Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

Rare coding variant analysis in a large cohort of Ashkenazi Jewish families with inflammatory bowel disease.

Rare variants are thought to contribute to the genetics of inflammatory bowel disease (IBD), which is more common amongst the Ashkenazi Jewish (AJ) population. A family-based approach using exome sequencing of AJ individuals with IBD was employed with a view to identify novel rare genetic variants for this disease. Exome sequencing was performed on 960 Jewish individuals including 513 from 199 multiplex families with up to eight cases. Rare, damaging variants in loci prioritized by linkage analysis and those shared by multiple affected individuals within the same family were identified. Independent evidence of association of each variant with disease was assessed. A number of candidate variants were identified, including in genes involved in the immune system. The ability to achieve statistical significance in independent case/control replication data was limited by power and was only achieved for variants in the well-established Crohn's disease gene, NOD2. This work demonstrates the challenges of identifying disease-associated rare damaging variants from exome data, even amongst a favorable cohort of familial cases from a genetic isolate. Further research of the prioritized rare candidate variants is required to confirm their association with the disease.

The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.

Previously, we have shown that shortening of telomeres by telomerase inhibition sensitized cancer cells to cisplatinum, slowed their migration, increased DNA damage and impaired DNA repair. The mechanism behind these effects is not fully characterized. Its clarification could facilitate novel therapeutics development and may obviate the time consuming process of telomere shortening achieved by telomerase inhibition. Here we aimed to decipher the microRNA and proteomic profiling of cancer cells with shortened telomeres and identify the key mediators in telomere shortening-induced damage to those cells. Of 870 identified proteins, 98 were differentially expressed in shortened-telomere cells. 47 microRNAs were differentially expressed in these cells; some are implicated in growth arrest or act as oncogene repressors. The obtained data was used for a network construction, which provided us with nodal candidates that may mediate the shortened-telomere dependent features. These proteins' expression was experimentally validated, supporting their potential central role in this system.

Selective expression and cellular localization of pro-inflammatory chemokine ligand/receptor pairs in the sciatic nerves of a severe murine experimental autoimmune neuritis model of Guillain-Barré syndrome.

AIMS: To determine if specific pro-inflammatory chemokine ligand/receptor pairs expressed in the peripheral nerves of Guillain-Barré syndrome patients are expressed in a severe murine experimental autoimmune neuritis (sm-EAN) model and to determine their cellular localization as a prerequisite to designing potentially therapeutic interventions in vivo. METHODS: Sm-EAN was induced in 8-12-week-old female SJL/J mice using bovine peripheral nerve myelin emulsified in complete Freund adjuvant with pertussis toxin and recombinant mouse interleukin-12 acting as co-adjuvants, with appropriate controls. Mice were evaluated for neuromuscular weakness and weighed daily. Dorsal caudal tail and sciatic nerve motor electrophysiological studies were performed at expected maximal severity. Sciatic nerves were harvested and specific chemokine ligand/receptor expression was determined using real-time quantitative reverse transcriptase polymerase chain reaction and indirect fluorescent immunohistochemistry. RESULTS: CCL2/CCR2, CXCL10/CXCR3 and CCL5/CCR1, CCR5 expression was significantly increased in the sciatic nerves of sm-EAN mice compared with controls. CCL2 was expressed on Schwann cells with CCR2 expressed on F4/80+ macrophages and CD3+ T cells. CXCL10 was expressed on endoneurial endothelial cells and within the endoneurial interstitium, with CXCR3 expressed on CD3+ T-lymphocytes. CCL5 co-localized to axons, with CCR1 and CCR5 expression on F4/80+ macrophages and rare CD3+ T cells. CONCLUSIONS: This study suggests that CCL2 expressed by Schwann cells and CXCL10 expressed by endoneurial endothelial cells may induce F4/80+ macrophage and CD3+ T cell-mediated inflammation and demyelination in sm-EAN. CCL2-CCR2 and CXCL10-CXCR3 signalling pathways are potential targets for therapeutic intervention in peripheral nerve inflammation.

A systems level strategy for analyzing the cell death network: implication in exploring the apoptosis/autophagy connection.

The mammalian cell death network comprises three distinct functional modules: apoptosis, autophagy and programmed necrosis. Currently, the field lacks systems level approaches to assess the extent to which the intermodular connectivity affects cell death performance. Here, we developed a platform that is based on single and double sets of RNAi-mediated perturbations targeting combinations of apoptotic and autophagic genes. The outcome of perturbations is measured both at the level of the overall cell death responses, using an unbiased quantitative reporter, and by assessing the molecular responses within the different functional modules. Epistatic analyses determine whether seemingly unrelated pairs of proteins are genetically linked. The initial running of this platform in etoposide-treated cells, using a few single and double perturbations, identified several levels of connectivity between apoptosis and autophagy. The knock down of caspase3 turned on a switch toward autophagic cell death, which requires Atg5 or Beclin-1. In addition, a reciprocal connection between these two autophagic genes and apoptosis was identified. By applying computational tools that are based on mining the protein-protein interaction database, a novel biochemical pathway connecting between Atg5 and caspase3 is suggested. Scaling up this platform into hundreds of perturbations potentially has a wide, general scope of applicability, and will provide the basis for future modeling of the cell death network.

Short UV luminescence for forensic applications: design of a real-time observation system for detection of latent fingerprints and body fluids.

An assembly that allows a pseudo real-time (one second delay) observation of latent fingerprints by their short ultraviolet luminescence was designed. It is composed of a mercury-xenon lamp and a CCD camera, both water-cooled and computer-controlled. The system is used to study the behaviour of latent fingerprints and stains of body fluids such as blood, semen and saliva under short-UV illumination.

Use of the Hartman sensor to measure the unisoplanatic wavefront tilt.

It is shown that the Hartman wavefront sensor can be used to measure the degree of unisoplanatism under atmospheric wavefront degradations. The measurements conform with theory and show the size of the isoplanatic patch in the object space and the coherent distance at the entrance of the pupil plane. These two measurements are unequal because of inhomogeneous turbulence. This inhomogeneity can be accounted for by using known theory and the height of the line of sight above the ground.

Platelet parameters and aggregation in essential and reactive thrombocytosis.

Platelet characteristics were assessed in 15 patients with essential thrombocytosis (ET), 89 patients with reactive thrombocytosis (RT), and 23 normal controls. A platelet volume distribution width (PDW) greater than or equal to 10.5 was found in 50%, 21%, and 14% of the three groups, respectively (P = 0.01 between patients with ET and patients with RT; P = 0.02 between patients with RT and controls), reflecting an excess of extreme values at both ends of the distribution. Compared with controls, the increase in platelet number in patients with RT was about twofold throughout the platelet volume range, whereas ET was characterized by a fivefold increase in small platelets less than 7.5 fL and threefold increase in larger size platelets. Mean platelet volume (MPV) was significantly lower in patients with ET versus patients with RT and in patients with RT versus controls (mean +/- SD 7.5 +/- 1.2 vs. 8.8 +/- 0.1 and 10.2 +/- 1.8 fL, respectively, P less than 0.01). Rate of in vitro platelet aggregation greater than or equal to 50% was significantly lower in patients with ET versus patients with RT and in patients with RT versus controls (0%, 23%, and 45%, respectively, P less than 0.01). Aggregation rate was positively correlated with MPV (r = 0.54; P less than 0.0001). Aggregation rate in patients with ET was significantly lower (P = 0.01) than expected from their reduced MPV alone. Despite these group differences, the overlap of individual platelet characteristics between the three groups precludes their usefulness for diagnostic purposes.

Significance of high HbA1 levels in normal glucose tolerance.

The significance of high hemoglobin A1 (HbA1) levels (greater than or equal to 8.0%) found in 12.1% of 648 individuals with normal glucose tolerance constituting a part of a representative population sample was examined. Measurement error in HbA1 and/or glucose-tolerance levels was precluded by HbA1 remaining in the same range over 3.5 yr in 89.7% of 29 individuals with initially high and 68.1% of 22 individuals with initially low (less than 6.5%) HbA1. Rate of deterioration to glucose intolerance (6.9%) in the high group during that period resembled the rate (11.8%) in a control group (n = 279). Fasting plasma glucose significantly accounted for only 2.4% of total HbA1-population variance. No correlation of HbA1 was found with other correlates of glucose tolerance or with daily caloric intake and physical activity. A small but significant increment in HbA1 was associated with smoking (7.1 vs. 6.8%, P less than .01) and with clinically overt atherosclerosis (7.3 vs. 6.9%, P less than .01). We conclude that factors unrelated to glucose metabolism are the main determinants of HbA1 level in normal glucose tolerance and play an important role in diabetes as well. These factors have bearing on evaluation of diabetic control by HbA1 and possibly on risk for diabetic complications.

Aperture averaging effects on the two-color correlation of scintillations.

The scintillation two-color correlation coefficient was measured using a variable aperture. The correlation, at constant aperture, vs turbulence strength and the aperture averaging effects at constant turbulence strength were obtained. The results show a strong decrease or correlation with increasing turbulence strength and a moderate increase with increasing aperture. These results cannot be accounted for by a constant shape turbulence spectrum. It is shown that a turbulence strength-dependent inner scale can explain most of the results using the Rytov approximation.

Sample size influence on optical scintillation analysis. Analytical treatment of the higher-order irradiance moments.

The statistical distribution of the experimentally obtained higher-order moments of optical scintillation probability density is studied. It is shown that this distribution is strongly dependent on the size of the data sample. At reasonable sample sizes the correct estimation of the theoretical value is improbable. At practically available sample sizes the region of the most probable values of the estimated higher-order moment is almost independent of the scintillation probability density function (PDF). The distinction between the candidate PDFs is almost impossible at reasonable sample sizes.

Sample size influence on optical scintillation analysis.2: Simulation approach.

This paper is the second part of the sample size influence analysis. We estimate this influence on different methods of irradiance probability density function (PDF) diagnostics. The estimation is achieved by a Monte Carlo-based simulation. The problem of the fastest effective sampling rate is also considered. The results indicate the low resolving power of conventional irradiance PDF integrating methods.

Temporal prediction of infrared images of ground terrain.

By measuring the IR image of a ground terrain at two different points of time, it is possible to calculate all the local scene invariants. Utilizing the heat balance equation, these scene invariants are used to calculate the IR image of the scene at another point of time. A good agreement with experimental results is obtained.