical effectiveness of antivenom therapy. To address this knowledge gap, we conducted phylogenetic and comparative venomics investigations of kraits in Southern and Western India. Phylogenetic reconstructions using mitochondrial markers revealed a new species of krait, Romulus’ krait (Bungarus romulusi sp. nov.), in Southern India. Additionally, we found that kraits with 17 mid-body dorsal scale rows in Western India do not represent a subspecies of the Sind Krait (B. sindanus walli) as previously believed, but are genetically very similar to B. sindanus in Pakistan. Furthermore, venom proteomics and comparative transcriptomics revealed completely contrasting venom profiles. While the venom gland transcriptomes of all three species were highly similar, venom proteomes and toxicity profiles differed significantly, suggesting the prominent role of post-genomic regulatory mechanisms in shaping the venoms of these cryptic kraits. In vitro venom recognition and in vivo neutralisation experiments revealed a strong negative impact of venom variability on the preclinical performance of commercial antivenoms. While the venom of B. caeruleus was neutralised as per the manufacturer’s claim, performance against the venoms of B. sindanus and B. romulusi was poor, highlighting the need for regionally-effective antivenoms in India.