1.Gene expression profile in osteoblastic differentiation of bone marrow stromal cells stimulated by simvastatin Gene chip analysis
Yaqiang MENG ; Liu ZHANG ; Faming TIAN ; Dacheng HAN ; Jie ZHENG ; Jun CAI
Chinese Journal of Tissue Engineering Research 2010;14(11):2081-2085
BACKGROUND:Simvastatin enhanced the expression of bone morphogenetic protein-2(BMP-2),which plays an anabolic role in bone metabolism and osteoblastic lineage differentiation.However,little is known about the molecular mechanism of simvastatin on regulation of bone marrow stromal cells differentiation.OBJECTIVE:To investigated the effect of simvastatin on osteoblastic differentiation of bone marrow stromal cells based on genetics level.METHODS:Bone marrow stromal cells derived from femur and tibia were cultured in different mediums with simvastatin or Vehicle for 7 days Following extraction and purification,mRNA was reverse-transcripted into cDNA.Fluorescence labelina was employed and the samples were then hybridized with oligonucleotide chip to screen the different genes,which were utillzed to analyze osteogenesis-related factors.Alkaline phosphatase and Von Kossa staining were performed at days 14 and 21,respectively.RESULTS AND CONCLUSIONS:At day 14,alkaline phosphatase-positive cells were more in the experimental group than control group.Von Kossa staining demonstrated that simvastatin could promote BMSCs osteoblastic differentiation and mineralization.Comparative analysis showed that 103 genes out of 22 575 rat genes had differential expression (≥2 fold or≤ 0.5 fold),and some genes were related to cell proliferation and ostoeblastic differentiation,including C/EBP δ,Cited,Ascl2,Ptpnl6,Wisp2,Tieg,etc.Simvastatin could induce osteoblastic differentiation of bone marrow stromal cells,involving in many osteogenetic-related genes.
2.Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome.
Zhenglin DU ; Liang MA ; Hongzhu QU ; Wei CHEN ; Bing ZHANG ; Xi LU ; Weibo ZHAI ; Xin SHENG ; Yongqiao SUN ; Wenjie LI ; Meng LEI ; Qiuhui QI ; Na YUAN ; Shuo SHI ; Jingyao ZENG ; Jinyue WANG ; Yadong YANG ; Qi LIU ; Yaqiang HONG ; Lili DONG ; Zhewen ZHANG ; Dong ZOU ; Yanqing WANG ; Shuhui SONG ; Fan LIU ; Xiangdong FANG ; Hua CHEN ; Xin LIU ; Jingfa XIAO ; Changqing ZENG
Genomics, Proteomics & Bioinformatics 2019;17(3):229-247
To unravel the genetic mechanisms of disease and physiological traits, it requires comprehensive sequencing analysis of large sample size in Chinese populations. Here, we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative (CASPMI) project launched by the Chinese Academy of Sciences, including the de novo assembly of a northern Han reference genome (NH1.0) and whole genome analyses of 597 healthy people coming from most areas in China. Given the two existing reference genomes for Han Chinese (YH and HX1) were both from the south, we constructed NH1.0, a new reference genome from a northern individual, by combining the sequencing strategies of PacBio, 10× Genomics, and Bionano mapping. Using this integrated approach, we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1. In order to generate a genomic variation map of Chinese populations, we performed the whole-genome sequencing of 597 participants and identified 24.85 million (M) single nucleotide variants (SNVs), 3.85 M small indels, and 106,382 structural variations. In the association analysis with collected phenotypes, we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males. Moreover, significant genetic diversity in MTHFR, TCN2, FADS1, and FADS2, which associate with circulating folate, vitamin B12, or lipid metabolism, was observed between northerners and southerners. Especially, for the homocysteine-increasing allele of rs1801133 (MTHFR 677T), we hypothesize that there exists a "comfort" zone for a high frequency of 677T between latitudes of 35-45 degree North. Taken together, our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine.