Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications

Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets and the nuclease-helicase Cas3 to degrade them. Among the seven subtypes, type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here, we use four cryoelectron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9 that strongly inhibit Neisseria lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through allosteric inhibition, whereas AcrIC9 achieves so through direct competition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for type I CRISPR eukaryotic genome engineering.

Preoperative diagnostic value of coronary CT angiography in acute Stanford type A aortic dissection involving the coronary arteries

AIM

To assess the diagnostic value of coronary computed tomography angiography (CCTA) in acute type A aortic dissection (ATAAD) with coronary artery involvement and to evaluate whether CCTA could provide potentially useful information for selecting the surgical method.

MATERIALS AND METHODS

Patients with ATAAD treated from January 2019 to December 2020 were reviewed retrospectively. Involvement of the coronary arteries based on CCTA findings were grouped into three major types and five subtypes. Interobserver and intraobserver diagnostic agreement for five subtypes were determined. The patients were divided into the coronary artery bypass grafting (CABG) and non-CABG groups, and the proportions of the five subtypes between the two groups were compared.

RESULTS

A total of 95 patients were enrolled in this study. Interobserver and intraobserver diagnostic agreement were both substantial in the left and right coronary arteries. Overall, the proportions of the five subtypes of coronary artery involvement were significantly different between the two groups (p<0.001). The proportion of Type A was elevated in the non-CABG group compared with the CABG group (22.6% versus 71.9%); by contrast, the proportions of Type B1 (35.5% versus 14.1%), Type B2 (19.4% versus 10.9%), Type C1 (6.5% versus 0%), and Type C2 (16.1% versus 3.1%) were elevated in the CABG group.

CONCLUSION

CCTA is reliable in evaluating coronary artery involvement by ATAAD. The present retrospective study indicated that CABG may be considered if the intimal flap disrupts the coronary orifice and causes luminal stenosis >50%, particularly Type B, or if an intimal tear occurs in the coronary orifice (Type C), which deserve further validation through prospective studies.

Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for Genome Editing Applications

Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets, and the nuclease-helicase Cas3 to degrade them. Among seven subtypes, Type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here we use four cryo-electron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling efficient NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9, that strongly inhibit N. lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through direct competition, whereas AcrIC9 achieves so through allosteric inhibition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for controllable Type I CRISPR genome engineering.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Snapshots of a tiny ancestral nuclease of Cas9

High-resolution structures solved by Schuler et al. shed light on how Cas9's evolutionary ancestor IscB operates as an RNA-guided nuclease. With only two-fifths the size of Cas9, IscB holds great promise for alleviating the cargo size constraint of in vivo CRISPR delivery.

Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems

Leading CRISPR-Cas technologies employ Cas9 and Cas12 enzymes that generate RNA-guided dsDNA breaks. Yet, the most abundant microbial adaptive immune systems, Type I CRISPRs, are under-exploited for eukaryotic applications. Here, we report the adoption of a minimal CRISPR-Cas3 from Neisseria lactamica (Nla) type I-C system to create targeted large deletions in the human genome. RNP delivery of its processive Cas3 nuclease and target recognition complex Cascade can confer ∼95% editing efficiency. Unexpectedly, NlaCascade assembly in bacteria requires internal translation of a hidden component Cas11 from within the cas8 gene. Furthermore, expressing a separately encoded NlaCas11 is the key to enable plasmid- and mRNA-based editing in human cells. Finally, we demonstrate that supplying cas11 is a universal strategy to systematically implement divergent I-C, I-D, and I-B CRISPR-Cas3 editors with compact sizes, distinct PAM preferences, and guide orthogonality. These findings greatly expand our ability to engineer long-range genome edits.

Introducing Large Genomic Deletions in Human Pluripotent Stem Cells Using CRISPR-Cas3

CRISPR-Cas systems provide researchers with eukaryotic genome editing tools and therapeutic platforms that make it possible to target disease mutations in somatic organs. Most of these tools employ Type II (e.g., Cas9) or Type V (e.g., Cas12a) CRISPR enzymes to create RNA-guided precise double-strand breaks in the genome. However, such technologies are limited in their capacity to make targeted large deletions. Recently, the Type I CRISPR system, which is prevalent in microbes and displays unique enzymatic features, has been harnessed to effectively create large chromosomal deletions in human cells. Type I CRISPR first uses a multisubunit ribonucleoprotein (RNP) complex called Cascade to find its guide-complementary target site, and then recruits a helicase-nuclease enzyme, Cas3, to travel along and shred the target DNA over a long distance with high processivity. When introduced into human cells as purified RNPs, the CRISPR-Cas3 complex can efficiently induce large genomic deletions of varying lengths (1-100 kb) from the CRISPR-targeted site. Because of this unique editing outcome, CRISPR-Cas3 holds great promise for tasks such as the removal of integrated viral genomes and the interrogation of structural variants affecting gene function and human disease. Here, we provide detailed protocols for introducing large deletions using CRISPR-Cas3. We describe step-by-step procedures for purifying the Type I-E CRISPR proteins Cascade and Cas3 from Thermobifida fusca, electroporating RNPs into human cells, and characterizing DNA deletions using PCR and sequencing. We focus here on human pluripotent stem cells due to their clinical potential, but these protocols will be broadly useful for other cell lines and model organisms for applications including large genomic deletion, full-gene or -chromosome removal, and CRISPR screening for noncoding elements, among others. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Expression and purification of Tfu Cascade RNP Support Protocol 1: Expression and purification of TfuCas3 protein Support Protocol 2: Culture of human pluripotent stem cells Basic Protocol 2: Introduction of Tfu Cascade RNP and Cas3 protein into hPSCs via electroporation Basic Protocol 3: Characterization of genomic DNA lesions using long-range PCR, TOPO cloning, and Sanger sequencing Alternate Protocol: Comprehensive analysis of genomic lesions by Tn5-based next-generation sequencing Support Protocol 3: Single-cell clonal isolation.

Symptomatic and Asymptomatic Chronic Carotid Artery Occlusion on High-Resolution MR Vessel Wall Imaging

BACKGROUND AND PURPOSE

Chronic carotid artery occlusion remains a poorly understood risk factor for subsequent stroke, and potential revascularization is dependent on understanding the anatomy and nature of the occlusion. Luminal imaging cannot assess the nature of an occlusion, so the internal structure of the occlusion must be inferred. The present study examines the signal characteristics of symptomatic and asymptomatic carotid occlusion that may point to management differentiation.

MATERIALS AND METHODS

We prospectively recruited patients who were diagnosed with chronic carotid artery occlusion defined as longer than 4 weeks and confirmed by DSA. All patients underwent high-resolution MR vessel wall imaging examinations after enrollment. Baseline characteristics, vessel wall imaging features, and DSA features were collected and evaluated. The vessel wall imaging features included segment involvement, signal intensity, contrast enhancement, and vessel wall thickness. The symptomatic and asymptomatic chronic carotid artery occlusions were compared.

RESULTS

A total of 44 patients with 48 lesions were included in this study from February 2020 to December 2020. Of the 48 lesions, 35 (72.9%) were symptomatic and 13 (27.1%) were asymptomatic. There was no difference in baseline and DSA features. On vessel wall imaging, C1 and C2 were the most commonly involved segments (91.7% and 68.8%, respectively). Compared with symptomatic lesions, asymptomatic lesions were more often isointense (69.2%) in the distal segment (P = .03). Both groups had diffuse wall thickening (80% and 100%).

CONCLUSIONS

Signal characteristics between those with symptomatic and asymptomatic carotid artery occlusions differ in a statistically significant fashion, indicating a different structure of the occlusion.

Cross-genera amplification and identification of Colpodella sp. with Cryptosporidium primers in fecal samples of zoo felids from northeast China

The protozoans include many intracellular human pathogens. Accurate detection of these pathogens is necessary to treat the diseases. In clinical epidemiology, molecular identification of protozoan is considered a more reliable and rapid method for identification than microscopy. Among these protozoans, Cryptosporidium considered being one of the important water-borne zoonotic pathogens and a major cause of a diarrheal disease named cryptosporidiosis in humans, domestic animals, and wild animals. This study was aimed to identify Cryptosporidium in zoo felids (N= 56) belonging to different zoo of China, but accidentlly Colpodella was encountered in the zoo felids sample and phylogenetic data confirmed this unexpected amplification from fecal samples using two-step nested-PCR. Phylogenetic analysis revealed the fact about the specific primers used previously by many researchers and cross-genera amplification. We came to know that genetically sequenced amplicon gives more accurate identification of species. This study suggests more investigation on Colpodella which has been neglected previously but gains the attention of researchers after identified from humans and animals and has been known to correlate with neurological symptoms in patients.

Impact of age and menopausal stage on serum anti-Müllerian hormone levels in middle-aged women

OBJECTIVE

This study aimed to evaluate the association between age, menopausal stage and serum anti-Müllerian hormone (AMH) levels in middle-aged women.

METHODS

In this cross-sectional study, the serum AMH levels of 288 healthy women aged 40-55 years (divided into age groups: 40-44, 45-49 and 50-55 years) were evaluated. Stages of Reproductive Aging Workshop + 10 criteria were used to categorize these women into menopausal stages: late reproductive, menopausal transition and early postmenopausal stages. The impact of age, menopausal stage and hormone replacement therapy on serum AMH levels was analyzed using multi-factor analysis of variance. Effects of body mass index, smoking status and oral contraceptive use were simultaneously considered.

RESULTS

The median AMH level was 0.140 ng/ml. Log-AMH levels varied according to age group (variance = 20.113, F = 88.538, p < 0.001) and menopausal stage (variance = 5.543, F = 24.501, p < 0.001). An exponential model defined as AMH = 227,421.757 × e^{(-0.301 × age)} was fit to describe the decline in AMH level with age. The 5th-95th percentiles of the AMH levels ranged from less than 0.020 to 3.150, less than 0.020 to 1.944 and less than 0.020 to 0.030 ng/ml in the aforementioned menopausal stages, respectively.

CONCLUSION

Age and menopausal stage were associated with AMH levels; age had a greater impact on AMH than menopausal stage in middle-aged women.

Traumatic fractures in China from 2012 to 2014: a National Survey of 512,187 individuals

The China National Fracture Study has been conducted to provide a national dataset of traumatic fractures across China. A national representative sample of 512,187 individuals was selected. The population-weighted incidence rates, distribution, injury mechanisms, and risk factors for traumatic fractures were identified for various groups of individuals.

INTRODUCTION

The China National Fracture Study (CNFS) has been conducted to provide a comprehensive and up-to-date national dataset of traumatic fractures across China. This study aims to report the national incidences and distributions of traumatic fractures that occurred in 2012, 2013, and 2014 and to analyze the risk factors.

METHODS

A national representative sample of individuals was selected from 24 rural counties and 24 urban cities of 8 provinces using stratified random sampling and the probability proportional to size (PPS) methodology. Participants were interviewed to identify whether they sustained traumatic fractures of the trunk and/or four extremities that had occurred in 2012, 2013, and 2014. The main risk factors associated with traumatic fractures were analyzed by multiple logistic regression models.

RESULTS

A total of 512,187 individuals, including 259,649 males and 252,538 females, participated in the CNFS. The population-weighted incidence rates of traumatic fractures in China were calculated to be 2.5 (95% CI, 2.2-2.8) per 1000 population in 2012, 2.8 (95% CI, 2.5-3.3) in 2013, and 3.2% (95% CI, 2.8-3.6) in 2014. The population-weighted incidence rates of fragility fractures among participants aged 65 years and older were calculated to be 27.4 (95% CI, 21.4-33.4) per 1000 population in 2012, 36.0 (95% CI, 28.6-43.5) in 2013, and 42.4 (95% CI, 34.9-49.9) in 2014. The most common cause of fracture was low-energy injuries, followed by traffic accidents. For all age groups, sleeping less than 7 h was a risk factor for traumatic fractures. Alcohol consumption and previous fracture history were identified as risk factors for adults aged 15 years and over. Cigarette smoking was found to be a risk factor for males aged 15-64 years old. For individuals aged 15-64 years old, underweight incurred a risk effect for males and overweight for females. Alcohol consumption, sleeping less than 7 h per day, living in the central and eastern regions, a body mass index less of than 18.5, and having a previous fracture history were identified as strong risk factors for fragility fractures.

CONCLUSION

The national incidence, distribution, and injury mechanisms for traumatic fractures were revealed in the CNFS. Risk factors were identified for various groups of individuals.

CDC6 is up-regulated and a poor prognostic signature in glioblastoma multiforme

PURPOSE

Glioblastoma multiforme (GBM) represents the most common and the most malignant type of brain tumor. Cell division cycle 6 (CDC6), a gene associated with DNA replication initiation, has been proven to be associated with the prognosis of multiple tumors. In this study, we aim to explore the association between CDC6 expression and GBM carcinogenesis and prognosis.

METHODS

CDC6 expression in normal cells and GBM cells was explored by analyzing TCGA dataset, as well as by RT-PCR and western blot methods. Survival analysis was performed by the Kaplan-Meier method. Multivariate Cox-regression analysis was adopted to estimate the independence of CDC6 as a GBM prognostic factor.

RESULTS AND CONCLUSIONS

Elevated CDC6 levels in GBM tumor tissues compared with those in normal brain tissues were illustrated by analyzing the gene expression profiles from TCGA dataset, and confirmed by RT-PCR and western blot assays in GBM tumor and normal human astrocyte cell lines. Kaplan-Meier analysis indicated the negative influence of high CDC6 expression on GBM overall survival (OS) probability and days to progression (D2P) after initial treatment, but not on days to recurrence (D2R) after initial treatment. Multivariate Cox regression analysis showed CDC6 as an independent signature marker gene for GBM prognosis. In addition, the combination of CDC6 mRNA expression and CpG island methylator phenotype (CIMP) could sensitively predict 3-year OS and D2P. In conclusion, our study uncovered the role of CDC6 in GBM carcinogenesis and prognosis for the first time, which could shed new light on GBM diagnosis and treatment.

Machine learning to predict developmental neurotoxicity with high-throughput data from 2D bio-engineered tissues

There is a growing need for fast and accurate methods for testing developmental neurotoxicity across several chemical exposure sources. Current approaches, such as in vivo animal studies, and assays of animal and human primary cell cultures, suffer from challenges related to time, cost, and applicability to human physiology. Prior work has demonstrated success employing machine learning to predict developmental neurotoxicity using gene expression data collected from human 3D tissue models exposed to various compounds. The 3D model is biologically similar to developing neural structures, but its complexity necessitates extensive expertise and effort to employ. By instead focusing solely on constructing an assay of developmental neurotoxicity, we propose that a simpler 2D tissue model may prove sufficient. We thus compare the accuracy of predictive models trained on data from a 2D tissue model with those trained on data from a 3D tissue model, and find the 2D model to be substantially more accurate. Furthermore, we find the 2D model to be more robust under stringent gene set selection, whereas the 3D model suffers substantial accuracy degradation. While both approaches have advantages and disadvantages, we propose that our described 2D approach could be a valuable tool for decision makers when prioritizing neurotoxicity screening.

Biochemical characterization of RNA-guided ribonuclease activities for CRISPR-Cas9 systems

The majority of bacteria and archaea rely on CRISPR-Cas systems for RNA-guided, adaptive immunity against mobile genetic elements. The Cas9 family of type II CRISPR-associated DNA endonucleases generates programmable double strand breaks in the CRISPR-complementary DNA targets flanked by the PAM motif. Nowadays, CRISPR-Cas9 provides a set of powerful tools for precise genome manipulation in eukaryotes and prokaryotes. Recently, a few Cas9 orthologs have been reported to possess intrinsic CRISPR-guided, sequence-specific ribonuclease activities. These discoveries fundamentally expanded the targeting capability of CRISPR-Cas9 systems, and promise to provide new CRISPR tools to manipulate specific cellular RNA transcripts. Here we present a detailed method for the biochemical characterization of Cas9's RNA-targeting potential.

Expression of C1q/TNF-related protein-3 (CTRP3) in serum of patients with gestational diabetes mellitus and its relationship with insulin resistance

OBJECTIVE

In this study, the changes of insulin resistance (IR) and pancreatic β-cell function in GDM patients were observed, changes of CTRP3 level in fasting serum and relationships with plasma glucose (PG) and pancreatic β-cell function were explored at the same time, and the correlation between serum CTRP3 and body mass index (BMI) was preliminarily discussed, providing a new way to identify the pathogenesis of GDM.

PATIENTS AND METHODS

Data of women from 24 to 28 weeks of pregnancy were collected. 100 women were selected to form gestational diabetes mellitus (GDM) group and another 100 women were chosen to constitute normal glucose tolerance (NGT) group according to the results of oral glucose tolerance test (OGTT). They were divided into GDM overweight/obesity (GDM + OW) group, GDM non-overweight/obesity (GDM + NW) group, simple overweight (OW) group and normal body weight (NW) group, according to whether the progestational body mass index (BMI) was higher than 24 kg/m2 before pregnancy. General information of all subjects, for example, age, last menstrual period, parity, diet, weight and height, were collected, and blood samples were taken from all subjects for use in detections of total cholesterol (TC), triglyceride (TG), very low-density lipoprotein (VLDL), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and serum C1q/tumor necrosis factor-related protein-3 (CTRP3).

RESULTS

The levels of FPG, 1 h PG, 2 h PG, fasting CP (FCP), fasting insulin (FINS), homeostasis model assessment of IR (HOMA-IR), TG and VLDL-C in the GDM group, were significantly higher than those in the NGT group. TC and LDL-C in the GDM group were greater than those in the NGT group. Compared with that in the NGT group, homeostasis model assessment of β (HOMA-β) index was lower in the GDM group. From the NGT group to the GDM group, FPG, 1 h PG, 2 h PG, FINS and FCP had rising tendencies, and the differences were of statistical significance. Pearson correlation analysis indicated that HOMA-IR was positively correlated with pre-pregnancy BMI, FPG, 2 h PG, FINS, 1 h INS, 2 h INS, FCP, 1 h CP and 2 h CP in the GDM group, HOMA-β was negatively related to FPG. In the NGT group, there was a positive correlation between HOMA-IR and pre-pregnancy BMI. The level of CTRP3 in fasting serum of the GDM group was distinctly lower than that of the NGT group. Pearson correlation analysis revealed that in the GDM group, fasting serum CTRP3 had positive correlations with HOMA-β and HDL-C, but negatively associated with pre-pregnancy BMI, FPG, 1 h PG, 2 h PG, FCP, HOMA-IR, TG and VLDL-C. In the NGT group, the fasting serum CTRP3 was negatively correlated with pre-pregnancy BMI. Multiple linear stepwise regression analysis showed FPG was an independent influencing factor for fasting serum CTRP3.

CONCLUSIONS

With the increase of FPG, the progression of GDM IR patients is increased, and pancreatic β-cell function progressively declines. The decrease of CTRP3 level in fasting serum in GDM patients plays a metabolic role in the pathogenesis of GDM.

Genetic variation and phylogenetic analysis of Porcine circovirus type 2 in China from 2016 to 2018

Infection with Porcine circovirus type 2 (PCV2), the essential cause of porcine circovirus (PCV) associated diseases, is a growing problem in swine industry around the world. High nucleotide alteration leads to the constant evolution of PCV2 and outbreak of disease caused by PCV2. In this study, 48 PCV2 strains were isolated in China between 2016 and 2018 and the genetic diversity of these PCV2 isolates was determined. Results showed that these PCV2 isolates were classified into genotypes PCV2a (4 of 48), PCV2b (13 of 48) and PCV2d (31 of 48). Among them, 54.5% isolated in 2016, 65.2% isolated in 2017 and 71.4% isolated in 2018 belonged to PCV2d. It indicated that the prevalence of PCV2d genotype increased. All strains shared 93.4%-100% nucleotide sequence identity for the whole genome. Results of the analysis using RDP 4.0 molecular recombination software showed there were no recombinant events among the 48 PCV2 isolates in this study. Further analysis indicated the presence of higher amino acid residues diversity in important epitopes (43D/G, 115D/G, 134N/T, 165P/T, 169G/R/S, and 210E/G/D) in the predominant genotype PCV2d. Animal tests showed the viral titer of the PCV2d strain LN-3 in sera was higher than that of PCV2b strain HeB-1 at 14 and 21 days post-challenge, however, the differences were not statistically significant. There were also no obvious differences between PCV2d strain LN-3 and PCV2b strain HeB-1 in the amount of PCV2 antigen in lymphoid tissues. On the account of the increasing prevalence of PCV2d genotype, it is necessary to find the cause of PCV2 genotype change, to evaluate the effect of existing commercial vaccines and to develop new vaccines based on PCV2d genotype, if necessary. Keywords: epitope; PCV2d; phylogeny; Porcine circovirus type 2; recombination; genetic diversity.

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas

CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.

[Derepression of CXCR7 indicates resistance to enzalutamide in castration resistant prostate cancer]

Objective: To investigate the effect of the derepression of chemokine receptor-7 (CXCR7) in prostatic tissues from patients with Castration Resistant Prostate Cancer (CRPC) on the resistance to enzalutamide (Enza). Methods: During the period of January 2015 to December 2017 all CRPC cases who underwent radical radiotherapy or androgen deprivation therapy (ADT) were evaluated. After prostatic puncture biopsy, the tissues were treated for immunostaining with CXCR7. Cox proportional hazard modeling and Kaplan-Meier analysis were used to determine PSA Progression-Free Survival (PSAP-FS) and Clinical or Radiographic Progression-Free Survival (CRP-FS) in the cohort. At last, PSA response rates and progression outcomes in CXCR7 negative cases and CXCR7 positive cases were analyzed. Results: Total 39 CRPC patients were enrolled in this study. And 23 cases derepress CXCR7, 16 cases negatively express CXCR7. The median follow-up duration was 12 months (range: 6-18) in the cohort. Chi-square analysis confirmed that PSA response rates after Enza treatment were significantly associated with CXCR7 derepression (χ(2)=22.129, P=0.000 06). Compared with CXCR7 positive expression group, CXCR7 negative expression group displayed improved median PSAP-FS (4.4 mon vs 11.7 mon, P=0.040 8) and CRP-FS (5.2 mon vs 13.1 mon, P=0.036 2) after Enza treatment. Conclusion: Derepression of CXCR7 in CRPC patients may be associated with resistance to enzalutamide. This protein may be novel target for treatment of CRPC.

Insights into a Mysterious CRISPR Adaptation Factor, Cas4

Cas4 nucleases are conserved factors in many CRISPR systems, yet their molecular role has remained enigmatic. In this issue of Molecular Cell, Shiimori et al. (2018) report that two Cas4 nucleases together determine the size, orientation, and PAM for foreign DNA snippets acquired by CRISPR loci as immunological memory.

Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics

Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.

Role of proton-coupled folate transporter in pemetrexed resistance of mesothelioma: clinical evidence and new pharmacological tools

BACKGROUND

Thymidylate synthase (TS) has a predictive role in pemetrexed treatment of mesothelioma; however, additional chemoresistance mechanisms are poorly understood. Here, we explored the role of the reduced-folate carrier (RFC/SLC19A1) and proton-coupled folate transporter (PCFT/SLC46A1) in antifolate resistance in mesothelioma.

PATIENTS AND METHODS

PCFT, RFC and TS RNA and PCFT protein levels were determined by quantitative RT-PCR of frozen tissues and immunohistochemistry of tissue-microarrays, respectively, in two cohorts of pemetrexed-treated patients. Data were analyzed by t-test, Fisher's/log-rank test and Cox proportional models. The contribution of PCFT expression and PCFT-promoter methylation to pemetrexed activity were evaluated in mesothelioma cells and spheroids, through 5-aza-2'-deoxycytidine-mediated demethylation and siRNA-knockdown.

RESULTS

Pemetrexed-treated patients with low PCFT had significantly lower rates of disease control, and shorter overall survival (OS), in both the test (N = 73, 11.3 versus 20.1 months, P = 0.01) and validation (N = 51, 12.6 versus 30.3 months, P = 0.02) cohorts. Multivariate analysis confirmed PCFT-independent prognostic role. Low-PCFT protein levels were also associated with shorter OS. Patients with both low-PCFT and high-TS levels had the worst prognosis (OS, 5.5 months), whereas associations were neither found for RFC nor in pemetrexed-untreated patients. PCFT silencing reduced pemetrexed sensitivity, whereas 5-aza-2'-deoxycytidine overcame resistance.

CONCLUSIONS

These findings identify for the first time PCFT as a novel mesothelioma prognostic biomarker, prompting prospective trials for its validation. Moreover, preclinical data suggest that targeting PCFT-promoter methylation might eradicate pemetrexed-resistant cells characterized by low-PCFT expression.

Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques

The aim of the present study was to test sample reproducibility for model neural tissues formed on synthetic hydrogels. Human embryonic stem (ES) cell-derived precursor cells were cultured on synthetic poly(ethylene glycol) (PEG) hydrogels to promote differentiation and self-organization into model neural tissue constructs. Neural progenitor, vascular, and microglial precursor cells were combined on PEG hydrogels to mimic developmental timing, which produced multicomponent neural constructs with 3D neuronal and glial organization, organized vascular networks, and microglia with ramified morphologies. Spearman's rank correlation analysis of global gene expression profiles and a comparison of coefficient of variation for expressed genes demonstrated that replicate neural constructs were highly uniform to at least day 21 for samples from independent experiments. We also demonstrate that model neural tissues formed on PEG hydrogels using a simplified neural differentiation protocol correlated more strongly to in vivo brain development than samples cultured on tissue culture polystyrene surfaces alone. These results provide a proof-of-concept demonstration that 3D cellular models that mimic aspects of human brain development can be produced from human pluripotent stem cells with high sample uniformity between experiments by using standard culture techniques, cryopreserved cell stocks, and a synthetic extracellular matrix. Impact statement Pluripotent stem (PS) cells have been characterized by an inherent ability to self-organize into 3D "organoids" resembling stomach, intestine, liver, kidney, and brain tissues, offering a potentially powerful tool for modeling human development and disease. However, organoid formation must be quantitatively reproducible for applications such as drug and toxicity screening. Here, we report a strategy to produce uniform neural tissue constructs with reproducible global gene expression profiles for replicate samples from multiple experiments.

RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations

Lead (Pb) is a well-known toxicant, especially for the developing nervous system, albeit the mechanism is largely unknown. In this study, we use time series RNA-seq to conduct a genome-wide survey of the transcriptome response of human embryonic stem cell-derived neural progenitor cells to lead treatment. Using a dynamic time warping algorithm coupled with statistical tests, we find that lead can either accelerate or decelerate the expression of specific genes during the time series. We further show that lead disrupts a neuron- and brain-specific splicing factor NOVA1 regulated splicing network. Using lead induced transcriptome change signatures, we predict several known and novel disease risks under lead exposure. The findings in this study will allow a better understanding of the mechanism of lead toxicity, facilitate the development of diagnostic biomarkers and treatment for lead exposure, and comprise a highly valuable resource for environmental toxicology. Our study also demonstrates that a human (embryonic stem) cell-derived system can be used for studying the mechanism of toxicants, which can be useful for drug or compound toxicity screens and safety assessment.

[Long-term oncologic outcomes of localized high-risk prostate cancer undergoing brachytherapy combined with external-beam radiation therapy and maximal androgen blockade]

Objective: To investigate the oncologic outcome and PSA kinetics of localized high-risk prostate cancer (PCa) patients treated with combination strategy of radiation therapy (RT) and maximal androgen blockade (MAB). Methods: We retrospectively reviewed the clinical data of 320 localized PCa patients undergoing RT+ MAB from 2001 to 2015. And radiation treatment protocol consisted of permanent prostate brachytherapy (PPB) at 110 Gy and EBRT at 45 Gy/23 fractions. Results: The median follow-up time was 90 (range: 12-186) months. And 117 (36.6%) cases underwent MAB + external-beam radiotherapy (EBRT), and other 203 (63.4%) cases received MAB+ EBRT+ PPB. Multivariate Cox regression analyses showed that PSA kinetics were positive indicators of oncologic outcomes. Furthermore, PSA kinetics were aberrantly improved by supplemental PPB to MAB+ EBRT as following, PSA nadir (1.3±0.7)μg/L vs(0.11±0.06)μg/L, time of PSA decrease to nadir (7.5±1.8)months vs (3.2±2.1)months, PSA doubling time (15.6±4.2)months vs (22.6±6.1)months, PSA decreasing amplitude (84.6±6.2)%vs(95.8±3.4)%. Additionally, the median time of several important oncologic events in MAB+ EBRT+ PPB group were also prolonged than that in MAB+ EBRT group as following, overall survival (12.3 years vs 9.1 years, P<0.001), biochemical recurrence-free survival (9.8 years vs 6.5 years, P<0.001), skeletal-related event (10.4years vs 8.2 years, P<0.001), and cytotoxic chemotherapy (11.6 years vs 8.8 years, P=0.007). Conclusion: MAB+ EBRT+ PPB is extremely effective combination strategy for localized high-risk PCa patients, and PPB plays the important synergistic role in improving PSA kinetics, which are independent predictor for oncologic outcomes.

Eyelid and fornix reconstruction in abortive cryptophthalmos: a single-center experience over 12 years

PurposeAbortive cryptophthalmos is a rare congenital eyelid anomaly with poor prognosis for vision and cosmesis. The study aims to present its varied manifestations and surgical outcomes.Patients and methodsThe medical records of patients with abortive cryptophthalmos treated at the Oculoplastic Clinic of Beijing Tongren Hospital between January 2004 and May 2016 were reviewed. Early surgical intervention was performed when exposure keratopathy occurs. Upper eyelid and superior fornix were mainly reconstructed with sliding myocutaneous flap and scleral and amniotic grafts. Post-operative upper eyelid contour, recurrence of symblepharon, and ability to retain prosthesis were evaluated.ResultsThe study included 41 eyes of 28 patients. The median age at first presentation was 5 years (ranging from 1 month to 58 years). The majority (79%) with concurrent craniofacial abnormalities tended to be associated with more severe cryptophthalmos. Nine eyes of 9 patients had recurrence of symblepharon. Acceptable functional and cosmetic outcomes were achieved in 20 of the 24 patients receiving repair procedures during the follow-up period.ConclusionOne-stage reconstruction of eyelid and fornix with scleral and amniotic grafts is an effective strategy to correct abortive cryptophthalmos.

Pretreatment Predictors of Early Response Revealed by Quantitative Cerebral Blood Flow in Major Depressive Disorder

Objective

The potential pattern of regional cerebral blood flow (rCBF) in major depressive disorder (MDD) underlies different response to antidepressants medication remain unclear. This study aimed to investigate the differences of rCBF between patients with different treatment response.

Methods

Eighty MDD patients [(44 treatment-responsive depression (RD) and 36 non-responding depression (NRD)] and 42 healthy controls (HC) underwent pulsed arterial spin labeling (PASL) scans in magnetic resonance imaging and clinical estimates. The exact rCBF values of each groups were obtained via quantification evaluation.

Results

Compared to NRD, the RD patients showed decreased rCBF values in frontal sensorimotor network (i.e. left paracentral lobule, left medial frontal gyrus, right superior frontal gyrus and right middle frontal gyrus), and further receiver operating curve (ROC) analyses demonstrated that the altered rCBF in these four regions exhibited outstanding performance on distinguishing NRD from RD. The NRD also exhibited reduced rCBF in bilateral cerebellum posterior lobe and right middle occipital gyrus and elevated rCBF in right postcentral gyrus and right middle frontal gyrus as compared to HC.

Conclusions

The decreased rCBF in frontal sensorimotor network appeared to be distinct characteristics for NRD, and might be severed as promising neuroimaging markers to differentiate depressed patients with weak early response to antidepressant medication. These findings expand our understanding of neural substrate underlying the antidepressant efficacy.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture

A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type. Endothelial cells cultured on tissue-culture polystyrene adopted a proliferative phenotype compared with cells cultured on or encapsulated in PEG hydrogels. The proliferative phenotype correlated to increased FAK-ERK activity, and knockdown or inhibition of ERK signaling reduced proliferation and expression for cell-cycle genes while increasing expression for “3D-like” vasculature development genes. Our results provide insight into the influence of 2D and 3D culture formats on global biological processes that regulate cell function.

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Defined, high-efficiency differentiation of human PSCs to endothelial cell

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Comprehensive genome-wide comparisons of 2D and 3D cell-culture formats

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Gene expression profiles for endothelial cells and pericytes in 3D cell culture

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Highly proliferative phenotypes on tissue-culture polystyrene surfaces

Antisense locked nucleic acids targeting agrA inhibit quorum sensing and pathogenesis of community-associated methicillin-resistant Staphylococcus aureus

AIM

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is commonly associated with nonnosocomial skin and soft tissue infections due to its virulence, which is mainly controlled by the accessory gene regulator (agr) quorum sensing (QS) system. In this study (KFF)₃ K peptide-conjugated locked nucleic acids (PLNAs) targeting agrA mRNA were developed to inhibit agr activity and arrest the pathogenicity of CA-MRSA.

METHODS AND RESULTS

Two PLNAs were designed, and synthesized, after predicting the secondary structure of agrA mRNA. The influence on bacterial growth was tested using a growth curve assay. RT-qPCR, haemolysis assay, lactate dehydrogenase release assay and chemotaxis assay were used to evaluate the effects of the PLNAs on inhibiting agr QS. A mouse skin infection model was employed to test the protective effect of the PLNAs in vivo. None of the PLNAs were found to be bacteriostatic or bactericidal in vitro. However, one PLNA, PLNA34, showed strong ability to suppress expression of agrA and the effector molecule RNAIII in USA300 LAC strain. Furthermore, PLNA34 inhibited the expression of virulence genes that are upregulated by agr, including hla, psmα, psmβ and pvl. The haemolytic activity of the supernatants from PLNA34-treated bacteria was also dramatically reduced, as well as the capacity to lyse and recruit neutrophils. Moreover, PLNA34 showed high levels of protection in the CA-MRSA mouse skin infection model.

CONCLUSIONS

The anti-agrA PLNA34 can effectively inhibit the agr QS and suppress CA-MRSA pathogenicity.

SIGNIFICANCE AND IMPACT OF THE STUDY

agrA is a promising target for the development of antisense oligonucleotides to block agr QS.

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm

BACKGROUND

Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states.

RESULTS

Here, we analyze the transcriptomes of human embryonic stem cell-derived lineage-specific progenitors by single-cell RNA-sequencing (scRNA-seq). We identify a definitive endoderm (DE) transcriptomic signature that leads us to pinpoint a critical time window when DE differentiation is enhanced by hypoxia. The molecular mechanisms governing the emergence of DE are further examined by time course scRNA-seq experiments, employing two new statistical tools to identify stage-specific genes over time (SCPattern) and to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to DE (Wave-Crest). Importantly, presumptive DE cells can be detected during the transitory phase from Brachyury (T) (+) mesendoderm toward a CXCR4 (+) DE state. Novel regulators are identified within this time window and are functionally validated on a screening platform with a T-2A-EGFP knock-in reporter engineered by CRISPR/Cas9. Through loss-of-function and gain-of-function experiments, we demonstrate that KLF8 plays a pivotal role modulating mesendoderm to DE differentiation.

CONCLUSIONS

We report the analysis of 1776 cells by scRNA-seq covering distinct human embryonic stem cell-derived progenitor states. By reconstructing a differentiation trajectory at single-cell resolution, novel regulators of the mesendoderm transition to DE are elucidated and validated. Our strategy of combining single-cell analysis and genetic approaches can be applied to uncover novel regulators governing cell fate decisions in a variety of systems.

Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels

Here, we describe an in vitro strategy to model vascular morphogenesis where human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) are encapsulated in peptide-functionalized poly(ethylene glycol) (PEG) hydrogels, either on standard well plates or within a passive pumping polydimethylsiloxane (PDMS) tri-channel microfluidic device. PEG hydrogels permissive towards cellular remodeling were fabricated using thiol-ene photopolymerization to incorporate matrix metalloproteinase (MMP)-degradable crosslinks and CRGDS cell adhesion peptide. Time lapse microscopy, immunofluorescence imaging, and RNA sequencing (RNA-Seq) demonstrated that iPSC-ECs formed vascular networks through mechanisms that were consistent with in vivo vasculogenesis and angiogenesis when cultured in PEG hydrogels. Migrating iPSC-ECs condensed into clusters, elongated into tubules, and formed polygonal networks through sprouting. Genes upregulated for iPSC-ECs cultured in PEG hydrogels relative to control cells on tissue culture polystyrene (TCP) surfaces included adhesion, matrix remodeling, and Notch signaling pathway genes relevant to in vivo vascular development. Vascular networks with lumens were stable for at least 14days when iPSC-ECs were encapsulated in PEG hydrogels that were polymerized within the central channel of the microfluidic device. Therefore, iPSC-ECs cultured in peptide-functionalized PEG hydrogels offer a defined platform for investigating vascular morphogenesis in vitro using both standard and microfluidic formats.

STATEMENT OF SIGNIFICANCE

Human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) cultured in synthetic hydrogels self-assemble into capillary networks through mechanisms consistent with in vivo vascular morphogenesis.

Association analysis of imbalanced interhemispheric functional coordination and early therapeutic efficacy in major depressive disorder: Evidence from resting state fMRI

Introduction

Emerging evidences indicate that the alteration of interhemispheric functional coordination may be involved in the pathogenesis of major depressive disorder (MDD). In present study, we aim to explore the potential marker by using the voxel-mirrored homotopic connectivity (VMHC) approach, which may be contributing to predict the clinical prognosis in MDD.

Methods

Eighty-two MDD patients and 50 normal control (NC) subjects participated in this study. We divided the MDD group into unremitted and remitted group according to the reduction rate of Hamilton Rating Scale for Depression (HAMD) within 2 weeks.

Results

The study detected significantly decreased VMHC in bilateral precuneus (pCu), inferior temporal gyrus (ITG) and increased VMHC in middle frontal gyrus (MFG) and caudate nucleus when compared remitted depression (RD) group to unremitted depression (URD) group. Meanwhile, when compared with NC group, the URD group presented reduced VMHC in bilateral cerebellum anterior lobe, thalamus and postcentral gyrus. Furthermore, the VHMC in media frontal gyrus, postcentral gyrus and precentral gyrus were significantly decreased in RD group. Correlation analysis suggested that reduced VMHC in bilateral pCu was negatively correlated with the baseline HAMD score of URD (r = −0.325, P = 0.041). Receiver operating characteristic (ROC) curve indicated that three regional VMHC changes could identify depressed patient with poorer treatment response: ITG [area under curve (AUC) = 0.699, P = 0.002, 95% CI = 0.586–0.812], MFG (AUC = 0.692, P = 0.003, 95% CI = 0.580–0.805), pCu (AUC = 0.714, P = 0.001, 95% CI = 0.603–0.825).

Conclusion

The current study combined with previous evidence indicates that the subdued intrinsic interhemispheric functional connectivity might represents a novel neural trait involved in the pathophysiology of MDD.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Decreased interhemispheric functional coordination underlying the cognitive impairment in late-onset depression

Background

The intuitive association between cognitive dysfunction in late onset depression (LOD) and the aberrant functional activity in the brain's default-mode network (DMN) has prompted interest in exploring the role of the DMN in LOD. The altered pattern of resting state voxel-mirrored homotopic connectivity (VMHC) in cognitive processes is not yet well understood in LOD.

Methods

The study was designed to examine the implicit coupling between the alteration of interhemispheric functional coordination and cognitive impairment in LOD. Thirty-one LOD patients and 37 matched healthy controls (HC) underwent neuropsychological tests and functional magnetic resonance imaging (fMRI) in this study.

Results

Compared to HC group, attenuated VMHC in superior frontal gyrus, superior temporal gyrus, posterior cerebellar lobe, postcentral and precentral gyrus was observed in LOD. Neuro-behavioral relevancy approach revealed that the imbalanced interhemispheric functional coordination in bilateral cerebellum was positively correlated with the performance of trail making test in LOD (r = 0.367, P = 0.040).

Conclusion

Altered linkage pattern of intrinsic homotopic connectivity and cognition was firstly investigated in LOD, and it would provide a novel clue to reveal the neural substrates underlying the cognitive dysfunction in LOD.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Impact of cataract surgery on vision-related life performances: the usefulness of Real-Life Vision Test for cataract surgery outcomes evaluation

PURPOSE

Real-Life Vision Test (RLVT) is a newly developed performance-based measures of functional vision. This present study is designed to determine whether it could be a meaningful assessment for cataract surgery outcomes evaluation.

PATIENTS AND METHODS

Age-related cataract patients (56) who scheduled for bilateral cataract surgery and 44 age-matched controls were evaluated by four types of measurements: (1) demographic, medical, cognitive and depressive evaluation, and the reaction time testing; (2) clinical measures (visual acuity, contrast sensitivity, stereopsis, and color perception); (3) the 25-item National Eye Institute's Visual Functioning Questionnaire (NEI-VFQ); (4) the RLVT. Spearman's coefficients and multiple regression analysis were conducted to investigate the relationship among RLVT, clinical measures, and self-report assessment of visual function.

RESULTS

The results of RLVT, clinical measures, and NEI-VFQ total scores were improved significantly after cataract surgery. There were no differences between control subjects and post-surgery patients with respect to NEI-VFQ-25 total scores, self-rating depression scale scores and three tasks of RLVT. Change of RLVT was significantly associated with the change of clinical measures in the cataract group. Multiple regression analysis demonstrated that change of distance, intermediate, and near visual acuity, and binocular contrast sensitivity were significant predictors of improvements of RLVT.

CONCLUSIONS

Cataract surgery could improve real-world visual ability effectively for cataract patients. Our study highlights the potential usefulness of RLVT as an adjunct to the current outcomes evaluation system for cataract surgery. The use of RLVT combined with clinical and self-survey methods may be the comprehensive strategy to manifest the impact of cataract surgery on patients' overall vision-related quality of life.

Annexin A5 promotes macrophage activation and contributes to pulmonary fibrosis induced by silica particles

OBJECTIVE

To investigate the contributions and underlying molecular mechanisms of annexin A5 toward silica-induced pulmonary fibrosis.

METHODS

Male C57BL/6 mice were randomly divided into three groups and instilled intratracheally with silica, saline, or air. Mice were euthanized at 3, 7, 14, or 28 days following treatment. Annexin A5 levels in serum and lung tissues were detected by enzyme-linked immunosorbant assay (ELISA) assays or Western blots. The association of annexin A5 levels with silica-induced lung fibrosis was further investigated in the macrophage cell line, RAW264.7. Following exposure of these cells to silica at a concentration of 200 μg/ml for 6 or 12 h, the expression levels of transforming growth factor β1 (TGF-β1), interleukin 1α (IL-1α), Fas ligand (FasL), and their downstream targets were evaluated by Western blots. Furthermore, annexin A5 and FasL were knocked down by small interfering ribonucleic acid (siRNA) and TGF-β1 secretion into the cell culture medium was measured by ELISA assays or Western blots.

RESULTS

Mice treated with silica demonstrated lung fibrosis at 28 days following exposure, whereas, in controls, only mild and transient inflammation was evident at day 3 and day 7 postinstillation and was not present at day 14. Furthermore, silica-exposed mice exhibited significantly (p < 0.05) elevated levels of annexin A5 in serum and lung tissues, relative to control groups. Consistent with these findings, silica exposure of RAW264.7 cells for 6 or 12 h, led to an annexin A5-dependent increase in the expression levels of TGF-β1, IL-1α, FasL, and their downstream target molecules. These silica-induced changes were reversed by siRNA-mediated knockdown of annexin A5, but downregulation of FasL led to increased annexin A5 expression and reduced levels of TGF-β1, IL-1α, and FasL downstream target molecules.

CONCLUSIONS

These findings define a role of annexin A5 in promoting macrophage activation via Fas/FasL pathways in silica-induced lung fibrosis.