49 research outputs found
Dual-functional surface of MXene anodes boosts long-term cyclability of lithium-metal batteries
No full textIntroducing seed elements with high lithiophilicity onto the anode is a promising strategy to mitigate dendrite growth in lithium metal batteries (LMBs). Two primary seed elements have been explored: (i) lithiophilic metals (e.g. Ag, Au, and Sn), and (ii) fluorine (-F) functionalities. Despite significant advancements, hybrid materials combining the two elements have not been realized. Moreover, it remains unclear which element enhances LMB performance more. In this study, we engineered, for the first time, a high-density dual-functional surface incorporating lithiophilic metals and -F functionalities. Through rapid Joule heating, we integrated high-density Au nanoparticles (Au NPs) onto the F-terminated Ti3C2Tx MXene anode surface. Our findings reveal distinct roles for each element: Au NPs reduce the size of deposited lithium, while -F functionalities promote uniform lithium distribution with a LiF-rich solid electrolyte interphase (SEI) layer. Notably, the synergistic effect of Au NPs and -F functionalities extended the lifespan of Au@F-rich Ti3C2Tx to 600 cycles compared to the initial 100 cycles of Ti3C2Tx and 240 cycles of Au@Ti3C2Tx. These results underscore the pivotal role of -F functionalities in prolonging and enhancing the performance of LMBs. This research highlights the importance of tailored surface functionalities and offers a promising pathway for the design of advanced LMB components.
Abstract 3378: Whole exome sequencing identifies recurrent alterations of genes in malignant phyllodes tumors in nine Korean individuals
No full textAbstract
Phyllodes tumors of the breast are rare fibroepithelial neoplasms with variable clinical behavior accounting for about 1% of all breast neoplasms. Phyllodes tumors are classified into benign, borderline, and malignant grades on the basis of histological features. Among those categories, Malignant phyllodes tumor has a higher propensity for local recurrence and distant metastasis, however the malignant potential of phyllodes tumors is difficult to assess on initial pathologic examination. In previous studies, an important role of mediator complex subunit 12 (MED12) in phyllodes tumors has been frequently revealed. However, except that, genetic abnormalities that drive tumor initiation and progress in malignant phyllodes tumor remain still unclear. Here, by performing whole exome sequencing of 9 malignant phyllodes tumors with matching normal cases, we frequently observed mutations in MED12 (3/9, 33.34%). Additionally, non-silent mutations in p53(TP53) and epidermal growth factor receptor (EGFR) were recurrently identified. Whole-gene amplifications of EGFR were also found in six cases (6/9, 66.67%). We suggest that EGFR has an underlying role in malignant phyllodes tumors. This study identifies potential therapeutic targets in malignant phyllodes tumors, including EGFR.
Citation Format: Jihui Yun, Hyeong-Gon Moon, Tae-Kyung Yoo, Eunshin Lee, Jeesoo Chae, Sam Hur, Jiwoo Lee, Jong-Il Kim, Dong-Young Noh. Whole exome sequencing identifies recurrent alterations of genes in malignant phyllodes tumors in nine Korean individuals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3378. doi:10.1158/1538-7445.AM2017-3378</jats:p
Abstract 4371: Genomic characterization of oropharyngeal squamous cell carcinoma in Korean population
No full textAbstract
Objective: Oropharyngeal squamous cell carcinoma (OPSCC) is a subtype of head and neck squamous cell carcinoma (HNSCC). Environmental risk factors such as tobacco, alcohol, and especially, human papillomavirus (HPV) are known to be associated with HNSCC. Also, large-scale sequencing studies identified several HNSCC-associated genes such as TP53, EGFR and PIK3CA. However, still the initiation and progression of OPSCC and mutational profiles of OPSCC in Korean population are unclear.
Methods: Frozen non-tumor mucosa, tumor tissues and blood were collected from nine OPSCC patients; 6 HPV positive and 3 negative. Adjacent non-tumor tissues were obtained about 1 cm apart from the tumor tissue and were histologically confirmed as non-neoplastic. We then performed whole exome sequencing with Agilent SureSelect Human All Exon Kit v4+UTR, yielding average on-target coverage of 100X.
Results: First, we compared somatic alterations of adjacent non-tumor and tumor tissue to understand the genomic status of non-tumor mucosa. Comparison of genome-wide copy number alterations (CNA) between non-tumor and OPSCCs showed that majority of somatic CNA (SCNA) was occurred after tumor progression. Also, non-tumor mucosa rarely harbored genomic changes, showing average nonsilent mutations rate of 0.07 per Mb. In contrast, OPSCC showed 1.0 mutations per Mb with few shared mutations with non-tumor. These results indicate occurrence of new distinct subclones after tumor progression. Second, somatic mutations and CNA analysis of 9 OPSCC identified two distinct groups divided by the HPV status of tumor. HPV(+) tumors showed lower mutation burden than HPV(-) tumors (0.63 and 1.73 mutations per Mb, respectively). And TP53 and CDKN2A mutations were detected exclusively in HPV(-) group, accounting for 66.6% of HPV(-) tumors. Furthermore, HPV(-) tumors showed greater degree of chromosomal alterations compared to HPV(+) tumors.
Conclusions: Although there are many studies to understand the relationships between premalignant and malignant tissue, there is a lack of understanding for genetic changes further from non-neoplastic mucosa. Our data show that genetic profile of normal crypt mucosa rarely changes and tumor develops in distinct subclones. This would provide a glimpse into the fundamental cellular changes of non-tumor cells of tonsillar crypts and oral cavity. Also, we provide a mutational landscape in HNSCC of Korean population. Although our OPSCC showed recurrent mutations and copy number alterations of genes related to RTK/PI(3)K- and differentiation-signaling pathways, similar as western, mutation burden in tumors was relatively lower, and somatic mutations on well-known HNSCC-associated genes such as PIK3CA, FAT1 and HRAS weren’t detected. Further investigation and molecular experiments are required to understand the mechanism of carcinogenesis and to discover early driver mutations of HNSCC.
Citation Format: Jeesoo Chae, Weon Seo Park, Dongwan Hong, Jong-Il Kim, Yuh-Seog Jung. Genomic characterization of oropharyngeal squamous cell carcinoma in Korean population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4371. doi:10.1158/1538-7445.AM2017-4371</jats:p
Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice
No full text© 2021, The Author(s).Secretory proteins are an essential component of interorgan communication networks that regulate animal physiology. Current approaches for identifying secretory proteins from specific cell and tissue types are largely limited to in vitro or ex vivo models which often fail to recapitulate in vivo biology. As such, there is mounting interest in developing in vivo analytical tools that can provide accurate information on the origin, identity, and spatiotemporal dynamics of secretory proteins. Here, we describe iSLET (in situ Secretory protein Labeling via ER-anchored TurboID) which selectively labels proteins that transit through the classical secretory pathway via catalytic actions of Sec61b-TurboID, a proximity labeling enzyme anchored in the ER lumen. To validate iSLET in a whole-body system, we express iSLET in the mouse liver and demonstrate efficient labeling of liver secretory proteins which could be tracked and identified within circulating blood plasma. Furthermore, proteomic analysis of the labeled liver secretome enriched from liver iSLET mouse plasma is highly consistent with previous reports of liver secretory protein profiles. Taken together, iSLET is a versatile and powerful tool for studying spatiotemporal dynamics of secretory proteins, a valuable class of biomarkers and therapeutic targets.11Nsciescopu
:중심체 단백질인 Rootletin과 Cep215의 구조적 기능적 연구
No full text학위논문 (박사) -- 서울대학교 대학원 : 자연과학대학 생명과학부, 2021. 2. 최희정.The centrosome is composed of two centrioles connected at right angles and the pericentriolar materials (PCM). The two centrioles are separated by disengagement in the G1 phase and connected to the linker fiber. Each centriole replicates the new daughter centriole and undergoes maturation of the centrosome. When the centrosome maturation progresses, nucleation of microtubules is generated at the PCM, and the mitotic spindle poles are formed.
In Chapter 1, I explain the structural study of rootletin, a centrosome linker protein. This content is based on a paper (Ko, D., Kim, J., Rhee, K., and Choi, H.J., Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin., Journal of Molecular Biology) published as a co-first author. Rootletin is a component of cilia's rootlet and is a coiled-coil protein that forms the linker fiber of two mother centrioles. According to the results of Prof. Kunsoo Rhee's laboratory, the coiled-coil domain 3 (CCD3) of Rootletin is essential for centrosomal localization and linking ability. A collaborative study for the structure and function of CCD3 was conducted. I analyzed the structural characteristics of CCD3 through the crystal structures of CCD3 1108-1200 and CCD3 1108-1317. In addition, the dynamic and oligomeric characteristics of the CCD3-6 fragment, which are essential for the function of rootletin, were investigated through biochemical analysis, such as crosslinking experiments and CD-analysis. Finally, the mutational study confirmed that the hydrophobic residues of CCD3 are important for the rootletin polymer formation, which is vital for the centriole linkage.
In Chapter 2, I demonstrate the interaction of Cep215 and Pericentrin (PCNT), which assemble the substances around the PCM during centrosome maturation. Centrosomin motif (CM2) of Cep215 is localized to the centrosome by interacting with PCNT, and recruits other PCM proteins. Centrosomin (Cnn), Cep215 homologous protein in Drosophila, contains phospho-regulated multimerization domain (PReM) and CM2, and these two domains assemble themselves through interaction with each other. PReM is not preserved in human Cep215, and instead, PCNT plays a crucial role in PCM assembly. I determined the minimal binding fragment of PCNT required for CM2 interaction, and proposed an interaction model of the two proteins using the crystal structure of Cnn as a guide. This interaction model of CM2-PCNT was verified through SAXS (small angle X-ray scattering) and ITC (isothermal titration calorimetry) experiments. Together with the result of cellular experiment, it was confirmed that the hydrophobic residues of CM2, L1860 and L1867, are important for hetero-tetramer formation.나는 중심체 단백질인 rootletin과 Cep215에 대한 구조적, 그리고 생화학적 연구를 수행하였다. 중심체는 직각으로 연결된 두 개의 중십립과 그 주변에 있는 중심체 주변 물질로 구성되어 있다. 두 중심립은 G1 기에 유리가 일어나고 연결 섬유로 이어진다. 그리고 각각의 중심립은 새로운 딸 중심립을 복제하며 중심체 주변 물질의 성숙 과정을 거친다. 중심체 성숙이 진행되면 미세소관의 결정핵이 중심체 주변 물질에 생성되며 방추사가 형성된다.
1장에서는 중심체 연결 단백질인 rootletin에 대한 구조 연구에 대해 설명하겠다. 이 내용은 본인이 공동 1저자로 참여하여 2020년 출판된 논문 (Ko, D., Kim, J., Rhee, K., and Choi, H.J. Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin. Journal of Molecular Biology) 을 기반으로 한다. Rootletin은 섬모의 뿌리구조의 구성요소이며 두 모중심립의 연결 섬유를 이루고 있는 또꼬인나선형 (coiled-coil) 단백질이다. Rootletin의 또꼬인나선 3번째 조각 (CCD3)이 중심체로 위치하는 것과 중심립 연결 능력에 중요하다는 이건수 교수님 실험실의 선행 연구 결과에 기반하여 CCD3에 대한 구조와 기능연구를 공동으로 진행하였다. 나는 CCD3 1108-1200와 CCD3 1108-1317의 X-선 결정 구조 규명을 통해 CCD3의 구조적 특징에 대해 분석하였다. 또한, rootletin의 기능에 중요한 CCD3-6 조각에 대해 교차결합 실험과 원이색성 분광광도계를 이용한 생화학 분석을 통하여 중합체를 형성하는 역동적인 특성을 밝혀냈다. 그리고, 중합체 형성에 중요한 CCD3의 소수성 아미노산 잔기들을 돌연변이 시킴으로써 중합체 형성이 억제되는 것을 확인하였고, 세포 내에서 이러한 돌연변이체는 연결 섬유의 역할을 제대로 수행하지 못함을 관찰하였다.
2장에서는 중심체 성숙과정에서 중심체 주변 물질들의 조립에 관여하는 Cep215와 Pericentrin (PCNT)의 상호작용에 대해 설명하였다. Cep215의 Centrosomin motif (CM2)는 PCNT와의 상호작용을 통하여 중심체 주변 물질에 도달하며 다른 단백질들을 모집한다. Drosophila의 centrosomin (Cnn)이라는 Cep215 상동 단백질은 PReM과 CM2를 가지고 있으며 이 두 부위가 서로 상호작용을 통해 스스로 조립된다. 사람의 Cep215에는 PReM이 보존 되어있지 않고 PCNT가 중심체 주변물질의 조립에 핵심적인 역할을 한다. 나는 CM2와 PCNT의 상호작용에 있어서 Cep215의 최소 조각 helix를 알아냈고, 이미 알려진 Cnn의 X-선 결정 구조를 기반으로 Cep215와 PCNT 두 단백질의 상호작용 모델을 제시하였다. 소각 X-선 산란 실험과 등온 적정형 열량계를 이용한 실험을 통해 이러한 두 단백질상호작용 모델을 검증하였고, 이형 4분자체 형성에서 Cep215의 소수성 잔기, L1860과 L1867이 중요하게 작용함을 확인하였다.Abstract 1
Contents 3
List of figures 6
Background 9
Centrosome 9
Centrosome Structure and functions 9
Centrosome cycle 10
CHAPTER 1. Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin 15
Introduction 16
Material and methods 24
Protein expression and purification 24
Crystallization, data collection, and structure determination 25
CD spectroscopy 26
SEC-MALS 26
Crosslinking experiment 27
Trypsin digestion assay 27
Negative-stain electron microscopy (EM) 27
Fluorescence-detection size-exclusion chromatography (FSEC) 28
Results 29
Structural analysis of rootletin CCD3 29
Biophysical analysis of rootletin fragment CCD3-6 45
Characterization of the rootletin CCD3 oligomer 48
Discussion 55
CHAPTER 2. Biophysical Analysis of the Interaction Between Cep215 and Pericentrin. 61
Introduction 62
Material and methods 71
Protein expression and purification 71
SEC-MALS 72
Small angle X-ray scattering 72
Isothermal titration calorimetry 73
Results 74
PCNT 2388-2420 interacts with CM2Cep215. 74
Sequence analysis of the CM2 and CM2Cep215 binding helix of PCNT 77
Each CM2Cep215 and CBH fragment constitutes a homodimer 80
CM2Cep215 and CBH form a hetero-tetramer similar to Cnn self-assembly module 83
Discussion 92
References 95
Appendix figure 103
국문초록 105Docto
Findings of a 1303 Korean whole-exome sequencing study
No full textEthnically specific data on genetic variation are crucial for understanding human biology and for clinical interpretation of variant pathogenicity. We analyzed data obtained by deep sequencing 1303 Korean whole exomes; the data were generated by three independent whole exome sequencing projects (named the KOEX study). The primary focus of this study was to comprehensively analyze the variant statistics, investigate secondary findings that may have clinical actionability, and identify loci that should be cautiously interpreted for pathogenicity. A total of 495 729 unique variants were identified at exonic regions, including 169 380 nonsynonymous variants and 4356 frameshift insertion/deletions. Among these, 76 607 were novel coding variants. On average, each individual had 7136 nonsynonymous single-nucleotide variants and 74 frameshift insertion/deletions. We classified 13 pathogenic and 13 likely pathogenic variants in 56 genes that may have clinical actionability according to the guidelines of the American College of Medical Genetics and Genomics, and the Association for Molecular Pathology. The carrier frequency of these 26 variants was 2.46% (95% confidence interval 1.73-3.46). To identify loci that require cautious interpretation in clinical sequencing, we identified 18 genes that are prone to sequencing errors, and 671 genes that are highly polymorphic and carry excess nonsynonymous variants. The catalog of identified variants, its annotation and frequency information are publicly available (http://koex.snu.ac.kr). These findings should be useful resources for investigating ethnically specific characteristics in human health and disease.Y
Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis
No full textTargeting proximity-labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice (MAX-Tg) expressing a mitochondrial matrix-targeted ascorbate peroxidase. Comparative analysis of matrix proteomes from the muscle tissues showed differential enrichment of mitochondrial proteins. We found that reticulon 4-interacting protein 1 (RTN4IP1), also known as optic atrophy-10, is enriched in the mitochondrial matrix of muscle tissues and is an NADPH oxidoreductase. Interactome analysis and in vitro enzymatic assays revealed an essential role for RTN4IP1 in coenzyme Q (CoQ) biosynthesis by regulating the O-methylation activity of COQ3. Rtn4ip1-knockout myoblasts had markedly decreased CoQ9 levels and impaired cellular respiration. Furthermore, muscle-specific knockdown of d Rtn4ip1 in flies resulted in impaired muscle function, which was reversed by dietary supplementation with soluble CoQ. Collectively, these results demonstrate that RTN4IP1 is a mitochondrial NAD(P)H oxidoreductase essential for supporting mitochondrial respiration activity in the muscle tissue. [Figure not available: see fulltext.] © 2023, The Author(s).11Nsciescopu
The interplay of cancer-associated fibroblasts and apoptotic cancer cells suppresses lung cancer cell growth through WISP-1-integrin ανβ3-STAT1 signaling pathway
No full textAbstract Background Cell death within the tumor microenvironment (TME) plays a crucial role in controlling cancer by influencing the balance of tumor-specific immunity. Cancer-associated fibroblasts (CAFs) significantly contribute to tumor progression through paracrine mechanisms. We found that reprogramming of CAFs by apoptotic cancer cells suppresses tumor volume and lung metastasis. Here, we investigated the mechanisms by which the interaction between apoptotic lung cancer cells and CAFs hinders tumor growth. Methods Experimental methods including CCK assay, colony formation assay, immunoblotting, co-immunoprecipitation, qRT-PCR analysis, qRT-PCR array, apoptosis assay, ELISA, and immunofluorescent staining were used in this study. Additionally, CAFs were isolated from lung tumors of Kras-mutant (KrasLA1) mice and human lung adenocarcinoma samples using magnetic-activated cell sorting. Murine lung cancer cells (344SQ cells) along with various human cancer cell lines (A549, HCT116, and LoVo) were cultured. In animal study, conditioned medium (CM) derived from CAFs (undiluted or 50% diluted) with or without neutralizing anti-WISP-1 antibody was administered into syngeneic mice to study anti-tumoral effects. To confirm the paracrine role of WISP-1, recombinant WISP-1 (rWISP-1) was administered via intratumoral injection. Results We demonstrate that treatment with CM from lung CAFs exposed to apoptotic cancer cells suppresses proliferation and promotes apoptosis in lung cancer cells through STAT1 signaling. Pharmacologic inhibition of Notch1 activation or siRNA-mediated Notch1 silencing in CAFs reversed the antiproliferative and proapoptotic effects. Similarly, knockdown of Wnt-induced signaling protein 1 (WISP-1) in CAFs or neutralizing the CM with anti-WISP-1 antibodies reversed the antiproliferative and proapoptotic effects. WISP-1 signaled through integrin ανβ3-STAT1 signaling pathway to inhibit cancer cell growth and promote apoptosis. The in vivo introduction of CM derived from apoptotic 344SQ-exposed CAFs (ApoSQ-CAF CM) potently decelerated tumor growth. This effect was observed alongside the downregulation of proliferative and anti-apoptotic markers, while simultaneously boosting the activation of phosphorylated STAT1 and pro-apoptotic markers in CD326+ tumor cells within syngeneic immunocompetent mice. rWISP-1 effectively replicates the in vivo effects of ApoSQ-CAF CM. Conclusions These findings suggest that CM from apoptotic cancer cell-exposed CAFs may offer a promising therapeutic approach by lung cancer suppression
Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants
No full textObjective: Genome wide association studies (GWAS) and meta-analyses for Crohn's disease (CD) have not fully explained the heritability of CD, suggesting that additional loci are yet to be found and that the known loci may contain high effect rare risk variants that have thus far gone undetected by GWAS. While the cost of deep sequencing remains too high to analyse many samples, targeted sequencing of pooled DNA samples allows the efficient and cost effective capture of all variations in a target region.
Design: We performed pooled sequencing in 500 Korean CD cases and 1000 controls to evaluate the coding exon and 5' and 3' untranslated regions of 131 CD associated genes. The identified genetic variants were validated using genotyping in an independent set of 500 CD cases and 1000 controls.
Results: Pooled sequencing identified 30 common/low single nucleotide variants (SNVs) in 12 genes and 3 rare SNVs in 3 genes. Our results confirmed a significant association of CD with the following previously reported risk loci: rs3810936 in TNFSF15 (OR=1.83, p<2.2×10(-16)), rs76418789 in IL23R (OR=0.47, p=1.14×10(-8)) and rs2241880 in ATG16L1 (OR=1.30, p=5.28×10(-6)). In addition, novel loci were identified in TNFSF8 (rs3181374, OR=1.53, p=1.03×10(-14)), BTNL2 (rs28362680, OR=1.47, p=9.67×10(-11)), HLA-DQA2 (rs3208181, OR=1.36, p=4.66×10(-6)), STAT3 (rs1053004, OR=1.29, p=2.07×10(-5)), NFKBIA (rs2273650, OR=0.80, p=3.93×10(-4)), NKX2-3 (rs888208, OR=0.82, p=6.37×10(-4)) and DNAH12 (rs4462937, OR=1.13, p=3.17×10(-2)). A novel rare SNV, rs200735402 in CARD9, was shown to have a protective effect (OR=0.09, p=5.28×10(-5)).
Conclusions: Our deep resequencing of 131 CD associated genes confirmed 3 reported risk loci and identified 8 novel risk loci for CD in Koreans, providing new insights into the genetic architecture of CD.restrictio
