Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment

Brain metastases are the most common tumor of the brain with a dismal prognosis. A fraction of patients with brain metastasis benefit from treatment with immune checkpoint inhibitors (ICI) and the degree and phenotype of the immune cell infiltration has been used to predict response to ICI. However, the anatomical location of brain lesions limits access to tumor material to characterize the immune phenotype. Here, we characterize immune cells present in brain lesions and matched cerebrospinal fluid (CSF) using single-cell RNA sequencing combined with T cell receptor genotyping. Tumor immune infiltration and specifically CD8 + T cell infiltration can be discerned through the analysis of the CSF. Consistently, identical T cell receptor clonotypes are detected in brain lesions and CSF, confirming cell exchange between these compartments. The analysis of immune cells of the CSF can provide a non-invasive alternative to predict the response to ICI, as well as identify the T cell receptor clonotypes present in brain metastasis. The use of CSF for diagnosis of metastatic brain tumors could be of clinical and patient benefit. Here the authors undertake a single-cell RNA analysis of CSF and brain to determine whether the phenotype in the CSF is reflective of the phenotype in the tumo

Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood appr

DIY Methods 2022 Conference Proceedings

As the past years have proven, the methods for conducting and distributing research that we’ve inherited from our disciplinary traditions can be remarkably brittle in the face of rapidly changing social and mobility norms. The ways we work and the ways we meet are questions newly opened for practical and theoretical inquiry; we both need to solve real problems in our daily lives and account for the constitutive effects of these solutions on the character of the knowledge we produce. Methods are not neutral tools, and nor are they fixed ones. As such, the work of inventing, repairing, and hacking methods is a necessary, if often underexplored, part of the wider research process. This conference aims to better interrogate and celebrate such experiments with method. Borrowing from the spirit and circuits of exchange in earlier DIY cultures, it takes the form of a zine ring distributed via postal mail. Participants will craft zines describing methodological experiments and/or how-to guides, which the conference organisers will subsequently mail out to all participants. Feedback on conference proceedings will also proceed through the mail, as well as via an optional Twitter hashtag. The conference itself is thus an experiment with different temporalities and medialities of research exchange. As a practical benefit, this format guarantees that the experience will be free of Zoom fatigue, timezone difficulties, travel expenses, and visa headaches. More generatively, it may also afford slower thinking, richer aesthetic possibilities, more diverse forms of circulation, and perhaps even some amount of delight. The conference format itself is part of the DIY experiment

Traces of trauma – a multivariate pattern analysis of childhood trauma, brain structure and clinical phenotypes

Background: Childhood trauma (CT) is a major yet elusive psychiatric risk factor, whose multidimensional conceptualization and heterogeneous effects on brain morphology might demand advanced mathematical modeling. Therefore, we present an unsupervised machine learning approach to characterize the clinical and neuroanatomical complexity of CT in a larger, transdiagnostic context. Methods: We used a multicenter European cohort of 1076 female and male individuals (discovery: n = 649; replication: n = 427) comprising young, minimally medicated patients with clinical high-risk states for psychosis; patients with recent-onset depression or psychosis; and healthy volunteers. We employed multivariate sparse partial least squares analysis to detect parsimonious associations between combinations of items from the Childhood Trauma Questionnaire and gray matter volume and tested their generalizability via nested cross-validation as well as via external validation. We investigated the associations of these CT signatures with state (functioning, depressivity, quality of life), trait (personality), and sociodemographic levels. Results: We discovered signatures of age-dependent sexual abuse and sex-dependent physical and sexual abuse, as well as emotional trauma, which projected onto gray matter volume patterns in prefronto-cerebellar, limbic, and sensory networks. These signatures were associated with predominantly impaired clinical state- and trait-level phenotypes, while pointing toward an interaction between sexual abuse, age, urbanicity, and education. We validated the clinical profiles for all three CT signatures in the replication sample. Conclusions: Our results suggest distinct multilayered associations between partially age- and sex-dependent patterns of CT, distributed neuroanatomical networks, and clinical profiles. Hence, our study highlights how machine learning approaches can shape future, more fine-grained CT research

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex

It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. (c) 2016 Wiley Periodicals, Inc

Crop Response to Leaf and Seed Applications of the Biostimulant ComCat® under Stress Conditions

Although clear evidence for benefits in crop production is partly missing, several natural compounds and microorganisms have been introduced to the market as biostimulants. They are supposed to enhance nutrient efficiency and availability in the rhizosphere, reduce abiotic stress, and improve crop quality parameters. Biostimulants often derive from natural compounds, such as microorganisms, algae, and plant extracts. In this study, the commercial plant extract-based biostimulant ComCat® was tested in two field experiments with maize in the communities of Banikoara and Matéri in Northern Benin and six pot experiments (four with maize and two with winter barley) at the University of Hohenheim in Germany. Maize was grown under nutrient deficiency, drought, and weed competition, and winter barley was stressed by the herbicide Luximo (cinmethylin). ComCat® was applied at half, full, and double the recommended field rate (50, 100, and 200 g ha−1) on the stressed and unstressed control plants as leaf or seed treatment. The experiments were conducted in randomized complete block designs with four replications. The above-ground biomass and yield data of one experiment in Benin were collected. The biostimulant did not promote maize and winter barley biomass production of the unstressed plants. When exposed to stress, ComCat® resulted only in one out of eight experiments in higher barley biomass compared to the stressed treatment without ComCat® application. There was a reduced phytotoxic effect of cinmethylin after seed treatment with ComCat®. Crop response to ComCat® was independent of the application rate. Basic and applied studies are needed to investigate the response of crops to biostimulants and their mechanisms of action in the plants before they should be used in practical farming

Repression of endogenous retroviruses prevents antiviral immune response and is required for mammary gland development

The role of heterochromatin in cell fate specification during development is unclear. We demonstrate that loss of the lysine 9 of histone H3 (H3K9) methyltransferase G9a in the mammary epithelium results in de novo chromatin opening, aberrant formation of the mammary ductal tree, impaired stem cell potential, disrupted intraductal polarity, and loss of tissue function. G9a loss derepresses long terminal repeat (LTR) retroviral sequences (predominantly the ERVK family). Transcriptionally activated endogenous retroviruses generate double-stranded DNA (dsDNA) that triggers an antiviral innate immune response, and knockdown of the cytosolic dsDNA sensor Aim2 in G9a knockout (G9acKO) mammary epithelium rescues mammary ductal invasion. Mammary stem cell transplantation into immunocompromised or G9acKO-conditioned hosts shows partial dependence of the G9acKO mammary morphological defects on the inflammatory milieu of the host mammary fat pad. Thus, altering the chromatin accessibility of retroviral elements disrupts mammary gland development and stem cell activity through both cell-autonomous and non-autonomous mechanisms