Exploring urinary modified nucleosides as biomarkers for diabetic retinopathy: Development and validation of a ultra performance liquid chromatography-tandem mass spectrometry method

The dynamic modification of RNA plays a crucial role in biological regulation and is strongly linked to human disease development and progression. Notably, modified nucleosides in urine have shown promising potential as early diagnostic biomarkers for various conditions. In this study, we developed and validated a rapid, sensitive, and accurate UPLC-MS/MS method for quantifying eight types of modified nucleosides (N1-methyladenosine (m1A), N6-methyladenosine (m6A), 5-methyluridine (m5U), 5-taurinomethyl-2-thiouridine (τm5s2U), 5-methylcytidine (m5C), 2'-O-methylcytidine (Cm), N1-methylguanosine (m1G), and N7-methylguanosine (m7G) in human urine. Using the method, we measured the urinary concentrations of m1A, m6A, m5U, τm5s2U, m5C, Cm, m1G, and m7G in a total of 21 control individuals and 23 patients diagnosed with diabetic retinopathy (DR). Cm levels showed promise as a diagnostic marker for diabetic retinopathy (DR), with a significant value (P < 0.01) and an AUC of 0.735. Other modified nucleosides also exhibited significant differences within specific subpopulations. As non-proliferative diabetic retinopathy (NPDR) signifies the latent early stage of diabetic retinopathy, we developed a multivariate linear model that integrates patients' sex, age, height, and urinary concentration of modified nucleosides which aims to predict and differentiate between healthy individuals, NPDR patients, and proliferative diabetic retinopathy (PDR) patients. Encouragingly, the model achieved satisfactory accuracy rates: healthy (81%), NPDR (75%), and PDR (80%). Our findings provide valuable insights into the development of an early, cost-effective, and noninvasive diagnostic approach for diabetic retinopathy.

Myokines and Biomarkers of Frailty in Older Inpatients with Undernutrition: A Prospective Study

BACKGROUND

Population aging might increase the prevalence of undernutrition in older people, which increases the risk of frailty. Numerous studies have indicated that myokines are released by skeletal myocytes in response to muscular contractions and might be associated with frailty. This study aimed to evaluate whether myokines are biomarkers of frailty in older inpatients with undernutrition.

METHODS

The frailty biomarkers were extracted from the Gene Expression Omnibus and Genecards datasets. Relevant myokines and health-related variables were assessed in 55 inpatients aged ≥ 65 years from the Peking Union Medical College Hospital prospective longitudinal frailty study. Serum was prepared for enzyme-linked immunosorbent assay using the appropriate kits. Correlations between biomarkers and frailty status were calculated by Spearman's correlation analysis. Multiple linear regression was performed to investigate the association between factors and frailty scores.

RESULTS

The prevalence of frailty was 13.21%. The bioinformatics analysis indicated that leptin, adenosine 5'-monophosphate-activated protein kinase (AMPK), irisin, decorin, and myostatin were potential biomarkers of frailty. The frailty group had significantly higher concentrations of leptin, AMPK, and MSTN than the robust group (p < 0.05). AMPK was significantly positively correlated with frailty (p < 0.05). The pre-frailty and frailty groups had significantly lower concentrations of irisin than the robust group (p < 0.05), whereas the DCN concentration did not differ among the groups. Multiple linear regression suggested that the 15 factors influencing the coefficients of association, the top 50% were the ADL score, MNA-SF score, serum albumin concentration, urination function, hearing function, leptin concentration, GDS-15 score, and MSTN concentration.

CONCLUSIONS

Proinflammatory myokines, particularly leptin, myostatin, and AMPK, negatively affect muscle mass and strength in older adults. ADL and nutritional status play major roles in the development of frailty. Our results confirm that identification of frailty relies upon clinical variables, myokine concentrations, and functional parameters, which might enable the identification and monitoring of frailty.

Alkaline humic acid fertilizer alters the distribution, availability, and translocation of cadmium and zinc in the acidic soil-Sauropus androgynus system

Humic acids (HA) are a popular soil additive to reduce metal availability, but they have the drawbacks of reduced effectiveness over time and a significant reduction in soil pH. An alkaline humic acid fertilizer (AHAF) combining alkaline additives with HA was developed to overcome such drawbacks. A field experiment was conducted to investigate the effects of different AHAF application rates on the physicochemical properties, bioavailability, accumulation, and translocation of Cd and Zn heavy metals in Sauropus androgynus grown in acidic soil. Based on our results, the 100AF (100% AHAF) treatment significantly increased soil pH, cation exchange capacity (CEC), and organic matter content (OM) after one year of application. Compared with the control treatment (CK), the application of different rates of AHAF resulted in a 37.1-40.3% decrease in soil exchangeable Cd fractions (Exc-Cd) and an increase in the humic acid-bound Cd fractions (HA-Cd) Fe- and Mn-oxide-bound Cd fractions (OX-Cd), and organic matter-bound Cd fractions (OM-Cd) by 9.5-64.6%, 24.8-45.1%, and 158.8-191.2%, respectively (P < 0.05). The different AHAF treatments decreased the Res-Zn, Exc-Zn, and OM-Zn fractions by 69.6-73.0%, 7.4-23.9%, and 18.1-23.2%, respectively (P < 0.05), and increased the HA-Zn fraction by 8.4-28.1%. In the control treatment, the bioconcentration factors (BCFs) for Cd and Zn in different S. androgynus plant organs were in the following order: (Cd) Leaves > Stems > Branches > Roots > Edible branches; (Zn) Roots > Stems > Leaves > Branches > Edible branches. The transfer factors (TFs) of Cd and Zn in S. androgynus were classified as follows: TF2 > TF1 > TF3 > TF4. Thus, S. androgynus stems, and roots had a strong ability to transport Cd and Zn to the leaves. Compared with CK, the 100AF treatment significantly increased the BCFs for Zn in all plant parts (except BCFedible branches). In contrast, it significantly decreased all BCFs and TFs for Cd and the TF4 for Zn, effectively reducing Cd and Zn accumulation in the edible branches of S. androgynus. Soil pH, CEC, OM, and HA-M fraction were highly and significantly negatively correlated with Cd and Zn content in edible branches (P < 0.001). Stepwise multiple linear regression analysis revealed that the soil HA-M fraction was the key contributing factor for Zn accumulation and translocation in S. androgynus. Moreover, based on our findings, the absorption, uptake, and translocation of Cd and Zn were mainly determined by metal speciation and the pH in the soil. Moreover, the competitive antagonistic mechanisms between Zn and Cd absorption also affected their accumulation in S. androgynus. Thus, AHAF can be used as a soil amendment to sustainably improve acidic soils and effectively reduce Cd and Zn accumulation in edible branches of S. androgynus.

Mitochondrial RNA m3C methyltransferase METTL8 relies on an isoform-specific N-terminal extension and modifies multiple heterogenous tRNAs

Methyltransferase-like 8 (METTL8) encodes a mitochondria-localized METTL8-Iso1 and a nucleolus-distributed METTL8-Iso4 isoform, which differ only in their N-terminal extension (N-extension), by mRNA alternative splicing. METTL8-Iso1 generates 3-methylcytidine at position 32 (m3C32) of mitochondrial tRNAThr and tRNASer(UCN). Whether METTL8-Iso4 is an active m3C32 methyltransferase and the role of the N-extension in mitochondrial tRNA m3C32 formation remain unclear. Here, we revealed that METTL8-Iso4 was inactive in m3C32 generation due to the lack of N-extension, which contains several absolutely conserved modification-critical residues; the counterparts were likewise essential in cytoplasmic m3C32 biogenesis by methyltransferase-like 2A (METTL2A) or budding yeasts tRNA N3-methylcytidine methyltransferase (Trm140), in vitro and in vivo. Cross-compartment/species tRNA modification assays unexpectedly found that METTL8-Iso1 efficiently introduced m3C32 to several cytoplasmic or even bacterial tRNAs in vitro. m3C32 did not influence tRNAThrN6-threonylcarbamoyladenosine (t6A) modification or aminoacylation. In addition to its interaction with mitochondrial seryl-tRNA synthetase (SARS2), we further discovered an interaction between mitochondrial threonyl-tRNA synthetase (TARS2) and METTL8-Iso1. METTL8-Iso1 substantially stimulated the aminoacylation activities of SARS2 and TARS2 in vitro, suggesting a functional connection between mitochondrial tRNA modification and charging. Altogether, our results deepen the mechanistic insights into mitochondrial m3C32 biogenesis and provide a valuable route to prepare cytoplasmic/bacterial tRNAs with only a m3C32 moiety, aiding in future efforts to investigate its effects on tRNA structure and function.

A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical Plant Cocos nucifera L

The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species of Cocos has only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2'-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.

Determination and dietary intake risk assessment of 35 pesticide residues in cowpea (Vigna unguiculata [L.] Walp) from Hainan province, China

The presence of pesticide residues in cowpea raises serious health concerns. In this study, a novel, sensitive, high-performance method was developed to simultaneously analyze the residues of 35 pesticides in cowpea samples from growing areas in the Hainan province of China, from November 2018 to June 2021. The method employs modified QuEChERS sample pretreatment coupled with gas chromatography-tandem mass spectrometry. The limits of quantification of the 35 pesticides in the cowpea matrix ranged from 1.0 to 8.0 μg/kg. Twenty-seven of the 35 pesticides were detected, twelve of which are banned for use on legumes in China. Residues for ten pesticides in 17.1% of the samples exceeded their MRLs, with the highest exceedance of 380% observed in difenoconazole. Moreover, 80.8% of the samples contained one or more pesticide residues, with the most frequently detected pesticide being chlorfenapyr with a detection rate of 46.3%. In addition, the pesticide triazophos was detected through different years and regions. Notably, the chronic dietary exposure risk (%ADI) of the detected pesticides, evaluated from the national estimated acceptable daily intake, was lower than 100% in Chinese people of different age groups.

THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates

Post-transcriptional modifications affect tRNA biology and are closely associated with human diseases. However, progress on the functional analysis of tRNA modifications in metazoans has been slow because of the difficulty in identifying modifying enzymes. For example, the biogenesis and function of the prevalent N2-methylguanosine (m2G) at the sixth position of tRNAs in eukaryotes has long remained enigmatic. Herein, using a reverse genetics approach coupled with RNA-mass spectrometry, we identified that THUMP domain-containing protein 3 (THUMPD3) is responsible for tRNA: m2G6 formation in human cells. However, THUMPD3 alone could not modify tRNAs. Instead, multifunctional methyltransferase subunit TRM112-like protein (TRMT112) interacts with THUMPD3 to activate its methyltransferase activity. In the in vitro enzymatic assay system, THUMPD3-TRMT112 could methylate all the 26 tested G6-containing human cytoplasmic tRNAs by recognizing the characteristic 3'-CCA of mature tRNAs. We also showed that m2G7 of tRNATrp was introduced by THUMPD3-TRMT112. Furthermore, THUMPD3 is widely expressed in mouse tissues, with an extremely high level in the testis. THUMPD3-knockout cells exhibited impaired global protein synthesis and reduced growth. Our data highlight the significance of the tRNA: m2G6/7 modification and pave a way for further studies of the role of m2G in sperm tRNA derived fragments.

Study on environmental behaviour of fluopyram in different banana planting soil

Fluopyram is commonly used to control banana leaf spot, anthracnose, and scab in tropical agricultural areas. To explore its behaviour in tropical agricultural environments, dissipation, adsorption, and leaching behaviours of fluopyram in three typical banana planting soils were studied. Also, its dissipation and migration capabilities in different regions and different soil types were evaluated. The results showed that the dissipation of fluopyram was in accordance with the first-order kinetic equation in the three banana soils, but the degradation rates were quite different. The degradation half-lives in the Hainan latosol, Yunnan sandy soil, and Fujian Plain alluvial soil were 46.21 days, 36.48 days and 57.76 days, respectively. Fluopyram also exhibited high adsorption and low leachability in the three soils. The Fujian Plain alluvial soil had the highest adsorption capacity for fluopyram, while fluopyram had the low leachability in the Yunnan sandy soil.

Long noncoding RNA PCAT-1 promoted ovarian cancer cell proliferation and invasion by suppressing KLF6

OBJECTIVE

Recently, the role of long noncoding RNAs (lncRNAs) in tumor progression has caught attention in numerous researchers. In our investigation, lncRNA PCAT-1 was studied to identify how it functioned in the progression of ovarian cancer.

PATIENTS AND METHODS

LncRNA PCAT-1 expression was detected by quantitative Real-time polymerase chain reaction (qRT-PCR) in both ovarian cancer cells and tissue samples. Furthermore, to identify the function of PCAT-1 in ovarian cancer, cell proliferation, transwell assay and Matrigel assay were conducted. In addition, by performing qRT-PCR and Western blot assay, the underlying mechanism was explored.

RESULTS

PCAT-1 expression was remarkably higher in ovarian cancer samples when compared with that in corresponding ones. Moreover, cell proliferation, migration and invasion were inhibited after PCAT-1 was knocked down in ovarian cancer cells. Moreover, the mRNA and protein expression of KLF6 (Krüppel-like factor 6) was upregulated after PCAT-1 was knocked down. Furthermore, the KLF6 expression level was negatively related to the PCAT-1 expression level in ovarian cancer samples.

CONCLUSIONS

We showed that PCAT-1 promotes the progression of ovarian cancer through enhancing cell metastasis and proliferation via suppressing KLF6, which might be a novel therapeutic strategy in ovarian cancer.