Specific expression of transmembrane protein 26 in retina and its association with primary open-angle glaucoma / 中华实验眼科杂志

Objective:To predict the transmembrane structure of transmembrane protein 26 (TMEM26), observe its expression in human retina and mouse retina, and investigate the relationship between it and primary open-angle glaucoma (POAG).Methods:The transmembrane structure of TMEM26 in human and mouse was obtained by inputting its amino acid sequences into the transmembrane protein structure prediction software, MemBrain.The expression and location of TMEM26 in human and mouse retinas were observed through frozen retinal sections stained with anti-TMEM26 antibody, which came from a human donor and five SPF-grade C57BL/6 mice.The possible function of TMEM26 gene and its influence on eyes were inferred on the basis of the specific expression of TMEM26 in retina.The single nucleotide polymorphism mutation of TMEM26 gene was searched in literature related to ocular diseases.The use and care of animals complied with the Regulations on the Management of Experimental Animals.This research protocol was approved by an Ethics Committee of Sichuan Provincial People's Hospital (No.2019-36). Results:Both human and mouse TMEM26 were eight transmembrane proteins with similar eight hydrophobic transmembrane domains, four hydrophilic cytoplasmic domains and five hydrophilic extracellular membrane domains.Small differences in the number of amino acid residues in the domains of TMEM26 were found.In both human and mouse retina, TMEM26 gene was only specifically expressed in the outer plexiform layer (OPL)and inner plexiform layer (IPL). TMEM26 was weakly associated with POAG in a published data. Conclusions:TMEM26 is a multi-pass transmembrane protein, mainly expressed in IPL and OPL of the retina. TMEM26 gene is weakly related to POAG.

Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19

The coronavirus disease 2019 (COVID-19) outbreak is an ongoing global health emergence, but the pathogenesis remains unclear. We revealed blood cell immune response profiles using 5 mRNA, TCR and BCR V(D)J transcriptome analysis with single-cell resolution. Data from 134,620 PBMCs and 83,387 TCR and 12,601 BCR clones was obtained, and 56 blood cell subtypes and 23 new cell marker genes were identified from 16 participants. The number of specific subtypes of immune cells changed significantly when compared patients with controls. Activation of the interferon-MAPK pathway is the major defense mechanism, but MAPK transcription signaling is inhibited in cured patients. TCR and BCR V(D)J recombination is highly diverse in generating different antibodies against SARS-CoV-2. Therefore, the interferon-MAPK pathway and TCR-and BCR-produced antibodies play important roles in the COVID-19 immune response. Immune deficiency or immune over-response may result in the condition of patients with COVID-19 becoming critical or severe.

Association between LIPC gene polymorphisms and choroidal neovascularization / 中华实验眼科杂志

Objective:To investigate the association between choroidal neovascularization (CNV) and the LIPC gene single nucleotide polymorphism (SNP) in a Chinese Han population from Shantou. Methods:A case-control study was designed.Two hundred and twenty-one patients with CNV who visited Shantou International Eye Center from January 2010 to December 2016 were enrolled and served as the CNV group, and 430 healthy volunteers matched in age and gender were enrolled and served as the normal control group.Each of 5 ml fasting peripheral blood of the subjects was extracted, and peripheral blood DNA was extracted after anticoagulation.PCR amplification was conducted on SNP loci of LIPC gene including rs10468017, rs920915 and rs2070895.After purification, genotyping was performed on the above SNP loci using the single base extension (SNaPshot) method.Hardy-weinberg equilibrium (HWE) test was used to determine the genotype frequency of the three SNPs of LIPC gene.The gene frequency and genotype frequency of the 3 loci between the CNV group and normal control group were compared.This study followed the Declaration of Helsinki.Written informed consent was obtained from each subject prior to entering the study cohort.The study protocol was approved by the Ethics Committee of Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong (No.11-004). Results:The genotype frequency distribution of rs10468017, rs920915 and rs2070895 of the three SNPs of LIPC gene reached genetic balance in the total samples ( P>0.05). The genotype frequencies of rs10468017 TT genotype, rs920915 CC genotype and rs2070895 AA genotype in CNV group were 3.62%, 5.43% and 12.22%, respectively, while those of normal control group were 2.56%, 5.58% and 14.19%, respectively, with no statistically significant difference (all at P>0.05). The minimum allele (T) frequency of rs10468017 was 18.1% and 17.2%, the minimum allele (C) frequency of rs920915 was 21.7% and 23.1%, and the minimum allele (A) frequency of rs2070895 was 33.7% and 38.7% in the CNV group and the normal control group, respectively (all at P>0.05). The odd ratio ( OR) values (95%confidence interval [ CI]) of rs10468017, rs920915 and rs2070895 in the CNV group and the normal control group were 1.06 (0.79-1.44), 0.92 (0.70-1.21) and 0.80 (0.63-1.02), respectively. Conclusions:The results from the present study do not indicate the association of LIPC SNPs (rsl0468017, rs920915 and rs2070895) with CNV in the Shantou Han population.

Association of ABCA1 rare nonsynonymous variants with primary open angle glaucoma / 中华实验眼科杂志

Objective To explore the rare nonsynonymous variants of ABCA1 gene in primary open angle glaucoma (POAG).Methods A prospective cohort study was carried out.Three hundred and ninety-eight POAG patients and 198 healthy controls matched in age and gender were recruited from March 2017 to March 2018 in Eye and Ear Nose Throat (ENT) Hospital of Fudan University.The periphery blood of 2-5 ml from all the subjects was collected for extraction of DNA,and rare variant analysis of the ABCA1 gene was conducted by whole exome sequencing (WES) data of these subjects.The study protocol was approved by Ethic Committee of Eye and Ear Nose Throat Hospital of Fudan University and Sichuan Provincial People's Hospital (No.2016-32-1,and written informed consent was obtained from each subject prior to entering the study cohort.Results A total of 21 rare nonsynonymous variants (minor allele frequency MAF＜0.O1) were detected in the coding regions of ABCA1 gene in 27 subjects of the 398 POAG,with the detection rate of 6.8％.Among them,c.4310C＞A (p.Thr1437Asn),c.3772G＞T(p.Asp1258Tyr),c.775A＞G (p.Lys259Glu) and c.1507_1508insGAGGT (p.Glu503GlyfsX7) were four novel variants.In the 198 healthy controls,five rare nonsynonymous variants were detected in the ABCA1 gene from five subjects respectively,with the detection rate of 2.5％,the detection rate of nonsynonymous in POAG group was higher than that in healthy control group,showing a significant difference (x2=4.72,P =0.03,OR =2.81).Conclusions Rare nonsynonymous variants in ABCA1 is associated with the pathogenesis of POAG.These variants can enrich the variation spectrum of ABCA1.

Analysis of MYOC gene variants among sporadic patients with primary open-angle glaucoma / 中华医学遗传学杂志

OBJECTIVE@#To screen for MYOC gene variants among sporadic patients with primary open angle glaucoma (POAG).@*METHODS@#For 398 patients with POAG, Sanger sequencing was applied to detect potential variants of the MYOC gene.@*RESULTS@#Eight patients (2.0%) were found to harbor variations of the MYOC gene. These included five types of variants, among which c.667C>T (p.Pro223Ser) and c.1138G>T (p.Asp380Tyr) were novel. c.382C>T (p.Arg128Trp), c.1109C>T(p.Pro370Leu) and c.1130C>A (p.Thr377Lys) were previously associated with POAG. Alignment of amino acid sequences of MYOC proteins of various species revealed that the two novel variants have occurred at highly conserved positions. c.1138G>T was predicted to be possible pathogenic by Bioinformatic analysis.@*CONCLUSION@#Two novel variants of the MYOC gene were detected among sporadic POAG patients, which enriched its variant spectrum.

Association of PLEKHA7, COL11A1 and PCMTD1-ST18 gene polymorphisms with primary angle closure glaucoma in ethnic Han Chinese from Sichuan / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To assess the association of single nucleotide polymorphisms (SNPs) of PLEKHA7, COL11A1 and PCMTD1-ST18 genes and primary angle closure glaucoma (PACG) among ethnic Han Chinese from Sichuan Province.</p><p><b>METHODS</b>In this study, 362 subjects with PACG and 1056 age- and sex-matched healthy controls were recruited. Genotypes of 3 reported SNPs, including PLEKHA7 rs11024102, COL11A1 rs3753841 and PCMTD1-ST18 rs1015213 were determined with a SNaPshot method.</p><p><b>RESULTS</b>The P values for the genotype frequencies of rs11024102, rs3753841 and rs1015213 between the patient and control groups were 0.62 (OR=1.09, 95%CI: 0.91-1.30), 0.42 (OR=1.04, 95%CI: 0.87-1.41) and 0.34 (OR=1.35, 95%CI: 0.73-2.49), respectively. And the P values for the allele frequency distributions of PLEKHA7 rs11024102, COL11A1 rs3753841 and PCMTD1-ST18 rs1015213 between the two groups were 0.347, 0.698 and 0.344, respectively.</p><p><b>CONCLUSION</b>No significant association of PLEKHA7 rs11024102, COL11A1 rs3753841 and PCMTD1-ST18 rs1015213 with PACG was found among ethnic Han Chinese from Sichuan.</p>

The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers.

BACKGROUND: The safflower, Carthamus tinctorius L., is a worldwide oil crop, and its flowers, which have a high flavonoid content, are an important medicinal resource against cardiovascular disease in traditional medicine. Because the safflower has a large and complex genome, the development of its genomic resources has been delayed. Second-generation Illumina sequencing is now an efficient route for generating an enormous volume of sequences that can represent a large number of genes and their expression levels. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the genes and pathways that might control flavonoids and other secondary metabolites in the safflower, we used Illumina sequencing to perform a de novo assembly of the safflower tubular flower tissue transcriptome. We obtained a total of 4.69 Gb in clean nucleotides comprising 52,119,104 clean sequencing reads, 195,320 contigs, and 120,778 unigenes. Based on similarity searches with known proteins, we annotated 70,342 of the unigenes (about 58% of the identified unigenes) with cut-off E-values of 10(-5). In total, 21,943 of the safflower unigenes were found to have COG classifications, and BLAST2GO assigned 26,332 of the unigenes to 1,754 GO term annotations. In addition, we assigned 30,203 of the unigenes to 121 KEGG pathways. When we focused on genes identified as contributing to flavonoid biosynthesis and the biosynthesis of unsaturated fatty acids, which are important pathways that control flower and seed quality, respectively, we found that these genes were fairly well conserved in the safflower genome compared to those of other plants. CONCLUSIONS/SIGNIFICANCE: Our study provides abundant genomic data for Carthamus tinctorius L. and offers comprehensive sequence resources for studying the safflower. We believe that these transcriptome datasets will serve as an important public information platform to accelerate studies of the safflower genome, and may help us define the mechanisms of flower tissue-specific and secondary metabolism in this non-model plant.