Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.

Spatial transcriptomics methods provide insight into the cellular heterogeneity and spatial architecture of complex, multicellular systems. Combining molecular and spatial information provides important clues to study tissue architecture in development and disease. Here, we present a comprehensive do-it-yourself (DIY) guide to perform such experiments at reduced costs leveraging open-source approaches.

3D in-system calibration method for PET detectors.

Background: Light-sharing detector designs for positron emission tomography (PET) systems have sparked interest in the scientific community. Particularly, (semi-)monoliths show generally good performance characteristics regarding 2D positioning, energy-, and timing resolution, as well as readout area. This is combined with intrinsic depth-of-interaction (DOI) capability to ensure a homogeneous spatial resolution across the entire field of view (FoV).

Three-dimensional chromatin mapping of sensory neurons reveals that promoter-enhancer looping is required for axonal regeneration.

The in vivo three-dimensional genomic architecture of adult mature neurons at homeostasis and after medically relevant perturbations such as axonal injury remains elusive. Here, we address this knowledge gap by mapping the three-dimensional chromatin architecture and gene expression program at homeostasis and after sciatic nerve injury in wild-type and cohesin-deficient mouse sensory dorsal root ganglia neurons via combinatorial Hi-C, promoter-capture Hi-C, CUT&Tag for H3K27ac and RNA-seq. We find that genes involved in axonal regeneration form long-range, complex chromatin loops, and that cohesin is required for the full induction of the regenerative transcriptional program.

Maternal immune activation exerts long-term effects on activity and sleep in male offspring mice.

Exposure to infectious or non-infectious immune activation during early development is a serious risk factor for long-term behavioural dysfunctions. Mouse models of maternal immune activation (MIA) have increasingly been used to address neuronal and behavioural dysfunctions in response to prenatal infections. One commonly employed MIA model involves administering poly(I:C) (polyriboinosinic-polyribocytdilic acid), a synthetic analogue of double-stranded RNA, during gestation, which robustly induces an acute viral-like inflammatory response.

Differential effects of purified low molecular weight Poly(I:C) in the maternal immune activation model depend on the laboratory environment.

The Poly (I:C) (polyriboinosinic-polyribocytidilic acid) paradigm of maternal immune activation (MIA) is most widely used as experimental model for the evaluation of the effects of gestational infection on the brain and behavior of the progeny. We have previously reported significant batch-to-batch variability in the effects of Poly (I:C), purchased from the same supplier (Sigma-Aldrich), on maternal and fetal immune responses and found these differences to be dependent on the relative amount of synthetic double-stranded RNA fragments in the high versus low molecular weight (LMW) range contained in the compound. We here resorted to Poly (I:C) purified for LMW dsRNA fragments to establish a MIA paradigm with increased reproducibility and enhanced standardization in an effort to refine the MIA paradigm and characterize its effect on offspring behavior.

Holistic evaluation of a machine learning-based timing calibration for PET detectors under varying data sparsity.

Modern PET scanners offer precise TOF information, improving the SNR of the reconstructed images. Timing calibrations are performed to reduce the worsening effects of the system components and provide valuable TOF information. Traditional calibration procedures often provide static or linear corrections, with the drawback that higher-order skews or event-to-event corrections are not addressed.

Prenatal immune activation in mice induces long-term alterations in brain mitochondrial function.

Prenatal exposure to infections is a risk factor for neurodevelopmental disorders in offspring, and alterations in mitochondrial function are discussed as a potential underlying factor. Here, using a mouse model of viral-like maternal immune activation (MIA) based on poly(I:C) (POL) treatment at gestational day (GD) 12, we show that adult offspring exhibit behavioral deficits, such as reduced levels of social interaction. In addition, we found increased nicotinamidadenindinucleotid (NADH)- and succinate-linked mitochondrial respiration and maximal electron transfer capacity in the prefrontal cortex (PFC) and in the amygdala (AMY) of males and females.

Microglia undergo molecular and functional adaptations to dark and light phases in male laboratory mice.

Microglia are increasingly recognized to contribute to brain health and disease. Preclinical studies using laboratory rodents are essential to advance our understanding of the physiological and pathophysiological roles of these cells in the central nervous system. Rodents are nocturnal animals, and they are mostly maintained in a defined light-dark cycle within animal facilities, with many laboratories investigating the molecular and functional profiles of microglia exclusively during the animals' light (sleep) phase.

Intrauterine position effects in a mouse model of maternal immune activation.

Rodent models of maternal immune activation (MIA) are increasingly used as experimental tools in preclinical research of immune-mediated neurodevelopmental disorders and mental illnesses. Using a viral-like MIA model that is based on prenatal poly(I:C) exposure in mice, we have recently identified the existence of subgroups of MIA-exposed offspring that show dissociable behavioral, transcriptional, brain network and inflammatory profiles even under conditions of genetic homogeneity and identical MIA. Here, we tested the hypothesis that the intrauterine positions of fetuses, which are known to shape individual variability in litter-bearing mammals through variations in fetal hormone exposure, may contribute to the variable outcomes of MIA in mice.

A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1.

The role and molecular mechanisms of intermittent fasting (IF) in non-alcoholic steatohepatitis (NASH) and its transition to hepatocellular carcinoma (HCC) are unknown. Here, we identified that an IF 5:2 regimen prevents NASH development as well as ameliorates established NASH and fibrosis without affecting total calorie intake. Furthermore, the IF 5:2 regimen blunted NASH-HCC transition when applied therapeutically.

Histopathological biomarkers for predicting the tumour accumulation of nanomedicines.

The clinical prospects of cancer nanomedicines depend on effective patient stratification. Here we report the identification of predictive biomarkers of the accumulation of nanomedicines in tumour tissue. By using supervised machine learning on data of the accumulation of nanomedicines in tumour models in mice, we identified the densities of blood vessels and of tumour-associated macrophages as key predictive features.

Antiviral Defence Mechanisms during Early Mammalian Development.

The type-I interferon (IFN) response constitutes the major innate immune pathway against viruses in mammals. Despite its critical importance for antiviral defence, this pathway is inactive during early embryonic development. There seems to be an incompatibility between the IFN response and pluripotency, the ability of embryonic cells to develop into any cell type of an adult organism.

pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging.

Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells.

RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell-mediated Rejection.

Background: Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell-mediated rejection (TCMR) may improve its management.

Methods: We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways.

A finely segmented semi-monolithic detector tailored for high-resolution PET.

Background: Preclinical research and organ-dedicated applications use and require high (spatial-)resolution positron emission tomography (PET) detectors to visualize small structures (early) and understand biological processes at a finer level of detail. Researchers seeking to improve detector and image spatial resolution have explored various detector designs. Current commercial high-resolution systems often employ finely pixelated or monolithic scintillators, each with its limitations.

Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells.

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors.

Transcriptomic signatures of chronic active antibody-mediated rejection deciphered by RNA sequencing of human kidney allografts.

Natural killer (NK) cells mediate spontaneous cell-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity. This dual functionality could enable their participation in chronic active antibody-mediated rejection (CA-ABMR). Earlier microarray profiling studies have not subcategorized antibody-mediated rejection into CA-ABMR and active-ABMR, and the gene expression pattern of CA-ABMR has not been compared with that of T cell-mediated rejection (TCMR).

A Method to Investigate Sterilization Processes and the Bacterial Inactivation Resolved in Time and Space.

In this study, a computational fluid dynamics (CFD) model was developed to predict all relevant phenomena occurring during a moist heat sterilization process at a high level of temporal and spatial resolution. The developed CFD model was used to simulate the distribution of, for example, pressure, temperature, and residual air within a large-scale industrial steam autoclave (multiphase flow models), which was not published until now. Moreover, the thermodynamic behavior and distribution of fluids and temperatures inside the sterilization load were simulated and were verified with measurements.

Comparison of transarterial bland embolization and drug-eluting beads transarterial chemoembolization for very early and early hepatocellular carcinoma not amenable for surgery or ablation: a single center retrospective data analysis.

Background: Transarterial chemoembolization (TACE) is the accepted therapy for intermediate hepatocellular carcinoma (HCC). Although recent data suggests that bland transarterial embolization (TAE) is equally effective in intermediate HCC, not much is known about the efficacy in very early and early HCC not amenable for ablation or resection. We aimed to compare the outcome of patients with very early and early HCC treated by drug-eluting beads TACE (DEB-TACE), a specific technique of TACE using DC beads, and TAE using microparticles with a size of 100 µm up to 700 µm.

The circadian clock time tunes axonal regeneration.

Nerve injuries cause permanent neurological disability due to limited axonal regeneration. Injury-dependent and -independent mechanisms have provided important insight into neuronal regeneration, however, common denominators underpinning regeneration remain elusive. A comparative analysis of transcriptomic datasets associated with neuronal regenerative ability revealed circadian rhythms as the most significantly enriched pathway.

Cognitive models for mentally visualizing a sharp instrument in a blind procedure.

Purpose: Our objective was to understand the cognitive strategies used by surgeons to mentally visualize navigation of a surgical instrument through blind space.

Methods: We conducted semi-structured interviews with 15 expert and novice surgeons following simulated retropubic trocar passage on 3D-printed models of pelvises segmented from preop MRIs. Midurethral sling surgery involves blind passage of a trocar among the urethra, bladder, iliac vessels, and bowel while relying primarily on haptic feedback from the suprapubic bone (SPB) for guidance.