3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing

The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular function and physiological processes. High-throughput chromosome conformation capture (Hi-C), Nanopore sequencing, and RNA-sequencing (RNA-seq) assays were performed on the liver of normal and NAFLD mice. A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops by Hi-C, and whole genome sequencing identifying structural variations (SVs) and copy number variations (CNVs) by Nanopore sequencing. We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements, between normal and NAFLD mice, and revealed gene dysregulation frequently accompanied by these variations. Candidate target genes were identified in NAFLD, impacted by genetic rearrangements and spatial organization disruption. Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations, revealed the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD. The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.

Clinical characteristics and management of asthma and COPD overlap syndrome in Nanchong / 公共卫生与预防医学

Objective To investigate the clinical characteristics and management of asthma and COPD overlap syndrome in Nanchong area. Methods The data of respiratory medicine patients in Nanchong area from October 2017 to November 2019 were collected. Patients who met the criteria were classified as asthma and COPD (ACOS) group (104 cases), asthma (BA) group (120 cases), and COPD group (116 cases). The clinical data of the three groups were compared and their general data and clinical characteristics were analyzed. Results The BA group had the highest proportion of patients with smoking history (92.50%), and had the least amount of smoking (P<0.05). The lung function indexes of ACOS group and COPD group were significantly lower than those of BA group (P<0.05). After inhaling bronchodilators, the variation rate of forced expiratory volume in the first second of the ACOS group was significantly higher than that of the COPD group (P<0.05). Patients in the COPD group had the lowest levels of immunoglobulin E (sIgE) and FeNO, while patients in the ACOS group had the highest level of EOS (P<0.05). Conclusion Compared with BA patients, ACOS patients were older and had a lower proportion of smoking but higher smoking quantity, and their lung function was significantly worse. Compared with COPD patients, ACOS patients had a higher proportion of smoking but lower smoking quantity, with better lung diffusion function, and high airway inflammation. The peripheral blood eosinophils in ACOS patients were specifically increased, which can be used as a reference for clinical diagnosis.

Circadian rhythm variation of the clock genes Per1 and cell cycle related genes in different stages of carcinogenesis of buccal mucosa in animal model / 中华口腔医学杂志

<p><b>OBJECTIVE</b>To investigate the expression and circadian rhythm variation of biological clock gene Per1 and cell cycle genes p53, CyclinD1, cyclin-dependent kinases (CDK1), CyclinB1 in different stages of carcinogenesis in buccal mucosa and its relationship with the development of buccal mucosa carcinoma.</p><p><b>METHODS</b>Ninety golden hamsters were housed under 12 hours light-12 hours dark cycles, and the model of buccal squamous cell carcinoma was established by using the dimethylbenzanthracene (DMBA) to smear the golden hamster buccal mucosa. Before the DMBA was used and after DMBA was used 6 weeks and 14 weeks respectively, the golden hamsters were sacrificed at 6 different time points (5 rats per time point) within 24 hour, including 4, 8, 12, 16, 20 and 24 hour after lights onset (HALO), and the normal buccal mucosa, precancerous lesions and cancer tissue were obtained, respectively. HE stained sections were prepared to observe the canceration of each tissue. Real time RT-PCR was used to detect the mRNA expression of Per1, p53, CyclinD1, CDK1 and CyclinB1, and a cosine analysis method was applied to determine the circadian rhythm variation of Per1, p53, CyclinD1, CDK1 and CyclinB1 mRNA expression, which were characterized by median, amplitude and acrophase.</p><p><b>RESULTS</b>The expression of Per1, p53, CDK1 and CyclinD1 mRNA in 6 different time points within 24 hours in the tissues of three different stages of carcinogenesis had circadian rhythm, respectively. However, the CyclinB1 mRNA was expressed with circadian rhythm just in normal and cancer tissue (P < 0.05), while in precancerous lesions the circadian rhythm was in disorder (P > 0.05). As the development of carcinoma, the median of Per1 and p53 mRNA expression were significantly decreased (P < 0.05), yet the median of CDK1, CyclinB1 and CyclinD1 mRNA expression were significantly increased (P < 0.05). The amplitude of Per1, p53 and CyclinD1 mRNA expression was significantly decreased as the development of carcinoma (P < 0.05), however the amplitude of CDK1 mRNA expression was significantly increased (P < 0.05). In addition, there was no significant difference in the amplitude of CyclinB1 mRNA expression. The time that the peak expression value of Per1 and CDK1 mRNA appeared (Acrophase) in precancerous lesions was remarkably earlier than that in normal tissues, but the acrophase of p53 and CyclinD1 mRNA expression was remarkably delayed. Moreover, the acrophase of CDK1 and CyclinB1 mRNA expression in cancer tissues was obviously earlier than that in normal tissues, yet there was no significant variation in acrophase of Per1, p53, CyclinD1 mRNA expression between normal tissues and cancer tissues.</p><p><b>CONCLUSIONS</b>The circadian rhythm of clock gene Per1 and cell cycle genes p53, CyclinD1, CDK1, CyclinB1 expression remarkably varied with the occurrence and development of carcinoma. Further research into the interaction between circadian and cell cycle of two cycle activity and relationship with the carcinogenesis may providenew ideas and methods of individual treatment and the mechanism of carcinogenesis.</p>

Circadian variation of clock gene Per2 and cancer-related clock-controlled genes in buccal mucosa carcinoma of golden hamster at different cancer stages / 华西口腔医学杂志

<p><b>OBJECTIVE</b>This study investigates the circadian variation rules of the clock gene Per2 and clock-controlled genes of vascular endothelial growth factor (VEGF), Ki67, c-Myc, and P53 in different stages of carcinogenesis in buccal mucosa carcinoma and their roles in the development of buccal mucosa carcinoma.</p><p><b>METHODS</b>Ninety Syrian golden hamsters were housed under. 12 h light/12 h dark cycles. Dimethylbenzanthracene (DMBA) was used to establish the carcinoma model by smearing the golden hamster buccal mucosa. Before DMBA painting and after 6 and 14 weeks, the hamsters were sacrificed at six time points within a period of 24 h (i.e., 4, 8, 12, 16, 20, and 24 h after light onset), and the normal buccal mucosa, precancerous lesions, and cancer tissues were simultaneously obtained. Hematoxylin and eosin stained sections were prepared to observe the canceration of each tissue. Real time polymerase chain reaction was used to detect the mRNA expression of Per2, VEGF, Ki67, c-Myc, and P53. Cosine analysis was employed to determine the circadian-rhythm variations of Per2, VEGF, Ki67, c-Myc, and P53 mRNA expression in terms of median, amplitude, and acrophase.</p><p><b>RESULTS</b>The expression of Per2, VEGF, P53, and c-Myc mRNA in three different stages appeared with circadian rhythms (P<0.05), whereas the Ki67 mRNA was expressed with circadian rhythm only in normal and precancerous lesion stages (P<0.05). The midline-estimating statistic of rhythms (MESORs) of Per2 and P53 mRNA were significantly down-regulated with the development of cancer (P<0.05), whereas the MESORs of VEGF, c-Myc, and Ki67 mRNA were up-regulated (P<0.05). The amplitude of P53 mRNA significantly decreased with the development of cancer (P<0.05). Moreover, compared with the normal group, the amplitudes of Per2, VEGF, Ki67, and c-Myc mRNA significantly increased in precancerous lesions and cancer tissue (P<0.05). In precancerous stage, the acrophases of Per2, VEGF, and c-Myc mRNA were earlier than that in the normal group, whereas that of Ki67 and P53 mRNA were delayed.</p><p><b>CONCLUSION</b>The circadian-rhythm characteristics of the clock gene Per2 and clock-controlled gene expression of VEGF, Ki67, c-Myc, and P53 mRNA have changed with the occurrence and development of carcinoma.</p>

Ribosomal DNA ITS sequence analysis of Aquilaria sinensis from different geographical origin in China / 中华中医药杂志

Objective: To study rDNA ITS (internal transcribed spacers) sequences variation from di erent population of Aquilaria sinensis in main habitat of China. Methods: The rDNA ITS regions of various A. sinensis were ampli ed by PCR method and sequenced, and they were analyzed by means of the software of CLUSTAL and MEGA. Results: The sequences of rDNA ITS region of A. sinensis were reported for the rst time, and the sequences of ITS region were 680bp (ITS1 246bp, 5.8S 163bp, ITS2 271bp). There were 6 variable sites among populations and the genetic distance were 0.0% to 1.1%,which indicated the intraspecific genetic variation was low of A. sinensis. Conclusion: The variation of rDNA ITS sequences can be used to authenticate A.sinensis from di erent geographical regions and their adulterants.

Construction and analysis of Polygonum multiflorum cDNA library / 中草药

Objective To construct a cDNA library of three-year old Polygonum multiflorum leaf tissues so as to further research the gene regulation of secondary metabolite biosynthesis of medicinal plants. Methods Total RNA from leaf tissues of P.multiflorum was extracted and mRNA was purified,which were synthesized to double strand cDNA through reverse transcription.After the cDNA termini was blunted,the 5' end of EcoR Ⅰ adapters phosphorylated was conjoined,and then digested by Xho Ⅰ,cDNA fragments were fractionated by Sepharose CL-2B spin column.The fragments longer than 400 bp were linked to Uni-ZAP XR vector.The primary cDNA library was established after the recombinants had been packaged.Uni-ZAP XR Vector might fleetly release pBluescript SK-phasmids at the presence of ExAssist helper phage of coinfection and inverted E.coli SOLR.Finally,PCR and double enzymes digestion were used to analyze the range of inserts,respectively. Results The titer of cDNA primary library was 1.07?106pfu/mL and the length of exogenous insert was at about 0.5-2.0 kb with 5.4?105 recombinants,the recombinants of amplified library were 4.25?1011 and the rate of recombination was 98.5%. Conclusion The results indicate that the cDNA library of P.multiflorum leaf tissues has enough volume for screening the desired genes and sets up a basis for studying on gene regulation of secondary metabolite biosynthesis of medicinal plants besides.