Citations

Objectives Important findings can be masked in gene expression studies of mixed cell populations. We examined single-cell gene expression in SLE patient monocytes in the context of clinical and immunological features. Methods Monocytes were purified from patients with SLE and controls, and individually isolated for single-cell gene expression measurement. A panel of monocyte-related transcripts were measured in individual classical (CL) and non-classical (NCL) monocytes. Results Analyses of both CL and NCL monocytes demonstrated that many genes had a lower expression rate in SLE monocytes than in controls. Unsupervised hierarchical clustering of the CL and NCL data sets demonstrated independent clusters of cells from the patients with SLE that were related to disease activity, type I interferon (IFN) and medication use. Thus, each of these factors exerted a different impact on monocyte gene expression that could be identified separately, and a number of genes correlated uniquely with disease activity. We found within-cell correlations between genes directly induced by type I IFN-induced and other non–IFN-induced genes, suggesting the downstream biological effects of type I IFN in individual human SLE monocytes which differed between CLs and NCLs. Conclusions In summary, single-cell gene expression in monocytes was associated with a wide range of clinical and biological features in SLE, providing much greater detail and insight into the cellular biology underlying the disease than previous mixed-cell population studies.

Background: Previous work shows that young athletes after anterior cruciate ligament reconstruction (ACLR) demonstrate single-leg (SL) landing movement asymmetries at the time of return to sport (RTS); however, the effect of movement asymmetries on longitudinal knee-related function after ACLR has not been examined. Hypothesis/Purpose: The purpose of this study was to examine the effect of SL drop-landing movement symmetry at the time of RTS on knee-related function 2 years later in young athletes after ACLR. The first hypothesis was that young athletes who demonstrated SL drop-landing asymmetries at RTS would demonstrate decreased knee function 2 years later compared with those who demonstrated symmetric SL drop-landing mechanics. The second hypothesis was that SL drop-landing movement symmetry at RTS would be associated with knee functional recovery 2 years later. Study Design: Cohort study; Level of evidence, 2. Methods: This study included 48 young athletes who had undergone ACLR and were assessed at the time of RTS (77% female; mean [±SD] age at RTS, 17.6 ± 2.6 years) and followed for 2 years after RTS. Three sagittal-plane landing variables of interest were calculated using 3-dimensional motion analysis during an SL drop-landing task at the time of RTS: knee flexion excursion, peak internal knee extension moment, and peak trunk flexion. The limb symmetry index (LSI) was calculated for each landing variable using the following: LSI = (involved/uninvolved) × 100%. The LSI was used to divide the cohort into symmetric (SYM) and asymmetric (ASYM) groups for each landing variable: knee flexion excursion (SYM: LSI ≥ 90% [n = 23]; ASYM: LSI < 85% [n = 18]), peak internal knee extension moment (SYM: LSI ≥ 90% [n = 19]; ASYM: LSI < 85% [n = 22]), and peak trunk flexion (SYM: LSI ≤ 105% [n = 25]; ASYM: LSI > 115% [n = 19]). At 2 years after RTS, knee-related function was evaluated using the Knee Injury and Osteoarthritis Outcome Score (KOOS), International Knee Documentation Committee (IKDC) subjective knee form, and performance on SL hop tests. Functional recovery was defined based on literature cutoffs for knee-related functional measures. Differences in 2-year function were compared between the symmetry groups using Mann-Whitney U tests because of nonnormality. Logistic regression was used to determine if landing symmetry at the time of RTS would be associated with 2-year knee functional recovery after RTS. Results: The ASYM knee flexion excursion group demonstrated decreased function at 2 years after RTS compared with the SYM group on the KOOS-Pain (ASYM: 93.0 ± 8.2; SYM: 98.4 ± 3.0; P = .008) and the KOOS–Quality of Life (ASYM: 81.6 ± 16.1; SYM: 94.1 ± 9.7; P = .008). Knee flexion excursion was associated with knee functional recovery on the KOOS-Pain and the KOOS–Quality of Life ( P = .033 and P = .012, respectively) at 2 years after RTS, after controlling for the quadriceps strength LSI and graft type. Conclusion: Young athletes after ACLR with asymmetries in knee kinematics at the time of RTS reported decreased self-reported function 2 years later; however, the clinical importance of these differences needs to be further understood.

Abstract Rationale Usual interstitial pneumonia (UIP) is the histopathologic hallmark of idiopathic pulmonary fibrosis. Although UIP can be detected by high-resolution computed tomography of the chest, the results are frequently inconclusive, and pathology from transbronchial biopsy (TBB) has poor sensitivity. Surgical lung biopsy may be necessary for a definitive diagnosis. Objectives To develop a genomic classifier in tissue obtained by TBB that distinguishes UIP from non-UIP, trained against central pathology as the reference standard. Methods Exome enriched RNA sequencing was performed on 283 TBBs from 84 subjects. Machine learning was used to train an algorithm with high rule-in (specificity) performance using specimens from 53 subjects. Performance was evaluated by cross-validation and on an independent test set of specimens from 31 subjects. We explored the feasibility of a single molecular test per subject by combining multiple TBBs from upper and lower lobes. To address whether classifier accuracy depends upon adequate alveolar sampling, we tested for correlation between classifier accuracy and expression of alveolar-specific genes. Results The top-performing algorithm distinguishes UIP from non-UIP conditions in single TBB samples with an area under the receiver operator characteristic curve (AUC) of 0.86, with specificity of 86% (confidence interval = 71–95%) and sensitivity of 63% (confidence interval = 51–74%) (31 test subjects). Performance improves to an AUC of 0.92 when three to five TBB samples per subject are combined at the RNA level for testing. Although we observed a wide range of type I and II alveolar–specific gene expression in TBBs, expression of these transcripts did not correlate with classifier accuracy. Conclusions We demonstrate proof of principle that genomic analysis and machine learning improves the utility of TBB for the diagnosis of UIP, with greater sensitivity and specificity than pathology in TBB alone. Combining multiple individual subject samples results in increased test accuracy over single sample testing. This approach requires validation in an independent cohort of subjects before application in the clinic.

Combined theoretical and experimental analysis of serotonin by quantum chemical density functional calculations and surface-enhanced Raman spectroscopy, respectively, is presented in this work to better understand phenomena related to this neurotransmitter’s detection and monitoring at very low concentrations specific to physiological levels. In addition to the successful ultrasensitive analyte detection on silver nanoparticles for concentrations as low as 10−11 molar, the relatively good agreement between the simulated and experimentally determined results indicates the presence of all serotonin molecular forms, such as neutral, ionic, and those oxidized through redox reactions. Obvious structural molecular deformations such as bending of lateral amino chains are observed for both ionic and oxidized forms. Not only does this combined approach reveal more probable adsorption of serotonin into the silver surface through hydroxyl/oxygen sites than through NH/nitrogen sites, but also that it does so predominantly in its neutral (reduced) form, somewhat less so in its ionic forms, and much less in its oxidized forms. If the development of opto-voltammetric biosensors and their effective implementation is envisioned for the future, this study provides some needed scientific background for comprehending changes in the vibrational signatures of this important neurotransmitter.

Objective To elucidate the genetic architecture of gene expression in pancreatic tissues. Design We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. Results We identified 38 615 cis -eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis -eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis -eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis -eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10 −8 ) and tumour-derived (p=8.3×10 −5 ) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the ‘O’ mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO ‘O’ mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. Conclusions We have identified cis -eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.

As potential treatments for C9ORF72‐associated amyotrophic lateral sclerosis (c9ALS) approach clinical trials, the identification of prognostic biomarkers for c9ALS becomes a priority. We show that levels of phosphorylated neurofilament heavy chain (pNFH) in cerebrospinal fluid (CSF) predict disease status and survival in c9ALS patients, and are largely stable over time. Moreover, c9ALS patients exhibit higher pNFH levels, more rapid disease progression, and shorter survival after disease onset than ALS patients without C9ORF72 expansions. These data support the use of CSF pNFH as a prognostic biomarker for clinical trials, which will increase the likelihood of successfully developing a treatment for c9ALS. Ann Neurol 2017;82:139–146

BACKGROUND: Patients with IBD have a higher baseline risk of venous thromboembolism, which further increases with surgery. Therefore, extended venous thromboembolism chemoprophylaxis has been suggested in certain high-risk cohorts. OBJECTIVE: The purpose of this study was to determine whether the underlying diagnosis, operative procedure, or both influence the incidence of postoperative venous thromboembolism. DESIGN: This was a retrospective review. SETTINGS: The American College of Surgeons–National Surgical Quality Improvement Project database was analyzed. PATIENTS: The NSQIP database was queried for patients with chronic ulcerative colitis and non-IBD undergoing colorectal resections using surgical Current Procedural Terminology codes modeled after the 3 stages used for the surgical management of chronic ulcerative colitis from 2005 to 2013. MAIN OUTCOME MEASURES: We measured 30-day postoperative venous thromboembolism risk in patients with chronic ulcerative colitis based on operative stage and risk factors for development of venous thromboembolism. RESULTS: A total of 18,833 patients met inclusion criteria, with an overall rate of venous thromboembolism of 3.8. Among procedure risk groups, venous thromboembolism rates were high risk, 4.4%; intermediate risk, 1.6%; and low risk, 0.7% (across risk groups, p < 0.01). Emergent case subjects exhibited a higher rate of venous thromboembolism than their elective counterparts (6.9% vs 3.1%). Factors significantly associated with venous thromboembolism on adjusted analysis included emergent risk case (adjusted OR = 7.85), high-risk elective case (adjusted OR = 5.07), intermediate-risk elective case (adjusted OR = 2.69), steroid use (adjusted OR = 1.54), and preoperative albumin <3.5 g/dL (adjusted OR = 1.45). LIMITATIONS: Because of its retrospective nature, correlation between procedures and venous thromboembolism risk can be demonstrated, but causation cannot be proven. In addition, data on inpatient and extended venous thromboembolism prophylaxis use are not available. CONCLUSIONS: Emergent status and operative procedure are the 2 highest risk factors for postoperative venous thromboembolism. Extended venous thromboembolism prophylaxis might be appropriate for patients undergoing these high-risk procedures or any emergent colorectal procedures. See Video Abstract at http://links.lww.com/DCR/A339.