Biology subjects

Nilsson, M.

Publications and source records attributed to Nilsson, M..

61 records · Page 4Linked to original sources

bioRxiv2020

Hybridization-based In Situ Sequencing (HybISS): spatial transcriptomic detection in human and mouse brain tissue

Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional dimension to investigate spatial cell typing and cell atlases, disease architecture or even data driven discoveries. The field of spatially resolved transcriptomic technologies is emerging as a vital tool to profile gene-expression, continuously pushing current methods to accommodate larger gene panels and larger areas without compromising throughput efficiency. Here, we describe a new version of the in situ sequencing (ISS) method based on padlock probes and rolling circle amplification. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes with high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. Here we present hybridization-based in situ sequencing (HybISS) that allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a target amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.

molecular biology↗

bioRxiv2019

Identification of spatial compartments in tissue from in situ sequencing data

Spatial organization of tissue characterizes biological function, and spatially resolved gene expression has the power to reveal variations of features with high resolution. Here, we propose a novel graph-based in situ sequencing decoding approach that improves recall, enabling precise spatial gene expression analysis. We apply our method on in situ sequencing data from mouse brain sections, identify spatial compartments that correspond with known brain regions, and relate them with tissue morphology.

neuroscience↗

bioRxiv2019

The dot-compartment revealed? Diffusion MRI with ultra-strong gradients and spherical tensor encoding in the living human brain

The so-called \"dot-compartment\" is conjectured in diffusion MRI to represent small spherical spaces, such as cell bodies, in which the diffusion is restricted in all directions. Previous investigations inferred its existence from data acquired with directional diffusion encoding which does not permit a straightforward separation of signals from sticks (axons) and signals from dots. Here we combine isotropic diffusion encoding with ultra-strong diffusion gradients (240 mT/m) to achieve high diffusion-weightings with high signal to noise ratio, while suppressing signal arising from anisotropic water compartments with significant mobility along at least one axis (e.g., axons). A dot-compartment, defined to have apparent diffusion coefficient equal to zero and no exchange, would result in a non-decaying signal at very high b-values (b {gtrsim} 7000 s/mm2). With this unique experimental setup, a residual yet slowly decaying, signal above the noise floor for b-values as high as 15000 s/mm2 was seen clearly in the cerebellar grey matter (GM), and in several white matter (WM) regions to some extent. Upper limits of the dot-signal-fraction were estimated to be ~2% in cerebellar GM and ~0.2% in WM. By relaxing the assumption of zero diffusivity, the signal at high b-values in cerebellar GM could be represented more accurately by an isotropic water pool with a low apparent diffusivity of 0.11 {micro}m2/ms and a substantial signal fraction of ~7-16%. This remaining signal at high b-values has potential to serve as a novel and simple marker for isotropically-restricted water compartments in cerebellar GM.

neuroscience↗

bioRxiv2019

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Granulomas are the pathological hallmark of Tuberculosis (TB), and the niche in which bacilli can either grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here, after in situ sequencing, thirty-four immune transcripts in lung sections from Mycobacterium tuberculosis-infected mice were aligned to the tissue morphology at cellular resolution, allowing the analysis of local immune interactions in the granuloma.\n\nCo-localizing transcript networks at <10 m in C57BL/6 mouse granulomas increased in complexity with time after infection. B-cell clusters developed late after infection. Transcripts from activated macrophages were enriched at subcellular distances from M. tuberculosis. Encapsulated C3HeB/FeJ granulomas showed necrotic centers with transcripts associated with immunosuppression (foxp3, il10), while those in the granuloma rims associated with activated T cells and macrophages. Highly diverse networks with common interactors were observed in similar lesions.\n\nThus, different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion and the proximity to bacteria were here defined.

immunology↗

bioRxiv2018

Low oxygen post conditioning improves stroke-induced cognitive impairment

Post-stroke cognitive impairment has proven to be notoriously difficult to treat. In the current study, we sought to both better understand cellular changes that underpin cognitive deficits and to consider the potential restorative benefits of low oxygen post conditioning (LOPC). We were motivated to use LOPC as an intervention as it is one of the few experimental interventions previously shown to improve cognitive function post-stroke. Experimental stroke was induced by photothrombotic occlusion in adult male C57BL/6 mice. Mice were randomly assigned to either a normal atmospheric air exposure or low oxygen (11% O2) exposure groups three days post-occlusion. On day 17 post-stroke, mice were euthanized for histology or biochemical analyses. Stroked mice exposed to LOPC was associated with marked reductions in amyloid-beta both in its absolute level and in the extent of its oligomerization. Exposure to LOPC post-stroke also improved cellular deficits induced by stroke including an increase in vessel density, a reduction in vascular leakage, and restoration of AQP4 polarisation. Critically, stroked mice exposed to LOPC exhibited robust improvements in cognitive function post-stroke, assessed using a touchscreen based paired-associate learning task. These findings provide compelling pre-clinical evidence of the potential clinical utility of LOPC for enhancing recovery post-stroke.

neuroscience↗

bioRxiv2018

A spatial atlas of inhibitory cell types in mouse hippocampus

Understanding the function of a tissue requires knowing the spatial organization of its constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has revealed the genome-wide expression patterns that define its many, closely related cell types, but cannot reveal their spatial arrangement. Here we introduce probabilistic cell typing by in situ sequencing (pciSeq), an approach that leverages prior scRNA-seq classification to identify cell types using multiplexed in situ RNA detection. We applied this method to map the inhibitory neurons of hippocampal area CA1, a cell system critical for memory function, for which ground truth is available from extensive prior work identifying the laminar organization of subtly differing cell types. Our method confidently identified 16 interneuron classes, in a spatial arrangement closely matching ground truth. This method will allow identifying the spatial organization of fine cell types across the brain and other tissues.

neuroscience↗

bioRxiv2017

High throughput expression profiling and in situ screening of circular RNAs in tissues

Circular RNAs (circRNAs) were recently discovered as a class of widely expressed noncoding RNA and have been implicated in regulation of gene expression. However, the function of the majority of circRNAs remains unknown. Studies of circRNAs have been hampered by a lack of essential approaches for detection, quantification and visualization. We therefore developed a target-enrichment sequencing method suitable for high-throughput screening of circRNAs and their linear counterparts. We also applied padlock probes and in situ sequencing to visualize and determine circRNAs localization in human brain tissue at subcellular levels. We measured circRNA abundance across different human samples and tissues. Our results demonstrate the potential of this RNA class to act as a specific diagnostic marker in blood and serum, by detection of circRNAs from genes exclusively expressed in the brain. The powerful and scalable tools we present will enable studies of circRNA function and facilitate screening of circRNA as diagnostic biomarkers.

genomics↗