Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China.

Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China. Methods: Over 48 months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared. Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups. Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.

Association Analysis of Gene Sequencing by NeoSeq Combined with Tandem Mass Spectrum and Four Neonatal Diseases.

BACKGROUND: NeoSeq is a new method of gene sequencing for newborn screening. The goal is to explore the relationship between gene sequencing by NeoSeq combined with tandem mass spectrum (TMS) and four neonatal diseases. METHODS: A total of 1,989 newborns from August 2010 to December 2021 were enrolled. The case number of congenital hypothyroidism, phenylketonuria, adrenocortical hyperplasia, and glucose-6-phosphate dehydrogenase deficiency was counted, and the results of gene sequencing by NeoSeq and TMS were analyzed. RESULTS: The proportion of male newborns was higher than that of female newborns (51.68% vs. 48.32%). The detection rate of glucose-6-phosphate dehydrogenase deficiency was higher than that of the other three diseases (0.60% vs. 0.05%, 0.05%, 0.15%). A total of 121 newborns were recalled from 1989 newborns by traditional screening technique, and TMS detected phenylketonuria, citrullinemia, glutaric acidemia type I, and 3-methylcro-tonyl-CoA carboxylase deficiency in 1 newborn each. Gene sequencing by NeoSeq of newborns with positive TMS results confirmed the presence of susceptibility genes, and 17 of 1,868 newborns with normal biochemical tests had pathogenic genes. CONCLUSIONS: The incidence of glucose-6-phosphate dehydrogenase deficiency is relatively higher in four neonatal diseases, and the detection rate of gene sequencing by NeoSeq combined with TMS is high.

A multicenter prospective study of next-generation sequencing-based newborn screening for monogenic genetic diseases in China.

BACKGROUND: Newborn screening (NBS) is an important and successful public health program that helps improve the long-term clinical outcomes of newborns by providing early diagnosis and treatment of certain inborn diseases. The development of next-generation sequencing (NGS) technology provides new opportunities to expand current newborn screening methodologies. METHODS: We designed a a newborn genetic screening (NBGS) panel targeting 135 genes associated with 75 inborn disorders by multiplex PCR combined with NGS. With this panel, a large-scale, multicenter, prospective multidisease analysis was conducted on dried blood spot (DBS) profiles from 21,442 neonates nationwide. RESULTS: We presented the positive detection rate and carrier frequency of diseases and related variants in different regions; and 168 (0.78%) positive cases were detected. Glucose-6-Phosphate Dehydrogenase deficiency (G6PDD) and phenylketonuria (PKU) had higher prevalence rates, which were significantly different in different regions. The positive detection of G6PD variants was quite common in south China, whereas PAH variants were most commonly identified in north China. In addition, NBGS identified 3 cases with DUOX2 variants and one with SLC25A13 variants, which were normal in conventional NBS, but were confirmed later as abnormal in repeated biochemical testing after recall. Eighty percent of high-frequency gene carriers and 60% of high-frequency variant carriers had obvious regional differences. On the premise that there was no significant difference in birth weight and gestational age, the biochemical indicators of SLC22A5 c.1400C > G and ACADSB c.1165A > G carriers were significantly different from those of non-carriers. CONCLUSIONS: We demonstrated that NBGS is an effective strategy to identify neonates affected with treatable diseases as a supplement to current NBS methods. Our data also showed that the prevalence of diseases has significant regional characteristics, which provides a theoretical basis for screening diseases in different regions.

[Prenatal diagnosis of partial deletion of NRXN1 gene with combined CNV-seq and qPCR assays].

OBJECTIVE: To summarize the genetic diagnosis, low-depth copy number variation sequencing (CNV-seq) and prenatal finding in 7 fetuses with 2p16.3 deletions only involving the NRXN1 gene. METHODS: The 7 fetuses have all been found to have loss of heterozygosity at 2p16.3 by CNV-seq, which were verified by quantitative real-time PCR (qPCR). Specific regions of NRXN1 gene deletions were identified, and the CNVs were verified in their parents. Outcome of the pregnancies were followed up. RESULTS: Among 16 502 prenatal samples, 7 fetuses were found to harbor a 120 kb ~ 900 kb microdeletion in the 2p16.3 region, which yielded a prevalence of 0.424‰. The deleted region mainly involved 50 200 000-51 880 000 positions of chromosome 2 and involved only the NRXN1 gene. All of the 7 fetal CNVs were confirmed by qPCR, including 2 cases with heterozygous deletion of exons 1 to 6, 1 with heterozygous deletion of exons 1 to 19, 1 with heterozygous deletion of exons 19 to 22, and 3 with heterozygous deletion of introns 6 to 7 of the NRXN1 gene. Verification in the parents had found that one deletion was inherited from the father, 1 was from the mother, 2 cases were de novo in origin, whilst the remaining 3 had refused parental verification. After genetic counseling, one couple had elected induced abortion, 1 case has not been born yet, whilst the other 5 cases were born healthy. Follow up had identified no mental abnormalities among the children. CONCLUSION: Seven fetuses with heterozygous 2p16.3 deletions only involving the NRXN1 gene were detected by CNV-seq. The specific deletion of the NRXN1 gene was verified by qPCR. Prenatal genetic counseling and fertility guidance has been provided to the particular family by combining the results of CNV testing, pedigree analysis and pregnancy outcome.

Stereochemically altered cephalosporins as potent inhibitors of New Delhi metallo-ß-lactamases.

Antibiotic resistance caused by ß-lactamases, particularly metallo-ß-lactamases, has been a major threat to public health globally. New Delhi metallo-ß-lactamase-1 (NDM-1) represents one of the most important metallo-ß-lactamases; the production of NDM-1 in bacterial pathogen significantly reduces the efficacy of ß-lactam antibiotics, including life-saving carbapenems. Herein, we have demonstrated stereochemically altered cephalosporins as potent inhibitors against NDM-1, as well as mutants of NDM. The structure and activity relationship (SAR) study on over twenty cephalosporin analogues discloses the stereochemistry and the substituents on 7-position and 3'-position of cephalosporin are critical to suppress the activity of NDM-1 and the optimal compound 1u exhibited an IC50 of 0.13 µM. Furthermore, a crystal complex of NDM-1 and 1u has been obtained, suggesting this cephalosporin derivative inhibits enzyme activity by the formation of a relatively stable hydrolytic product-NDM-1 intermediate. The discovery in this study may pave the way to turn cephalosporin, a natural substrate of ß-lactamase, into an effective NDM-1 inhibitor to combat antibiotic resistance.

Screening aptamers for serine ß-lactamase-expressing bacteria with Precision-SELEX.

Klebsiella pneumoniae carbapenemase 2 (KPC-2) is a serine ß-lactamase that can hydrolyze almost all ß-lactam antibiotics. The drug resistant problem of bacteria expressing carbapenemases is currently a global problem, therefore, rapid and specific detection of pathogenic bacteria is urgent. In order to obtain an aptamer that can specifically recognize bacteria expressing KPC-2, we have established a method called Precision-SELEX. Precision-SELEX combined protein SELEX and bacterium SELEX. In this method, KPC-2 was used as a target protein, and Escherichia coli expressing KPC-2 (KPC-2 E. coli) was used as a target bacterium. After precision-SELEX, the same aptamer named XK-10 that can recognize KPC-2 and KPC-2 E. coli was obtained while the screening process could be shortened to 4 rounds. Dissociation equilibrium constants were calculated as 0.81 nM by SPR. In addition, XK-10 could specifically bind to KPC-2 E. coli, which was confirmed through flow cytometry and molecular Docking Simulations. The high-content imaging method could detect KPC-2 E. coli. In all, the Precision-SELEX provides an accurate and efficient method to screening aptamers for bacteria.

A minor structure modification serendipitously leads to a highly carbapenemase-specific fluorogenic probe.

Reported herein is a fluorogenic probe for the detection of carbapenemase activity. This reagent features carbapenem as an enzyme recognition motif and a carbon-carbon double bond between carbapenem and the fluorophore, exhibiting high specificity to all carbapenemases, including metallo carbapenemases and serine carbapenemases, over other ß-lactamases.

Highly selective and wash-free visualization of resistant bacteria with a relebactam-derived fluorogenic probe.

Reported herein is a relebactam-derived fluorogenic reagent for covalent labeling of serine ß-lactamases (SBLs), which are the major causes of bacterial resistance to ß-lactam antibiotics. This highly selective imaging reagent generates over 300-fold stronger near-infrared fluorescence signals upon covalently bonding to SBLs, allowing wash-free visualization of live antimicrobial-resistant bacteria.

A carbapenem-based fluorescence assay for the screening of metallo-ß-lactamase inhibitors.

Reported herein is a fluorescence assay for the rapid screening of metallo-ß-lactamase (MBL) inhibitors. This assay employs a fluorogenic carbapenem CPC-1 as substrate and is compatible with all MBLs, including B1, B2 and B3 subclass MBLs. The efficiency of this assay was demonstrated by the rapid inhibition screening of a number of molecules against B2 MBL CphA and 2,3-dimercaprol was identified as a potent CphA inhibitor.

[Research progress of serum pharmacochemistry of traditional Chinese medicine].

Serum pharmacochemistry of traditional Chinese medicine(TCM) is an effective method to rapidly screen the effective substances and reveal the compatibility law of compound by identification and analysis of constituents migrating to blood after oral administration. In the last two decades, it has been universally accepted and widely applied in the field. With the cross-fusion with other disciplines, such as serum pharmacology, pharmacokinetics, metabolomics, network pharmacology and systems biology, serum pharmacochemistry shows comprehensive superiority in explaining drug changes in vivo and in vitro, interactions between drugs, interactions between drug and body, which coincides with the complexity of TCM compatibility, multi-components, multi-targets and multi-mechanisms. Based on the references related with the serum pharmacochemistry from CNKI scholar and Pubmed in 2013-2016, the research results of serum pharmacochemistry were statistically analyzed, and the key technical problems during the study of serum pharmacochemistry, for example, preparation of test sample, selection of experimental animal, determination of drug delivery scheme, method and time of the adoption blood, preparation and pretreatment of blood sample, as well as analysis of constituents migrating to blood, and the solving ways were empirically introduced. In addition, the development and comprehensive application of serum pharmacochemistry in TCM were summarized in this paper, hoping to lay a foundation for the further application of this method in TCM research.

Estimation of herbage intake and digestibility of grazing sheep in Zhenglan Banner of Inner Mongolia by using n-alkanes.

To reveal the seasonal dynamics of herbage intake, diet composition and digestibility and clarify the relationship of those with herbage nutrient and botanical composition of grazing sheep in Zhenglan Banner of Inner Mongolia, the n-alkane technique was used to test in sheep grazed during June, August and December. The results showed that the sheep mainly ate Fringed sagebrush, Stipa krylovii and Carex in proportions of 33.5, 17.9 and 21.2%, respectively, in spring. In summer, the sheep consumed cleistogenes, Potentilla tanacetifolia, Thyme, etc; the intake of Fringed sagebrush, Carex and Stipa declined. In winter, Fringed sagebrush accounted for 50.1% of herbage intake, and the intakes of Cleistogenes and Stipa krylovii increased to 15.3 and 18.4%, respectively. Herbage intake by the sheep in spring was 1.8 kg DM/d, and digestibility was 71.4%. Herbage intake and digestibility decreased slightly to 1.7 kg DM/d and 68.4% during the summer, respectively and decreased significantly to 1.2 kg DM/d and 36.4% in winter. There were significant correlations between diet composition and CP content in winter, diet composition and botanical composition in summer. A highly positive correlation between herbage intake and digestibility was observed in grazing sheep.