Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.

Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expression (heterochromatin), little is known about mechanisms silencing ERVs residing in open regions of the genome (euchromatin). This is particularly important during embryonic development, where induction and repression of distinct classes of ERVs occur in short temporal windows. Here, we demonstrate that transcription-associated RNA degradation by the nuclear RNA exosome and Integrator is a regulatory mechanism that controls the productive transcription of most genes and many ERVs involved in preimplantation development. Disrupting nuclear RNA catabolism promotes dedifferentiation to a totipotent-like state characterized by defects in RNAPII elongation and decreased expression of long genes (gene-length asymmetry). Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards RNAPII activity, ERV expression, cell identity, and developmental potency.

Greater geographic sharing and heart transplantation waitlist outcomes following the 2018 heart allocation policy.

BACKGROUND: In 2018, a new heart allocation policy was introduced to reduce variability in access to and outcomes after transplantation, in part, through attempts at broader geographic sharing of donor hearts. We evaluated how this policy affected geographic sharing and waitlist outcomes by donation service area (DSA). METHODS: This retrospective study of the Scientific Registry of Transplant Recipients database included adult patients waitlisted between October 2016 and October 2020, stratified by policy period. Our primary outcomes were mean proportion of imported and exported hearts aggregated by DSA as well as time to transplant. RESULTS: Following the policy change, there was substantial evidence of sharing across DSAs. The mean proportion of imported hearts transplanted by a DSA increased from 32% (95% CI: 27%-36%) to 74% (95% CI: 71%-78%; p < 0.001), and the mean proportion of exported hearts increased from 37% (95% CI: 33%-42%) to 75% (95% CI: 71%-79%; p < 0.001). The mean sharing ratio, defined as the log-transformed ratio of imported to exported hearts per DSA, shifted from 1.15 (95% CI: 0.88-1.42) to 1.02 (95% CI: 0.96-1.07), with a 76% decline in the variance across DSAs. As sharing increased, time to transplant per DSA declined from 153.9 days (95% CI, 143.4-164.4 days) pre-policy to 89.6 days (95% CI, 83.1-96.1 days) post-policy (p < 0.001). A larger decrease in waitlist time was associated with a higher proportion of exported hearts. CONCLUSIONS: The 2018 heart allocation policy was associated with more uniform access to heart transplantation and improved waitlist outcomes.

Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease.

Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer's disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs from the human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration.

Machine-learning-optimized Cas12a barcoding enables the recovery of single-cell lineages and transcriptional profiles.

The development of CRISPR-based barcoding methods creates an exciting opportunity to understand cellular phylogenies. We present a compact, tunable, high-capacity Cas12a barcoding system called dual acting inverted site array (DAISY). We combined high-throughput screening and machine learning to predict and optimize the 60-bp DAISY barcode sequences. After optimization, top-performing barcodes had ∼10-fold increased capacity relative to the best random-screened designs and performed reliably across diverse cell types. DAISY barcode arrays generated ∼12 bits of entropy and ∼66,000 unique barcodes. Thus, DAISY barcodes-at a fraction of the size of Cas9 barcodes-achieved high-capacity barcoding. We coupled DAISY barcoding with single-cell RNA-seq to recover lineages and gene expression profiles from ∼47,000 human melanoma cells. A single DAISY barcode recovered up to ∼700 lineages from one parental cell. This analysis revealed heritable single-cell gene expression and potential epigenetic modulation of memory gene transcription. Overall, Cas12a DAISY barcoding is an efficient tool for investigating cell-state dynamics.

Genome-wide association study and functional validation implicates JADE1 in tauopathy.

Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-ß (Aß) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aß toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.

Radiomics signature based on computed tomography images for the preoperative prediction of lymph node metastasis at individual stations in gastric cancer: A multicenter study.

BACKGROUND: Specific diagnosis and treatment of gastric cancer (GC) require accurate preoperative predictions of lymph node metastasis (LNM) at individual stations, such as estimating the extent of lymph node dissection. This study aimed to develop a radiomics signature based on preoperative computed tomography (CT) images, for predicting the LNM status at each individual station. METHODS: We enrolled 1506 GC patients retrospectively from two centers as training (531) and external (975) validation cohorts, and recruited 112 patients prospectively from a single center as prospective validation cohort. Radiomics features were extracted from preoperative CT images and integrated with clinical characteristics to construct nomograms for LNM prediction at individual lymph node stations. Performance of the nomograms was assessed through calibration, discrimination and clinical usefulness. RESULTS: In training, external and prospective validation cohorts, radiomics signature was significantly associated with LNM status. Moreover, radiomics signature was an independent predictor of LNM status in the multivariable logistic regression analysis. The radiomics nomograms revealed good prediction performances, with AUCs of 0.716-0.871 in the training cohort, 0.678-0.768 in the external validation cohort and 0.700-0.841 in the prospective validation cohort for 12 nodal stations. The nomograms demonstrated a significant agreement between the actual probability and predictive probability in calibration curves. Decision curve analysis showed that nomograms had better net benefit than clinicopathologic characteristics. CONCLUSION: Radiomics nomograms for individual lymph node stations presented good prediction accuracy, which could provide important information for individual diagnosis and treatment of gastric cancer.

Assessment of a Deep Learning Model to Predict Hepatocellular Carcinoma in Patients With Hepatitis C Cirrhosis.

Importance: Deep learning, a family of machine learning models that use artificial neural networks, has achieved great success at predicting outcomes in nonmedical domains. Objective: To examine whether deep learning recurrent neural network (RNN) models that use raw longitudinal data extracted directly from electronic health records outperform conventional regression models in predicting the risk of developing hepatocellular carcinoma (HCC). Design, Setting, and Participants: This prognostic study included 48 151 patients with hepatitis C virus (HCV)-related cirrhosis in the national Veterans Health Administration who had at least 3 years of follow-up after the diagnosis of cirrhosis. Patients were identified by having at least 1 positive HCV RNA test between January 1, 2000, to January 1, 2016, and were followed up from the diagnosis of cirrhosis to January 1, 2019, for the development of incident HCC. A total of 3 models predicting HCC during a 3-year period were developed and compared, as follows: (1) logistic regression (LR) with cross-sectional inputs (cross-sectional LR); (2) LR with longitudinal inputs (longitudinal LR); and (3) RNN with longitudinal inputs. Data analysis was conducted from April 2018 to August 2020. Exposures: Development of HCC. Main Outcomes and Measures: Area under the receiver operating characteristic curve, area under the precision-recall curve, and Brier score. Results: During a mean (SD) follow-up of 11.6 (5.0) years, 10 741 of 48 151 patients (22.3%) developed HCC (annual incidence, 3.1%), and a total of 52 983 samples (51 948 [98.0%] from men) were collected. Patients who developed HCC within 3 years were older than patients who did not (mean [SD] age, 58.2 [6.6] years vs 56.9 [6.9] years). RNN models had superior mean (SD) area under the receiver operating characteristic curve (0.759 [0.009]) and mean (SD) Brier score (0.136 [0.003]) than cross-sectional LR (0.689 [0.009] and 0.149 [0.003], respectively) and longitudinal LR (0.682 [0.007] and 0.150 [0.003], respectively) models. Using the RNN model, the samples with the mean (SD) highest 51% (1.5%) of HCC risk, in which 80% of all HCCs occurred, or the mean (SD) highest 66% (1.2%) of HCC risk, in which 90% of all HCCs occurred, could potentially be targeted. Among samples from patients who achieved sustained virologic response, the performance of the RNN models was even better (mean [SD] area under receiver operating characteristic curve, 0.806 [0.025]; mean [SD] Brier score, 0.117 [0.007]). Conclusions and Relevance: In this study, deep learning RNN models outperformed conventional LR models, suggesting that RNN models could be used to identify patients with HCV-related cirrhosis with a high risk of developing HCC for risk-based HCC outreach and surveillance strategies.

Atomically dispersed metal sites stabilized on a nitrogen doped carbon carrier via N2 glow-discharge plasma.

A novel, facile and universal N2 plasma approach to form single atom metal sites (Pt, Pd, Ag, Cu, and Co) is proposed. Fast nucleation and slow growth of metal ions under low temperature plasma are the premise to form single atoms. These isolated metal atoms are subsequently trapped by in situ doped nitrogen. We provide a new route to expand the toolbox of single-atoms preparation.

BCL11A Promotes the Progression of Laryngeal Squamous Cell Carcinoma.

Background: We report functional and clinical data uncovering the significance of B-cell lymphoma/leukemia 11A (BCL11A) in laryngeal squamous cell carcinoma (LSCC). Methods: We examined BCL11A expression in a cohort of LSCC patients and evaluated the association between BCL11A expression and clinicopathological features. We investigated the consequences of overexpressing BCL11A in the LSCC cell line on proliferation, migration, invasion, cell cycle, chemosensitivity, and growth in vivo. We explored the relationship between BCL11A and MDM2 in LSCC and tumorigenesis pathways by using the Human Cancer PathwayFinder Array. Results: High levels of BCL11A were found in LSCC tissues and were more frequently associated with advanced lymphatic metastasis stages with poor prognoses. BCL11A overexpression enhanced LSCC proliferation in vitro and vivo. A positive correlation between MDM2 and BCL11A expression was identified. Conclusions: These data uncover important functions of BCL11A in LSCC and identify BCL11A as a prognostic biomarker and potential therapeutic target in LSCC.

Cost Effectiveness of Bosentan for Pulmonary Arterial Hypertension: A Systematic Review.

Objectives: Although many studies have reported on the cost-effectiveness of bosentan for treating pulmonary arterial hypertension (PAH), a systematic review of economic evaluations of bosentan is currently lacking. Objective evaluation of current pharmacoeconomic evidence can assist decision makers in determining the appropriate place in therapy of a new medication. Methods: Systematic literature searches were conducted in English-language databases (MEDLINE, EMBASE, EconLit databases, and the Cochrane Library) and Chinese-language databases (China National Knowledge Infrastructure, WanFang Data, and Chongqing VIP) to identify studies assessing the cost-effectiveness of bosentan for PAH treatments. Results: A total of 8 published studies were selected for inclusion. Among them were two studies comparing bosentan with epoprostenol and treprostinil. Both results indicated that bosentan was more cost-effective than epoprostenol, while the results of bosentan and treprostinil were not consistent. Four studies compared bosentan with other endothelin receptor antagonists, which indicated ambrisentan might be the drug of choice for its economic advantages and improved safety profile. Only two economic evaluations provided data to compare bosentan versus sildenafil, and the results favored the use of sildenafil in PAH patients. Four studies compared bosentan with conventional, supportive, or palliative therapy, and whether bosentan was cost-effective was uncertain. Conclusions: Bosentan may represent a more cost-effective option compared with epoprostenol and conventional or palliative therapy. There was unanimous agreement that bosentan was not a cost-effective front-line therapy compared with sildenafil and other endothelin receptor antagonists. However, high-quality cost-effectiveness analyses that utilize long-term follow-up data and have no conflicts of interest are still needed.

Role of T helper 17 cytokines in the tumour immune inflammation response of patients with laryngeal squamous cell carcinoma.

Altered cytokine production can lead to immune dysfunction in patients with cancer. The present study investigated the expression of T helper (Th)17 cytokines in patients with laryngeal squamous cell carcinoma (LSCC) and their clinical significance in providing new therapeutic insights. The prevalence of Th17 cells and their receptors in patients with LSCC was studied using immunohistochemical analysis via tissue microarray technology. Flow cytometry was used to investigate the percentage of Th17 and Th1 cells in peripheral blood mononuclear cells. Furthermore, the proliferation of Th17 cells and Th17-associated cytokines, including interleukin (IL)17, IL23 and RAR-related orphan receptor γt, was analyzed by reverse transcription-quantitative polymerase chain reaction. The results revealed that the prevalence of Th17 cells in patients with LSCC was elevated in their primary tumors, as well as in peripheral blood, compared with that in healthy controls. It was further demonstrated that Th17 cells could be induced and expanded in the tumor microenvironment through cytokines produced by the tumor cells. In conclusion, Th17 cells have a substantial impact on the carcinogenesis of LSCCs, and could serve as a potential therapeutic target to modulate the anti-tumor response in these carcinomas.

Association of the microsatellite (GT)n repeat polymorphisms of the HO-1 gene promoter and corresponding serum levels with the risk of laryngeal squamous cell carcinoma.

CONCLUSION: Long (GT)n repeat polymorphisms in the heme oxygenase-1 (HO-1) gene promoter and decreased serum HO-1 levels are associated with a higher susceptibility to laryngeal squamous cell carcinoma (LSCC). OBJECTIVE: In this case-control study, the association of HO-1 microsatellite (GT)n repeat polymorphisms and serum levels with the risk of LSCC was investigated. METHODS: A total of 142 LSCC patients, 54 vocal leukoplakia patients and 98 healthy controls, were examined for (GT)n polymorphisms by sequencing, and the serum HO-1 levels were detected in a sub-set from participants above by ELISA. RESULTS: Compared with the controls, the LSCC group had significantly higher frequencies of L-allele (> 29 repeats) and L-allele carriers (p < 0.001, OR = 2.037 and p = 0.005, OR = 2.152, respectively). The frequencies of lymph node metastasis and of moderate or poor differentiation were significantly higher in L-allele carriers compared to non-L-allele carriers (p < 0.05). Significantly lower serum HO-1 levels were detected in LSCC patients (p < 0.001), and patients with lower serum HO-1 levels had more advanced cancer stage and a higher lymph node metastasis rate (p < 0.05). Furthermore, the L-allele carriers had lower serum HO-1 concentrations compared with the non-L-allele carriers (p = 0.019).

The ratio of CD4/CD8 T-cells in human papillomavirus-positive laryngeal squamous cell carcinoma accounts for improved outcome.

CONCLUSION: Improved prognosis associated with HPV-positive status may depend on lower CD4/CD8 ratio. Th1 CD4(+ )T cells were found to be the major sub-set of T lymphocytes in the HPV positive laryngeal squamous cell carcinoma microenvironment. BACKGROUND: To examine the prognostic significance of human papillomavirus (HPV) status in relation to the ratio of CD4/CD8 in LSCC. METHODS: In this study, 46 LSCC biopsy samples were retrospectively assessed using immunohistochemistry for CD4(+ )and CD8(+ )tumor infiltrating lymphocytes (TILs). HPV status was determined by HPV in situ hybridization (ISH) and p16(INK4A) immunohistochemistry. Of the 46 samples, 21 were evaluated for the expression of IFN-γ and IL-4 by quantitative real-time PCR (qRT-PCR). The influence of HPV status on locoregional tumor control and T-cell sub-sets infiltrating tumor microenvironment were investigated. RESULTS: Nineteen patients (41.3%) were classified as HPV positive, who had improved disease-free survival (28% in reduction, hazard ratio =0.10; 95% CI =0.011-0.938). A direct correlation between the HPV status and the ratio of CD4/CD8 or mean levels of CD8(+ )T cells was observed. Compared with the HPV-negative samples, HPV-positive samples had a higher ratio of IFN-γ/IL-4 (24.43 ± 29.89 vs 3.90 ± 4.03; p = 0.0375).

[Association of IL-10 promoter polymorphism and plasma levels with susceptibility to vocal cords leukoplakia].

OBJECTIVE: To investigated the association between interleukin-10(IL-10)-1082/-819/-592 promoter polymorphism, plasma IL-10 levels and risk of vocal leukoplakia. METHODS: A case-control study of 61 patients with vocal cords leukoplakia and 119 healthy subjects were performed. Genotypes for the IL-10 gene (IL-10 -1082 G/A, -819 C/T and -592 C/A) were determined using pyrosequencing and plasma IL-10 levels were analyzed by ELISA. RESULTS: Smoking and alcohol consumption increased the risk of vocal leukoplakia (OR = 4.73, 95%CI:2.4-9.1;OR = 5.70, 95%CI:2.9-11.2, P < 0.01) . Patients with vocal cord leukoplakia had significantly higher frequencies of AC at -592 and -819 (OR = 1.93, 95%CI:0.97-3.81, P = 0.05) and AG at -1082(OR = 2.14, 95%CI:0.87-5.27, P = 0.092) than control. Vocal leukoplakia patients had higher concentration of plasma IL-10 (21.6 ± 0.5) pg/ml (X(-) ± s) than controls (19.0 ± 1.1)pg/ml(t = 2.08, P = 0.043) and the haplotype containing the G allele was associated with higher plasma IL-10 concentrations (24.3 ± 5.7) pg/ml compared with the ATA haplotype(19.9 ± 4.7) pg/ml (t = -2.64, P = 0.008). CONCLUSIONS: IL-10-1082/-819/-592 promoter polymorphism and high concentration of plasma IL-10 are associated with vocal cord leukoplakia, and the concentration of plasma IL-10 is associated with the genotypes of IL-10 promoter polymorphism.

[The change of negative pressure in the cupping-cup and its influence on the depth of filiform-needle insertion].

This study was designed to observe the negative pressure in the cup during cupping, and to investigate the influence of negative pressure on the depth of filiform-needle inserted and retained. In the beginning, the change of pressure after cupping on acupoint BL23 for a span of 20 minutes was recorded. Acupuncture on acupoint BL23 was performed; the filiform-needle was retained and followed by cupping at different levels of negative pressure, and the changes of the depth of needle insertion was measured. The results showed: the absolute value of the negative pressure in the cup goes down with time and is significantly lower after 20 minutes (P < 0.05); the negative pressure in the cup causes the retreat of the inserted needle; and under the same pressure, there is a greater length measurement in needle retreat for male than for female (P < 0.01). The length of needle retreat is related to the pressure in the cupping-cup and to gender.