Blood molecular markers associated with COVID-19 immunopathology and multi-organ damage.

COVID-19 is characterized by dysregulated immune responses, metabolic dysfunction and adverse effects on the function of multiple organs. To understand host responses to COVID-19 pathophysiology, we combined transcriptomics, proteomics, and metabolomics to identify molecular markers in peripheral blood and plasma samples of 66 COVID-19-infected patients experiencing a range of disease severities and 17 healthy controls. A large number of expressed genes, proteins, metabolites, and extracellular RNAs (exRNAs) exhibit strong associations with various clinical parameters. Multiple sets of tissue-specific proteins and exRNAs varied significantly in both mild and severe patients suggesting a potential impact on tissue function. Chronic activation of neutrophils, IFN-I signaling, and a high level of inflammatory cytokines were observed in patients with severe disease progression. In contrast, COVID-19-infected patients experiencing milder disease symptoms showed robust T-cell responses. Finally, we identified genes, proteins, and exRNAs as potential biomarkers that might assist in predicting the prognosis of SARS-CoV-2 infection. These data refine our understanding of the pathophysiology and clinical progress of COVID-19.

Expression analysis of immune-associated genes in hemocytes of mud crab Scylla paramamosain under low salinity challenge.

To gain knowledge on the immune response in Scylla paramamosain under low salinity challenge, S. paramamosain we investigated digital gene expression (DEG) in S. paramamosain hemocytes using the deep-sequencing platform Illumina Hiseq XTen. A total of 97,257 high quality unigenes with mean length 786.59 bp were found to be regulated by low salinity challenge, among which 93 unigenes were significantly up regulated, and 71 were significantly down regulated. Functional categorization and pathways analysis of differentially expressed genes revealed that immune signaling pathway including cAMP and cGMP signaling pathway were affected in low salinity stress. Cellular immunity-related genes including low-density lipoprotein receptor-related protein 6 (LRP6) and xanthine dehydrogenase (XDH) were down-regulated, indicating phagocytosis and oxygen dependent mechanism of phagocyte were suppressed in low salinity stress; Humoral immunity-related genes serine proteases and serpins 3 were up- and down-regulated, respectively, suggest that the proPO system was influenced by low salinity significantly; Moreover, processes related to immune response including carbohydrate metabolism, protein synthesis and lipid transport were found differentially regulated, implying the integrity of the immune response in low salinity stress. This study gained comprehensive insights on the immune mechanism of S. paramamosain at low salinity stress at the molecular level. The findings provide a theoretical basis for understanding immune mechanisms of S. paramamosain under low salinity stress, and technical reference for evaluating physiological adaptation in fresh water environment.

The long non-coding RNA NEAT1 regulates epithelial to mesenchymal transition and radioresistance in through miR-204/ZEB1 axis in nasopharyngeal carcinoma.

Long non-coding RNAs (lncRNAs) play a critical role in cancer progression, including in nasopharyngeal carcinoma (NPC). However, it is still poorly understood whether lncRNA regulates epithelial to mesenchymal transition (EMT) and radioresistance of NPC cells. We found that lncRNA NEAT1 was significantly upregulated in NPC cell lines and tissues. Knockdown of NEAT1 could sensitize NPC cells to radiation in vitro. Further investigation found that NEAT1 regulated radioresistance by modulating EMT phenotype. Furthermore, we found that there was reciprocal repression between NEAT1 and miR-204. ZEB1 was identified as a downstream target of miR-204 and NEAT1 upregulated ZEB1 expression by negatively regulating miR-204 expression. Taking together, we proposed that NEAT1 regulated EMT phenotype and radioresistance by modulating the miR-204/ZEB1 axis in NPC.

Simultaneously quantifying hundreds of acylcarnitines in multiple biological matrices within ten minutes using ultrahigh-performance liquid-chromatography and tandem mass spectrometry.

Acylcarnitines are metabolic intermediates of fatty acids and branched-chain amino acids having vital biofunctions and pathophysiological significances. Here, we developed a high-throughput method for quantifying hundreds of acylcarnitines in one run using ultrahigh performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS). This enabled simultaneous quantification of 1136 acylcarnitines (C0-C26) within 10-min with good sensitivity (limit of detection < 0.7 fmol), linearity (correlation coefficient > 0.992), accuracy (relative error < 20%), precision (coefficient of variation (CV), CV < 15%), stability (CV < 15%), and inter-technician consistency (CV < 20%, n = 6). We also established a quantitative structure-retention relationship (goodness of fit > 0.998) for predicting retention time (tR) of acylcarnitines with no standards and built a database of their multiple reaction monitoring parameters (tR, ion-pairs, and collision energy). Furthermore, we quantified 514 acylcarnitines in human plasma and urine, mouse kidney, liver, heart, lung, and muscle. This provides a rapid method for quantifying acylcarnitines in multiple biological matrices.

Comprehensive metabolomic and lipidomic alterations in response to heat stress during seed germination and seedling growth of Arabidopsis.

Temperature affects seed germination and seedling growth, which is a critical and complex stage in plant life cycle. However, comprehensive metabolic basis on temperature implicating seed germination and seedling growth remains less known. Here, we applied the high-throughput untargeted metabolomic and advanced shotgun lipidomic approaches to profile the Arabidopsis 182 metabolites and 149 lipids under moderate (22°C, 28°C) and extreme high (34°C, 40°C) temperatures. Our results showed that a typical feature of the metabolism related to organic acids/derivates and amines was obviously enriched at the moderate temperature, which was implicated in many cellular responses towards tricarboxylic acid cycle (TCA), carbohydrates and amino acids metabolism, peptide biosynthesis, phenylpropanoid biosynthesis and indole 3-acetate (IAA) biosynthetic pathway. Whereas, under extreme high temperatures, there was no seed germination, but 148 out of total 182 metabolites were highly enriched, involving in the galactose metabolism, fatty acid degradation, tryptophan/phenylalanine metabolism, and shikimic acid-mediated pathways especially including alkaloids metabolism and glucosinolate/flavone/flavonol biosynthesis. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) also exhibited the gradually increased tendency from moderate temperatures to extreme high temperatures; whereas phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG) were contrary to decrease. Another typical feature of the distinguished metabolites between 22°C and 28°C, the TCA, disaccharides, nucleotides, polypeptides, SQDG and the biosynthesis of fatty acids and glucobrassicin-mediated IAA were obviously decreased at 28°C, while amino acids, trisaccharides, PE, PC, PA, PS, MGDG, DGDG and diacylglycerol (DAG) preferred to enrich at 28°C, which characterized the alteration of metabolites and lipids during fast seedling growth. Taking together, our results provided the comprehensive metabolites phenotyping, revealed the characteristics of metabolites necessary for seed germination and/or seedling growth under different temperatures, and provided insights into the different metabolic regulation of metabolites and lipid homeostasis for seed germination and seedling growth.

Relative Validity and Reproducibility of Dietary Measurements Assessed by a Semiquantitative Food Frequency Questionnaire among Chinese Healthy Adults.

This study aimed to evaluate the relative validity and reproducibility of a semiquantitative food frequency questionnaire (SFFQ) in adult populations in China. Among the 49 recruited healthy participants (age range: 20-60 years), the relative validity of a 79-item SFFQ was assessed in two ways: (1) by comparing its dietary intake estimates with those from the average measurements of three inconsecutive 24 h dietary records (24-HDRs); and (2) by comparing its estimates of dietary fatty acids with the measured plasma levels of fatty acids. The reproducibility of the SFFQ was evaluated by a comparison of two SFFQ measurements from the same participants collected one year apart. In the relative validity study, the average Spearman correlation coefficient (r) was 0.27 among 18 prespecified food group intakes estimated from the SFFQ and the 24-HDRs; nevertheless, that of five food group intakes (e.g., red meat and seafood) was higher (all rs > 0.40, p < 0.05). In addition, a moderate correlation between the SFFQ estimate of polyunsaturated fatty acid intakes (energy-adjusted percentage of total fatty acids) and its plasma level was observed (r = 0.42, p < 0.05). Regarding the one-year reproducibility of the SFFQ-assessed intakes, the average rank intraclass correlation coefficient (ICC) was 0.35 for the 18 food group estimates. In particular, moderately reproducible estimates of seven food group intakes (e.g., refined grains and red meat, all ICCs ≥ 0.40, p < 0.05) were observed. In conclusion, the SFFQ provides valid and reproducible estimates of dietary intakes for various food groups in general and performs well as a potential tool for estimating habitual dietary intakes of some unsaturated fatty acids.

Rapid quantification of 50 fatty acids in small amounts of biological samples for population molecular phenotyping.

Efficient quantification of fatty-acid (FA) composition (fatty-acidome) in biological samples is crucial for understanding physiology and pathophysiology in large population cohorts. Here, we report a rapid GC-FID/MS method for simultaneous quantification of all FAs in numerous biological matrices. Within eight minutes, this method enabled simultaneous quantification of 50 FAs as fatty-acid methyl esters (FAMEs) in femtomole levels following the efficient transformation of FAs in all lipids including FFAs, cholesterol-esters, glycerides, phospholipids and sphingolipids. The method showed satisfactory inter-day and intra-day precision, stability and linearity (R2 > 0.994) within a concentration range of 2-3 orders of magnitude. FAs were then quantified in typical multiple biological matrices including human biofluids (urine, plasma) and cells, animal intestinal content and tissue samples. We also established a quantitative structure-retention relationship (QSRR) for analytes to accurately predict their retention time and aid their reliable identification. We further developed a novel no-additive retention index (NARI) with endogenous FAMEs reducing inter-batch variations to 15 seconds; such NARI performed better than the alkanes-based classical RI, making meta-analysis possible for data obtained from different batches and platforms. Collectively, this provides an inexpensive high-throughput analytical system for quantitative phenotyping of all FAs in 8-minutes multiple biological matrices in large cohort studies of pathophysiological effects.

Identification of Veratrum Species in Pimacao Based on ITS2 Sequences and Steroidal Alkaloids by a Pseudo-Targeted Metabolomics Method.

Pimacao is a traditional Chinese folk medicine and is the main component of the famous Chinese herbal remedy "Yunnan Baiyao" for its significant analgesic activity in the treatment of wounds. Due to increases in consumption, its wild population is now difficult to find, and adulterant from the same genus has occurred. However, this is challenging to distinguish the species of Veratrum in Pimacao using dried roots and rhizomes or medicinal powder. ITS2 sequences and steroidal alkaloids by the non-targeted and pseudo-targeted metabolomics methods were taken advantage of establishing an effective identification method. Based on the ITS2 sequence, metabolite profiling of steroidal alkaloids and morphological characteristics, the classification of two distinct subspecies in V. mengzeanum has been reinforced. In addition, the new subspecies V. mengzeanum subsp. phuwae was collected in China for the first time. The ITS2 sequence could be used in the identification of V. taliense, V. mengtzeanum, V. stenophyllum, and V. nigrum, but is insufficient for intraspecific identification. Simultaneously, 147 variables were labeled by non-targeted analysis accomplished utilizing an ultra-high-performance liquid chromatography electrospray ionization orbitrap tandem mass spectrometry (UPLC-ESI-QE-Orbitrap-MS) system consisting of an Orbitrap QE HF-X. Followed by a pseudo-targeted analysis method developed for the Qtrap 6500-plus mass spectrometry system coupled with an ESI source, 29 labeled steroidal alkaloids detected by the MRM mode could distinguish between four species. Notably, 25 labeled steroidal alkaloids could distinguish between three closely related species. These have the potential to be used as markers for identification. Furthermore, there were several variables with statistical differences between two subspecies of V. mengtzeanum and populations of V. taliense, V. mengtzeanum, and V. stenophyllum.

Lipidomics Approach in High-Fat-Diet-Induced Atherosclerosis Dyslipidemia Hamsters: Alleviation Using Ether-Phospholipids in Sea Urchin.

Ether-phospholipids (ether-PLs) in sea urchins, especially eicosapentaenoic-acid-enriched plasmenyl phosphatidylethanolamine (PE-P) and plasmanyl phosphatidylcholine (PC-O), exhibit potential lipid-regulating effects. However, their underlying regulatory mechanisms have not yet been elucidated. Herein, we integrated an untargeted lipidomics strategy and biochemical analysis to investigate these mechanisms in high-fat-induced atherosclerotic hamsters. Dietary supplementation with PE-P and PC-O decreased total cholesterol and low-density lipoprotein cholesterol concentrations in serum. The lipid regulatory effects of PE-P were superior to those of PC-O. Additionally, 20 lipid molecular species, including phosphatidylethanolamine, cholesteryl ester, triacylglycerol, and phosphatidylinositol, were identified as potential lipid biomarkers in the serum of hamsters with PC-O and PE-P treatment (95% confidence interval; p < 0.05). The variations of lipids may be attributed to downregulation of adipogenesis genes and upregulation of lipid ß-oxidation genes and bile acid biosynthesis genes. The improved lipid homeostasis by ether-PLs in sea urchins might be a key pathway underlying the antiatherosclerosis effect.

Identification of ceramide 2-aminoethylphosphonate molecular species from different aquatic products by NPLC/Q-Exactive-MS.

Ceramide 2-aminoethylphosphonate (CAEP) is a type of phosphonosphingolipids with potential trophic activity. In this work, complicated CAEP species from different aquatic products were comprehensively identified and semi-quantified by utilizing normal phase liquid chromatography/Q-Exactive mass spectrometry (NPLC/Q-Exactive-MS). We elucidated the fragment schemes of CAEP molecules and found the presence of methylated CAEP (Me-CAEP) species. Remarkably, quantitative results revealed that Loligo chinensis had the highest CAEP content of 4.9 ±â€¯0.4 mg/g dry weight and the most complex molecular species composition, whereas Asterias amurenis had the lowest CAEP content of 1.9 ±â€¯0.6 mg/g dry weight. The most common molecule was CAEP (d19:3-16:0). Additionally, statistical analysis revealed that five aquatic products can be effectively distinguished from their CAEP species; thus, CAEP molecules can play an important role in identifying processed products from aquatic products.

Growth and Lipidomic Responses of Juvenile Pacific White Shrimp Litopenaeus vannamei to Low Salinity.

The Pacific white shrimp (Litopenaeus vannamei), a euryhaline penaeid species, can tolerate a wide range of salinities, but little is known on its strategies to cope with low salinity fluctuations from the aspect of lipidomics. Thus, in this study, L. vannamei were grown in two different salinities [3 and 30‰ (control)] for 8 weeks, and then an liquid chromatography (LC)-mass spectrometry (MS)-based lipidomics analysis was performed to reveal the lipid profile differences in gill and muscle. L. vannamei under low salinity had lower weight gain and condition factor than the control shrimp at 30‰, but no differences were found in survival and hepatopancreas index. A higher number of differential lipid metabolites were identified in gill than in muscle in L. vannamei at salinity 3‰ relative to the control shrimp at salinity of 30‰ (159 versus 37), which belonged to 11 and 6 lipids classes, respectively. Of these lipids, phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidic acid (PA), phosphatidylethanolamine (PE), and triglyceride (TG) were the main lipids in both shrimp gill and muscle, regardless of salinities. Compared with the control shrimp at salinity 30‰, the percentage of PC significantly reduced, but TG and PA significantly increased in gill of shrimp at salinity 3‰. Moreover, the relative fatty acid abundances showed significant changes in L. vannamei between the two salinity groups, but the patterns of the changes were complex and were fatty acid dependent. Neither lipid nor fatty acid composition in muscle was affected by salinity. Further pathway analysis showed that these metabolites were closely related to lipid and fatty acid metabolic pathways. All the findings in this study reveal that the lipid variations are closely related to bio-membrane structure, mitochondrial function, energy supply, or organic osmolyte contents in hemolymph for improving osmoregulatory capacity of L. vannamei under low salinity.

Mechanism of Phospholipid Hydrolysis for Oyster Crassostrea plicatula Phospholipids During Storage Using Shotgun Lipidomics.

A fast and efficient shotgun lipidomics strategy was applied to analyze phospholipids (PL) in the oyster Crassostrea plicatula, including 29 species of phosphatidylcholine (PtdCho), 23 species of phosphatidylethanolamine (PtdEtn), 11 species of phosphatidylserine (PtdSer), 6 species of phosphatidylinositol (PtdIns), and 17 species of lysophospholipids (Lyso-PL). During storage at 4 °C for 7 days, the PL content decreased by 68.08%, but a significant increase in the FFA content was observed (from 63.11 to 318.72 µg/g). PtdCho and PtdIns decreased relatively by 64.97 and 67.49%, and PtdSer decreased most markedly by 74.15%. However, the PtdEtn content increased slightly during the early stages of storage but subsequently began to decrease. Moreover, PL with eicosapentaenoic acid (EPA-PL) and docosahexaenoic acid (DHA-PL) decreased by 51.77 and 50.61%, whereas plasmalogens were relatively stable showing only a 25.46% decrease. In particular, through enzyme activity analysis of lipase, phospholipase A1 (PLA1), phospholipase A2 (PLA2), phospholipase C (PLC), and phospholipase D (PLD), it was observed that the activities of all these enzymes increased at the early stage at 4 °C, but their activities were at lower levels when the oysters were stored at -20 °C. During the storage period at 4 °C, correlation analysis suggests that the degradation of PtdCho was mostly correlated to PLA2 (p < 0.05), whereas PtdEtn and PtdSer were more markedly correlated to lipase and PLD, respectively. The above result indicates that the hydrolysis mechanism of PL during seafood storage was correlated to the lipid hydrolytic enzyme activities under different storage temperatures.

Erratum to: Mechanism of Phospholipid Hydrolysis for Oyster Crassostrea plicatula Phospholipids During Storage Using Shotgun Lipidomics.

Erratum to: Lipids https://doi.org/10.1007/s11745-017-4305-7.

Dosimetry of a thyroid uptake detected in seed migration survey following a patient's iodine-125 prostate implant and in vitro measurements of intentional seed leakages.

As a quality control procedure, a post-implant seed migration survey has been accomplished on 340 prostate cancer patients since November 2001. Pulmonary seed embolization and intracardiac seed embolization have been detected. A case of thyroid uptake due to leaking iodine-125 (I-125) sources was also seized. In order to determine the dose to the thyroid, a dosimetry method was developed to link in vivo measurements and the cumulated dose to the thyroid. The calculated source leakage half-life in the case was approximately 15 days based on the measurements and the estimated cumulated dose to thyroid was 204 cGy. It is concluded that one seed was leaking. In order to verify the in vivo measurements, intentional in vitro seed leakage tests were performed. A seed was cut open and placed in a sealed glass container filled with a given volume of saline. The I-125 concentration in the saline was subsequently measured over a period of six months. Consistent in vivo and in vitro results were obtained. Recent incidents of seed leaks reported from other centers have drawn practitioners' attention to this problem. In order to make the measurements more useful, the seed leakage tests were expanded to include I-125 seeds from six other vendors. The results show that the leakage half-lives of those seeds varied from nine days to a half-year. Two seed models demonstrated least leakage. Since the measurements lasted for six months, the escape of iodine resulted from oxidation of iodide in the saline was a concern for the measurement accuracy. As a reference, another set of leakage tests were performed by adding sodium thiosulfate salt (Na2S2O3 x 5 H2O) to the saline. Sodium thiosulfate is a reducing agent that prevents the conversion of iodide to iodate so as to minimize I-125 evaporation. As a result, significantly shortened leakage half-lives were observed in this group. Seed agitation was also performed and no significant deviations of the leakage rates were observed. Considering the body fluid is more complex than saline, the in vivo leakage half-life, in case a source leak is encountered, may vary significantly from what is presented in this paper due to chemical reactions. In vivo measurements thus may produce a more accurate estimation of leakage half-life and thyroid uptake dose.

In vivo detection of an 125I seed located in the intracardiac region after prostate permanent brachytherapy.

PURPOSE: The purpose of this investigation is to determine the mechanism of seed migration after prostate implant and to develop procedures to minimize the risk of seed migration. METHODS AND MATERIALS: Radioactivity survey of prostate cancer patients after permanent brachytherapy with (125)I to detect pulmonary seed embolization is routinely performed using a seed migration detector. The seed migration detector is made from a low-energy, high-sensitivity scintillation survey meter by adding a single-hole collimation cap to the scintillation probe. If a seed migration is suspected, a pair of chest radiographs is ordered to document the location of the migrated seed. A comprehensive investigation is elicited if there are discrepancies between the seed migration detector survey and the radiographic examination. RESULTS: One hundred five patients have been surveyed, and 20 patients have demonstrated pulmonary seed embolization. In 1 patient, the seed migration detector sensed radioactivity in the thorax, but repeat chest radiographic examinations failed to show a radiopaque foreign body in the chest cavity. Owing to the signal variation mimicking heart rate, an (125)I seed located in the intracardiac region was suspected. This suspicion was confirmed in a high-quality fluoroscopy examination. CONCLUSIONS: Seed embolization to the intracardiac region is rarely reported. The true rate may be higher, but has not been adequately documented owing to the limitation of diagnostic quality of chest radiographs to detect seed migration to the intracardiac region. The seed migration detector, on the other hand, demonstrated its efficacy in the detection of seed migration, particularly in the detection of a seed located in the intracardiac region.

Accurate and efficient detection of pulmonary seed embolization in prostate iodine-125 permanent brachytherapy with a collimated gamma scintillation survey meter.

Pulmonary seed embolization is frequently observed in permanent prostate brachytherapy. Postoperative chest radiographic examination does not always detect seed embolization. To overcome this deficiency, a low energy gamma scintillation survey meter was converted to a seed-migration detector by adding a cone-shaped single-hole collimation cap to the window end of the scintillation probe. The response functions of the seed-migration detector to iodine-125 (I-125) for different source-to-detector distances in air and in water were measured. The spatial discrimination power of the survey meter, represented by the full width at half maximum measured in water, is typically improved from more than 7 cm to about 3 cm. Seventy-nine patients with I-125 implantation were scanned with the seed-migration detector at the patients' 30-day postevaluation visit. Fifteen patients showed single-seed embolization to the chest region and four patients displayed two-seed embolization. In other words, 24% of the patients present with embolized seeds. The detection accuracy of each patient was validated by a comprehensive investigation procedure. The comprehensive investigation consists of reviewing the patient's treatment history, orally questioning the patient for possible seed loss via the urethra route outside the hospital, examining all available chest radiographs before and after the seed implantation, and counting the seeds on the postevaluation CT scans. In comparison, examinations relying only on the analysis of postoperative chest radiographs yielded a false-positive detection in four patients and a false-negative detection in two patients. Another advantage of the seed-migration detector is that multiple seed-migration scans can be performed without exposing the patient to any additional radiation, for this device is a passive detector. Our clinical implementation also demonstrated that the seed-migration detector is a convenient and cost-effective method. As a result of this study, we stopped ordering the postoperative chest radiographs in a patient's regular postevaluation visit. Only if the detector shows radioactivity outside a patient's pelvis are a pair of anteroposterior and lateral chest radiographs of the patient ordered to document the location of the embolized seeds.

Thyroid uptake of 125iodine after prostate permanent brachytherapy.

PURPOSE: To decrease the seed migration rate after 125I prostate brachytherapy and improve the quality of implants to our knowledge we report for the first time the detection of thyroid uptake, possibly from a damaged seed, in a patient after 125I implantation. MATERIALS AND METHODS: Seed migration detection is routinely offered to our patients at the post-evaluation visit. A seed migration detector and comprehensive investigation procedure have been developed for the task. Chest radiographs are ordered to document the location of the detected seed. A fluoroscopic study may be performed if intracardiac radioactivity is detected. RESULTS: Since November 2001, 246 patients have been studied for seed migration. A total of 23,184 125I seeds were implanted, of which 75 were lost through the urethra and 25 migrated to the thorax. In the routine survey of a patient on February 13, 2003 radioactivity in the chest-neck region was sensed. Repeat radiographs and fluoroscopic examinations were negative for seed migration. Using a gamma camera butterfly-shaped uptake was noted in the thyroid region. The energy peak of the uptake matched the spectrum of the 125I source. The patient denied any intake of other iodine medication. The results suggested possible 125I leakage from at least 1 seed implanted in the prostatic region. CONCLUSIONS: Improved control of seed migration has been achieved. The detection of thyroid uptake is reported. Detection techniques and subsequent actions are described.