A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

Chen, Han,Li, Chunyan,Peng, Xinxin,Zhou, Zhicheng,Weinstein, John N.,Caesar-Johnson, Samantha J.,Demchok, John A.,Felau, Ina,Kasapi, Melpomeni,Ferguson, Martin L.,Hutter, Carolyn M.,Sofia, Heidi J.,Ta Elsevier 2018 Cell Vol.173 No.2

<P><B>Summary</B></P> <P>The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Systematic analysis of enhancer expression across ∼9,000 samples of 33 cancer types </LI> <LI> Global enhancer activation positively correlates with aneuploidy but not mutations </LI> <LI> A computational method that infers causal enhancer-target-gene relationships </LI> <LI> Enhancers as key regulators of therapeutic targets, including PD-L1 </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

A Queuing Model of the N-design Multi-skill Call Center with Impatient Customers

Chunyan Li,Dequan Yue 보안공학연구지원센터 2015 International Journal of u- and e- Service, Scienc Vol.8 No.4

This paper studies a queuing model of the N-design multi-skill call center. In this model, there are two types of customers and two server groups who have different skills. Group 1 consists of specialized servers who can only serve one type of customers, Group 2 consists of flexible servers who can serve both two types of customers. The customers waiting for the service in the queue may leave the system due to impatience. By dividing the system’s state space into several sets of sates, we obtain the equilibrium equations and the steady-state probabilities of the system. We also obtain the computational formula of the service level and the computational procedure of the staffing problem.

Mechanistic target of rapamycin and an extracellular signalingregulated kinases 1 and 2 signaling participate in the process of acetate regulating lipid metabolism and hormone-sensitive lipase expression

Li Yujuan,Fu Chunyan,Liu Lei,Liu Yongxu,Li Fuchang 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.9

Objective: Acetate plays an important role in host lipid metabolism. However, the network of acetate-regulated lipid metabolism remains unclear. Previous studies show that mitogen-activated protein kinases (MAPKs) and mechanistic target of rapamycin (mTOR) play a crucial role in lipid metabolism. We hypothesize that acetate could affect MAPKs and/or mTOR signaling and then regulate lipid metabolism. The present study investigated whether any cross talk occurs among MAPKs, mTOR and acetate in regulating lipid metabolism.Methods: The ceramide C6 (an extracellular signaling-regulated kinases 1 and 2 [ERK1/2] activator) and MHY1485 (a mTOR activator) were used to treat rabbit adipose-derived stem cells (ADSCs) with or without acetate, respectively.Results: It indicated that acetate (9 mM) treatment for 48 h decreased the lipid deposition in rabbit ADSCs. Acetate treatment decreased significantly phosphorylated protein levels of ERK1/2 and mTOR but significantly increased mRNA level of hormone-sensitive lipase (HSL). Acetate treatment did not significantly alter the phosphorylated protein level of p38 MAPK and c-Jun aminoterminal kinase (JNK). Activation of ERK1/2 and mTOR by respective addition in media with ceramide C6 and MHY1485 significantly attenuated decreased lipid deposition and increased HSL expression caused by acetate.Conclusion: Our results suggest that ERK1/2 and mTOR signaling pathways are associated with acetate regulated HSL gene expression and lipid deposition.

The Effect of Web2.0 on Learning Management System

Li Chunyan,Cui Haitao,Li Guolin 보안공학연구지원센터 2014 International Journal of Multimedia and Ubiquitous Vol.9 No.10

Detecting Human Head and Shoulders Trajectory in a Smart Classroom

Li Chunyan,Zhu Yulian,Xue Zhimei 보안공학연구지원센터 2014 International Journal of Smart Home Vol.8 No.1

Engineering a Highly Thermostable and Stress Tolerant Superoxide Dismutase by N-terminal Modification and Metal Incorporation

Mingchang Li,Shuyi Guo,Xiaomin Li,Quan Wang,Lin Zhu,Chunyan Yin,Wei Wang 한국생물공학회 2017 Biotechnology and Bioprocess Engineering Vol.22 No.6

Thermophilic or hyperthermophilic SODs (superoxide dismutase) usually offer substantial biotechnological advantages over mesophilic SODs. Previously a 244-amino acid N-terminal domain (NTD) from a heatresistant SOD of Geobacillus thermodenitrificans NG80-2 was discovered and demonstrated to be able to confer thermostability to homologous mesophilic SODs, which revealed a new type of heat resistance mechanism. To further improve the heat resistance and stress tolerance of thermophilic cambialistic superoxide dismutase (Fe/Mn- SODAp) from Aeropyrum pernix K1 through metal incorporation and fusion with the newly found peptide NTD for broadening its industrial application, the wildtype SODAp and NTD-fused ntdSODAp were expressed in E. coli BL21 and incorporated with metal cofactors by two ways. Recombinant fusion SOD obtained by in vitro reconstitution (Mn-rec ntdSODAp) exhibited improved optimum temperature at 70oC and dramatically enhanced thermostability especially at 110oC with enhanced pH stability from 4 to 10 and higher tolerance for denaturants and organic media than Mn-rec SODAp. To the best of our knowledge, Mn-rec ntdSODAp could be the most heat resistant SOD. In addition, metal incorporation of SODAp and ntdSODAp via in vivo modification have been developed and proved to be more practical for industrial use. These results indicate that fusion with NTD along with metal incorporation can generate superimposed effect and be applied to enhance the stability of cambialistic thermophilic SODs, thus providing a universal and convenient bioengineering method for generating extremely stable SODs.

Cast Iron Smelting and Fining: An Iron Smelting Site of the Eastern Han Dynasty in Xuxiebian, Sichuan Province, China

( Yuniu Li ),( Chunyan Ma ),( Yasuyuki Murakami ),( Zhiqing Zhou ),( Yingdong Yang ),( Yingfu Li ) 성균관대학교 동아시아학술원 2019 Sungkyun Journal of East Asian Studies Vol.19 No.1

In this article, we introduce the excavation of an iron smelting site at Xuxiebian 許鞋匾, Pujiang 蒲江 County, Sichuan 四川 Province in the PRC. Two excavations were carried out in 2007 and 2011, and a total of four bowl-shaped furnaces, five pits, two trenches, and one posthole were excavated. The site is dated from the mid-late Eastern Han dynasty to the Jin dynasty (ca. AD 150-420) according to the local pottery assemblage. It is possible that the sole functions of the Xuxiebian site were the production of pig iron ingots and the conversion of pig iron to wrought iron. The iron ingots were likely transported to areas with stronger administrative control by the central government near the ancient city of Chengdu or even to the Central Plains, where they were then cast into different objects.

Dietary Niacin Supplementation Suppressed Hepatic Lipid Accumulation in Rabbits

Liu, Lei,Li, Chunyan,Fu, Chunyan,Li, Fuchang Asian Australasian Association of Animal Productio 2016 Animal Bioscience Vol.29 No.12

An experiment was conducted to investigate the effect of niacin supplementation on hepatic lipid metabolism in rabbits. Rex Rabbits (90 d, n = 32) were allocated to two equal treatment groups: Fed basal diet (control) or fed basal diet with additional 200 mg/kg niacin supplementation (niacin). The results show that niacin significantly increased the levels of plasma adiponectin, hepatic apoprotein B and hepatic leptin receptors mRNA (p<0.05), but significantly decreased the hepatic fatty acid synthase activity and adiponectin receptor 2, insulin receptor and acetyl-CoA carboxylase mRNA levels (p<0.05). Plasma insulin had a decreasing tendency in the niacin treatment group compared with control (p = 0.067). Plasma very low density lipoproteins, leptin levels and the hepatic adiponectin receptor 1 and carnitine palmitoyl transferase 1 genes expression were not significantly altered with niacin addition to the diet (p>0.05). However, niacin treatment significantly inhibited the hepatocytes lipid accumulation compared with the control group (p<0.05). In conclusion, niacin treatment can decrease hepatic fatty acids synthesis, but does not alter fatty acids oxidation and triacylglycerol export. And this whole process attenuates lipid accumulation in liver. Besides, the hormones of insulin, leptin and adiponectin are associated with the regulation of niacin in hepatic lipid metabolism in rabbits.

Long Noncoding RNA Expression Profiling During the Neuronal Differentiation of Glial Precursor Cells from Rat Dorsal Root Ganglia

Yunfei Dai,Wei Ma,Tong Zhang,Jinwei Yang,Chenghao Zang,Kuangpin Liu,Xianbin Wang,Jiawei Wang,Zhen Wu,Xingkui Zhang,Chunyan Li,Junjun Li,Xiangpeng Wang,Jianhui Guo,Liyan Li 한국생물공학회 2020 Biotechnology and Bioprocess Engineering Vol.25 No.3

Long noncoding RNAs (lncRNAs) play important roles in the process of cell fate determination. However, their function and expression profiles have not yet been systematically investigated during the transdifferentiation of glial precursor cells derived from dorsal root ganglia (DRG) in the peripheral nervous system. Our results demonstrated significant differences in gene architecture and expression among the three transcript types (lncRNA, mRNA, and TUCP). Distinct differences in transcript length, exon number, and ORF length were identified between lncRNAs and mRNAs after comparative analysis of their structure and sequence conservation. We found that the upregulated lncRNAs outnumbered the downregulated lncRNAs in glial precursor cells cultured with proBDNF antiserum compared with the levels in glial precursor cells cultured without proBDNF antiserum. By a series of GO and KEGG analyses, we found that the effects of some lncRNAs on their target genes in cis were related to nerve growth factor-induced cell cycle, cell phenotype change, and neuronal differentiation. The qRT-PCR verification results of lncRNAs ENSRNOT00000091991, ENSRNOT00000087717, and LNC_000429 were mostly consistent with the sequencing results. The candidate lncRNAs may be associated with the neuronal transdifferentiation of glial precursor cells. Our study provides the first evidence for a remarkably diverse pattern of lncRNA expression during neuronal differentiation of glial precursor cells from rat DRG, and also provides a resource for lncRNA studies in the field of cell differentiation.

Synthesis and Photovoltaic Properties of Alternating Conjugated Polymers Derived from Thiophene-Benzothiadiazole Block and Fluorene/Indenofluorene Units

Li, Jianfeng,Tong, Junfeng,Zhang, Peng,Yang, Chunyan,Chen, Dejia,Zhu, Yuancheng,Xia, Yangjun,Fan, Duowang Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.2

A new donor-accepter-donor-accepter-donor (D-A-D-A-D) type 2,1,3-benzothiadiazole-thiophene-based acceptor unit 2,5-di(4-(5-bromo-4-octylthiophen-2-yl)-2,1,3-benzothiadiazol-7-yl)thiophene ($DTBTTBr_2$) was synthesized. Copolymerized with fluorene and indeno[1,2-b]fluorene electron-rich moieties, two alternating narrow band gap (NBG) copolymers PF-DTBTT and PIF-DTBTT were prepared. And two copolymers exhibit broad and strong absorption in the range of 300-700 nm with optical band gap of about 1.75 eV. The highest occupied molecular orbital (HOMO) energy levels vary between -5.43 and -5.52 eV and the lowest unoccupied molecular orbital (LUMO) energy levels range from -3.64 to -3.77 eV. Potential applications of the copolymers as electron donor material and $PC_{71}BM$ ([6,6]-phenyl-$C_{71}$ butyric acid methyl ester) as electron acceptors were investigated for photovoltaic solar cells (PSCs). Photovoltaic performances based on the blend of PF-DTBTT/$PC_{71}BM$ (w:w; 1:2) and PIF-DTBTT/$PC_{71}BM$ (w:w; 1:2) with devices configuration as ITO/PEDOT: PSS/blend/Ca/Al, show an incident photon-to-current conversion efficiency (IPCE) of 2.34% and 2.56% with the open circuit voltage ($V_{oc}$) of 0.87 V and 0.90 V, short circuit current density ($J_{sc}$) of $6.02mA/cm^2$ and $6.12mA/cm^2$ under an AM1.5 simulator ($100mA/cm^2$). The photocurrent responses exhibit the onset wavelength extending up to 720 nm. These results indicate that the resulted narrow band gap copolymers are viable electron donor materials for polymer solar cells.