The impact of age and number of mutations on the size of clonal hematopoiesis.

Clonal hematopoiesis (CH) represents the clonal expansion of hematopoietic stem cells and their progeny driven by somatic mutations. Accurate risk assessment of CH is critical for disease prevention and clinical decision-making. The size of CH has been showed to associate with higher disease risk, yet, factors influencing the size of CH are unknown. In addition, the characteristics of CH in long-lived individuals are not well documented. Here, we report an in-depth analysis of CH in longevous (≥90 y old) and common (60~89 y old) elderly groups. Utilizing targeted deep sequencing, we found that the development of CH is closely related to age and the expression of aging biomarkers. The longevous elderly group exhibited a significantly higher incidence of CH and significantly higher frequency of TET2 and ASXL1 mutations, suggesting that certain CH could be beneficial to prolong life. Intriguingly, the size of CH neither correlates significantly to age, in the range of 60 to 110 y old, nor to the expression of aging biomarkers. Instead, we identified a strong correlation between large CH size and the number of mutations per individual. These findings provide a risk assessment biomarker for CH and also suggest that the evolution of the CH is influenced by factor(s) in addition to age.

ETS1 acts as a regulator of human healthy aging via decreasing ribosomal activity.

Adaptation to reduced energy production during aging is a fundamental issue for maintaining healthspan or prolonging life span. Currently, however, the underlying mechanism in long-lived people remains poorly understood. Here, we analyzed transcriptomes of 185 long-lived individuals (LLIs) and 86 spouses of their children from two independent Chinese longevity cohorts and found that the ribosome pathway was significantly down-regulated in LLIs. We found that the down-regulation is likely controlled by ETS1 (ETS proto-oncogene 1), a transcription factor down-regulated in LLIs and positively coexpressed with most ribosomal protein genes (RPGs). Functional assays showed that ETS1 can bind to RPG promoters, while ETS1 knockdown reduces RPG expression and alleviates cellular senescence in human dermal fibroblast (HDF) and embryonic lung fibroblast (IMR-90) cells. As protein synthesis/turnover in ribosomes is an energy-intensive cellular process, the decline in ribosomal biogenesis governed by ETS1 in certain female LLIs may serve as an alternative mechanism to achieve energy-saving and healthy aging.

miR-206-G6PD axis regulates lipogenesis and cell growth in hepatocellular carcinoma cell.

miR-206 plays an essential role in repressing the growth of multiple cancer cells. Glucose-6-phosphate dehydrogenase (G6PD) is the rate-limiting enzyme of the pentose phosphate pathway. However, it is mostly unknown whether G6PD is associated with miR-206-mediated growth repression of hepatocellular carcinoma (HCC) cells. In this study, we found that the expression of G6PD was upregulated in HCC patients and cell lines, whereas the expression of miR-206 was negatively associated with the clinical staging criterion of primary liver cancer. Overexpression of G6PD increased lipid accumulation and promoted cell proliferation. Conversely, inhibition of G6PD expression decreased lipid accumulation and suppressed cell proliferation. Moreover, miR-206 could directly bind to G6PD mRNA 3´-UTR and downregulate G6PD level. Overexpression of G6PD significantly attenuated the miR-206 mimic-mediated suppression of lipid accumulation and cell proliferation. In summary, the results demonstrated that miR-206 could inhibit lipid accumulation and growth of HCC cells by targeting G6PD, suggesting that the miR-206-G6PD axis may be a promising target for treating HCC.

NGS-based spinal muscular atrophy carrier screening of 10,585 diverse couples in China: a pan-ethnic study.

In this study, we performed a spinal muscular atrophy carrier screening investigation with NGS-based method. First, the validation for NGS-based method was implemented in 2255 samples using real-time PCR. The concordance between the NGS-based method and real-time PCR for the detection of SMA carrier and patient were up to 100%. Then, we applied this NGS-based method in 10,585 self-reported normal couples (34 Chinese ethnic groups from 5 provinces in South China) for SMA carrier screening. The overall carrier frequency was 1 in 73.8 (1.4%). It varied substantially between ethnic groups, highest in Dai ethnicity (4.3%), and no significant difference was found between five provinces. One couple was detected as carriers with an elevated risk of having an SMA affected baby. The distribution of SMN1:SMN2 genotype was also revealed in this study. Among the individuals with normal phenotype, the exon 7 copy-number ratio of SMN1 to SMN2 proved the gene conversion between them. With NGS-based method, we investigated SMA carrier status in Chinese population for the first time, and our results demonstrated that it is a promising alternative for SMA carrier screening and could provide data support and reference for future clinical application.

Metabolic profiling reveals alterations in the erythrocyte response to fava bean ingestion in G6PD-deficient mice.

BACKGROUND: Favism is an acute hemolytic syndrome caused by fava bean (FB) ingestion. The purpose of this study was to investigate the possible influences of FB on the metabonomic profile of erythrocytes in glucose-6-phosphate dehydrogenase (G6PD)-deficient (G6PDx) and wild-type (WT) mice. RESULTS: Ninety-two metabolites were identified in the comparison of the G6PDx and WT groups. Eighty-seven metabolites were identified in the erythrocytes of WT and G6PDx mice after FB ingestion. Thirty-eight metabolites were identified in the comparison of the FB-treated G6PDx and the FB-treated WT mouse groups. Among them, the number of glycerophospholipids (GPLs) and polyunsaturated fatty acids (PUFAs) changed significantly, which suggests that GPLs and PUFAs may be responsible for FB stress. CONCLUSION: This study demonstrates that G6PD deficiency might affect the metabonomic profile of erythrocytes in response to FB. © 2020 Society of Chemical Industry.

Aggregation kinetics of fragmental PET nanoplastics in aqueous environment: Complex roles of electrolytes, pH and humic acid.

The aggregation kinetics of fragmental polyethylene glycol terephthalate (PET) nanoplastics under various chemistry conditions in aqueous environment were firstly investigated in this work. The aggregation of PET nanoplastics increased with increasing electrolyte concentrations and decreasing solution pH, which became stronger with the presence of divalent cations (e.g. Ca2+ and Mg2+) than that of monovalent cations (e.g. Na+ and K+). The effect of cations with the same valence on the aggregation of PET nanoplastics was similar. The measured critical coagulation concentrations (CCC) for PET nanoplastics at pH 6 were 55.0 mM KCl, 54.2 mM NaCl, 2.1 mM CaCl2 and 2.0 mM MgCl2, which increased to 110.4 mM NaCl and 5.6 mM CaCl2 at pH 10. In addition, the aggregation of PET nanoplastics was significantly inhibited with the presence of humic acid (HA), and the CCC values increased to 558.8 mM NaCl and 12.3 mM CaCl2 (1 mg L-1 HA). Results from this study showed that the fragmental PET nanoplastics had the quite higher CCC values and stability in aqueous environment. In addition, the aggregation behaviors of PET nanoplastics can be successfully predicted by the Derjguin Landau Verwey Overbeek (DLVO) theory.

Seasonal and spatial distributions of morpho-functional phytoplankton groups and the role of environmental factors in a subtropical river-type reservoir.

Phytoplankton is capable of responding to aquatic conditions and can therefore be used to monitor freshwater reservoir water quality. Numerous classification techniques, including morpho-functional approaches, have been developed. This study examined changes in phytoplankton assemblages and water quality, which were sampled quarterly from July 2018 to April 2019. The purpose was to contrast the applicability of three classification approaches (functional, morpho-functional and morphological-based functional groupings) for understanding the spatial and seasonal distribution of the biomass variance in phytoplankton functional groups and their driving environmental factors in the ecological zones of the Shanxi Reservoir through multivariate analysis. The results showed that the phytoplankton biomass was highest in the watercourse zone and lowest in the transition zone. Furthermore, the Shanxi Reservoir was characterized by several cyanobacteria (Microcystis spp.) and numerous bacillariophytes (Asterionella sp., Navicula spp. and Aulacoseira granulata). After evaluating the advantages and disadvantages of morpho-functional classifications, we determined that water temperature appeared to be an essential factor, and the morphology-based functional group approach provided the best results for demonstrating phytoplankton succession, despite having lower sensitivity than the others. Nevertheless, these approaches are all appropriate for identifying and monitoring phytoplankton community structure in aquatic systems of reservoirs with complex terrains.

Spatial variations of soil phosphorus in bars of a mountainous river.

As an important part of the riparian zone, bars are an important barrier for the interception of phosphorus (P) originated from leaching and runoff. The spatial variation in P as well as the influence of factors on the said spatial variation in mountainous river (Lingshan River) bars was investigated. A total of 100 soil samples were collected from 11 sampling sites. Soil total phosphorus (TP) and soil available P were determined to explore the spatial variation of soil P in mountainous river bars. One-way analysis of variance, Pearson's correlation analyses, stepwise multiple linear regressions and curve fitting were used to explore the dominant factors affecting the spatial variation of soil P in mountainous river bars. Affected by erosion effect of flowing water, the TP of the bar soils decreased in the longitudinal direction, the TP and available P of the bar soils increased in the cross-sectional direction and the variation in TP between the surface and deep soils firstly increased and then decreased as the height of the bar above the water surface increased. The stronger the erosion effect of flowing water, the more P releases to the water, which may cause the spatial variation of soil P in mountainous river bars, and the results of this study facilitated control of non-point source pollution in mountainous river and restoration of the ecosystems in mountainous river bars.

Combined effect of physicochemical factors on the retention and transport of g-C3N4 in porous media.

The environmental behaviors of graphitic carbon nitride (g-C3N4) have drawn increasing attention in recent. Understanding the fate and transport of g-C3N4 in porous media is necessary for evaluating its environmental risks. Column experiments were used in this study to investigate the combined effect of ionic strength (IS) and other common physicochemical factors (i.e. sand grain size, solution pH, and humic acid concentration) on g-C3N4 transport. The one-site kinetic models were applied to simulate the retention and transport of g-C3N4 in porous media, which fitted the breakthrough curves very well. Experimental and model results showed that g-C3N4 had a weak mobility with the transport mass recovery (TMR) less than 39.6% at pH 6.0 in absence of humic acid (HA). The mobility of g-C3N4 was inhibited with decreasing sand grain size, and the inhibited efficiency was enhanced with IS. However, g-C3N4 transport was significantly enhanced with increasing pH and HA concentration, and the enhanced efficiency was more obviously at high IS. The maximum TMR (78.3%) of g-C3N4 was observed with the presence of 5 mg L-1 HA. These results indicated that physicochemical factors played an important and combined role in controlling g-C3N4 transport in porous media, which would lead to the more complex evaluation on the environmental behaviors of g-C3N4.

Aggregation behavior of graphitic C3N4 nanosheets in aqueous environment: Kinetics and mechanisms.

The aggregation behaviors of graphitic carbon nitride (g-C3N4) nanosheets under various electrolytes and pH conditions were systematically investigated. The aggregation of g-C3N4 nanosheets was significantly enhanced with increasing electrolyte concentrations. The divalent electrolytes (CaCl2 and MgCl2) were more effective than monovalent electrolytes (NaCl and KCl) in promoting the aggregation of g-C3N4 nanosheets. At the same valence, cations with higher atomic weight were more effective in enhancing the aggregation of g-C3N4 nanosheets. The measured critical coagulation concentrations (CCC) of g-C3N4 nanosheets were 4.7 mM KCl, 9.2 mM NaCl, 1.0 mM CaCl2 and 1.9 mM MgCl2 at pH 6.0, which were lower than some of other two-dimensional nanoparticles. The CCC values of g-C3N4 nanosheets were decreased to 5.5 mM NaCl at pH 2.0, but increased to 29.0 mM NaCl and 2.1 mM CaCl2 at pH 10.0, indicating that the aggregation degree of g-C3N4 nanosheets was decreased with increasing pH. The Fe/Al hydrated complexes generated at the specific pH inhibited the aggregation of g-C3N4 nanosheets and enhanced the stability. Overall, findings from this study demonstrated that the electrolytes and pH conditions played important and combined roles on the aggregation of g-C3N4 nanosheets. In addition, the aggregation behaviors of g-C3N4 nanosheets could be well predicted with the DLVO theory.

LOVD-DASH: A comprehensive LOVD database coupled with diagnosis and an at-risk assessment system for hemoglobinopathies.

Hemoglobinopathies are the most common monogenic disorders worldwide. Substantial effort has been made to establish databases to record complete mutation spectra causing or modifying this group of diseases. We present a variant database which couples an online auxiliary diagnosis and at-risk assessment system for hemoglobinopathies (DASH). The database was integrated into the Leiden Open Variation Database (LOVD), in which we included all reported variants focusing on a Chinese population by literature peer review-curation and existing databases, such as HbVar and IthaGenes. In addition, comprehensive mutation data generated by high-throughput sequencing of 2,087 hemoglobinopathy patients and 20,222 general individuals from southern China were also incorporated into the database. These sequencing data enabled us to observe disease-causing and modifier variants responsible for hemoglobinopathies in bulk. Currently, 371 unique variants have been recorded; 265 of 371 were described as disease-causing variants, whereas 106 were defined as modifier variants, including 34 functional variants identified by a quantitative trait association study of this high-throughput sequencing data. Due to the availability of a comprehensive phenotype-genotype data set, DASH has been established to automatically provide accurate suggestions on diagnosis and genetic counseling of hemoglobinopathies. LOVD-DASH will inspire us to deal with clinical genotyping and molecular screening for other Mendelian disorders.

Activation of AKT/AP1/FoxM1 signaling confers sorafenib resistance to liver cancer cells.

Sorafenib is the first­line drug used in the treatment of liver cancer; however, drug resistance seriously limits the clinical response to sorafenib. The present study investigated the molecular mechanisms of sorafenib resistance in liver cancer cells. The data indicated that forkhead box M1 (FoxM1) was significantly overexpressed in sorafenib­resistant cells, at the mRNA and protein levels. Knockdown of FoxM1 rendered drug­tolerant cells sensitive to sorafenib. Furthermore, FoxM1 was upregulated at the transcriptional level. Overexpression of c­jun was associated with the upregulation of FoxM1. The results of a reporter gene assay, electrophoretic mobility shift assay and chromatin immunoprecipitation assay demonstrated that there is an activator protein­1 (AP1) binding site in the promoter of FoxM1, located at ­608 to ­618. Knockdown of c­jun significantly decreased the levels of FoxM1, accompanied by enhanced cell sensitivity to sorafenib. Furthermore, the activation of AKT contributed to the upregulation of c­jun and FoxM1. Inhibition of AKT using BEZ­235 markedly suppressed the upregulation of c­jun and FoxM1, and increased the sensitivity of drug­resistant cells to sorafenib in vitro and in vivo. The data indicated that the activation of the AKT/AP1/FoxM1 signaling axis is an important determinant of sorafenib tolerance.

Intestinal transcriptional profiling reveals fava bean-induced immune response in DBA/1 mice.

BACKGROUND: Fava beans (FBs) have long been used as food, and their principal disadvantage is derived from their haemotoxicity. We hypothesized that FB ingestion alters the intestinal gene expression pattern, thereby inducing an immune response. RESULTS: In-depth sequence analysis identified 769 differentially expressed genes (DEGs) associated with the intestine in FB-treated DBA/1 mouse intestines. The identified genes were shown to be associated with biological processes (such as response to stimulus and immune system processes), human disease pathways (such as infectious diseases, endocrine and metabolic diseases, and immune diseases), and organismal system pathways (such as the digestive system, endocrine system, environmental adaptation, and immune system). Moreover, plasma total immunoglobulin E (IgE), histamine, interleukin (IL)-4 and IL-13 levels were significantly increased when the mice were treated with FBs. CONCLUSIONS: These results demonstrated that FBs affect the intestinal immune response and IgE and cytokine secretion in DBA/1 mice.

Pilot study of expanded carrier screening for 11 recessive diseases in China: results from 10,476 ethnically diverse couples.

Expanded carrier screening (ECS) has been demonstrated to increase the detection rate of carriers compared with traditional tests. The aim of this study was to assess the potential value of ECS for clinical application in Southern China, a region with high prevalence of thalassemia and with diverse ethnic groups, and to provide a reference for future implementations in areas with similar population characteristics. A total of 10,476 prenatal/preconception couples from 34 self-reported ethnic groups were simultaneously tested and analyzed anonymously for 11 Mendelian disorders using targeted next-generation sequencing. Overall, 27.49% of individuals without self-reported family history of disorders were found to be carriers of at least 1 of the 11 conditions, and the carrier frequency varied greatly between ethnic groups, ranging from 4.15% to 81.35%. Furthermore, 255 couples (2.43%) were identified as carrier couples at an elevated risk having an affected baby, sixty-five of which would not have been identified through the existing screening strategy, which only detects thalassemia. The modeled risk of fetuses being affected by any of the selected disorders was 531 per 100,000 (95% CI, 497-567 per 100,000). Our data demonstrate the feasibility of ECS, and provide evidence that ECS is a promising alternative to traditional one-condition screening strategies. The lessons learned from this experience should be applicable for other countries or regions with diverse ethnic groups.

Carrying the T Allele of the SNP rs574344, an eQTL of GSTM1, Contributes to Longevity in the Han Chinese Population.

BACKGROUND: There has been recent recognition that the GSTM1 gene is associated with successful aging and longevity. It has been hypothesized that individuals with a GSTM1 deletion are at a greater risk for developing a plethora of diseases. This study was carried out to investigate the association between the rs574344 single nucleotide polymorphism, an expression quantitative trait locus of GSTM1, and longevity in the Han Chinese population. MATERIALS AND METHODS: We performed a case-control study that comprised 526 long-lived subjects (>97 years of age) and 783 younger subjects (aged 19-80 years) from the general population who served as controls. Identification of the genotypes of rs574344 was accomplished by combining polymerase chain reaction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RESULTS: The long-lived study population, when compared with the controls, showed a significantly higher frequency of the T/T genotype and the T allele of rs574344. We determined that the T/T genotype is associated with a longer lifespan (OR = 5.972, 95% CI 1.798-19.833, p = 0.001, for all genders; p = 0.006 adjusted by gender). We also observed a significant difference (p < 0.05) in the distribution of alleles and genotypes in both the male group (TT vs. TA, OR = 1.043, 95% CI 1.022-1.067, p = 0.043) and the female group (TT vs. TA, OR = 3.592, 95% CI 0.982-13.147, p = 0.039) Conclusion: We found significant associations between both the T allele and the T/T genotype of rs574344 with longevity in the Han Chinese population.

Intestinal transcriptional profiling reveals fava bean-induced immune response in DBA/1 mice

BACKGROUND: Fava beans (FBs) have long been used as food, and their principal disadvantage is derived from their haemotoxicity. We hypothesized that FB ingestion alters the intestinal gene expression pattern, thereby inducing an immune response. RESULTS: In-depth sequence analysis identified 769 differentially expressed genes (DEGs) associated with the intestine in FB-treated DBA/1 mouse intestines. The identified genes were shown to be associated with biological processes (such as response to stimulus and immune system processes), human disease pathways (such as infectious diseases, endocrine and metabolic diseases, and immune diseases), and organismal system pathways (such as the digestive system, endocrine system, environmental adaptation, and immune system). Moreover, plasma total immunoglobulin E (IgE), histamine, interleukin (IL)-4 and IL-13 levels were significantly increased when the mice were treated with FBs. CONCLUSIONS: These results demonstrated that FBs affect the intestinal immune response and IgE and cytokine secretion in DBA/1 mice.

Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians.

Centenarians (CENs) are excellent subjects to study the mechanisms of human longevity and healthy aging. Here, we analyzed the transcriptomes of 76 centenarians, 54 centenarian-children, and 41 spouses of centenarian-children by RNA sequencing and found that, among the significantly differentially expressed genes (SDEGs) exhibited by CENs, the autophagy-lysosomal pathway is significantly up-regulated. Overexpression of several genes from this pathway, CTSB, ATP6V0C, ATG4D, and WIPI1, could promote autophagy and delay senescence in cultured IMR-90 cells, while overexpression of the Drosophila homolog of WIPI1, Atg18a, extended the life span in transgenic flies. Interestingly, the enhanced autophagy-lysosomal activity could be partially passed on to their offspring, as manifested by their higher levels of both autophagy-encoding genes and serum beclin 1 (BECN1). In light of the normal age-related decline of autophagy-lysosomal functions, these findings provide a compelling explanation for achieving longevity in, at least, female CENs, given the gender bias in our collected samples, and suggest that the enhanced waste-cleaning activity via autophagy may serve as a conserved mechanism to prolong the life span from Drosophila to humans.

A rare variant in MLKL confers susceptibility to ApoE ɛ4-negative Alzheimer's disease in Hong Kong Chinese population.

Alzheimer's disease (AD) is the most common neurodegenerative disorders in the elderly. To identify rare genetic factors other than apolipoprotein E ɛ4 allele (ApoE ɛ4) contributing to the pathogenesis of late-onset AD (LOAD), we conducted a whole-exome analysis of 246 ApoE ɛ4-negative LOAD cases and 172 matched controls in Hong Kong Chinese population. LOAD patients showed a significantly higher burden of rare loss-of-function variants in genes related to immune function than healthy controls. Among the genes involved in immune function, we identified a rare stop-gain variant (p.Q48X) in mixed lineage kinase domain like pseudokinase (MLKL) gene present exclusively in 6 LOAD cases. MLKL is expressed in neurons, and the its expression levels in the p.Q48X carriers were significantly lower than that in age-matched wild-type controls. The ratio of Aß42 to Aß40 significantly increased in MLKL knockdown cells compared to scramble controls. MLKL loss-of-function mutation might contribute to late-onset ApoE ɛ4-negative AD in the Hong Kong Chinese population.

Hepatic transcriptional profiling response to fava bean-induced oxidative stress in glucose-6-phosphate dehydrogenase-deficient mice.

Favism is an acute hemolytic syndrome caused by the ingestion of fava bean (FB) in glucose 6-phosphate dehydrogenase (G6PD) deficient individuals. However, little is known about the global transcripts alteration in liver tissue after FB ingestion in G6PD-normal and -deficient states. In this study, deep sequencing was used to analyze liver genes expression alterations underlying the effects of FB in C3H (Wild Type, WT) and G6PD-deficient (G6PDx) mice and to evaluate and visualize the collective annotation of a list of genes to Gene Ontology (GO) terms associated with favism. Our results showed that FB resulted in a decrease of glutathione (GSH)-to-oxidized glutathione (GSSG) ratio and an increase of malondialdehyde (MDA) both in the G6PDx and WT-control check (CK) mice plasma. Significantly, liver transcript differences were observed between the control and FB-treated groups of both WT and G6PDx mice. A total of 320 differentially expressed transcripts were identified by comparison of G6PDx-CK with WT-CK and were associated with immune response and oxidation-reduction function. A total of 149 differentially expressed genes were identified by comparison of WT-FB with WT-CK. These genes were associated with immune response, steroid metabolic process, creatine kinase activity, and fatty acid metabolic process. A total of 438 differential genes were identified by comparing G6PDx-FB with G6PD-CK, associated with the negative regulation of fatty acid metabolic process, endoplasmic reticulum, iron binding, and glutathione transferase activity. These findings indicate that G6PD mutations may affect the functional categories such as immune response and oxidation-reduction.