• 대한예방한의학회지
• /
• 제27권2호
• /
• pp.35-48
• /
• 2023

Objective : We studied prognostic biomarkers discovery for lung cancer based on the pattern identification for the personalized Korean medicine. Methods : Using 30 tissue samples, we performed a whole exome sequencing to examine the genetic differences among three groups. Results : The exome sequencing identified among 23,490 SNPs germline variants, 12 variants showed significant frequency differences between Xu and Stasis groups (P<0.0005). As similar, 18 and 10 variants were identified in analysis for Xu vs. Gentleness group and Stasis vs. Gentleness group, respectively (P<0.001). Our exome sequencing also found 8,792 lung cancer specific variants and among the groups identified 6, 34, and 12 variants which showed significant allele frequency differences in the comparison groups; Xu vs. Stasis, Xu vs. Gentleness group, and Stasis vs. Gentleness group. As a result of PCA analysis, in germline data set, Xu group was divided from other groups. Analysis using somatic variants also showed similar result. And in gene ontology analysis using pattern identification variants, we found genes like as FUT3, MYCBPAP, and ST5 were related to tumorigenicity, and tumor metastasis in comparison between Xu and Stasis. Other significant SNPs for two were responsible for eye morphogenesis and olfactory receptor activity. Classification of somatic pattern identification variants showed close relationship in multicellular organism reproduction, anion-anion antiporter activity, and GTPase regulator activity. Conclusions : Taken together, our study identified 40 variants in 29 genes in association with germline difference of pattern identification groups and 52 variants in 47 genes in somatic cancer tissues.

• Genomics & Informatics
• /
• 제21권4호
• /
• pp.46.1-46.10
• /
• 2023

Colon adenocarcinoma (COAD) is the predominant type of colorectal cancer. Early diagnosis and treatment can significantly improve the prognosis of COAD patients. Anoctamin 7 (ANO7), an anion channel protein, has been implicated in prostate cancer and other types of cancer. In this study, we analyzed the expression of ANO7 and its correlation with clinicopathological characteristics among COAD patients using the Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and the University of Alabama at Birmingham CANcer (UALCAN) databases. The GEPIA2, Kaplan-Meier plotter, and the Survival Genie platform were employed for survival analysis. The co-expression network and potential function of ANO7 in COAD were analyzed using GeneFriends, the Database for Annotation, Visualization and Integrated Discovery (DAVID), GeneMANIA, and Pathway Studio. Our data analysis revealed a significant reduction in ANO7 expression levels within COAD tissues compared to normal tissues. Additionally, ANO7 expression was found to be associated with race and histological subtype. The COAD patients exhibiting low ANO7 expression had lower survival rates compared to those with high ANO7 expression. The genes correlated with ANO7 were significantly enriched in proteolysis and mucin type O-glycan biosynthesis pathway. Furthermore, ANO7 demonstrated a direct interaction and a positive co-expression correlation with mucin 2 (MUC2). In conclusion, our findings suggest that ANO7 might serve as a potential prognostic biomarker and potentially plays a role in proteolysis and mucin biosynthesis in the context of COAD.

• Molecules and Cells
• /
• 제43권11호
• /
• pp.909-920
• /
• 2020

Cytosolic Ca²⁺ levels ([Ca²⁺]_c) change dynamically in response to inducers, repressors, and physiological conditions, and aberrant [Ca²⁺]_c concentration regulation is associated with cancer, heart failure, and diabetes. Therefore, [Ca²⁺]_c is considered as a good indicator of physiological and pathological cellular responses, and is a crucial biomarker for drug discovery. A genetically encoded calcium indicator (GECI) was recently developed to measure [Ca²⁺]_c in single cells and animal models. GECI have some advantages over chemically synthesized indicators, although they also have some drawbacks such as poor signal-to-noise ratio (SNR), low positive signal, delayed response, artifactual responses due to protein overexpression, and expensive detection equipment. Here, we developed an indicator based on interactions between Ca²⁺-loaded calmodulin and target proteins, and generated an innovative GECI sensor using split nano-luciferase (Nluc) fragments to detect changes in [Ca²⁺]_c. Stimulation-dependent luciferase activities were optimized by combining large and small subunits of Nluc binary technology (NanoBiT, LgBiT:SmBiT) fusion proteins and regulating the receptor expression levels. We constructed the binary [Ca²⁺]_c sensors using a multicistronic expression system in a single vector linked via the internal ribosome entry site (IRES), and examined the detection efficiencies. Promoter optimization studies indicated that promoter-dependent protein expression levels were crucial to optimize SNR and sensitivity. This novel [Ca²⁺]_c assay has high SNR and sensitivity, is easy to use, suitable for high-throughput assays, and may be useful to detect [Ca²⁺]_c in single cells and animal models.

• Asian Pacific Journal of Cancer Prevention
• /
• 제17권4호
• /
• pp.1801-1810
• /
• 2016

Recent discovery showing the presence of microRNAs (miRNAs) in the circulation sparked interest in their use as potential biomarkers. Our previous studies showed the diagnostic potential of miR-451 as a serological marker for inflammatory breast cancer (IBC), miR-337-5p and miR-30b for non-inflammatory breast cancer (non-IBC). The aim of this study is to investigate the prognostic values of circulating miRNAs by comparing the amounts of 12 circulating miRNAs in the serum of IBC and non-IBC from Tunisian breast cancer patients, and by determinating whether correlated pairs of miRNAs could provide useful information in the diagnosis of IBC and non-IBC patients. TaqMan qPCR was performed to detect circulating expression of miRNAs in serum of 20 IBC, 20 non-IBC and 20 healthy controls. Nonparametric rank Spearman rho correlation coefficient was used to examine the prognostic value of miRNAs and to assess the correlation profile between miRNAs expression. Further, a large number of miRNAs were highly correlated (rho>0.5) in both patients groups and controls. Also, the correlations profiles were different between IBC, non-IBC and healthy controls indicating important changes in molecular pathways in cancer cells. Our results showed that miR-335 was significantly overexpressed in premenopausal non-IBC patients; miR-24 was significantly overexpressed in non-IBC postmenopausal patients. Patients with previous parity had higher serum of miR-342-5p levels than those without. Furthermore, patients with HER2+ IBC present lower serum levels of miR-15a than patients with HER2-disease. Together, these results underline the potential of miRNAs to function as diagnostic and prognostic markers for IBC and non-IBC, with links to the menopausal state, Her2 status and parity.

• Journal of Gastric Cancer
• /
• 제19권3호
• /
• pp.301-314
• /
• 2019

Purpose: Peritoneal carcinomatosis in gastric cancer (GC) patients results in extremely poor prognosis. Malignant ascites samples are the most appropriate biological material to use to evaluate biomarkers for peritoneal carcinomatosis. This study identified exosomal MicroRNAs (miRNAs) differently expressed between benign liver cirrhosis-associated ascites (LC-ascites) and malignant gastric cancer-associated ascites (GC-ascites), and validated their role as diagnostic biomarkers for GC-ascites. Materials and Methods: Total RNA was extracted from exosomes isolated from 165 ascites samples (73 LC-ascites and 92 GC-ascites). Initially, microarrays were used to screen the expression levels of 2,006 miRNAs in the discovery cohort (n=22). Subsequently, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analyses were performed to validate the expression levels of selected exosomal miRNAs in the training (n=70) and validation (n=73) cohorts. Furthermore, carcinoembryonic antigen (CEA) levels were determined in ascites samples. Results: The miR-574-3p, miR-181b-5p, miR-4481, and miR-181d were significantly downregulated in the GC-ascites samples compared to the LC-ascites samples, and miR-181b-5p showed the best diagnostic performance for GC-ascites (area under the curve [AUC]=0.798 and 0.846 for the training and validation cohorts, respectively). The diagnostic performance of CEA for GC-ascites was improved by the combined analysis of miR-181b-5p and CEA (AUC=0.981 and 0.946 for the training and validation cohorts, respectively). Conclusions: We identified exosomal miRNAs capable of distinguishing between non-malignant and GC-ascites, showing that the combined use of miR-181b-5p and CEA could improve diagnosis.

• 생명과학회지
• /
• 제25권8호
• /
• pp.861-869
• /
• 2015

가축화된 동물종 중 하나인 개는, 다양한 목적을 위해 인간에 의하여 선택적으로 육종되었다. 개는 많은 품종을 갖고 있고, 특정한 행동과 형태를 갖도록 인공적으로 선택되어 왔다. 개들은 그들의 삶을 안내, 구조 혹은 탐지 등의 특수 목적에 대하여 인간에게 헌신하고 있다. 특수 목적견에게 요구되는 좋은 품성, 이를테면 온순함, 강건성, 그리고 인내심과 같은 특성은 그들의 특수 임무를 수행하는 데 필요하다. 많은 연구들이 우수한 특수 목적견의 선정을 위한 유전적 마커를 찾는 데 집중되었다. 본 연구에서는, 뇌에서 발현함으로써 기능하는 것으로 알려진 총 8개의 유전자(ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2; BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 그리고 TBR1; T-Box, Brain, 1)들의 정량적인 발현 양상을 개의 네 품종의 뇌 조직에서 확인하였다. 특히, BARX2, SEPT9, SLC10A4, TBR1 그리고 WNT1 유전자들은 비글과 진돗개에서 많이 발현되는데 반하여, 삽살이와 세퍼드에서는 반대되는 발현 양상을 보여 주었다. 본 연구의 유전자들에 대한 Gene ontology (GO) 결정을 위하여 DAVID (Database for annotation, visualization and integrated discovery) 분석이 수행되었고, 이러한 유전자들이 뇌 발생과 개체의 지능에 중요한 기능을 제공할 것이라고 예상하였다. 결론적으로, 이러한 결과들을 통하여, 뇌에서의 기능과 관련된 인자들과 관련된 바이오마커를 발굴하는 데 중요한 단서를 제공해 줌과 동시에, 우수한 특수 목적견을 선발하는 데 도움을 줄 것이라 기대한다.

• 지능정보연구
• /
• 제26권3호
• /
• pp.127-147
• /
• 2020

세계는 신형 코로나바이러스 감염증(COVID-19)으로 수 많은 인명 피해와 경제적 손실을 기록하고 있는 상황이다. 우리나라 정부는 연구개발(Research & Development)을 통해 국가 감염병 위기를 극복하려는 전략을 수립하고 실행하기 위한 투자방향을 수립하였다. 기존 기술분류나 과학기술 표준분류에 따른 통계를 활용하면 특정 R&D 분야의 특이점 및 변화를 발견하기 어렵다는 한계가 존재해왔다. 최근 우리나라 감염병 연구개발 과제를 대상으로 수요자의 목적에 맞게 분류체계를 수립하고 연구비 비교 분석을 통해 투자가 요구되는 연구 분야를 제시하는 연구들이 진행되었다. 하지만 현재 국가 보건 안보와 신성장 산업육성이라는 목표를 달성하기 위한 실행방안으로 요구되고 있는 전염병 연구분야의 국가간 협력전략 수립에 필요한 정보를 체계적으로 제공하고 있지 못한 상황이다. 따라서 국가 공동 연구개발 전략 수립을 위한 분류체계와 분류모델기반의 정보서비스에 대한 연구가 요구되고 있다. 우선 감염병관련 NTIS 과제데이터를 기반으로 정성분석을 통해 7개의 분류체계를 도출하였다. 스코퍼스(Scopus) 데이터와 양방향 RNN모델을 사용하여, 분류체계 모델을 학습시켰다. 최종적인 모델의 분류 성능은 90%이상의 높은 정확도와 강건성을 확보하였다. 실증연구를 위해 주요 국가의 코로나바이러스 연구개발 과제를 대상으로 전염병 분류체계를 적용하였다. 주요 국가의 감염병(코로나바이러스) 연구개발 과제를 분류체계별로 분석한 결과, 세계적으로 유행하는 바이러스의 예상치 못한 창궐이 확산되는 속도에 비해 백신과 치료제 개발이 제대로 이뤄지지 않는 원인의 배경을 간접적으로 확인할 수 있었다. 국가별 비교분석을 통해 미국과 일본은 상대적으로 모든 영역에 골고루 연구개발 투자를 하고 있는 것으로 나타난 반면, 유럽은 상대적으로 특정 연구분야에 많은 투자를 하는 집중화 전략을 취하는 것으로 나타났다. 동시에 주요 국가의 코로나 바이러스 주요 연구조직에 대한 정보를 분류체계별로 제공하여 국제 공동R&D 전략의 기초정보를 제공하였다. 본 연구 결과를 통해 세 가지 정책적 의미를 도출할 수 있다. 첫째, 데이터기반 과학기술정책 관점에서 수요자 관심분야에 대한 국가 R&D사업의 정보를 글로벌 기준으로 문서를 분류하는 방안을 제시하였다. 둘째, 감염병관련 국가 R&D사업 영역에 대한 정보분석 서비스 기획의 기반을 마련하였다. 마지막으로 국가 감염병 R&D 분류체계 수립을 통해 분류 체계의 궁극적 목표인 산업, 기업, 정책 정보를 제공할 수 있는 기반을 마련한 것이다.