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>

강원도에서 토양과 기후 데이터베이스를 이용한 청보리의 재배 적지 구분

김경대 ( K D Kim ),성경일 ( K I Sung ),주진호 ( J H Joo ),김병완 ( B W Kim ),팽경륜 ( J L Peng ),이배훈 ( B H Lee ),잘일가세미네자드 ( J G Nejad ),조무환 ( M H Jo ),임영철 ( Y C Lim ) 강원대학교 농업생명과학연구원(구 농업과학연구소) 2013 강원 농업생명환경연구 Vol.25 No.3

본 연구는 토양과 기후 데이터베이스를 이용하여 조사료 재배적지 기준 설정 연구의 일환으로 청보리를 대상으로 강원도에서의 재배가능지역을 추정하였다. 토양요인항목으로는 토양 물리성인 토성, 배수, 경사, 유효토심 및 암반노출, 토양화학성인 토양산도, 토양염류도 및 유기물함량을 선정하고 기준값 및 가중치를 설정하였다. 기후요인항목으로는 1월 일최저온도 평균, 3-5월의 평균온도, 9-12월의 5℃ 이상 일수, 10-5월의 강수일수와 강수량 그리고 3월에서 5월까지의 일조시간을 선정하고 기준값 및 가중치를 설정하였다. 토양요인의 관점에서 강원도에서 청보리의 재배가능지 및 재배최적지는 영동지방의 경우 고성, 속초, 양양, 강릉, 동해 및 삼척이며 주로 경사가 완만한 해안지역에 분포하고 있었다. 영서지방은 철원, 양구, 춘천, 원주, 횡성, 평창 및 정선에 주로 분포하고 있었다. 기후요인의 관점에서 강원도는 대부분이 50점이상이었으며, 재배가능지는 고성, 속초, 양양, 강릉, 동해 및 삼척의 해안지역과 철원, 양구, 춘천, 원주, 횡성, 평창 및 정선 일부 지역이 포함되었다. 이상의 결과로부터 강원도에서 토양과 기후요인을 고려한 청보리의 재배가능지 및 재배최적지는 영동지방의 고성, 속초, 양양, 강릉, 동해 및 삼척의 해안지역을 중심으로 가능하였고, 영서지방의 철원, 양구, 춘천, 원주, 횡성, 평창 및 정선 일부지역에서 재배가능지로 나타나고 있다. 향후 청보리의 재배적지 연구를 위해서는 일조시간에 대한 전자정보의 확보가 이루어진다면, 더욱 정밀한 청보리 재배 적지의 예상이 가능할 것으로 판단된다. As a part of establishing suitability classification for forage production, use of the national soil and climate database was attempted for Whole crop barley (Hordeum vulgare var. hexastichon (L.) Asch.) in Gangwon Province. The soil data base were from Heugtoram of the National Academy of Agricultural Science, and the climate data base were from the National Center for Agro-Meteorology, respectively. Soil physical properties including soil texture, drainage, slope available depth and surface rock contents, and soil chemical properties including soil acidity and salinity, organic matter content were selected as soil factors. The criteria and weighting factors of these elements were scored. Climate factors including average daily minimum temperature in January, average temperature from March to May, the number of days of which average temperature was higher than 5℃ from September to December, the number of days of precipitation and its amount from October to May of the following year, and sunshine hours from March to May were selected, and criteria and weighting factors were scored. The electronic maps were developed with these scores using the national data base of soil and climate. Based on soil scores, the area of Goseong, Sogcho, Yangyang, Gangreung, Donghea and Samcheog in east coastal region with gentle slope were classified as the possible and/or the proper area for Whole crop barley cultivation in Gangwon Province. The lands with gentle or moderate slope of Cheolwon, Yanggu, Chuncheon, Wonju, Hweongseong, Pyungchang and Jeongsun in west side slope of Taebaeg mountains were classified as the possible and/or proper area as well. Based on climate score, the east coastal area of Goseong, Sogcho, Yangyang, Gangreung and Samcheog could be classified as the possible or proper area. Most area located on west side of the Taebaeg mountains were classified as not suitable for Whole crop barley production. In scattered area in Cheolwon, Yanggu, Chuncheon, Wonju, Hweongseong, Pyungchang and Jeongsun, where the scores exceeded 50, the Whole crop barley cultivation should be carefully managed for good production. As a results, based on soil with climate the area of Goseong, Sogcho, Yangyang, Gangreung, Donghea and Samcheog in east coastal region with gentle slope and some area of Cheolwon, Yanggu, Chuncheon, Wonju, Hweongseong, Pyungchang and Jeongsun were classified as the possible and/or the proper area for Whole crop barley cultivation in Gangwon Province. For better application of electronic maps of whole crop barley, acurate study will be possible if a data comfirmed on th shine hours is achieved.

46. Detecting the Reason for the Negative Effects of Accumulated Precipitation on the Yield of Whole Crop Maize and Sorghum-sudangrass Hybrid Based on Field Experimental Data in Korea

J. L. Peng,M. J. Kim,M. H. Jo,B. H. Lee,J. Y. Kim,S. C. Kim,C. Befekadu,J. G. Nejad,B. W. Kim,K. I. Sung 한국초지조사료학회 2017 한국초지조사료학회 학술대회논문집 Vol.2017 No.09

Maximum concrete stress developed in unconfined flexural RC members

J.C.M. Ho,H.J. Pam,J. Peng,Y.L. Wong 사단법인 한국계산역학회 2011 Computers and Concrete, An International Journal Vol.8 No.2

In flexural strength design of unconfined reinforced concrete (RC) members, the concrete compressive stress-strain curve is scaled down from the uni-axial stress-strain curve such that the maximum concrete stress adopted in design is less than the uni-axial strength to account for the strain gradient effect. It has been found that the use of this smaller maximum concrete stress will underestimate the flexural strength of unconfined RC members although the safety factors for materials are taken as unity. Herein, in order to investigate the effect of strain gradient on the maximum concrete stress that can be developed in unconfined flexural RC members, several pairs of plain concrete (PC) and RC inverted T-shaped specimens were fabricated and tested under concentric and eccentric loads. From the test results, the maximum concrete stress developed in the eccentric specimens under strain gradient is determined by the modified concrete stress-strain curve obtained from the counterpart concentric specimens based on axial load and moment equilibriums. Based on that, a pair of equivalent rectangular concrete stress block parameters for the purpose of flexural strength design of unconfined RC members is determined.

Accuracy evaluation of the crop-weather yield predictive models of Italian ryegrass and forage rye using cross-validation

Peng, J. L.,Kim, M. J.,Jo, M. H.,Min, D. H.,Kim, K. D.,Lee, B. H.,Kim, B. W.,Sung, K. I. Korean Society of Crop Science 2017 Journal of crop science and biotechnology Vol.20 No.4

Complex molecules in the W51 North region

Rong, J.,Qin, S.-L.,Zapata, L. A.,Wu, Y.,Liu, T.,Zhang, C.,Peng, Y.,Zhang, L.,Liu, Y. Oxford University Press 2016 MONTHLY NOTICES- ROYAL ASTRONOMICAL SOCIETY Vol.455 No.2

New Evidence of Alleles (V199I and G52S) at the PRKAG3 (RN) Locus Affecting Pork Meat Quality

Chen, J.F.,Dai, L.H.,Peng, J.,Li, J.L.,Zheng, R.,Zuo, B.,Li, F.E.,Liu, M.,Yue, K.,Lei, M.G.,Xiong, Y.Z.,Deng, C.Y.,Jiang, S.W. Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.4

The porcine PRKAG3 (RN) gene encodes the regulatory gamma subunit of adenosine monophosphate-activated protein kinase (AMPK), which is a good candidate gene affecting meat quality. In this study, the effects of two missense mutations A595G (Ile199Val) and G154A (Gly52Ser) in porcine PRKAG3 gene on meat quality traits were studied in M. Longissimus dorsi (LD), M. Semispinalis capitis (SC) and M. Biceps femoris (BF) from different populations of 326 pigs. The PRKAG3 alleles 199I, 199IV, 52S and 52G were identified with PCR-RFLPs and all genotypes - 199I/199I, 199I/199V, 199V/199V, 52S/52S, 52S/52G and 52G/52G - were found. The frequency of V allele was larger than that of I allele in all populations. I allele frequency was zero in Chinese Meishan pigs (population D) especially. G allele frequency was larger than that of S allele in all populations except Large White (population A). Both variations at the PRKAG3 locus significantly affected these meat quality traits. The pork meat quality has not previously been established in Meishan or crosses thereof. The results suggested that generally pH of LD, SC and BF was higher in Meishan pigs than that in other populations. Moreover, Meishan pigs showed higher water-holding capacity and intramuscular fat (IMF), lower water content and water loss percentage compared to other populations in terms of the two variations. The results present here supply new evidence that alleles V199I and G52S at the PRKAG3 locus affect pork meat quality and provide useful information on pork production.

Observation of the topological surface state in the nonsymmorphic topological insulator KHgSb

Liang, A. J.,Jiang, J.,Wang, M. X.,Sun, Y.,Kumar, N.,Shekhar, C.,Chen, C.,Peng, H.,Wang, C. W.,Xu, X.,Yang, H. F.,Cui, S. T.,Hong, G. H.,Xia, Y.-Y.,Mo, S.-K.,Gao, Q.,Zhou, X. J.,Yang, L. X.,Felser, C. American Physical Society 2017 Physical review. B Vol.96 No.16

<P>Topological insulators represent unusual topological quantum states, typically with gapped bulk band structure but gapless surface Dirac fermions protected by time-reversal symmetry. Recently, a distinct kind of topological insulator resulting from nonsymmorphic crystalline symmetry was proposed in the KHgX (X = As, Sb, Bi) compounds. Unlike regular topological crystalline insulators, the nonsymmorphic glide-reflection symmetry in KHgX guarantees the appearance of an exotic surface fermion with hourglass shape dispersion (where two pairs of branches switch their partners) residing on its (010) side surface, contrasting to the usual two-dimensional Dirac fermion form. Here, by using high-resolution angle-resolved photoemission spectroscopy, we systematically investigate the electronic structures of KHgSb on both (001) and (010) surfaces and reveal the unique in-gap surface states on the (010) surface with delicate dispersion consistent with the 'hourglass Fermion' recently proposed. Our experiment strongly supports that KHgSb is a nonsymmorphic topological crystalline insulator with hourglass fermions, which serves as an important step to the discovery of unique topological quantum materials and exotic fermions protected by nonsymmorphic crystalline symmetry.</P>

Quantitative Trait Loci Mapping for Porcine Backfat Thickness

Wu, X.L.,Lee, C.,Jiang, J.,Peng, Y.L.,Yan, H.F.,Yang, S.L.,Xiao, B.N.,Liu, X.C.,Shi, Q.S. Asian Australasian Association of Animal Productio 2002 Animal Bioscience Vol.15 No.7

A partial genome scan using porcine microsatellites was carried out to detect quantitative trait loci (QTL) for backfat thickness (BFT) in a pig reference population. This population carried QTL on chromosomes 1, 13 and 18. The QTL on chromosome 1 was located between marker loci S0113 and SW1301. The QTL corresponded to very low density lipoprotein receptor gene (VLDLR) in location and in biological effects, suggesting that VLDLR might be a candidate gene. The QTL found on chromosome 13 was found between marker loci SWR1941 and SW864, but significance for the marker-trait association was inconsistent by using data with different generations. The QTL on chromosome 18 was discovered between markers S0062 and S0117, and it was in proximity of the regions where IGFBP3 and GHRHR were located. The porcine obese gene might be also a candidate gene for the QTL on chromosome 18. In order to understand genetic architecture of BFT better, fine mapping and positional comparative candidate gene analyses are necessary.

Mapping a Quantitative Trait Locus for Growth and Backfat on Porcine Chromosome 18

Wu, X.L.,Lee, C.,Jiang, J.,Peng, Y.L.,Yang, S.L.,Xiao, B.N.,Liu, X.C.,Shi, Q.S. Asian Australasian Association of Animal Productio 2001 Animal Bioscience Vol.14 No.12

A QTL was localized near S0120 on porcine chromosome 18. The QTL was significant (p<0.05) for average daily gain (ADG) of body weight and backfat thickness (BFT). The estimates of additive and dominance effects for the QTL were 0.0135 kg/day (p<0.001) and 0.0138 kg/day (p>0.5) for ADG and 1.6115 mm (p<0.001) and 0.9281 mm (p>0.05) for BFT. The location of this QTL coincided with a few growth hormone pathway genes. This study suggested that a QTL allele probably resulted from a mutation responsible for physiological lipase deficiency favoring obesity. This QTL might be important to obesity as well as growth in pigs.