ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.

Alternative lengthening of telomeres (ALTs) mechanism is activated in some somatic, germ cells, and human cancer cells. However, the key regulators and mechanisms of the ALT pathway remain elusive. Here we demonstrated that ZBTB40 is a novel telomere-associated protein and binds to telomeric dsDNA through its N-terminal BTB (BR-C, ttk and bab) or POZ (Pox virus and Zinc finger) domain in ALT cells. Notably, the knockout or knockdown of ZBTB40 resulted in the telomere dysfunction-induced foci and telomere lengthening in the ALT cells. The results also show that ZBTB40 is associated with ALT-associated promyelocytic leukemia nuclear bodies, and the loss of ZBTB40 induces the accumulation of the ALT-associated promyelocytic leukemia nuclear bodies in U2OS cells. Taken together, our results implicate that ZBTB40 is a key player of telomere protection and telomere lengthening regulation in human ALT cells.

Association of BMAL1 clock gene polymorphisms with fasting glucose in children.

BACKGROUND: The brain and muscle Arnt-like protein-1 (BMAL1) gene is an important circadian clock gene and previous studies have found that certain polymorphisms are associated with type 2 diabetes in adults. However, it remains unknown if such polymorphisms can affect fasting glucose in children and if other factors modify the associations. METHODS: A school-based cross-sectional study with 947 Chinese children was conducted. A multivariable linear regression model was used to analyze the association between BMAL1 gene polymorphisms and fasting glucose level. RESULTS: After adjusting for age, sex, body mass index (BMI), physical activity, and unhealthy diet, GG genotype carriers of BMAL1 rs3789327 had higher fasting glucose than AA/GA genotype carriers (b = 0.101, SE = 0.050, P = 0.045). Adjusting for the same confounders, rs3816358 was shown to be significantly associated with fasting glucose (b = 0.060, SE = 0.028, P = 0.032). Furthermore, a significant interaction between rs3789327 and nutritional status on fasting glucose was identified (Pinteraction = 0.009); rs3789327 was associated with fasting glucose in the overweight/obese subgroup (b = 0.353, SE = 0.126, P = 0.006), but not in non-overweight/non-obese children. CONCLUSIONS: BMAL1 polymorphisms were significantly associated with the fasting glucose level in children. Additionally, the observed interaction between nutritional status and BMAL1 supports promoting an optimal BMI in children genetically predisposed to higher glucose level. IMPACT: Polymorphisms in the essential circadian clock gene BMAL1 were associated with fasting blood glucose levels in children. Additionally, there was a significant interaction between nutritional status and BMAL1 affecting fasting glucose levels. BMAL1 rs3789327 was associated with fasting glucose only in overweight/obese children. This finding could bring novel insights into mechanisms by which nutritional status influences fasting glucose in children.

A Quick Method to Synthesize Extrachromosomal Circular DNA In Vitro.

Extrachromosomal circular DNA (eccDNA) is a special class of circular DNA in eukaryotes. Recent studies have suggested that eccDNA is the product of genomic instability and has important biological functions to regulate many downstream biological processes. While NGS (Next-Generation Sequencing)-based eccDNA sequencing has led to the identification of many eccDNAs in both healthy and diseased tissues, the specific biological functions of individual eccDNAs have yet to be clearly elucidated. Synthesizing eccDNAs longer than 1 kb with specific sequences remains a major challenge in the field, which has hindered our ability to fully understand their functions. Current methods for synthesizing eccDNAs primarily rely on chemical oligo synthesis, ligation, or the use of a specific gene editing and recombination systems. Therefore, these methods are often limited by the length of eccDNAs and are complex, expensive, as well as time-consuming. In this study, we introduce a novel method named QuickLAMA (Ligase-Assisted Minicircle Accumulation) for rapidly synthesizing eccDNAs up to 2.6 kb using a simple PCR and ligation approach. To validate the efficacy of our method, we synthesized three eccDNAs of varying lengths from cancer tissue and PC3 cells and confirmed successful circularization through sequencing and restriction enzyme digestion. Additional analyses have demonstrated that this method is highly efficient, cost-effective, and time-efficient, with good reproducibility. Using the method, a well-trained molecular biologist can synthesize and purify multiple eccDNAs within a single day, and it can be easily standardized and processed in a high-throughput manner, indicating the potential of the method to produce a wide range of desired eccDNAs and promote the translation of eccDNA research into clinical applications.

[Association between regional fat mass and risk of nonalcoholic fatty liver disease in overweight/obese adults].

OBJECTIVE: To explore the relationship between fat distribution and non-alcoholic fatty liver(NAFLD) in overweight/obese adults. METHODS: This cross-sectional study included 736(190 men and 546 women) 19-56 years old overweight/obese people in Beijing were selected by convenient sampling. Their age and body mass index(BMI) distribution were 36(31-46) years old and 28.0(26.2-30.7), respectively. The body fat mass and regional fat mass were measured by dual energy X-ray absorptiometry(DXA), and Logistic regression model was used to analyze the association between regional fat mass and the risk of NAFLD. RESULTS: The prevalence of NAFLD was 70.0%(515/736) in overweight/obese population. In the multivariate Logistic model, after adjusting for age, gender, BMI, hypertension and body fat mass, waist circumference(WC), thigh fat mass and android fat mass were significantly association with NAFLD risk(P<0.05), but no association was found between arms, trunk and gynoid fat mass and NAFLD risk. There were interactions between thigh fat mass and age(P_(interaction)<0.001) and BMI group(P_(interaction)=0.001). Subgroup analysis showed that thigh fat mass and NAFLD risk were significantly associated in ≤36-year-old(OR=0.62, 95%CI 0.48-0.81), male(OR=0.32, 95%CI 0.16-0.64) and overweight(OR=0.48, 95%CI 0.36-0.64) groups, but in the >36-year-old, female and the obesity group this association was not statistically significant. There was an interaction between trunk fat mass and age group(P_(interaction)=0.009). There was a positive correlation between trunk fat mass and NAFLD risk in >36-year-old group(OR=1.63, 95%CI 1.35-1.97), but no association was found in ≤36-year-old group. In addition, we also found that a significant interaction between gynoid fat mass and BMI group on NAFLD(P_(interaction)<0.001). In overweight, gynoid fat mass was negatively correlated with the risk of NAFLD(OR=0.12, 95% CI 0.06-0.25), but in the obesity group, the association was not statistically significant. There were no statistically significant interactions between WC, arms fat mass and android mass and age, sex and BMI groups. CONCLUSION: WC, android fat mass and thigh fat mass are associated with the risk of NAFLD. Thigh fat mass has a significant interaction with age and BMI group on the risk of NAFLD(only in ≤36-year-old group, male and overweight group a significant protective effect of thigh fat on NAFLD was found, but not in >36-year-old group, female and obesity group). Trunk fat mass had an interaction with age(the association between trunk fat mass and NAFLD was significant in >36-year-old group). Gynoid fat mass and BMI group also have a significant interaction on NAFLD(the detrimental effect of gynoid fat on NAFLD is much more profound in the obesity group).

BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS.

BACKGROUND: Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethylated cytosines into thymines (BS conversion). Incomplete conversion of unmethylated cytosines can introduce false positive methylation call. Developing a quick method to evaluate bisulfite conversion ratio (BCR) is benefit for both quality control and data analysis of WGBS. RESULTS: Here we provide a computational method named "BCREval" to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control. We tested the method by using public WGBS data and found that it is very stable and most of BS conversion assays can achieve> 99.5% efficiency. The non-CpG DNA methylation at telomere fits a binomial model and may result from a random process with very low possibility (the ratio < 0.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571-1572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter. CONCLUSION: Our method is a simple but robust method to QC and speculates BCR for WGBS experiments to make sure it achieves acceptable level. It is faster and more efficient than current tools and can be easily integrated into presented WGBS pipelines.

The roles and mechanisms of Leydig cells and myoid cells in regulating spermatogenesis.

Spermatogenesis is fundamental to the establishment and maintenance of male reproduction, whereas its abnormality results in male infertility. Somatic cells, including Leydig cells, myoid cells, and Sertoli cells, constitute the microenvironment or the niche of testis, which is essential for regulating normal spermatogenesis. Leydig cells are an important component of the testicular stroma, while peritubular myoid cells are one of the major cell types of seminiferous tubules. Here we addressed the roles and mechanisms of Leydig cells and myoid cells in the regulation of spermatogenesis. Specifically, we summarized the biological features of Leydig cells and peritubular myoid cells, and we introduced the process of testosterone production and its major regulation. We also discussed other hormones, cytokines, growth factors, transcription factors and receptors associated with Leydig cells and myoid cells in mediating spermatogenesis. Furthermore, we highlighted the issues that are worthy of further studies in the regulation of spermatogenesis by Leydig cells and peritubular myoid cells. This review would provide novel insights into molecular mechanisms of the somatic cells in controlling spermatogenesis, and it could offer new targets for developing therapeutic approaches of male infertility.

Actl6a protects embryonic stem cells from differentiating into primitive endoderm.

Actl6a (actin-like protein 6A, also known as Baf53a or Arp4) is a subunit shared by multiple complexes including esBAF, INO80, and Tip60-p400, whose main components (Brg1, Ino80, and p400, respectively) are crucial for the maintenance of embryonic stem cells (ESCs). However, whether and how Actl6a functions in ESCs has not been investigated. ESCs originate from the epiblast (EPI) that is derived from the inner cell mass (ICM) in blastocysts, which also give rise to primitive endoderm (PrE). The molecular mechanisms for EPI/PrE specification remain unclear. In this study, we provide the first evidence that Actl6a can protect mouse ESCs (mESCs) from differentiating into PrE. While RNAi knockdown of Actl6a, which appeared highly expressed in mESCs and downregulated during differentiation, induced mESCs to differentiate towards the PrE lineage, ectopic expression of Actl6a was able to repress PrE differentiation. Our work also revealed that Actl6a could interact with Nanog and Sox2 and promote Nanog binding to pluripotency genes such as Oct4 and Sox2. Interestingly, cells depleted of p400, but not of Brg1 or Ino80, displayed similar PrE differentiation patterns. Mutant Actl6a with impaired ability to bind Tip60 and p400 failed to block PrE differentiation induced by Actl6a dysfunction. Finally, we showed that Actl6a could target to the promoters of key PrE regulators (e.g., Sall4 and Fgf4), repressing their expression and inhibiting PrE differentiation. Our findings uncover a novel function of Actl6a in mESCs, where it acts as a gatekeeper to prevent mESCs from entering into the PrE lineage through a Yin/Yang regulating pattern.

The trithorax group protein Ash2l is essential for pluripotency and maintaining open chromatin in embryonic stem cells.

Embryonic stem (ES) cells exhibit general characteristics of open chromatin, a state that may be necessary for ES cells to efficiently self-renew while remaining poised for differentiation. Histone H3K4 and H3K9 trimethylation associate as a general rule, with open and silenced chromatin, respectively, for ES cell pluripotency maintenance. However, how histone modifications are regulated to maintain open chromatin in ES cells remains largely unknown. Here, we demonstrate that trithorax protein Ash2l, homologue of the Drosophila Ash2 (absent, small, homeotic-2) protein, is a key regulator of open chromatin in ES cells. Consistent with Ash2l being a core subunit of mixed lineage leukemia methyltransferase complex, RNAi knockdown of Ash2l was sufficient to reduce H3K4 methylation levels and drive ES cells to a silenced chromatin state with high H3K9 trimethylation. Genome-wide ChIP-seq analysis indicated that Ash2l is recruited to target loci through two distinct modes and enriched at a family of genes implicated in open chromatin regulation, including chromatin remodeler Cdh7, transcription factor c-Myc, and H3K9 demethylase Kdm4c. Our results underscore the importance of Ash2l in open chromatin regulation and provide insight into how the open chromatin landscape is maintained in ES cells.

Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells.

As a member of the Tet (Ten-eleven translocation) family proteins that can convert 5-methylcytosine (5mC) to 5-hydroxylmethylcytosine (5hmC), Tet1 has been implicated in regulating global DNA demethylation and gene expression. Tet1 is highly expressed in embryonic stem (ES) cells and appears primarily to repress developmental genes for maintaining pluripotency. To understand how Tet1 may regulate gene expression, we conducted large scale immunoprecipitation followed by mass spectrometry of endogenous Tet1 in mouse ES cells. We found that Tet1 could interact with multiple chromatin regulators, including Sin3A and NuRD complexes. In addition, we showed that Tet1 could also interact with the O-GlcNAc transferase (Ogt) and be O-GlcNAcylated. Depletion of Ogt led to reduced Tet1 and 5hmC levels on Tet1-target genes, whereas ectopic expression of wild-type but not enzymatically inactive Ogt increased Tet1 levels. Mutation of the putative O-GlcNAcylation site on Tet1 led to decreased O-GlcNAcylation and level of the Tet1 protein. Our results suggest that O-GlcNAcylation can positively regulate Tet1 protein concentration and indicate that Tet1-mediated 5hmC modification and target repression is controlled by Ogt.

Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells.

Detection of low-affinity or transient interactions can be a bottleneck in our understanding of signaling networks. To address this problem, we developed an arrayed screening strategy based on protein complementation to systematically investigate protein-protein interactions in live human cells, and performed a large-scale screen for regulators of telomeres. Maintenance of vertebrate telomeres requires the concerted action of members of the Telomere Interactome, built upon the six core telomeric proteins TRF1, TRF2, RAP1, TIN2, TPP1, and POT1. Of the ∼12,000 human proteins examined, we identified over 300 proteins that associated with the six core telomeric proteins. The majority of the identified proteins have not been previously linked to telomere biology, including regulators of post-translational modifications such as protein kinases and ubiquitin E3 ligases. Results from this study shed light on the molecular niche that is fundamental to telomere regulation in humans, and provide a valuable tool to investigate signaling pathways in mammalian cells.

Zbtb40 Deficiency Leads to Morphological and Phenotypic Abnormalities of Spermatocytes and Spermatozoa and Causes Male Infertility.

Studies on the gene regulation of spermatogenesis are of unusual significance for maintaining male reproduction and treating male infertility. Here, we have demonstrated, for the first time, that a loss of ZBTB40 function leads to abnormalities in the morphological and phenotypic characteristics of mouse spermatocytes and spermatids as well as male infertility. We revealed that Zbtb40 was expressed in spermatocytes of mouse testes, and it was co-localized with γH2AX in mouse secondary spermatocytes. Interestingly, spermatocytes of Zbtb40 knockout mice had longer telomeres, compromised double-strand break (DSB) repair in the sex chromosome, and a higher apoptosis ratio compared to wild-type (WT) mice. The testis weight, testicular volume, and cauda epididymis body weight of the Zbtb40+/- male mice were significantly lower than in WT mice. Mating tests indicated that Zbtb40+/- male mice were able to mate normally, but they failed to produce any pups. Notably, sperm of Zbtb40+/- mice showed flagellum deformities and abnormal acrosome biogenesis. Furthermore, a ZBTB40 mutation was associated with non-obstructive azoospermia. Our results implicate that ZBTB40 deficiency leads to morphological and phenotypic abnormalities of spermatocytes and spermatids and causes male infertility. This study thus offers a new genetic mechanism regulating mammalian spermatogenesis and provides a novel target for gene therapy in male infertility.

Deep convolutional neural networks using an active learning strategy for cervical cancer screening and diagnosis.

Cervical cancer (CC) is the fourth most common malignant tumor among women worldwide. Constructing a high-accuracy deep convolutional neural network (DCNN) for cervical cancer screening and diagnosis is important for the successful prevention of cervical cancer. In this work, we proposed a robust DCNN for cervical cancer screening using whole-slide images (WSI) of ThinPrep cytologic test (TCT) slides from 211 cervical cancer and 189 normal patients. We used an active learning strategy to improve the efficiency and accuracy of image labeling. The sensitivity, specificity, and accuracy of the best model were 96.21%, 98.95%, and 97.5% for CC patient identification respectively. Our results also demonstrated that the active learning strategy was superior to the traditional supervised learning strategy in cost reduction and improvement of image labeling quality. The related data and source code are freely available at https://github.com/hqyone/cancer_rcnn.

Machine Learning Prediction Model of Tuberculosis Incidence Based on Meteorological Factors and Air Pollutants.

BACKGROUND: Tuberculosis (TB) is a public health problem worldwide, and the influence of meteorological and air pollutants on the incidence of tuberculosis have been attracting interest from researchers. It is of great importance to use machine learning to build a prediction model of tuberculosis incidence influenced by meteorological and air pollutants for timely and applicable measures of both prevention and control. METHODS: The data of daily TB notifications, meteorological factors and air pollutants in Changde City, Hunan Province ranging from 2010 to 2021 were collected. Spearman rank correlation analysis was conducted to analyze the correlation between the daily TB notifications and the meteorological factors or air pollutants. Based on the correlation analysis results, machine learning methods, including support vector regression, random forest regression and a BP neural network model, were utilized to construct the incidence prediction model of tuberculosis. RMSE, MAE and MAPE were performed to evaluate the constructed model for selecting the best prediction model. RESULTS: (1) From the year 2010 to 2021, the overall incidence of tuberculosis in Changde City showed a downward trend. (2) The daily TB notifications was positively correlated with average temperature (r = 0.231), maximum temperature (r = 0.194), minimum temperature (r = 0.165), sunshine duration (r = 0.329), PM2.5 (r = 0.097), PM10 (r = 0.215) and O3 (r = 0.084) (p < 0.05). However, there was a significant negative correlation between the daily TB notifications and mean air pressure (r = -0.119), precipitation (r = -0.063), relative humidity (r = -0.084), CO (r = -0.038) and SO2 (r = -0.034) (p < 0.05). (3) The random forest regression model had the best fitting effect, while the BP neural network model exhibited the best prediction. (4) The validation set of the BP neural network model, including average daily temperature, sunshine hours and PM10, showed the lowest root mean square error, mean absolute error and mean absolute percentage error, followed by support vector regression. CONCLUSIONS: The prediction trend of the BP neural network model, including average daily temperature, sunshine hours and PM10, successfully mimics the actual incidence, and the peak incidence highly coincides with the actual aggregation time, with a high accuracy and a minimum error. Taken together, these data suggest that the BP neural network model can predict the incidence trend of tuberculosis in Changde City.

TIN2 protein dyskeratosis congenita missense mutants are defective in association with telomerase.

Dyskeratosis congenita (DC) is a progressive and heterogeneous congenital disorder that affects multiple systems and is characterized by bone marrow failure and a triad of abnormal skin pigmentation, nail dystrophy, and oral leukoplakia. One common feature for all DC patients is abnormally short telomeres and defects in telomere biology. Most of the known DC mutations have been found to affect core components of the telomerase holoenzyme. Recently, multiple mutations in the gene encoding the telomeric protein TIN2 have been identified in DC patients with intact telomerase genes, but the molecular mechanisms underlying TIN2 mutation-mediated DC remain unknown. Here, we demonstrate that ectopic expression of TIN2 with DC missense mutations in human cells led to accelerated telomere shortening, similar to the telomere phenotypes found in DC patients. However, this telomere shortening was not accompanied by changes in total telomerase activity, localization of TIN2, or telomere end protection status. Interestingly, we found TIN2 to participate in the TPP1-dependent recruitment of telomerase activity. Furthermore, DC mutations in TIN2 led to its decreased ability to associate with TERC and telomerase activity. Taken together, our data suggest that TIN2 mutations in DC may compromise the telomere recruitment of telomerase, leading to telomere shortening and the associated pathogenesis.

SGK3 is associated with estrogen receptor expression in breast cancer.

While breast cancer mortality rate has seen a steady decline in the last few decades, advances in better treatment and diagnostic tools remain important as we come into the age of personalized therapy. In this report, we describe our studies of SGK3's role in breast cancer. SGK3 (also known as CISK) is a member of the AGC family of kinases. Our previous work indicates that SGK3 functions downstream of the PI 3-kinase cascade and shares molecular and biochemical similarities with Akt. Here, we show that SGK3 expression is linked to estrogen receptor (ER) both in breast caner cell lines and in primary tumor samples. Our analysis also indicated a positive correlation between SGK3 expression and tumor prognosis. Importantly, our immunochemistry analysis of human tumor samples established a clinical link between SGK3 expression and ER+ tumors. These findings implicate SGK3 as an additional component to a complex and heterogeneous disease, and point to the potential benefits of incorporating SGK3 into the process of breast cancer diagnosis and treatment.

The effects of the interaction between BMI and dyslipidemia on hypertension in adults.

Body mass index (BMI) and dyslipidemia are indicators of human health and are often associated with high blood pressure. In this study,we explored the relationship between BMI or dyslipidemia and the risk of hypertension and further verified the possible interacting influences of BMI with dyslipidemia on the risk of hypertension. The aim is to explore the possible risk factors of hypertension and to provide scientific basis for the prevention and treatment of hypertension. Eligible subjects were selected from a cross-sectional survey in Changsha City, and we collected relevant data and clinical indicators for each participant. Body mass index (BMI) was calculated as weight (kg)/height2 (m2), and divided into four categories according to the Chinese standard. Dyslipidemia is defined according to Chinese guideline. Unconditional logistic regression models were used for dichotomous variables to determine the risk or protective factors of dependent variables. Multivariate Logistic model was used to study the influence of BMI and dyslipidemia on hypertension. The following indicators were used to assess the interaction effects: (1) Relative excess risk due to interaction (RERI); (2) Attributable proportion due to interaction(AP); (3) Synergy index (SI). SPSS software was used for statistical analysis. A total of 2740 eligible participants were enrolled in the cross-sectional study, of which 765 subjects (27.9%) were diagnosed with hypertension. Multivariate Logistic model showed that overweight (OR: 1.70, 95%CI: 1.39-2.09) or obese (OR: 2.60, 95%CI: 1.84-3.66) subjects had a significantly higher risk of hypertension than normal weight people, and underweight was a protective factor for hypertension(OR: 0.52, 95%CI: 0.29-0.93). People with dyslipidemia have a higher risk of hypertension than those with normal lipids (OR: 3.05, 95%CI: 2.36-3.90). In addition,there was a significant potentiating interaction effect between overweight or obesity and dyslipidemia(overweight: RERI (1.91, 95%CI: 0.17-3.66), AP (0.40, 95%CI:0.14-0.66), SI (2.03, 95%CI:1.11-3.74) and obesity: RERI (2.20, 95%CI:1.01-3.40), AP (0.38, 95%CI:0.18-0.58), SI (1.84, 95%CI:1.18-2.89), while no interaction was found between underweight and dyslipidemia. Low body weight is an independent protective factor for hypertension, but overweight, obesity and dyslipidemia are risk factors for hypertension, and dyslipidemia significantly shared interactions with overweight and obesity that influenced the risk of hypertension.

Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation.

Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.

Systematic analysis of gene expression level with tissue-specificity, function and protein subcellular localization in human transcriptome.

Recent studies have shown that, in mammals, the highly expressed genes have shorter gene length and their protein products have relatively lower evolutionary rates. However, the global relationship between genes' expression level and their features such as tissue-specificity, function and protein subcellular localization has not been investigated extensively, especially in mammalian. In order to solve it, we analysed 8,570 genes across 46 human tissues. Our results suggest that widely expressed genes have higher mean expression levels than tissue-specific ones and genes encoding zinc-finger proteins have low expression levels similar to that of DNA-binding proteins. In the analysis of protein subcellular localization, it is shown that nuclear and Golgi apparatus proteins have lower mean expression levels than those of mitochondria, endoplasmic reticulum and membrane proteins, while genes encoding cytoplasm and extracellular components display the highest expression levels. When comparing the gene expression levels and the number of expressed genes in different tissues, we found that some tissues have less active genes while single gene encodes relatively more transcripts. Taken together, gene expression levels are clearly correlated with their tissue-specificity, function and protein subcellular localization, and are highly conserved during evolution.

ATP2B1 gene polymorphisms rs2681472 and rs17249754 are associated with susceptibility to hypertension and blood pressure levels: A systematic review and meta-analysis.

OBJECTIVE: The present study aimed to conduct a systematic review and meta-analysis to evaluate the relationships between ATP2B1 gene polymorphisms with blood pressure (BP) level and susceptibility to hypertension. METHODS: PubMed, Web of Science, Embase and China National Knowledge Infrastructure (CNKI) Databases were systematically searched by 2 independent researchers to screen studies on ATP2B1 gene polymorphisms and BP related phenotypes. The records retrieval period was limited from the formation of the database to March 4, 2021. Pooled odds rations (ORs) or ß and their 95% confidence intervals (95%CI) were calculated to assess the association between ATP2B1 gene polymorphisms and the risk of hypertension or BP levels. Publication bias and sensitivity analysis were conducted to find potential bias. All the statistical analysis were conducted with Stata version 11.0 software. RESULTS: A total of 15 articles were ultimately included in the present study, including 15 polymorphisms of ATP2B1 gene. Nine articles (N = 65,362) reported the polymorphism rs17249754, and 7 articles(N = 91,997) reported rs2681472 (both loci were reported in 1 article). Meta-analysis showed that rs17249754 (G/A) and rs2681472 (A/G) were associated with the susceptibility to hypertension (rs17249754: OR = 1.19, 95%CI: 1.10-1.28; rs2681472: OR = 1.15, 95%CI: 1.12-1.17), and were positively associated with systolic BP (SBP) and diastolic blood pressure (DBP) (rs17249754: SBP, ß=1.01, 95%CI: 0.86-1.16, DBP, ß=0.48, 95%CI: 0.30-0.66; rs2681472: SBP, ß=0.92, 95%CI: 0.77-1.07, DBP, ß=0.50, 95%CI: 0.42-0.58) in the additive genetic model. Subgroup analysis stratified by race, population, sample size, and BP measurement method revealed that the association between A allele in rs2681472 polymorphism and risk of hypertension was slightly stronger in European (EUR) populations (OR = 1.16, 95%CI: 1.13-1.20) than in East Asians (OR = 1.14, 95%CI: 1.10-1.17). While in East Asians, relation between rs17249754 with risk of hypertension (OR = 1.19, 95%CI: 1.10-1.28) is stronger than rs2681472 (OR = 1.14, 95%CI: 1.10-1.17). CONCLUSIONS: Our study demonstrated that ATP2B1 gene polymorphism rs2681472 and rs17249754 were associated with BP levels and the susceptibility to hypertension.

Nuclear Factor Related to KappaB Binding Protein (NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development.

Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.