Regulation and functions of non-m6A mRNA modifications.

Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.

CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons.

Nonsense mutations, accounting for >20% of disease-associated mutations, lead to premature translation termination. Replacing uridine with pseudouridine in stop codons suppresses translation termination, which could be harnessed to mediate readthrough of premature termination codons (PTCs). Here, we present RESTART, a programmable RNA base editor, to revert PTC-induced translation termination in mammalian cells. RESTART utilizes an engineered guide snoRNA (gsnoRNA) and the endogenous H/ACA box snoRNP machinery to achieve precise pseudouridylation. We also identified and optimized gsnoRNA scaffolds to increase the editing efficiency. Unexpectedly, we found that a minor isoform of pseudouridine synthase DKC1, lacking a C-terminal nuclear localization signal, greatly improved the PTC-readthrough efficiency. Although RESTART induced restricted off-target pseudouridylation, they did not change the coding information nor the expression level of off-targets. Finally, RESTART enables robust pseudouridylation in primary cells and achieves functional PTC readthrough in disease-relevant contexts. Collectively, RESTART is a promising RNA-editing tool for research and therapeutics.

Epigenetic regulation of innate lymphoid cells.

Innate lymphoid cells (ILCs) lack antigen-specific receptors and are considered the innate arm of the immune system, phenotypically and functionally mirroring CD4+ helper T cells. ILCs are categorized into groups 1, 2, and 3 based on transcription factors and cytokine expression. ILCs predominantly reside in mucosal tissues and play important roles in regional immune responses. The development and function of ILC subsets are controlled by both transcriptional and epigenetic mechanisms, which have been extensively studied in recent years. Epigenetic regulation refers to inheritable changes in gene expression that occur without affecting DNA sequences. This mainly includes chromatin status, histone modifications, and DNA methylation. In this review, we summarize recent discoveries on epigenetic mechanisms regulating ILC development and function, and how these regulations affect disease progression under pathological conditions. Although the ablation of specific epigenetic regulators can cause global changes in corresponding epigenetic modifications to the chromatin, only partial genes with altered epigenetic modifications change their mRNA expression, resulting in specific outcomes in cell differentiation and function. Therefore, elucidating epigenetic mechanisms underlying the regulation of ILCs will provide potential targets for the diagnosis and treatment of inflammatory diseases.

GLP-1 receptor agonists alleviate colonic inflammation by modulating intestinal microbiota and the function of group 3 innate lymphoid cells.

Glucagon-like peptide-1 receptor agonists (GLP-1RAs), which are drugs used for treating type 2 diabetes, have been reported to exert anti-inflammatory effects on inflammatory bowel disease (IBD), the mechanism of which remains elusive. Here, we report that GLP-1RAs ameliorate dextran sulfate sodium (DSS)-induced colitis in both wild-type and T/B-cell-deficient mice through modulating group 3 innate lymphoid cells (ILC3s), a subset of innate lymphoid cells that regulate intestinal immunity. GLP-1RAs promote IL-22 production by ILC3, and the protective effect of GLP-1RAs on DSS-induced colitis was abrogated in ILC3-deficient RORgtgfp/gfp mice. Furthermore, the treatment effect of GLP-RAs on colitis, as well as the generation of IL-22-producing ILC3s by GLP-RAs, is dependent on the gut microbiota. GLP-1RAs increase the abundance of Firmicutes and Proteobacteria in the gut, particularly beneficial bacteria such as Lactobacillus reuteri, and decrease the abundance of enteropathogenic Staphylococcus bacteria. The untargeted gas chromatography (GC)/liquid chromatography (LC)-mass spectrometry (MS) of faecal metabolites further revealed enrichment of N,N-dimethylsphingosine (DMS), an endogenous metabolite derived from sphingosine, in the GLP-1RA-treated group. Strikingly, DMS ameliorates colitis while promoting intestinal IL-22-producing ILC3s. Taken together, our findings show that GLP-1RAs exert a therapeutic effect on colitis possibly by regulating the microbiota-DMS-IL-22+ILC3 axis, highlighting the potential beneficial role of GLP-RAs in inflammatory intestinal disorders with diabetes complications.

Carotenoids in maternal and cord blood, breast milk and their association with maternal dietary intake: a longitudinal study in Shanghai, China.

Carotenoids are important bioactive substances in breast milk, the profile of which is seldom studied. This study aimed to explore the profile of carotenoids in breast milk and maternal/cord plasma of healthy mother-neonate pairs in Shanghai, China, and their correlation with dietary intake. Maternal blood, umbilical cord blood and breast milk samples from five lactation stages (colostrum, transitional milk and early-, mid- and late-term mature milk) were collected. Carotenoid levels were analysed by HPLC. Carotenoid levels in breast milk changed as lactation progressed (P < 0·001). ß-Carotene was the primary carotenoid in colostrum. Lutein accounted for approximately 50 % of total carotenoids in transitional milk, mature milk and cord blood. Positive correlations were observed between five carotenoids in umbilical cord blood and maternal blood (P all < 0·001). ß-Carotene levels were also correlated between maternal plasma and three stages of breast milk (r = 0·605, P < 0·001; r = 0·456, P = 0·011, r = 0·446; P = 0·013, respectively). Dietary carotenoid intakes of lactating mothers also differed across lactation stages, although no correlation with breast milk concentrations was found. These findings suggest the importance of exploring the transport mechanism of carotenoids between mothers and infants and help guide the development of formulas for Chinese infants as well as the nutritional diets of lactating mothers.

The impact of global and local Polynesian genetic ancestry on complex traits in Native Hawaiians.

Epidemiological studies of obesity, Type-2 diabetes (T2D), cardiovascular diseases and several common cancers have revealed an increased risk in Native Hawaiians compared to European- or Asian-Americans living in the Hawaiian islands. However, there remains a gap in our understanding of the genetic factors that affect the health of Native Hawaiians. To fill this gap, we studied the genetic risk factors at both the chromosomal and sub-chromosomal scales using genome-wide SNP array data on ~4,000 Native Hawaiians from the Multiethnic Cohort. We estimated the genomic proportion of Native Hawaiian ancestry ("global ancestry," which we presumed to be Polynesian in origin), as well as this ancestral component along each chromosome ("local ancestry") and tested their respective association with binary and quantitative cardiometabolic traits. After attempting to adjust for non-genetic covariates evaluated through questionnaires, we found that per 10% increase in global Polynesian genetic ancestry, there is a respective 8.6%, and 11.0% increase in the odds of being diabetic (P = 1.65×10-4) and having heart failure (P = 2.18×10-4), as well as a 0.059 s.d. increase in BMI (P = 1.04×10-10). When testing the association of local Polynesian ancestry with risk of disease or biomarkers, we identified a chr6 region associated with T2D. This association was driven by an uniquely prevalent variant in Polynesian ancestry individuals. However, we could not replicate this finding in an independent Polynesian cohort from Samoa due to the small sample size of the replication cohort. In conclusion, we showed that Polynesian ancestry, which likely capture both genetic and lifestyle risk factors, is associated with an increased risk of obesity, Type-2 diabetes, and heart failure, and that larger cohorts of Polynesian ancestry individuals will be needed to replicate the putative association on chr6 with T2D.

m6Am RNA modification detection by m6Am-seq.

Reversible and dynamic RNA modifications play important roles in fine-tuning gene expression. N6, 2'-O-dimethyladenosine (m6Am), a terminal modification at mRNA cap, mediates various biological effects. However, limitations of the current m6Am detection methods lead to a lack of potential applications. Here, we describe a specific and sensitive method, termed m6Am-seq, that can detect m6Am at single-base resolution. m6Am-seq is based on optimized in-vitro demethylation assay and RNA immunoprecipitation, which can distinguish m6Am from 5'-UTR m6A. We provide a step by step protocol to perform m6Am-seq, including experimental procedures and sequencing data analysis. Collectively, we describe m6Am-seq, a robust tool to reveal both m6Am and 5'-UTR m6A methylome, enabling further functional and mechanistic study of m6Am modification.

Aberrant alteration of peripheral B lymphocyte subsets in hepatocellular carcinoma patients.

Although B lymphocytes are widely known to participate in the immune response, the conclusive roles of B lymphocyte subsets in the antitumor immune response have not yet been determined. Single-cell data from GEO datasets were first analyzed, and then a B cell flow cytometry panel was used to analyze the peripheral blood of 89 HCC patients and 33 healthy controls recruited to participate in our research. Patients with HCC had a higher frequency of B10 cells and a lower percentage of MZB cells than healthy controls. And the changes in B cell subsets might occur at an early stage. Moreover, the frequency of B10 cells decreased after surgery. Positively correlated with B10 cells, the elevated IL-10 level in HCC serum may be a new biomarker in HCC identification. For the first time, our results suggest that altered B cell subsets are associated with the development and prognosis of HCC. Increased B10 cell percentage and IL-10 in HCC patients suggest they might augment the development of liver tumors. Hence, B cell subsets and related cytokines may have predictive value in HCC patients and could be potential targets for immunotherapy in HCC.

Numerical Investigation of Exergy Loss of Ammonia Addition in Hydrocarbon Diffusion Flames.

In this paper, a theoretical numerical analysis of the thermodynamics second law in ammonia/ethylene counter-flow diffusion flames is carried out. The combustion process, which includes heat and mass transfer, as well as a chemical reaction, is simulated based on a detailed chemical reaction model. Entropy generation and exergy loss due to various reasons in ammonia/ethylene and argon/ethylene flames are calculated. The effects of ammonia addition on the thermodynamics efficiency of combustion are investigated. Based on thermodynamics analysis, a parameter, the lowest emission of pollutant (LEP), is proposed to establish a relationship between the available work and pollutant emissions produced during the combustion process. Chemical reaction paths are also analyzed by combining the chemical entropy generation, and some important chemical reactions and substances are identified. The numerical results reveal that ammonia addition has a significant enhancement on heat transfer and chemical reaction in the flames, and the total exergy loss rate increases slightly at first and then decreases with an increase in ammonia concentration. Considering the factors of thermodynamic efficiency, the emissions of CO2 and NOx reach a maximum when ammonia concentration is near 10% and 30%, respectively. In terms of the chemical reaction path analysis, ammonia pyrolysis and nitrogen production increase significantly, while ethylene pyrolysis and carbon monoxide production decrease when ammonia is added to hydrocarbon diffusion flames.

Carotenoid profile in breast milk and maternal and cord plasma: a longitudinal study in Southwest China.

Carotenoids are increasingly being implicated to have an important role in brain and eye development. This study aimed to quantify the content and profile of carotenoids in human breast milk, maternal plasma and neonatal umbilical cord plasma in Chengdu, an urban area in Southwest China. In this study, fifty-four healthy mothers were enrolled. Maternal blood, umbilical cord blood, colostrum, transitional milk and mature milk were collected. Concentrations of carotenoids (lutein, zeaxanthin, ß-cryptoxanthin, ß-carotene and lycopene) were analysed by HPLC. We found that carotenoid concentrations decreased from colostrum to mature milk. Hydrocarbon carotenoids with weaker polarity decreased more than the polar carotenoids. Lycopene concentrations dropped by 99 %, ß-carotene by 92 %, ß-cryptoxanthin by 83 %, lutein by 32 % and zeaxanthin by 22 %. Lycopene and ß-carotene accounted for 70 % of the total carotenoids in colostrum, and lutein predominated amongst carotenoids in transitional milk and mature milk (51-55 %). Carotenoid concentrations in maternal plasma were much higher than that in cord plasma. Lutein predominated in cord plasma. The concentrations of all carotenoids in maternal plasma were correlated with those of cord plasma and human milk. These results are consistent with selective transport mechanisms in the mammary gland related to the polarity of carotenoids, and each carotenoid has its own implications, which may have different priorities in the early life development of infants. These findings may help guide dietary recommendations for carotenoid inclusion in infant formulas.

Using Machine Learning-Based Approaches for the Detection and Classification of Human Papillomavirus Vaccine Misinformation: Infodemiology Study of Reddit Discussions.

BACKGROUND: The rapid growth of social media as an information channel has made it possible to quickly spread inaccurate or false vaccine information, thus creating obstacles for vaccine promotion. OBJECTIVE: The aim of this study is to develop and evaluate an intelligent automated protocol for identifying and classifying human papillomavirus (HPV) vaccine misinformation on social media using machine learning (ML)-based methods. METHODS: Reddit posts (from 2007 to 2017, N=28,121) that contained keywords related to HPV vaccination were compiled. A random subset (2200/28,121, 7.82%) was manually labeled for misinformation and served as the gold standard corpus for evaluation. A total of 5 ML-based algorithms, including a support vector machine, logistic regression, extremely randomized trees, a convolutional neural network, and a recurrent neural network designed to identify vaccine misinformation, were evaluated for identification performance. Topic modeling was applied to identify the major categories associated with HPV vaccine misinformation. RESULTS: A convolutional neural network model achieved the highest area under the receiver operating characteristic curve of 0.7943. Of the 28,121 Reddit posts, 7207 (25.63%) were classified as vaccine misinformation, with discussions about general safety issues identified as the leading type of misinformed posts (2666/7207, 36.99%). CONCLUSIONS: ML-based approaches are effective in the identification and classification of HPV vaccine misinformation on Reddit and may be generalizable to other social media platforms. ML-based methods may provide the capacity and utility to meet the challenge involved in intelligent automated monitoring and classification of public health misinformation on social media platforms. The timely identification of vaccine misinformation on the internet is the first step in misinformation correction and vaccine promotion.

miR-330-3p promotes lung cancer cells invasion, migration, and metastasis by directly targeting hSOD2b.

Lung cancer is a serious threat to human health. Studies have revealed that human manganese superoxide dismutase (hSOD2) and miRNAs play an essential role in the metastasis process of lung cancer. However, the miRNAs that associated with hSOD2 and involved in metastasis, remain elusive. After databases analysis and dual luciferase reporter validation, we demonstrated that miR-330-3p expression inversely correlated with hSOD2b expression level, and that miR-330-3p directly targeted the 3'untranslated region (3'UTR) of hSOD2b. Furthermore, overexpression of miR-330-3p promoted whereas knockdown of miR-330-3p inhibited invasion/migration and the epithelial-mesenchymal transition (EMT) process of lung cancer cells in vitro. Knockdown of miR-330-3p inhibited metastasis of lung cancer cells in vivo. Moreover, miR-330-3p-mediated enhancement of invasion/migration in 95-D cells could be rescued by over-expression of hSOD2. In conclusion, we demonstrated that miR-330-3p promoted metastasis of lung cancer cells by suppressing hSOD2b expression and unveiled a new clinical application of miR-330-3p in the therapy of lung cancer.

[Marine fish bone collagen oligopeptide combined with calcium aspartate increases bone mineral density in obariectomized rats].

OBJECTIVE: To investigate the effect of marine fish collagen oligopeptide and calcium aspartate alone or in combination on bone mineral density in ovariectomized rats. METHODS: Sixty three-month-old SPF Wistar female rats were randomly divided into 6 groups according to their body weight: sham operation group, model control group(ovariectomy), calcium aspartate group(ovariectomy), marine fish collagen oligopeptide group(ovariectomy), aspartate calcium + marine fish collagen oligopeptide group(ovariectomy) and calcium carbonate control group(ovariectomy), 10 rats in each group. The sham operation group and the model control group were given the same volume of pure water by gavage, and the other groups were intragastrically administered with calcium aspartate(116. 7 mg/kg), marine fish collagen oligopeptide(250 mg/kg), calcium aspartate(116. 7 mg/kg) + marine fish collagen oligopeptide(250 mg/kg), calcium carbonate(35. 6 mg/kg), and the test substance was continuously administered for 90 days. After 90 days, the animals were sacrificed, and the liver and kidney of the rats were taken to calculate the organ coefficient and pathological examination. The rat femurs were taken to measure bone mineral density and bone calcium content and rat serum was used to determine serum calcium, phosphorus concentration and alkaline phosphatase(ALP) activity. RESULTS: Bone mineral density and bone calcium content in the model group were significantly lower than those in the sham operation group(P<0. 05), indicating that the osteoporosis model was successfully established by oophorectomy. There was no significant difference in the organ index of each group(P>0. 05), liver/kidney HE staining microscopic examination showed no abnormal changes, indicating the safety of the test substances. The bone mineral density of the aspartate calcium + marine fish collagen oligopeptide group was significantly greater than that of the model group(P<0. 05). The bone mineral density of the aspartate calcium group and the marine fish collagen oligopeptide group was larger than that of the model group, but there was no significant difference(P>0. 05). Compared with that in the model group, the calcium content of calcium aspartate + marine fish collagen oligopeptide group was significantly higher(P<0. 05). Compared with that in the calcium aspartate group, the calcium content of calcium aspartate + marine fish collagen oligopeptide group was higher(P<0. 05), there was no significant difference in serum calcium concentration between groups(P>0. 05). Compared with that in the model group, serum phosphorus concentration in the aspartate calcium group, marine fish collagen oligopeptide group, aspartate calcium + marine fish collagen oligopeptide group was significantly higher(P<0. 05) and ALP activity was significantly reduced(P<0. 05). CONCLUSION: The combination of calcium aspartate and marine fish collagen oligopeptide has a significant effect on increasing bone mineral density, also indicating that marine fish bone collagen oligopeptide could promote absorption of calcium aspartate.

The novel truncated isoform of human manganese superoxide dismutase has a differential role in promoting metastasis of lung cancer cells.

Growing evidences have demonstrated alternative splicing makes great contribution to tumor metastasis since multiple protein isoforms from a single gene that often display different functions in the cell. Human manganese superoxide dismutase (hMnSOD) was revealed dysregulation in progress of tumor metastasis, while the effect of hMnSOD isoforms on metastasis remained unclear. In this study, we showed a novel truncated hMnSOD isoform hMnSOD183, which lacked 39 amino acids compared with hMnSOD222. We expressed two hMnSOD protein isoforms in Escherichia coli, respectively, and found that the MnSOD activity of truncated hMnSOD isoform was especially weaker. In 95-D cells, mRNA levels of hMnSOD variants and MnSOD activity were significantly increased than that in A549 cells. Furthermore, the hMnSODc exhibited lower mRNA level than hMnSODa/b in A549 and 95-D cells. Additionally, the effects of two isoforms were assessed about cell invasion, overexpression of hMnSOD222 but not hMnSOD183 promoted 95-D cells metastasis, and hMnSOD knockdown significantly reduced cells invasive behavior. Overexpression of hMnSOD isoforms also caused changes of metastasis associated proteins, such as up-regulation of MMPs, VEGF and Vimentin and down-regulation of E-cadherin. Moreover, overexpression of hMnSOD183 had weaker effect on metastasis related signaling proteins, such as Akt, JNK and IKKß, compared to hMnSOD222. In conclusion, our study identified that hMnSOD isoforms induced lung cancer cells invasion through Akt-JNK-IKKß signaling pathways and the hMnSOD183 isoform played a weaker role than hMnSOD222. Characterization of hMnSOD isoforms is useful for future investigation on metastasis of lung cancer cells.

Urinary exosomes as a novel biomarker for evaluation of α-lipoic acid's protective effect in early diabetic nephropathy.

BACKGROUND: Long-term administration of α-lipoic acid (α-LA) is proved to ameliorate renal impairment. Herein we assessed serum, urinary biomarkers and vascular endothelium function to evaluate its short-period therapeutic effect and identify novel biomarkers for diabetic nephropathy (DN). METHODS: Sixty-two microalbuminuria-stage DN patients were randomly divided into two groups and received the following treatment for 8 weeks: (1) routine treatment(DM group); (2) routine treatment with 600 mg/d α-lipoic acid intravenously (α-LA group). Another total of 21 patients were recruited for the second-stage study and randomly divided into two groups: normoalbuminuria (UAER <30 mg/24 h) and microalbuminuria (UAER from 30-300 mg/24 h). RESULTS: With α-LA treatment, urinary albumin excretion rates (UAER), serum creatinine (SCr) and malonaldehyde (MDA) declined significantly, whereas plasma superoxide dismutase (SOD)activity increased and endothelium-dependent flow mediated vasodilation (FMD) flexibility improved dramatically. Furthermore, the improvement of FMD showed positive correlation with the variation in MDA and SOD as well (r values are .516 and .435, P<.01 and P<.05, respectively). In contrast, these markers have no significant difference in the DM group with routine treatment. Notably, the CD63 expressing of exosomes in urine was found higher in the normoalbuminuria patients compared with those in microalbuminuria, parallelly only declined markedly after α-LA administration in normoalbuminuria patients. CONCLUSION: In summary, we emphasize short-term α-LA could protect the kidney in the early DN against general oxidative stress, particularly the urinary CD63-positive exosome could be a potential sensitive and therapeutic indicator.

Resistance to high-fat diet-induced obesity in male heterozygous Pprc1 knockout mice.

Peroxisome proliferator-activated receptor gamma, co-activator-related 1 (Pprc1) is the third member of the Pgc1 family. Other than the well-characterized Pgc1a and Pgc1b that act as regulators of mitochondrial biogenesis and oxidative metabolism, the function of Pprc1 in vivo is rarely reported, due to embryonic lethality of whole-body Pprc1 knockout mice. To investigate the biological and physiological function of Pprc1 in metabolic processes, male Pprc1(+/-) mice fed with a high fat diet (HFD) showed resistance to diet-induced obesity with a decrease of adipose tissue in Pprc1(+/-) mice, which was a result of elevated energy expenditure. In skeletal muscle of Pprc1(+/-) mice, Pprc1 level showed haplo-insufficiency with down-regulation of Pgc1b and Pgc1a, whereas in adipose tissue, Pprc1 expression remained normal, with significant compensatory increase of other Pgc1 family members to induce an up-regulation of respiratory chain genes. Taken together, as the first report on the metabolic roles of Pprc1 in vivo, these results indicated an elevated basal metabolic rate and lipid metabolic alteration of male Pprc1(+/-) mice on HFD, suggesting the significant role of Pprc1 in controlling mitochondrial gene expression and energy metabolic processes, synergistically with Pgc1a and Pgc1b.

A recombinant trans-membrane protein hMnSOD-R9 inhibits the proliferation of cervical cancer cells in vitro.

Human manganese superoxide dismutase (hMnSOD) is a new type of cancer suppressor. Nonamer of arginine (R9) is an efficient protein transduction domain (PTD). The aim of the study was to improve the transduction efficiency of hMnSOD and investigate its activity in vitro. In this study, we designed, constructed, expressed, and purified a novel fusion protein containing the hMnSOD domain and R9 PTD (hMnSOD­R9). The DNA damaged by Fenton's reagent was found to be significantly reduced when treated with hMnSOD­R9. hMnSOD­R9 fusion protein was successfully delivered into HeLa cells. The MTT assay showed that proliferation of various cancer cell lines were inhibited by hMnSOD­R9 in a dose-dependent manner. In addition, the cell cycle of HeLa cells was arrested at the sub-G0 phase by hMnSOD­R9. hMnSOD­R9 induced apoptosis of HeLa cells in a dose-dependent manner. With hMnSOD­R9 treatment, Bax, JNK, TBK1 gene expression was increased and STAT3 gene expression was gradually down-regulated in HeLa cells. We also found that apoptosis was induced by hMnSOD­R9 in HeLa cells via up-regulation of cleaved caspase-3 and down-regulation phospho-STAT3 pathway. These results indicated that hMnSOD­R9 may provide benefits to cervical cancer treatment.

Association between metabolic syndrome and bone fractures: a meta-analysis of observational studies.

BACKGROUND: Emerging epidemiological evidence suggest an association between metabolic syndrome and fractures. However, whether metabolic syndrome is an independent risk or protective factor of fractures remains controversial. Our goal is to provide a quantitative assessment of the association between metabolic syndrome and bone fractures by conducting a meta-analysis of observational studies. METHODS: The PubMed and Embase database were searched through to March 2013 to identify studies that met pre-established inclusion criteria. Reference lists of retrieved articles were also reviewed. Summary effect estimates with 95% confidence intervals (CI) were derived using a fixed or random effects model, depending on the heterogeneity of the included studies. RESULTS: Eight epidemiologic studies involving 39,938 participants were included in the meta-analysis. In overall analysis, metabolic syndrome was not associated with prevalent fractures [pooled odds ratio (OR) 0.93, 95% CI 0.84 - 1.03] in cross-sectional studies or incident fractures [pooled relative risk (RR) 0.88, 95% CI 0.37 - 2.12] in prospective cohort studies. No evidence of heterogeneity was found in cross-sectional studies (p = 0.786, I2 = 0.0%). A substantial heterogeneity was detected in cohort studies (p = 0.001, I2 = 85.7%). No indication of significant publication bias was found either from Begg's test or Egger's test. Estimates of total effects were substantially consistent in the sensitivity and stratification analyses. CONCLUSIONS: The present meta-analysis of observational studies suggests that the metabolic syndrome has no explicit effect on bone fractures.

The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility.

The most common epigenetic modification of messenger ribonucleic acids (mRNAs) is N6-methyladenosine (m6A), which is mainly located near the 3' untranslated region of mRNAs, near the stop codons, and within internal exons. The biological effect of m6A is dynamically modified by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). By controlling post-transcriptional gene expression, m6A has a significant impact on numerous biological functions, including RNA transcription, translation, splicing, transport, and degradation. Hence, m6A influences various physiological and pathological processes, such as spermatogenesis, oogenesis, embryogenesis, placental function, and human reproductive system diseases. During gametogenesis and embryogenesis, genetic material undergoes significant changes, including epigenomic modifications such as m6A. From spermatogenesis and oogenesis to the formation of an oosperm and early embryogenesis, m6A changes occur at every step. m6A abnormalities can lead to gamete abnormalities, developmental delays, impaired fertilization, and maternal-to-zygotic transition blockage. Both mice and humans with abnormal m6A modifications exhibit impaired fertility. In this review, we discuss the dynamic biological effects of m6A and its regulators on gamete and embryonic development and review the possible mechanisms of infertility caused by m6A changes. We also discuss the drugs currently used to manipulate m6A and provide prospects for the prevention and treatment of infertility at the epigenetic level.

Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.

Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.