scholarly journals Spatial heterogeneity of the immune compartment within the lungs of critical COVID-19 patients

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Amy Cross
Keyword(s):  
In Situ Hybridisation ◽  
Severe Infection ◽  
Spatial Separation ◽  
Spatially Resolved ◽  
Spatial Profiling ◽  
Cancer Transcriptome ◽  
Tcr Activation ◽  
Interferon Gamma Response ◽  
Viral Nucleocapsid

Cross AR, Sansom S, Roberts I, Cerundolo L, Melero I, De Andrea C, Landecho MF, Klenerman P,Hester J, Issa F Acute respiratory distress syndrome (ARDS) is a defining feature of severe infection with theSARS-CoV-2 virus. Approaches to understand the immune response during COVID-19 are largelyconfined to characterisation of circulating leukocytes, however this approach excludes the mostrelevant cells that are active at the site of infection and injury. The aim of this study was to characterise the immune landscape across the lungs of COVID-19patients. Lung samples from three critical COVID-19 patients were assessed for histopathology,viral load, and distribution using qPCR, in situ hybridisation and immunohistochemistry.Leukocyte distribution was then assessed, and the transcript profile of selected areas examinedagainst the >1800 genes in the Cancer Transcriptome Atlas panel on the NanoString GeoMxDigital Spatial Profiling platform. Lung samples exhibited a spectrum of typical COVID-19 pathology with diffuse alveolar damageconsistent with hyaline membrane and type II pneumocyte hyperplasia, interstitialinflammation, organising pneumonia and thrombi. All tissues tested positive for SARS-CoV-2RNA using qPCR, whilst spatially resolved techniques revealed only few and sparsely distributedcells carrying the viral nucleocapsid protein. Multiplexed immunofluorescence for lymphocytes(CD3+) and macrophages (CD68+) was used to select areas of immune enrichment for spatialtranscriptomic profiling. These targeted analyses highlighted functional pathways involved inthe interferon gamma response, TCR activation and antigen presentation. Comparison acrossimmune-enriched areas identified a heterogeneity in lung infiltrates with spatial separation ofchemokine and complement production. Our data identify pathological immune pathways thatare amenable to therapeutic intervention in critical disease.

scholarly journals Elucidating spatially-resolved changes in host signaling during Plasmodium liver-stage infection

2021 ◽  
Author(s):  
Elizabeth K.K. Glennon ◽  
Tinotenda Tongogara ◽  
Veronica I. Primavera ◽  
Sophia M. Reeder ◽  
Ling Wei ◽  
...  
Keyword(s):  
Blood Stream ◽  
Plasmodium Yoelii ◽  
Infected Hepatocyte ◽  
Spatially Resolved ◽  
Spatial Profiling ◽  
Host Signaling ◽  
Infected Cells ◽  
Spatial Locations

AbstractUpon transmission to the human host, Plasmodium sporozoites exit the skin, are taken up by the blood stream, and then travel to the liver where they infect and significantly modify a single hepatocyte. Low infection rates within the liver have made proteomic studies of infected hepatocytes challenging, particularly in vivo, and existing studies have been largely unable to consider how protein and phosphoprotein differences are altered at different spatial locations within the heterogeneous liver. Using digital spatial profiling, we characterized changes in host signaling during Plasmodium yoelii infection in vivo without disrupting the liver tissue, and measured variation between infected cells. Moreover, we measured alterations in protein expression around infected hepatocytes and identified a subset of CD163+ Kupffer cells that migrate towards infected cells during infection. These data offer the first insight into the heterogeneity of the infected hepatocyte in situ and provide insights into how the parasite may alter the local microenvironment to influence its survival and modulate immunity.

scholarly journals Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortex

2021 ◽  
Author(s):  
Kenny Roberts ◽  
Alexander Aivazidis ◽  
Vitalii Kleshchevnikov ◽  
Tong Li ◽  
Robin Fropf ◽  
...  
Keyword(s):  
Gene Expression ◽  
New Technology ◽  
In Situ Hybridisation ◽  
Cell Types ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Human Neocortex ◽  
Formalin Fixed Tissue ◽  
Spatial Profiling

Spatial genomic technologies can map gene expression in tissues, but provide limited potential for transcriptome-wide discovery approaches and application to fixed tissue samples. Here, we introduce the GeoMX Whole Transcriptome Atlas (WTA), a new technology for transcriptome-wide spatial profiling of tissues with cellular resolution. WTA significantly expands the Digital Spatial Profiling approach to enable in situ hybridisation against 18,190 genes at high-throughput using a sequencing readout. We applied WTA to generate the first spatial transcriptomic map of the fetal human neocortex, validating transcriptome-wide spatial profiling on formalin-fixed tissue material and demonstrating the spatial enrichment of autism gene expression in deep cortical layers. To demonstrate the value of WTA for cell atlasing, we integrated single-cell RNA-sequencing (scRNA-seq) and WTA data to spatially map dozens of neural cell types and showed that WTA can be used to directly measure cell type specific transcriptomes in situ. Moreover, we developed computational tools for background correction of WTA data and accurate integration with scRNA-seq. Our results present WTA as a versatile transcriptome-wide discovery tool for cell atlasing and fixed tissue spatial transcriptomics.

FT-IR microspectroscopic analysis of diseased white matter brain tissues

1995 ◽  
Vol 53 ◽  
pp. 968-969
Author(s):  
Steven M. Le Vine ◽  
David L. Wetzel
Keyword(s):  
White Matter ◽  
Gray Matter ◽  
Twitcher Mouse ◽  
Grid Pattern ◽  
Marked Contrast ◽  
Spatially Resolved ◽  
Ft Ir ◽  
Ir Microspectroscopy ◽  
Chemical Evidence

In situ FT-IR microspectroscopy has allowed spatially resolved interrogation of different parts of brain tissue. In previous work the spectrrscopic features of normal barin tissue were characterized. The white matter, gray matter and basal ganglia were mapped from appropriate peak area measurements from spectra obtained in a grid pattern. Bands prevalent in white matter were mostly associated with the lipid. These included 2927 and 1469 cm-1 due to CH2 as well as carbonyl at 1740 cm-1. Also 1235 and 1085 cm-1 due to phospholipid and galactocerebroside, respectively (Figs 1and2). Localized chemical changes in the white matter as a result of white matter diseases have been studied. This involved the documentation of localized chemical evidence of demyelination in shiverer mice in which the spectra of white matter lacked the marked contrast between it and gray matter exhibited in the white matter of normal mice (Fig. 3).The twitcher mouse, a model of Krabbe’s desease, was also studied. The purpose in this case was to look for a localized build-up of psychosine in the white matter caused by deficiencies in the enzyme responsible for its breakdown under normal conditions.

Bio-P and non-bio-P bacteria identification by a novel microbial approach

1999 ◽  
Vol 39 (6) ◽  
pp. 13-20 ◽  
Author(s):  
Philip L. Bond ◽  
Jürg Keller ◽  
Linda L. Blackall
Keyword(s):  
In Situ Hybridisation ◽  
Microbial Populations ◽  
Biological Phosphorus Removal ◽  
Gram Positive Bacteria ◽  
P Content ◽  
Identification Of Bacteria ◽  
Widespread Belief ◽  
Biological Phosphorus ◽  
P Removal

Culturing bacteria from activated sludge with enhanced biological phosphorus removal (EBPR) has strongly implicated Acinetobacter with the process. However, using fluorescent in-situ hybridisation (FISH) probing to analyse microbial populations, we have shown evidence opposing this widespread belief. We describe the phosphorus (P) removing performance and microbial population analyses of sludges obtained in a laboratory scale EBPR reactor. Two sludges with extremely high P removing capabilities were examined, the P content of these sludges was 8.6% (P sludge) and 12.3% (S sludge) of the MLSS. Identification of bacteria using FISH probing indicated both sludges were dominated by microbes from the beta proteobacteria and high mol% G+C Gram positive bacteria. Acinetobacter could make up only a small proportion of the cells in these sludges. Sludge with extremely poor P removal (P content of 1.5%, referred to as T sludge) was then generated by reducing the P in the influent. Bacteria resembling the G-bacteria became abundant in this sludge and these were identified using FISH probing. The anaerobic transformations of the T and P sludges correlated well with that of the non-EBPR and EBPR biological models respectively, indicating that bacteria in the T sludge have the potential to inhibit P removal in EBPR systems.

scholarly journals Spatially Resolved Experimental Modal Analysis on High-Speed Composite Rotors Using a Non-Contact, Non-Rotating Sensor

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4705
Author(s):  
Julian Lich ◽  
Tino Wollmann ◽  
Angelos Filippatos ◽  
Maik Gude ◽  
Juergen Czarske ◽  
...  
Keyword(s):  
High Speed ◽  
Natural Frequencies ◽  
Mode Shapes ◽  
Fiber Reinforced ◽  
Structural Dynamic ◽  
Spatially Resolved ◽  
Glass Fiber Reinforced ◽  
Vibration Responses ◽  
And Performance

Due to their lightweight properties, fiber-reinforced composites are well suited for large and fast rotating structures, such as fan blades in turbomachines. To investigate rotor safety and performance, in situ measurements of the structural dynamic behaviour must be performed during rotating conditions. An approach to measuring spatially resolved vibration responses of a rotating structure with a non-contact, non-rotating sensor is investigated here. The resulting spectra can be assigned to specific locations on the structure and have similar properties to the spectra measured with co-rotating sensors, such as strain gauges. The sampling frequency is increased by performing consecutive measurements with a constant excitation function and varying time delays. The method allows for a paradigm shift to unambiguous identification of natural frequencies and mode shapes with arbitrary rotor shapes and excitation functions without the need for co-rotating sensors. Deflection measurements on a glass fiber-reinforced polymer disk were performed with a diffraction grating-based sensor system at 40 measurement points with an uncertainty below 15 μrad and a commercial triangulation sensor at 200 measurement points at surface speeds up to 300 m/s. A rotation-induced increase of two natural frequencies was measured, and their mode shapes were derived at the corresponding rotational speeds. A strain gauge was used for validation.

scholarly journals Rapid Multi-Hybridisation FISH Screening for Balanced Porcine Reciprocal Translocations Suggests a Much Higher Abnormality Rate Than Previously Appreciated

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Rebecca E O’Connor ◽  
Lucas G Kiazim ◽  
Claudia C Rathje ◽  
Rebecca L Jennings ◽  
Darren K Griffin
Keyword(s):  
Semen Analysis ◽  
In Situ Hybridisation ◽  
Economic Loss ◽  
Environmental Damage ◽  
Fluorescence In Situ Hybridisation ◽  
Reciprocal Translocations ◽  
Chromosome Translocations ◽  
Farrowing Rate ◽  
Significant Economic Loss

With demand rising, pigs are the world’s leading source of meat protein; however significant economic loss and environmental damage can be incurred if boars used for artificial insemination (AI) are hypoprolific (sub-fertile). Growing evidence suggests that semen analysis is an unreliable tool for diagnosing hypoprolificacy, with litter size and farrowing rate being more applicable. Once such data are available, however, any affected boar will have been in service for some time, with significant financial and environmental losses incurred. Reciprocal translocations (RTs) are the leading cause of porcine hypoprolificacy, reportedly present in 0.47% of AI boars. Traditional standard karyotyping, however, relies on animal specific expertise and does not detect more subtle (cryptic) translocations. Previously, we reported development of a multiple hybridisation fluorescence in situ hybridisation (FISH) strategy; here, we report on its use in 1641 AI boars. A total of 15 different RTs were identified in 69 boars, with four further animals XX/XY chimeric. Therefore, 4.5% had a chromosome abnormality (4.2% with an RT), a 0.88% incidence. Revisiting cases with both karyotype and FISH information, we reanalysed captured images, asking whether the translocation was detectable by karyotyping alone. The results suggest that chromosome translocations in boars may be significantly under-reported, thereby highlighting the need for pre-emptive screening by this method before a boar enters a breeding programme.

scholarly journals α-Fetoprotein mRNA in situ hybridisation is a highly specific marker of hepatocellular carcinoma: a multi-centre study

2021 ◽  
Author(s):  
Shi-Xun Lu ◽  
Yu-Hua Huang ◽  
Li-Li Liu ◽  
Chris Zhiyi Zhang ◽  
Xia Yang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
In Situ Hybridisation ◽  
Diagnostic Value ◽  
Detection Sensitivity ◽  
Specific Marker ◽  
Specific Method ◽  
Multi Centre Study ◽  
Arginase 1 ◽  
Afp Mrna

Abstract Background Pathologic diagnosis of hepatocellular carcinoma (HCC) can be challenging in differentiating from benign and non-hepatocytic malignancy lesions. The aim of this study was to investigate the potential utility of α-fetoprotein (AFP) mRNA RNAscope, a sensitive and specific method, in the diagnosis of HCC. Methods Three independent retrospective cohorts containing 2216 patients with HCC, benign liver lesions, and non-hepatocytic tumours were examined. AFP was detected using ELISA, IHC (Immunohistochemistry), and RNAscope. Glypican3 (GPC3), hepatocyte paraffin-1 (HepPar-1), and arginase-1 (Arg-1) proteins were detected using IHC. Results AFP RNAscope improved the HCC detection sensitivity by 24.7–32.7% compared with IHC. In two surgical cohorts, a panel of AFP RNAscope and GPC3 provided the best diagnostic value in differentiating HCC from benign hepatocytic lesions (AUC = 0.905 and 0.811), and a panel including AFP RNAscope, GPC3, HepPar-1, and Arg-1 yielded the best AUC (0.971 and 0.977) when distinguishing HCC from non-hepatocytic malignancies. The results from the liver biopsy cohort were similar, and additional application of AFP RNAscope improved the sensitivity by 18% when distinguishing HCC from benign hepatocytic lesions. Conclusions AFP mRNA detected by RNAscope is highly specific for hepatocytic malignancy and may serve as a novel diagnostic biomarker for HCC.

scholarly journals Abnormal mucus in cap polyposis

Gut ◽  
1998 ◽  
Vol 42 (1) ◽  
pp. 135-138 ◽  
Author(s):  
M P Buisine ◽  
J F Colombel ◽  
M Lecomte-Houcke ◽  
P Gower ◽  
J P Aubert ◽  
...  
Keyword(s):  
In Situ Hybridisation ◽  
Clinical Manifestations ◽  
Goblet Cells ◽  
Biopsy Specimens ◽  
Mucin Genes ◽  
Cap Polyposis ◽  
Abnormal Glycosylation ◽  
Histochemical Examination ◽  
Mrna In Situ Hybridisation

Background—Cap polyposis is a rare disease characterised by mucoid and bloody diarrhoea, with polyps covered by a cap of mucoid and fibrinopurulent exudate. The pathogenesis is not known.Aims—To pour some light on cap polyposis pathogenesis, by examining the mucus of patients and analysing the expression of five mucin genes, MUC2, MUC3,MUC4, MUC5AC, and MUC5B.Patient and methods—The study was performed on biopsy specimens taken from a patient with recurrent cap polyposis. Histochemical examination, electron microscopy, and mRNA in situ hybridisation were used.Results—The mucus of cap polyposis differed in three respects from that of normal adult colon: abnormal ultrastructure of the mucus in the goblet cells, predominance of non-sulphated mucins, abnormal expression of the MUC4, MUC3, andMUC5AC genes.Conclusions—Most of these abnormalities have been reported for other pathological situations, suggesting that the abnormalities observed in the mucus of this patient with cap polyposis are probably secondary phenomena rather than primary. However, the mucin abnormalities detected, which reflect deregulation of the expression of three apomucin genes, abnormal glycosylation, and abnormalities of the secretion process, are also probably involved in the clinical manifestations of cap polyposis.

Sign in / Sign up

Export Citation Format

Share Document