Publications by authors named "Rui Qin"

242 Publications

Effect of psychological nursing combined with health education on postpartum quality of life of parturients undergoing cesarean section.

Minerva Surg 2021 Nov 17. Epub 2021 Nov 17.

Department of Obstetrics, Cangzhou Maternal and Child Health Care Hospital, Cangzhou, China -

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http://dx.doi.org/10.23736/S2724-5691.21.09181-4DOI Listing
November 2021

Evaluation of leachate production and level in municipal solid waste landfills considering secondary compression.

Environ Sci Pollut Res Int 2021 Nov 5. Epub 2021 Nov 5.

MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Institute of Geotechnical Engineering, Zhejiang University, Hangzhou, China.

Landfilled municipal solid waste (MSW) in developing countries generally produces a large amount of leachate due to high moisture content. The estimation of leachate production and level is of great importance to the capacity design of leachate treatment plants and the stability analysis of landfills. In this study, the leachate production ratios (the ratio of leachate mass to waste mass) in different countries and cities were first summarized to reveal the basic status of leachate generation. Then, a model was established to calculate the leachate production and level that considers the rainfall infiltration and the water released from MSW due to both primary and secondary compression (ignored in previous models). Finally, the proposed model was used in a case study of Laogang Landfill in Shanghai, China. It was found that the leachate proportion produced by compression was much higher compared with that produced by rainfall infiltration, ranging from 49 (rainy season) to 93% (dry season). The leachate released from waste due to secondary compression accounted for a high proportion (up to 25%) of the total leachate production, especially for aged MSW. The calculated leachate discharge amount and leachate level were close to the measured values because the possible low permeability layer at the bottom of the landfill was considered in this model.
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http://dx.doi.org/10.1007/s11356-021-17209-8DOI Listing
November 2021

Experimental study on anisotropy of hydraulic conductivity for municipal solid waste.

Waste Manag 2021 Oct 31;137:39-49. Epub 2021 Oct 31.

MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Institute of Geotechnical Engineering, Zhejiang University, Hangzhou 310058, China.

Anisotropy of hydraulic conductivity is an important parameter controlling fluid movement in municipal solid waste (MSW) landfills, while measurements of anisotropy are rare. In this study, a laboratory-scale enhanced reactor was built to create MSW samples with different degrees of degradation. Vertical and horizontal hydraulic conductivities of these samples were measured in a self-designed permeameter to study the effects of compression and degradation on anisotropy of MSW. CT scanning was performed to observe the internal pore-structure of MSW under compression. A prediction model of anisotropy under compression was established. It was found that as degradation time increased from 0 month to 18 months, the dry mass percent of 0D particles increased from 12.3% to 38.8%, while 2D particles content decreased from 78.7% to 47.2%. As vertical stress increased from 50 kPa to 400 kPa, dry unit weight (γ) increased from 3.26 kN/m to 5.51 kN/m, anisotropy (A) increased from 1.26 to 5.17. It was because that the size and continuity of pores decreased and the angle of pore arrangement tended to be horizontal as the vertical stress increased. The relation between anisotropy and vertical stress could be well fitted with the prediction model. When degradation time increased from 0 month to 18 months, A decreased linearly from 5.02 to 2.75 due to the decreasing content of 2D particles. Anisotropy also decreased with the decreasing C/L. Compression has much greater influence on waste anisotropy than that of degradation. Anisotropy of MSW at different depths of landfills could be determined based on the trend lines in this study.
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http://dx.doi.org/10.1016/j.wasman.2021.10.030DOI Listing
October 2021

Construction of CF-Functionalized Fully Substituted Benzonitriles through Rauhut-Currier Reaction Initiated [3 + 3] Benzannulation.

J Org Chem 2021 Nov 1;86(21):14844-14854. Epub 2021 Oct 1.

State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.

Though numerous cyanation reactions have been developed for the synthesis of benzonitriles, the construction of valuable fully substituted benzonitriles is still a challenging task. Herein, we reported a tertiary amine-catalyzed [3 + 3]-benzannulation for the green synthesis of CF-functionalized fully substituted benzonitriles. This strategy features exclusive chemoselectivity, high atom-economy, and good step-economy with environment-friendly reagents and mild conditions. Unique triphenyl-substituted dicyanobenzoate products could be rapidly constructed using this method. The practicality and reliability of this reaction were proved by the successful scale-up synthesis. A mechanistic study indicates that the [3 + 3]-benzannulation was initiated by an intermolecular Rauhut-Currier reaction.
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http://dx.doi.org/10.1021/acs.joc.1c01631DOI Listing
November 2021

Complete chloroplast genome sequence of (Saxifragaceae).

Mitochondrial DNA B Resour 2021 22;6(10):3028-3030. Epub 2021 Sep 22.

Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, College of Science, Tibet University, Lhasa, China.

Bunge, Tibetan name 'Yajima,' growing in the highlands of China is a perennial herb belonging to the genus Saxifragaceae. As a traditional Chinese medicine, it has been used to treat digestive diseases for hundreds of years. The complete chloroplast genome of is 152,775 bp in length and comprises two inverted repeats (IR, 25,962 bp), a large single-copy region (LSC, 83,533 bp), and a small single-copy region (SSC, 17,318 bp). It harbors 112 genes, including 78 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. In addition, the gene was deleted. The GC content of the whole chloroplast genome is 37.54%. This chloroplast genome resource will be useful for study on the evolution and genetic diversity of in the future.
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http://dx.doi.org/10.1080/23802359.2021.1978893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462875PMC
September 2021

Phase I study of cediranib, an oral VEGFR inhibitor, in combination with selumetinib, an oral MEK inhibitor, in patients with advanced solid malignancies.

Invest New Drugs 2021 Sep 13. Epub 2021 Sep 13.

Division of Medical Oncology, Mayo Clinic, Rochester, MN, 55905, USA.

Purpose: Targeting the vascular endothelial growth factor (VEGF) pathway improves progression free survival in multiple advanced malignancies but durable responses are uncommon. Inhibition of the VEGF pathway at multiple levels of signal transduction may improve clinical outcomes. Preclinical data with cediranib, an inhibitor of all 3 VEGF receptors, in combination with selumetinib, an inhibitor of MEK 1/2, demonstrated improved tumor control experimentally. This phase I trial was designed to test the two agents in combination to evaluate the tolerability, safety and assess disease response.

Methods: Patients with advanced solid malignancies were enrolled into this phase I trial. Cediranib and selumetinib were dosed using a toxicity-adaptive isotonic design for the dose escalation/de-escalation of each agent. Both cediranib and selumetinib were administered daily and continuously. Cycles were 28 days in length.

Results: Eighteen patients were enrolled. At all dose levels, dose limiting toxicities (DLT) were observed, which limited dose escalation and further evaluation. The maximum tolerated dose of cediranib and selumetinib in combination could not be determined. The best response of stable disease was observed in eight patients.

Conclusions: Cediranib and selumetinib in combination on a continuous schedule was not tolerable, with patients experiencing cardiovascular and other DLTs. Intermittent schedules may be needed to establish a safe and tolerable combination of cediranib and selumetinib.
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http://dx.doi.org/10.1007/s10637-021-01175-6DOI Listing
September 2021

phase1RMD: An R package for repeated measures dose-finding designs with novel toxicity and efficacy endpoints.

PLoS One 2021 2;16(9):e0256391. Epub 2021 Sep 2.

Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States of America.

Traditional dose-finding designs are substantially inefficient for targeted agents and cancer immunotherapies by failing to incorporate efficacy signals, mild and moderate adverse events, and late, cumulative toxicities. However, the lack of user-friendly software is a barrier to the practical use of the novel phase I designs, despite their demonstrated superiority of traditional 3+3 designs. To overcome these barriers, we present an R package, phase1RMD, which provides a comprehensive implementation of novel designs with repeated toxicity measures and early efficacy. A novel phase I repeated measures design that used a continuous toxicity score from multiple treatment cycles was implemented. Furthermore, in studies where preliminary efficacy is evaluated, an adaptive, multi-stage design to identify the most efficacious dose with acceptable toxicity was demonstrated. Functions are provided to recommend the next dose based on the data collected in a phase I trial, as well as to assess trial characteristics given design parameters via simulations. The repeated measure designs accurately estimated both the magnitude and direction of toxicity trends in late treatment cycles, and allocated more patients at therapeutic doses. The R package for implementing these designs is available from the Comprehensive R Archive Network. To our best knowledge, this is the first software that implement novel phase I dose-finding designs that simultaneously accounts for the multiple-grade toxicity events over multiple treatment cycles and a continuous early efficacy outcome. With the software published on CRAN, we will pursue the implementation of these designs in phase I trials in real-life settings.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0256391PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8412295PMC
November 2021

Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of sect. Turanga in Northwest China.

Front Plant Sci 2021 11;12:705083. Epub 2021 Aug 11.

Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China.

sect. Turanga (hereafter referred to as ""), including and , are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of (59 and 26 populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of . Both and populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among and populations could be explained by both geographical and environmental distance. The genetic diversity of showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.
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http://dx.doi.org/10.3389/fpls.2021.705083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8385373PMC
August 2021

DTYMK promote hepatocellular carcinoma proliferation by regulating cell cycle.

Cell Cycle 2021 Sep 9;20(17):1681-1691. Epub 2021 Aug 9.

Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, China.

Overexpression of DTYMK is related with tumorigenesis and progression in several human tumors. However, the role of upregulated DTYMK in hepatocellular carcinoma (HCC) patients still remains unclear. In this study, the DTYMK expression in HCC tumors was evaluated in three GEO series (GSE14520, GSE54236, GSE63898), TCGA-LIHC, and ICGC-IRLR-JP cohorts. Survival analysis of DTYMK based on TCGA-LIHC and ICGC-LIRI-JP cohorts was conducted. We found that DTYMK was dramatically upregulated in tumor tissue compared with that in adjacent liver tissue. Kaplan-Meier analysis revealed that high expression of DTYMK in HCC patients' tumor tissue was significantly corresponded to worse overall survival (OS) (P < 0.05). Further analysis showed that overexpressing DTYMK led to poor relapse free survival (RFS) and disease-specific survival (DSS) (all P < 0.05). In conclusion, DTYMK is upregulated in tumors and correlated with poor prognosis in HCC patients. In our report, DTYMK is higher expression in HCC cancer tissue and cell line than tumor adjacent tissue and normal liver cell line. Knocking down DTYMK can inhabit tumor cell proliferation by interfering cell cycle, whereas overexpression of DTYMK can promote tumor cell proliferation. These findings indicate that upregulation of DTYMK enhances tumor growth and proliferation by promoting cell cycle.
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http://dx.doi.org/10.1080/15384101.2021.1958502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8489954PMC
September 2021

A Chromosome-level Assembly of A Wild Castor Genome Provides New Insights into the Adaptive Evolution in A Tropical Desert.

Genomics Proteomics Bioinformatics 2021 Jul 30. Epub 2021 Jul 30.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China. Electronic address:

Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiation, strong light, and extremely dry condition. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence assembly of the wild castor accession WT05, with a genome size of 316 Mb, a scaffold N50 of 31.93 Mb, and a contig N50 of 8.96 Mb, respectively. Compared with cultivated castor and other Euphorbiaceae species, the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis, and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.
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http://dx.doi.org/10.1016/j.gpb.2021.04.003DOI Listing
July 2021

Tryptophan potentiates CD8 T cells against cancer cells by TRIP12 tryptophanylation and surface PD-1 downregulation.

J Immunother Cancer 2021 07;9(7)

State Key Laboratory of Genetic Engineering, School of Life Sciences and Obstetrics & Gynecology Hospital of Fudan University, Shanghai, China

Background: Tryptophan catabolites suppress immunity. Therefore, blocking tryptophan catabolism with indoleamine 2,3-dioxygenase (IDO) inhibitors is pursued as an anticancer strategy.

Methods: The intracellular level of tryptophan and kynurenine was detected by mass spectrum analysis. The effect of tryptophan and IDO inhibitors on cell surface programmed cell death protein 1 (PD-1) level were measured by flow cytometry. A set of biochemical analyses were used to figure out the underlying mechanism. In vitro co-culture system, syngeneic mouse models, immunofluorescent staining, and flow cytometry analysis were employed to investigate the role of tryptophan and IDO inhibitor in regulating the cytotoxicity of CD8 T cells.

Results: Here, we reported that IDO inhibitors activated CD8 T cells also by accumulating tryptophan that downregulated PD-1. Tryptophan and IDO inhibitors administration, both increased intracellular tryptophan, and tryptophanyl-tRNA synthetase (WARS) overexpression decreased Jurkat and mice CD8 T cell surface PD-1. Mechanistically, WARS tryptophanylated lysine 1136 of and activated E3 ligase TRIP12 to degrade NFATc1, a PD-1 transcription activator. SIRT1 de-tryptophanylated TRIP12 and reversed the effects of tryptophan and WARS on PD-1. Tryptophan or IDO inhibitors potentiated CD8 T cells to induce apoptosis of co-cultured cancer cells, increased cancer-infiltrating CD8 T cells and slowed down tumor growth of lung cancer in mice.

Conclusions: Our results revealed the immune-activating efficacy of tryptophan, and suggested tryptophan supplemental may benefit IDO inhibitors and PD-1 blockade during anticancer treatments.
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http://dx.doi.org/10.1136/jitc-2021-002840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323461PMC
July 2021

Screening of genes related to survival prognosis of cervical squamous cell carcinoma and construction of prognosis prediction model.

J Obstet Gynaecol Res 2021 Sep 4;47(9):3310-3321. Epub 2021 Jul 4.

Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China.

Aim: We aimed to screen for the genes related to survival prognosis of cervical squamous cell carcinoma (CSCC) and then constructed a prognosis prediction model.

Methods: The GSE63514 dataset was obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). The CSCC gene dataset and the GSE44001 dataset were obtained from The Cancer Genome Atlas and NCBI GEO, respectively. The Kaplan-Meier (KM) curve was used to evaluate the association between high and low prognosis that was with the actual survival prognosis information. The Cox proportional hazards model was used to screen out the optimized prognostic-related signature differentially expressed gene (DEG) combinations. Gene set enrichment analysis was used to perform pathway enrichment annotation analysis for DEGs that were related to risk grouping.

Results: In total, 16 399 DEGs were obtained and 23 gene ontology biological processes and 8 Kyoto Encyclopedia of Genes and Genomes pathways were screened. Nine optimized DEG groups related to independent prognosis were selected. The KM curves of pathologic N0 and N1 showed that low-risk group were associated with a better overall survival (p = 1.518e; p = 1.704e-01). The pathways related to risk grouping were cytokine-cytokine receptor interaction, JAK stat signaling pathway, and glycolysis-gluconeogenesis.

Conclusion: On the basis of this study, we established a prognostic risk model, which provided a reliable prognostic tool and was of great significance for locating the biomarkers related to survival prognosis in CSCC.
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http://dx.doi.org/10.1111/jog.14827DOI Listing
September 2021

Adherence and Efficacy of Smoking Cessation Treatment Among Patients with COPD in China.

Int J Chron Obstruct Pulmon Dis 2021;16:1203-1214. Epub 2021 Apr 30.

Tobacco Medicine and Tobacco Cessation Centre, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.

Background: Smoking cessation is a key intervention for all smokers with chronic obstructive pulmonary disease (COPD). Poor treatment adherence is a challenge in clinical practice that might contribute to the lower efficacy of medication (eg, oral drug). However, it is unclear what factors will influence adherence among smokers with COPD.

Methods: This study was based on an open-label randomized controlled trial (RCT) of varenicline and bupropion for smoking cessation among patients with COPD in China. The medication was given for 12 weeks, and visits and assessments were conducted at weeks 0, 1, 2, 4, 6, 9, 12, and 24. We assessed whether the adherence to smoking cessation treatment affects the smoking cessation efficacy and evaluated predictors of adherence.

Results: A total of 136 participants were recruited from February 2019 to June 2020, and analyzed using the intention-to-treat (ITT) method. In this study, 48.5% (66/136) of the total participants had good adherence to smoking cessation, and good adherence significantly improved the efficacy of smoking cessation (OR=9.60, 95% CI 4.02-22.96, P < 0.001). After adjusting for age, gender, nationality, education, and marital status, we found older age, higher education level, having more previous quitting attempts, stronger self-efficacy and preparation in quitting smoking, recognizing hazards of smoking, longer duration of COPD, and higher St. George's Respiratory Questionnaire (SGRQ) scores were relevant to good adherence (P < 0.05).

Conclusion: To our best knowledge, this is the first study to evaluate adherence to smoking cessation treatment among patients with COPD in China. Our study found that good adherence to smoking cessation treatment significantly improved the smoking cessation efficacy, and predictors of adherence were evaluated. We call on the medical community to pay attention to the adherence to smoking cessation among patients with COPD.
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http://dx.doi.org/10.2147/COPD.S301579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096422PMC
July 2021

The characteristics of laboratory tests at admission and the risk factors for adverse clinical outcomes of severe and critical COVID-19 patients.

BMC Infect Dis 2021 Apr 20;21(1):371. Epub 2021 Apr 20.

Hubei Provincial Academy of Tranditional Chinese Medicine, Wuhan, China.

Background: The current coronavirus disease 2019 (COVID-19) is a public health emergency. In this study, we aimed to evaluate the risk factors for mortality in severe and critical COVID-19 patients.

Methods: We performed a retrospective study of patients diagnosed with severe and critical COVID-19 from four hospitals in Wuhan, China, by evaluating the clinical characteristics and laboratory results, and using Cox proportional hazards model to assess the risk factors involved in disease progression.

Results: In total, 446 patients with COVID-19 were enrolled. The study indicated a high mortality rate (20.2%) in severe and critical COVID-19 patients. At the time of admission, all patients required oxygen therapy, and 52 (12%) required invasive mechanical ventilation, of which 50 (96%) died. The univariate Cox proportional hazards model showed a white blood cell count of more than 10 × 10/L (HR 3.993,95%CI 2.469 to 6.459) that correlated with an increased mortality rate. The multivariable Cox proportional hazards model demonstrated that older age (HR 1.066, 95% CI 1.043 to 1.089) and higher white blood cell count (HR 1.135, 95% CI 1.080 to 1.192) were independent risk factors for determining COVID-19 associated mortality.

Conclusions: COVID-19 is associated with a significant risk of morbidity and mortality in the population. Older age and higher white blood cell count were found to be independent risk factors for mortality.
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http://dx.doi.org/10.1186/s12879-021-06057-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057654PMC
April 2021

Sweet systems: technologies for glycomic analysis and their integration into systems biology.

Crit Rev Biochem Mol Biol 2021 06 5;56(3):301-320. Epub 2021 Apr 5.

Department of Chemistry, New York University, New York City, NY, USA.

Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.
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http://dx.doi.org/10.1080/10409238.2021.1908953DOI Listing
June 2021

Heat stress interferes with formation of double-strand breaks and homolog synapsis.

Plant Physiol 2021 04;185(4):1783-1797

College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China.

Meiotic recombination (MR) drives novel combinations of alleles and contributes to genomic diversity in eukaryotes. In this study, we showed that heat stress (36°C-38°C) over the fertile threshold fully abolished crossover formation in Arabidopsis (Arabidopsis thaliana). Cytological and genetic studies in wild-type plants and syn1 and rad51 mutants suggested that heat stress reduces generation of SPO11-dependent double-strand breaks (DSBs). In support, the abundance of recombinase DMC1, which is required for MR-specific DSB repair, was significantly reduced under heat stress. In addition, high temperatures induced disassembly and/or instability of the ASY4- but not the SYN1-mediated chromosome axis. At the same time, the ASY1-associated lateral element of the synaptonemal complex (SC) was partially affected, while the ZYP1-dependent central element of SC was disrupted, indicating that heat stress impairs SC formation. Moreover, expression of genes involved in DSB formation; e.g. SPO11-1, PRD1, 2, and 3 was not impacted; however, recombinase RAD51 and chromosome axis factors ASY3 and ASY4 were significantly downregulated under heat stress. Taken together, these findings revealed that heat stress inhibits MR via compromised DSB formation and homolog synapsis, which are possible downstream effects of the impacted chromosome axis. Our study thus provides evidence shedding light on how increasing environmental temperature influences MR in Arabidopsis.
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http://dx.doi.org/10.1093/plphys/kiab012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133540PMC
April 2021

The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis.

Plant Biotechnol J 2021 09 8;19(9):1725-1742. Epub 2021 Apr 8.

Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China.

Safflower (Carthamus tinctorius L.), a member of the Asteraceae, is a popular crop due to its high linoleic acid (LA) and flavonoid (such as hydroxysafflor yellow A) contents. Here, we report the first high-quality genome assembly (contig N50 of 21.23 Mb) for the 12 pseudochromosomes of safflower using single-molecule real-time sequencing, Hi-C mapping technologies and a genetic linkage map. Phyloge nomic analysis showed that safflower diverged from artichoke (Cynara cardunculus) and sunflower (Helianthus annuus) approximately 30.7 and 60.5 million years ago, respectively. Comparative genomic analyses revealed that uniquely expanded gene families in safflower were enriched for those predicted to be involved in lipid metabolism and transport and abscisic acid signalling. Notably, the fatty acid desaturase 2 (FAD2) and chalcone synthase (CHS) families, which function in the LA and flavonoid biosynthesis pathways, respectively, were expanded via tandem duplications in safflower. CarFAD2-12 was specifically expressed in seeds and was vital for high-LA content in seeds, while tandemly duplicated CarFAD2 genes were up-regulated in ovaries compared to CarFAD2-12, which indicates regulatory divergence of FAD2 in seeds and ovaries. CarCHS1, CarCHS4 and tandem-duplicated CarCHS5˜CarCHS6, which were up-regulated compared to other CarCHS members at early stages, contribute to the accumulation of major flavonoids in flowers. In addition, our data reveal multiple alternative splicing events in gene families related to fatty acid and flavonoid biosynthesis. Together, these results provide a high-quality reference genome and evolutionary insights into the molecular basis of fatty acid and flavonoid biosynthesis in safflower.
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http://dx.doi.org/10.1111/pbi.13586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428823PMC
September 2021

Vitamin D status and its dietary and lifestyle factors in children during the first 5 years of life: A cross-sectional multicentre Jiangsu bone study.

J Hum Nutr Diet 2021 10 9;34(5):792-806. Epub 2021 Apr 9.

Department of Child Health Care, Xinghua Maternity and Child Health Care Hospital, Xinghua, China.

Background: To explore the vitamin D status with its demographic and lifestyle factors including dietary, supplementation, and physical activity in 0-5 years old children.

Methods: This was a large population-based cross-sectional multicentre study in which the children were recruited from 12 Children's Health Care Centers by a stratified cluster random-sampling method in 10 cities in Jiangsu Province, China.

Results: A total number of 5289 children were investigated. The prevalence of vitamin D deficiency was 30.1%. The concentration of 25 hydroxyvitamin D was 64.0 (46.3-83.0) nmol mL after adjustment for covariates. Children with higher risk of vitamin D deficiency were more likely to be at older age, girls, survey conducted in spring, location in southern Jiangsu province, residence in urban, outdoor activity < 2 h day (all p < 0.05). Moreover, those with lower risk were more likely to be the number of parity ≥ 2 times, vitamin D supplementation from birth to 6 months, the initial time of vitamin D supplementation after birth ≤ 1 months, vitamin D and calcium supplementation in the last 3 months, and dose of vitamin D supplementation > 400 IU day (all p < 0.05). Children with preferences for sweets, meat consumption > 150.0 g day , milk consumption < 250 mL day , time of sleeping < 10 h day had higher risks of vitamin D deficiency. However, these relationships were affected by demographics.

Conclusions: Vitamin D status during the first five years of life was suboptimal and was associated with demographic and lifestyle determinants including milk, meat, sweets, vitamin D and calcium supplementation, sleeping and outdoor activity.
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http://dx.doi.org/10.1111/jhn.12883DOI Listing
October 2021

Applicability and cost-effectiveness of the Systolic Blood Pressure Intervention Trial (SPRINT) in the Chinese population: A cost-effectiveness modeling study.

PLoS Med 2021 03 4;18(3):e1003515. Epub 2021 Mar 4.

Department of Epidemiology and Health Statistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China.

Background: The Systolic Blood Pressure Intervention Trial (SPRINT) showed significant reductions in death and cardiovascular disease (CVD) risk with a systolic blood pressure (SBP) goal of <120 mm Hg compared with a SBP goal of <140 mm Hg. Our study aimed to assess the applicability of SPRINT to Chinese adults. Additionally, we sought to predict the medical and economic implications of this intensive SBP treatment among those meeting SPRINT eligibility.

Methods And Findings: We used nationally representative baseline data from the China Health and Retirement Longitudinal Study (CHARLS) (2011-2012) to estimate the prevalence and number of Chinese adults aged 45 years and older who meet SPRINT criteria. A validated microsimulation model was employed to project costs, clinical outcomes, and quality-adjusted life-years (QALYs) among SPRINT-eligible adults, under 2 alternative treatment strategies (SBP goal of <120 mm Hg [intensive treatment] and SBP goal of <140 mm Hg [standard treatment]). Overall, 22.2% met the SPRINT criteria, representing 116.2 (95% CI 107.5 to 124.8) million people in China. Of these, 66.4%, representing 77.2 (95% CI 69.3 to 85.0) million, were not being treated for hypertension, and 22.9%, representing 26.6 (95% CI 22.4 to 30.7) million, had a SBP between 130 and 139 mm Hg, yet were not taking antihypertensive medication. We estimated that over 5 years, compared to standard treatment, intensive treatment would reduce heart failure incidence by 0.84 (95% CI 0.42 to 1.25) million cases, reduce CVD deaths by 2.03 (95% CI 1.44 to 2.63) million cases, and save 3.84 (95% CI 1.53 to 6.34) million life-years. Estimated reductions of 0.069 (95% CI -0.28, 0.42) million myocardial infarction cases and 0.36 (95% CI -0.10, 0.82) million stroke cases were not statistically significant. Furthermore, over a lifetime, moving from standard to intensive treatment increased the mean QALYs from 9.51 to 9.87 (an increment of 0.38 [95% CI 0.13 to 0.71]), at a cost of Int$10,997 per QALY gained. Of all 1-way sensitivity analyses, high antihypertensive drug cost and lower treatment efficacy for CVD death resulted in the 2 most unfavorable results (Int$25,291 and Int$18,995 per QALY were gained, respectively). Simulation results indicated that intensive treatment could be cost-effective (82.8% probability of being below the willingness-to-pay threshold of Int$16,782 [1× GDP per capita in China in 2017]), with a lower probability in people with SBP 130-139 mm Hg (72.9%) but a higher probability among females (91.2%). Main limitations include lack of specific SPRINT eligibility information in the CHARLS survey, uncertainty about the implications of different blood pressure measurement techniques, the use of several sources of data with large reliance on findings from SPPRINT, limited information about the serious adverse event rate, and lack of information and evidence for medication effectiveness on renal disease.

Conclusions: Although adoption of the SPRINT treatment strategy would increase the number of Chinese adults requiring SBP treatment intensification, this approach has the potential to prevent CVD events, to produce gains in life-years, and to be cost-effective under common thresholds.
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http://dx.doi.org/10.1371/journal.pmed.1003515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971845PMC
March 2021

Complete chloroplast genome of (Umbelliferae).

Mitochondrial DNA B Resour 2021 Feb 11;6(2):536-537. Epub 2021 Feb 11.

Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China.

(Miq.) Koidz. is a perennial herbaceous plant belonging to the genus , Umbelliferae. As a plant with dual-purpose as food and medicine, it has the potential for the future development of high-value functional products. The complete chloroplast genome has a total size of 147,007 bp, consisting of two inverted repeats (IR, 18,508 bp, each), and separated by a large single-copy region (LSC, 92,415 bp) and a small single-copy region (SSC, 17,576 bp). Further annotation revealed the chloroplast genome contains 128 genes, including 84 protein-coding genes (80 PCG species), 36 tRNA genes (30 tRNA species), and 8 rRNA genes (4 rRNA species). A total of 83 simple sequence repeats (SSRs) were identified in the chloroplast genome. This chloroplast genome resource will be useful for the study of the evolution and genetic diversity of in the future.
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http://dx.doi.org/10.1080/23802359.2021.1873711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889118PMC
February 2021

A novel prognostic prediction model based on seven immune-related RNAs for predicting overall survival of patients in early cervical squamous cell carcinoma.

BMC Med Genomics 2021 02 15;14(1):49. Epub 2021 Feb 15.

Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, No 126, Xiantai Street, Changchun, Jilin, 130033, People's Republic of China.

Background: In this study, we aimed to mine immune-related RNAs expressed in early cervical squamous cell carcinoma to construct prognostic prediction models.

Methods: The RNA sequencing data of 309 cervical squamous cell carcinoma (CSCC) cases, including data of individuals with available clinical information, were obtained from The Cancer Genome Atlas (TCGA) database. We included 181 early-stage CSCC tumor samples with clinical survival and prognosis information (training dataset). Then, we downloaded the GSE44001 gene expression profile data from the National Center for Biotechnology Information Gene Expression Omnibus (validation dataset). Gene ontology annotation and the Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to analyze the biological functions of differentially expressed immune-related genes (DEIRGs). We established protein-protein interactions and competing endogenous RNA networks using Cytoscape. Using the Kaplan-Meier method, we evaluated the association between the high- and low-risk groups and the actual survival and prognosis information. Our univariate and multivariate Cox regression analyses screened for independent prognostic factors.

Results: We identified seven prognosis-related signature genes (RBAKDN, CXCL2, ZAP70, CLEC2D, CD27, KLRB1, VCAM1), the expression of which was markedly associated with overall survival (OS) in CSCC patients. Also, the risk score of the seven-gene signature discripted superior ability to categorize CSCC patients into high-risk and low-risk groups, with a observablydifferent OS in the training and validation datasets. We screened two independent prognostic factors (Pathologic N and prognostic score model status) that correlated significantly by univariate and multivariate Cox regression analyses in the TCGA dataset. To further explore the potential mechanism of immune-related genes, we observed associated essential high-risk genes with a cytokine-cytokine receptor interaction.

Conclusions: This study established an immune-related RNA signature, which provided a reliable prognostic tool and may be of great significance for determining immune-related biomarkers in CSCC.
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http://dx.doi.org/10.1186/s12920-021-00885-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885601PMC
February 2021

Metabolism and global protein glycosylation are differentially expressed in healthy and osteoarthritic equine carpal synovial fluid.

Equine Vet J 2021 Feb 15. Epub 2021 Feb 15.

Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.

Background: Carpal osteochondral fragmentation and subsequent post-traumatic osteoarthritis (PTOA) are leading causes of wastage in the equine athlete. Identification of synovial fluid biomarkers could contribute to the diagnosis and understanding of osteoarthritis (OA) pathophysiology.

Objective: The aim of this study was to identify differentially expressed metabolic and glycosylation pathways in synovial fluid from healthy horses and horses with naturally occurring carpal OA.

Study Design: Cross-sectional, in vivo metabolomics and glycomics study.

Methods: In cohort 1, carpal synovial fluid (n = 12 horses; n = 6 healthy, n = 6 OA) was analysed using high-resolution liquid chromatography mass spectrometry (LC-MS). In cohort 2 (n = 40 horses; n = 20 healthy, n = 20 OA), carpal synovial fluid was analysed using lectin microarrays and a lubricin sandwich ELISA.

Results: Metabolomic analysis identified >4900 LC-MS features of which 84 identifiable metabolites were differentially expressed (P < .05) between healthy and OA joints, including key pathways related to inflammation (histidine and tryptophan metabolism), oxidative stress (arginine biosynthesis) and collagen metabolism (lysine metabolism). Principle Component Analysis and Partial Least Squares Discriminant Analysis demonstrated separation between healthy and OA synovial fluid. Lectin microarrays identified distinct glycosylation patterns between healthy and OA synovial fluid, including increased Core 1/Core 3 O-glycosylation, increased α-2,3 sialylation and decreased α-1,2 fucosylation in OA. O-glycans predominated over N-glycans in all synovial fluid samples, and synovial fluid lubricin was increased in OA joints as compared to controls.

Main Limitations: The sample size in cohort 1 was limited, and there is inherent variation in severity and duration of joint injury in naturally occurring OA. However, LC-MS identified up to 5000 unique features.

Conclusions: These data suggest new potential diagnostic and therapeutic targets for equine OA. Future targeted metabolomic and glycomic studies should be performed to verify these results. Lectin microarrays could be investigated as a potential screening tool for the diagnosis and therapeutic monitoring of equine OA.
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http://dx.doi.org/10.1111/evj.13440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364562PMC
February 2021

Complete chloroplast genome sequence of and (Saxifragaceae).

Mitochondrial DNA B Resour 2020 Jul 15;5(3):2837-2838. Epub 2020 Jul 15.

Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China.

The complete chloroplast genome of Maxim. and L. were reported in this study. The chloroplast genomes were 153,460 bp for and 152,619 bp for . LSC and SSC of 83,670 bp and 17,342 bp were separated by two IRs of 26,224 bp each in . While contained IRs of 25,992 bp, LSC of 83,524 bp and SSC of 17,111 bp. The chloroplast genome of contains 112 unique genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. And the chloroplast genome of contains 112 unique genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. In addition, the rps12 gene was recognized as a trans-spliced gene and 17 intron-containing genes were also detected.
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http://dx.doi.org/10.1080/23802359.2020.1790313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850371PMC
July 2020

The host glycomic response to pathogens.

Curr Opin Struct Biol 2021 06 30;68:149-156. Epub 2021 Jan 30.

Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada. Electronic address:

Glycans play important roles in the biology of infectious diseases. Although glycans are expressed on both the pathogens and the host, the functions and dynamics of the host glycome during infection are not well understood. Recent years have witnessed new discoveries on the host glycome respsonse to infection, as well as related mechanisms and their implications. Herein, we present a brief review on the latest findings in this field and put them in the context of host immunity.
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http://dx.doi.org/10.1016/j.sbi.2020.12.011DOI Listing
June 2021

Comparative multi-omics analyses reveal differential expression of key genes relevant for parasitism between non-encapsulated and encapsulated Trichinella.

Commun Biol 2021 01 29;4(1):134. Epub 2021 Jan 29.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Genome assemblies provide a powerful basis of comparative multi-omics analyses that offer insight into parasite pathogenicity, host-parasite interactions, and invasion biology. As a unique intracellular nematode, Trichinella consists of two clades, encapsulated and non-encapsulated. Genomic correlation of the distinct differences between the two clades is still unclear. Here, we report an annotated draft reference genome of non-encapsulated Trichinella, T. pseudospiralis, and perform comparative multi-omics analyses with encapsulated T. spiralis. Genome and methylome analyses indicate that, during Trichinella evolution, the two clades of Trichinella exhibit differential expansion and methylation of parasitism-related multi-copy gene families, especially for the DNase II members of the phospholipase D superfamily and Glutathione S-transferases. Further, methylome and transcriptome analyses revealed divergent key excretory/secretory (E/S) genes between the two clades. Among these key E/S genes, TP12446 is significantly more expressed across three life stages in T. pseudospiralis. Overexpression of TP12446 in the mouse C2C12 skeletal muscle cell line could induce inhibition of myotube formation and differentiation, further indicating its key role in parasitism of T. pseudospiralis. This multi-omics study provides a foundation for further elucidation of the mechanism of nurse cell formation and immunoevasion, as well as the identification of pharmacological and diagnostic targets of trichinellosis.
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http://dx.doi.org/10.1038/s42003-021-01650-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846577PMC
January 2021

Complete chloroplast genome sequence of Schrenk from PacBio Sequel II Platform.

Mitochondrial DNA B Resour 2020 Sep 29;5(3):3452-3454. Epub 2020 Sep 29.

Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.

Schrenk plays an important role on ecological services in desert areas. The complete chloroplast genome was reported in this study using the PacBio Sequel II Platform. The chloroplast genome with a total size of 157,856 bp consists of two inverted repeats (IR, 27,673 bp) separated by a large single-copy region (LSC, 85,867 bp) and a small single-copy region (SSC, 16,645 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 151 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of in the future.
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http://dx.doi.org/10.1080/23802359.2020.1824593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782250PMC
September 2020

Complete chloroplast genome sequence of and (Saxifragaceae).

Mitochondrial DNA B Resour 2020 May 12;5(3):2040-2041. Epub 2020 May 12.

Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China.

The complete chloroplast genome of Oliv. and Fr. Schmidt. were reported in this study. The chloroplast genomes were 152,837 bp for and 151,679 bp for . LSC and SSC of 83,584 bp and 17,265 bp were separated by two IRs of 25,994 bp each in . While contained IRs of 25,973 bp, LSC of 82,772 bp and SSC of 16,961 bp, for a total 151,679 bp length. The chloroplast genome of contains 130 genes, including 85 protein-coding genes (78 PCG species), 8 ribosomal RNA genes (4 rRNA species), 37 transfer RNA genes (30 tRNA species). And the chloroplast genome of contains 130 genes, including 85 protein-coding genes (78 PCG species), 8 ribosomal RNA genes (4 rRNA species), 37 transfer RNA genes (30 tRNA species).
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http://dx.doi.org/10.1080/23802359.2020.1760152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782184PMC
May 2020

Stereoselective synthesis of trifluoroethyl 3,2'-spirooxindole γ-lactam through the organocatalytic cascade reaction of 3-((2,2,2-trifluoroethyl)amino)indolin-2-one.

Org Biomol Chem 2021 01;19(2):467-475

School of Basic Medical Sciences, School of Pharmacy, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.

Newly designed 3-((2,2,2-trifluoroethyl)amino)indolin-2-ones were used for the facile synthesis of chiral fluoroalkyl-containing 3,2'-spirooxindole γ-lactam products. The secondary amine-catalysed Michael/hemiaminalization cascade reaction of 3-((2,2,2-trifluoroethyl)amino)indolin-2-one with α,β-unsaturated aldehydes followed by oxidation can easily produce the desired products in high yields (up to 86%) with excellent enantioselectivities (up to 99% ee) and diastereoselectivities (up to >95 : 5 dr).
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http://dx.doi.org/10.1039/d0ob02166kDOI Listing
January 2021

Prognostic and Predictive Value of a 15 Transcription Factors (TFs) Panel for Hepatocellular Carcinoma.

Cancer Manag Res 2020 1;12:12349-12361. Epub 2020 Dec 1.

Department of Pathology, Affiliated Hospital of Jining Medical University, Jining 272000, People's Republic of China.

Purpose: Hepatocellular carcinoma (HCC) is one of the most devastating diseases worldwide. Limited performance of clinicopathologic parameters as prognostic factors underscores more accurate and effective biomarkers for high-confidence prognosis that guide decision-making for optimal treatment of HCC. The aim of the present study was to establish a novel panel to improve prognosis prediction of HCC patients, with a particular interest in transcription factors (TFs).

Materials And Methods: A TF-related prognosis model of liver cancer with data from ICGC-LIRP-JI cohort successively were processed by univariate and multivariate Cox regression analysis. Then, for evaluating the prognostic prediction value of the model, receiver operating characteristic (ROC) curve and survival analysis were performed both with internal data from the International Cancer Genome Consortium (ICGC) and external data from The Cancer Genome Atlas (TCGA). Furthermore, we verified the expression of three genes in HCC cell lines by Western blot and qPCR and protein expression level by IHC in liver cancer patients' sample. Finally, we constructed a TF clinical characteristics nomogram to furtherly predict liver cancer patient survival probability with TCGA cohort.

Results: By Cox regression analysis, a panel of 15 TFs (, , , , , , , , , , , , , , ) was identified to present with powerful predictive performance for overall survival of HCC patients based on internal ICGC cohort and external TCGA cohort. A nomogram that integrates these factors was established, allowing efficient prediction of survival probabilities and displaying higher clinical utility.

Conclusion: The 15-TF panel is an independent prognostic factor for HCC, and 15 TF-based nomogram might provide implication an effective approach for HCC patient management and treatment.
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http://dx.doi.org/10.2147/CMAR.S279194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7719121PMC
December 2020
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