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Characterization of TNNC1 as a Novel Tumor Suppressor of Lung Adenocarcinoma
Kim, Suyeon,Kim, Jaewon,Jung, Yeonjoo,Jun, Yukyung,Jung, Yeonhwa,Lee, Hee-Young,Keum, Juhee,Park, Byung Jo,Lee, Jinseon,Kim, Jhingook,Lee, Sanghyuk,Kim, Jaesang Korean Society for Molecular and Cellular Biology 2020 Molecules and cells Vol.43 No.7
In this study, we describe a novel function of TNNC1 (Troponin C1, Slow Skeletal and Cardiac Type), a component of actin-bound troponin, as a tumor suppressor of lung adenocarcinoma (LUAD). First, the expression of TNNC1 was strongly down-regulated in cancer tissues compared to matched normal lung tissues, and down-regulation of TNNC1 was shown to be strongly correlated with increased mortality among LUAD patients. Interestingly, TNNC1 expression was enhanced by suppression of KRAS, and ectopic expression of TNNC1 in turn inhibited KRAS<SUP>G12D</SUP>-mediated anchorage independent growth of NIH3T3 cells. Consistently, activation of KRAS pathway in LUAD patients was shown to be strongly correlated with down-regulation of TNNC1. In addition, ectopic expression of TNNC1 inhibited colony formation of multiple LUAD cell lines and induced DNA damage, cell cycle arrest and ultimately apoptosis. We further examined potential correlations between expression levels of TNNC1 and various clinical parameters and found that low-level expression is significantly associated with invasiveness of the tumor. Indeed, RNA interference-mediated down-regulation of TNNC1 led to significant enhancement of invasiveness in vitro. Collectively, our data indicate that TNNC1 has a novel function as a tumor suppressor and is targeted for down-regulation by KRAS pathway during the carcinogenesis of LUAD.
금강 주요지점에서의 환경 인자와 남조류 세포수의 배타적 인과성분석
김연화 ( Yeonhwa Kim ),이은형 ( Eunhyung Lee ),김경현 ( Kyunghyun Kim ),김상현 ( Sanghyun Kim ) 한국환경과학회 2016 한국환경과학회지 Vol.25 No.7
Algal blooming in 4 major rivers introduces substantial impacts to water front activity. Concentrations of algae are increasing at major points along the Geum River. Ecosystem food webs can be affected by algal blooming because blue-green algae release toxic materials. Even though there have been many studies on blue-green algae, its causality to environmental factors has not been completely determined yet. This study analyzed the exclusive correlation between various hydrometeorological, water quality, and hydrologic variables and the cell number of cyanobacteria to understand causality of blue-green algae in the Geum River. A prewhitening process was introduced to remove the autocorrelation structure and periodicity, which is useful to evaluate the effective relationship between two time series.
Proteogenomic Characterization of Human Early-Onset Gastric Cancer
Mun, Dong-Gi,Bhin, Jinhyuk,Kim, Sangok,Kim, Hyunwoo,Jung, Jae Hun,Jung, Yeonjoo,Jang, Ye Eun,Park, Jong Moon,Kim, Hokeun,Jung, Yeonhwa,Lee, Hangyeore,Bae, Jingi,Back, Seunghoon,Kim, Su-Jin,Kim, Jieun Cell Press 2019 Cancer Cell Vol. No.
<P><B>Summary</B></P> <P>We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and <I>N</I>-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Mutation-phosphorylation correlation suggests possible signaling interplays in EOGCs </LI> <LI> mRNA-protein correlation suggests genes with high association with patient survival </LI> <LI> Integrated analysis of mRNA and protein data identified four subtypes </LI> <LI> Phosphorylation data provide cellular signaling pathways underlying the subtypes </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>
Kim, Jinwoo,Kang, Yongsung,Choi, Okhee,Jeong, Yeonhwa,Jeong, Jae-Eun,Lim, Jae Yun,Kim, Minkyun,Moon, Jae Sun,Suga, Hiroaki,Hwang, Ingyu Blackwell Scientific Publications 2007 Molecular microbiology Vol.64 No.1
<P>Summary</P><P>The bacterium <I>Burkholderia glumae</I> causes rice grain rot by producing toxoflavin, whose expression is regulated by quorum sensing (QS). We report a major deviation from the current paradigm for the regulation of bacterial polar flagellum genes. The <I>N</I>-octanoyl homoserine lactone (C8-HSL)-deficient mutant of <I>B. glumae</I> is aflagellate and has lost the ability to swim and swarm at 37°C. Mutagenesis of the bacterium with the mini-Tn<I>5rescue</I> identified an IclR-type transcriptional regulator, called QsmR, which is important for flagellum formation. TofR, which is a cognate C8-HSL receptor, activated <I>qsmR</I> expression by binding directly to the <I>qsmR</I> promoter region. From the flagellum gene cluster, we identified <I>flhDC</I> homologues that are directly activated by QsmR. FlhDC in turn activates the expression of genes involved in flagellum biosynthesis, motor functions and chemotaxis in <I>B. glumae</I>. Non-motile <I>qsmR</I>, <I>fliA</I> and <I>flhDC</I> mutants produced toxoflavin, but lost pathogenicity for rice. The unexpected discovery of FlhDC in a polarly flagellate bacterium suggests that exceptions to the typical regulatory mechanisms of flagellum genes exist in Gram-negative bacteria. The finding that functional flagella play critical roles in the pathogenicity of <I>B. glumae</I> suggests that either QS or flagellum formation constitutes a good target for the control of rice grain rot.</P>
Maintenance of stem cell characteristics after long-term cryopreservation
Yeonhwa Song,Sujin Yun,Jiyoung Kim,Hyun Mi Kang,Seah Park,Hye Jin Yang,A young Yoon,Sun Young Baek,Si Hyung Yoo,Sun Hee Kim,Haekwon Kim 한국발생생물학회 2011 한국발생생물학회 학술발표대회 Vol.30 No.-
The human eyelid adipose-derived stem cells (HEACs) are known as a candidate source for stem cell-based therapy. HEACs possess the ability to proliferate in vitro and multipotency to differentiate into adipogenic, osteogenic and chondrogenic cells. To be used later than the time of collection, a long-term storage is needed. In this study, we investigated stem cell characteristics after cryopreservation of HEACs for 6 months and 1 year in liquid nitrogen. Frozen-thawed stem cells have shown that cumulative cell and doubling numbers were similar to those of fresh HEACs. After thawing, HEACs expressed stem cell-related genes of SCF, NANOG, OCT4, and TERT, ectoderm-related genes of NCAM and FGF5, mesoderm/endoderm-related genes of CK18 and VIM. They also consistently expressed transcripts of the immune-related genes of HLA-ABC and β2M. To induce mesodermal differentiation, cell were cultivated in adipogenic, osteogenic or chondrogenic medium for 2~3 weeks. After each differentiation culture, HEACs expressed adipocyte-, osteocyte- and chondrocytespecific genes. They were also stained with Oil red O, von Kossa, or alcian blue, revealing adipogenic, osteogenic, or chondrogenic character, respectively. The results suggest that long-term storage up to 1 year do not affect their biological properties, HEACs may be suitable for clinical application on cell-based therapies.
Jo, Yeonhwa,Choi, Hoseong,Bae, Miah,Kim, Sang-Min,Kim, Sun-Lim,Lee, Bong Choon,Cho, Won Kyong,Kim, Kook-Hyung The Korean Society of Plant Pathology 2017 Plant Pathology Journal Vol.33 No.5
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
JEONG, YEONHWA,CHEONG, HOON,CHOI, OKHEE,KIM, JUNG KYU,KANG, YONGSUNG,KIM, JINWOO,LEE, SEUNGDON,KOH, SERRY,MOON, JAE SUN,HWANG, INGYU Blackwell Publishing Ltd 2011 Molecular plant pathology Vol.12 No.4
<P><B>SUMMARY</B></P><P>The host specificity of <I>Ralstonia solanacearum</I>, the causal organism of bacterial wilt on many solanaceous crops, is poorly understood. To identify a gene conferring host specificity of the bacterium, SL341 (virulent to hot pepper but avirulent to potato) and SL2029 (virulent to potato but avirulent to hot pepper) were chosen as representative strains. We identified a gene, <I>rsa1</I>, from SL2029 that confers avirulence to SL341 in hot pepper. The <I>rsa1</I> gene encoding an 11.8‐kDa protein possessed the perfect consensus hrp<SUB>II</SUB> box motif upstream of the gene. Although the expression of <I>rsa1</I> was activated by HrpB, a transcriptional activator for <I>hrp</I> gene expression, Rsa1 protein was secreted in an Hrp type III secretion‐independent manner. Rsa1 exhibited weak homology with an aspartic protease, cathepsin D, and possessed protease activity. Two specific aspartic protease inhibitors, pepstatin A and diazoacetyl‐<SMALL>d</SMALL>,<SMALL>l</SMALL>‐norleucine methyl ester, inhibited the protease activity of Rsa1. Substitution of two aspartic acid residues with alanine at positions 54 and 59 abolished protease activity. The SL2029 <I>rsa1</I> mutant was much less virulent than the wild‐type strain, but did not induce disease symptoms in hot pepper. These data indicate that Rsa1 is an extracellular aspartic protease and plays an important role for the virulence of SL2029 in potato.</P>