1.Mutation-Driven Immune Microenvironments in Non-Small Cell Lung Cancer: Unrevealing Patterns through Cluster Analysis
Youngtaek KIM ; Joon Yeon HWANG ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(12):683-694
Purpose:
We aimed to comprehensively analyze the immune cell and stromal components of tumor microenvironment at the single-cell level and identify tumor heterogeneity among the major top-derived oncogene mutations in non-small cell lung cancer (NSCLC) using single-cell RNA sequencing (scRNA-seq) data.
Materials and Methods:
The scRNA-seq dataset utilized in this study comprised 64369 primary tumor tissue cells from 21 NSCLC patients, focusing on mutations in EGFR, ALK, BRAF, KRAS, TP53, and the wild-type.
Results:
Tumor immune microenvironment (TIM) analysis revealed differential immune responses across NSCLC mutation subtypes. TIM analysis revealed different immune responses across the mutation subtypes. Two mutation clusters emerged: KRAS, TP53, and EGFR+TP53 mutations (MC1); and EGFR, BRAF, and ALK mutations (MC2). MC1 showed higher tertiary lymphoid structures signature scores and enriched populations of C2-T-IL7R, C3-T/NK-CXCL4, C9-T/NK-NKG, and C1-B-MS4A1 clusters than cluster 2. Conversely, MC2 cells exhibited higher expression levels of TNF, IL1B, and chemokines linked to alternative immune pathways. Remarkably, co-occurring EGFR and TP53 mutations were grouped as MC1. EGFR+TP53 mutations showed upregulation of peptide synthesis and higher synthetic processes, as well as differences in myeloid and T/NK cells compared to EGFR mutations. In T/NK cells, EGFR+TP53 mutations showed a higher expression of features related to cell activity and differentiation, whereas EGFR mutations showed the opposite.
Conclusion
Our research indicates a close association between mutation types and tumor microenvironment in NSCLC, offering insights into personalized approaches for cancer diagnosis and treatment.
2.Mutation-Driven Immune Microenvironments in Non-Small Cell Lung Cancer: Unrevealing Patterns through Cluster Analysis
Youngtaek KIM ; Joon Yeon HWANG ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(12):683-694
Purpose:
We aimed to comprehensively analyze the immune cell and stromal components of tumor microenvironment at the single-cell level and identify tumor heterogeneity among the major top-derived oncogene mutations in non-small cell lung cancer (NSCLC) using single-cell RNA sequencing (scRNA-seq) data.
Materials and Methods:
The scRNA-seq dataset utilized in this study comprised 64369 primary tumor tissue cells from 21 NSCLC patients, focusing on mutations in EGFR, ALK, BRAF, KRAS, TP53, and the wild-type.
Results:
Tumor immune microenvironment (TIM) analysis revealed differential immune responses across NSCLC mutation subtypes. TIM analysis revealed different immune responses across the mutation subtypes. Two mutation clusters emerged: KRAS, TP53, and EGFR+TP53 mutations (MC1); and EGFR, BRAF, and ALK mutations (MC2). MC1 showed higher tertiary lymphoid structures signature scores and enriched populations of C2-T-IL7R, C3-T/NK-CXCL4, C9-T/NK-NKG, and C1-B-MS4A1 clusters than cluster 2. Conversely, MC2 cells exhibited higher expression levels of TNF, IL1B, and chemokines linked to alternative immune pathways. Remarkably, co-occurring EGFR and TP53 mutations were grouped as MC1. EGFR+TP53 mutations showed upregulation of peptide synthesis and higher synthetic processes, as well as differences in myeloid and T/NK cells compared to EGFR mutations. In T/NK cells, EGFR+TP53 mutations showed a higher expression of features related to cell activity and differentiation, whereas EGFR mutations showed the opposite.
Conclusion
Our research indicates a close association between mutation types and tumor microenvironment in NSCLC, offering insights into personalized approaches for cancer diagnosis and treatment.
3.Mutation-Driven Immune Microenvironments in Non-Small Cell Lung Cancer: Unrevealing Patterns through Cluster Analysis
Youngtaek KIM ; Joon Yeon HWANG ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(12):683-694
Purpose:
We aimed to comprehensively analyze the immune cell and stromal components of tumor microenvironment at the single-cell level and identify tumor heterogeneity among the major top-derived oncogene mutations in non-small cell lung cancer (NSCLC) using single-cell RNA sequencing (scRNA-seq) data.
Materials and Methods:
The scRNA-seq dataset utilized in this study comprised 64369 primary tumor tissue cells from 21 NSCLC patients, focusing on mutations in EGFR, ALK, BRAF, KRAS, TP53, and the wild-type.
Results:
Tumor immune microenvironment (TIM) analysis revealed differential immune responses across NSCLC mutation subtypes. TIM analysis revealed different immune responses across the mutation subtypes. Two mutation clusters emerged: KRAS, TP53, and EGFR+TP53 mutations (MC1); and EGFR, BRAF, and ALK mutations (MC2). MC1 showed higher tertiary lymphoid structures signature scores and enriched populations of C2-T-IL7R, C3-T/NK-CXCL4, C9-T/NK-NKG, and C1-B-MS4A1 clusters than cluster 2. Conversely, MC2 cells exhibited higher expression levels of TNF, IL1B, and chemokines linked to alternative immune pathways. Remarkably, co-occurring EGFR and TP53 mutations were grouped as MC1. EGFR+TP53 mutations showed upregulation of peptide synthesis and higher synthetic processes, as well as differences in myeloid and T/NK cells compared to EGFR mutations. In T/NK cells, EGFR+TP53 mutations showed a higher expression of features related to cell activity and differentiation, whereas EGFR mutations showed the opposite.
Conclusion
Our research indicates a close association between mutation types and tumor microenvironment in NSCLC, offering insights into personalized approaches for cancer diagnosis and treatment.
4.Analysis of papers published in The Journal of Korean Academic Society of Nursing Education over 30 Years
Seungmi PARK ; SuJeong YU ; Kyung Choon LIM ; Subin CHOI ; Eunyoung, E SUH
Journal of Korean Academic Society of Nursing Education 2024;30(4):382-390
Purpose:
This study aims to explore the trend of nursing education and major research themes in the Journal of Korean Academic Society of Nursing Education (JKASNE) over 30 years. Methods: A total of 1,026 articles, published in the JKASNE from 1995 to 2023, were analyzed using the Microsoft Excel program for descriptive statistics and NetMiner for a word cloud of Korean keywords.
Results:
Most research subjects were healthy people (n=841). Education-related research topics (n=619) were categorized into nine domains: educational methods, educational curriculum, study type and methods, knowledge level and contents, psychosocial variables related to knowledge and education, attitude, behavior, development and evaluation of educational programs, and effects of educational programs. Quantitative (n=835) and descriptive studies (n=497) were determined to be the most common research designs. Self-reported questionnaires were the most common method used in surveys (n=581) and experimental studies (n=153). Descriptive statistics, Pearson's correlation coefficient, and other statistical techniques were used. The keywords in the JKASNE reflected various aspects of nursing research. General terms related to nursing education, such as "nursing students," "nurses," and "nursing education," appeared with high frequency, while more specific terms and phrases reflecting educational competencies and characteristics, such as "self-efficacy," "clinical performance ability," and "communication knowledge," were also prominently featured.
Conclusion
The JKASNE has published mainly education-focused papers. Analyzing the full set of papers published in JKASNE and examining their characteristics is very meaningful and helpful for the future development of Korean nursing education.
5.Analysis of papers published in The Journal of Korean Academic Society of Nursing Education over 30 Years
Seungmi PARK ; SuJeong YU ; Kyung Choon LIM ; Subin CHOI ; Eunyoung, E SUH
Journal of Korean Academic Society of Nursing Education 2024;30(4):382-390
Purpose:
This study aims to explore the trend of nursing education and major research themes in the Journal of Korean Academic Society of Nursing Education (JKASNE) over 30 years. Methods: A total of 1,026 articles, published in the JKASNE from 1995 to 2023, were analyzed using the Microsoft Excel program for descriptive statistics and NetMiner for a word cloud of Korean keywords.
Results:
Most research subjects were healthy people (n=841). Education-related research topics (n=619) were categorized into nine domains: educational methods, educational curriculum, study type and methods, knowledge level and contents, psychosocial variables related to knowledge and education, attitude, behavior, development and evaluation of educational programs, and effects of educational programs. Quantitative (n=835) and descriptive studies (n=497) were determined to be the most common research designs. Self-reported questionnaires were the most common method used in surveys (n=581) and experimental studies (n=153). Descriptive statistics, Pearson's correlation coefficient, and other statistical techniques were used. The keywords in the JKASNE reflected various aspects of nursing research. General terms related to nursing education, such as "nursing students," "nurses," and "nursing education," appeared with high frequency, while more specific terms and phrases reflecting educational competencies and characteristics, such as "self-efficacy," "clinical performance ability," and "communication knowledge," were also prominently featured.
Conclusion
The JKASNE has published mainly education-focused papers. Analyzing the full set of papers published in JKASNE and examining their characteristics is very meaningful and helpful for the future development of Korean nursing education.
6.Mutation-Driven Immune Microenvironments in Non-Small Cell Lung Cancer: Unrevealing Patterns through Cluster Analysis
Youngtaek KIM ; Joon Yeon HWANG ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(12):683-694
Purpose:
We aimed to comprehensively analyze the immune cell and stromal components of tumor microenvironment at the single-cell level and identify tumor heterogeneity among the major top-derived oncogene mutations in non-small cell lung cancer (NSCLC) using single-cell RNA sequencing (scRNA-seq) data.
Materials and Methods:
The scRNA-seq dataset utilized in this study comprised 64369 primary tumor tissue cells from 21 NSCLC patients, focusing on mutations in EGFR, ALK, BRAF, KRAS, TP53, and the wild-type.
Results:
Tumor immune microenvironment (TIM) analysis revealed differential immune responses across NSCLC mutation subtypes. TIM analysis revealed different immune responses across the mutation subtypes. Two mutation clusters emerged: KRAS, TP53, and EGFR+TP53 mutations (MC1); and EGFR, BRAF, and ALK mutations (MC2). MC1 showed higher tertiary lymphoid structures signature scores and enriched populations of C2-T-IL7R, C3-T/NK-CXCL4, C9-T/NK-NKG, and C1-B-MS4A1 clusters than cluster 2. Conversely, MC2 cells exhibited higher expression levels of TNF, IL1B, and chemokines linked to alternative immune pathways. Remarkably, co-occurring EGFR and TP53 mutations were grouped as MC1. EGFR+TP53 mutations showed upregulation of peptide synthesis and higher synthetic processes, as well as differences in myeloid and T/NK cells compared to EGFR mutations. In T/NK cells, EGFR+TP53 mutations showed a higher expression of features related to cell activity and differentiation, whereas EGFR mutations showed the opposite.
Conclusion
Our research indicates a close association between mutation types and tumor microenvironment in NSCLC, offering insights into personalized approaches for cancer diagnosis and treatment.
7.Analysis of papers published in The Journal of Korean Academic Society of Nursing Education over 30 Years
Seungmi PARK ; SuJeong YU ; Kyung Choon LIM ; Subin CHOI ; Eunyoung, E SUH
Journal of Korean Academic Society of Nursing Education 2024;30(4):382-390
Purpose:
This study aims to explore the trend of nursing education and major research themes in the Journal of Korean Academic Society of Nursing Education (JKASNE) over 30 years. Methods: A total of 1,026 articles, published in the JKASNE from 1995 to 2023, were analyzed using the Microsoft Excel program for descriptive statistics and NetMiner for a word cloud of Korean keywords.
Results:
Most research subjects were healthy people (n=841). Education-related research topics (n=619) were categorized into nine domains: educational methods, educational curriculum, study type and methods, knowledge level and contents, psychosocial variables related to knowledge and education, attitude, behavior, development and evaluation of educational programs, and effects of educational programs. Quantitative (n=835) and descriptive studies (n=497) were determined to be the most common research designs. Self-reported questionnaires were the most common method used in surveys (n=581) and experimental studies (n=153). Descriptive statistics, Pearson's correlation coefficient, and other statistical techniques were used. The keywords in the JKASNE reflected various aspects of nursing research. General terms related to nursing education, such as "nursing students," "nurses," and "nursing education," appeared with high frequency, while more specific terms and phrases reflecting educational competencies and characteristics, such as "self-efficacy," "clinical performance ability," and "communication knowledge," were also prominently featured.
Conclusion
The JKASNE has published mainly education-focused papers. Analyzing the full set of papers published in JKASNE and examining their characteristics is very meaningful and helpful for the future development of Korean nursing education.
8.Mutation-Driven Immune Microenvironments in Non-Small Cell Lung Cancer: Unrevealing Patterns through Cluster Analysis
Youngtaek KIM ; Joon Yeon HWANG ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(12):683-694
Purpose:
We aimed to comprehensively analyze the immune cell and stromal components of tumor microenvironment at the single-cell level and identify tumor heterogeneity among the major top-derived oncogene mutations in non-small cell lung cancer (NSCLC) using single-cell RNA sequencing (scRNA-seq) data.
Materials and Methods:
The scRNA-seq dataset utilized in this study comprised 64369 primary tumor tissue cells from 21 NSCLC patients, focusing on mutations in EGFR, ALK, BRAF, KRAS, TP53, and the wild-type.
Results:
Tumor immune microenvironment (TIM) analysis revealed differential immune responses across NSCLC mutation subtypes. TIM analysis revealed different immune responses across the mutation subtypes. Two mutation clusters emerged: KRAS, TP53, and EGFR+TP53 mutations (MC1); and EGFR, BRAF, and ALK mutations (MC2). MC1 showed higher tertiary lymphoid structures signature scores and enriched populations of C2-T-IL7R, C3-T/NK-CXCL4, C9-T/NK-NKG, and C1-B-MS4A1 clusters than cluster 2. Conversely, MC2 cells exhibited higher expression levels of TNF, IL1B, and chemokines linked to alternative immune pathways. Remarkably, co-occurring EGFR and TP53 mutations were grouped as MC1. EGFR+TP53 mutations showed upregulation of peptide synthesis and higher synthetic processes, as well as differences in myeloid and T/NK cells compared to EGFR mutations. In T/NK cells, EGFR+TP53 mutations showed a higher expression of features related to cell activity and differentiation, whereas EGFR mutations showed the opposite.
Conclusion
Our research indicates a close association between mutation types and tumor microenvironment in NSCLC, offering insights into personalized approaches for cancer diagnosis and treatment.
9.Exploring the Expression and Function of T Cell Surface Markers Identified through Cellular Indexing of Transcriptomes and Epitopes by Sequencing
Joon Yeon HWANG ; Youngtaek KIM ; Kwangmin NA ; Dong Kwon KIM ; Seul LEE ; Seong-san KANG ; Sujeong BAEK ; Seung Min YANG ; Mi Hyun KIM ; Heekyung HAN ; Seong Su JEONG ; Chai Young LEE ; Yu Jin HAN ; Jie-Ohn SOHN ; Sang-Kyu YE ; Kyoung-Ho PYO
Yonsei Medical Journal 2024;65(9):544-555
Purpose:
By utilizing both protein and mRNA expression patterns, we can identify more detailed and diverse immune cells, providing insights into understanding the complex immune landscape in cancer ecosystems.
Materials and Methods:
This study was performed by obtaining publicly available Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data of peripheral blood mononuclear cells (PBMCs) from the Gene Expression Omnibus database. A total of 94674 total cells were analyzed, of which 32412 were T cells. There were 228 protein features and 16262 mRNA features in the data.The Seurat package was used for quality control and preprocessing, principal component analysis was performed, and Uniform Manifold Approximation and Projection was used to visualize the clusters. Protein and mRNA levels in the CITE-seq were analyzed.
Results:
We observed that a subset of T cells in the clusters generated at the protein level divided better. By identifying mRNA markers that were highly correlated with the CD4 and CD8 proteins and cross-validating CD26 and CD99 markers using flow cytometry, we found that CD4 + and CD8+ T cells were better discriminated in PBMCs. Weighted Nearest Neighbor clustering results identified a previously unobserved T cell subset.
Conclusion
In this study, we used CITE-seq data to confirm that protein expression patterns could be used to identify cells more precisely. These findings will improve our understanding of the heterogeneity of immune cells in the future and provide valuable insights into the complexity of the immune response in health and disease.
10.A study on the Textbook on Nursing published in Korea in 1918
Ggodme YI ; SuJeong YU ; Chan Sook PARK
Journal of Korean Academic Society of Nursing Education 2023;29(4):415-426
Purpose:
The purpose of this study is to better understand nursing education in the early years of the Japanese colonial rule.
Methods:
We compared the 1918 Textbook on Nursing with the first Textbook on Nursing and to the original text, Grade A Textbook on Nursing, by the Japanese Red Cross Society (JRCS) using the historical research method. The background of its publication and its use in nursing education were exploring, too.
Results:
After Korea’s annexation by Japan, the nursing textbook by the JRCS was appointed as the standard textbook in nursing education by the Government-General in Korea (GGK). Missionary nurse got the permission for the nursing textbook by JRCS and the Textbook on Nursing was published in 1918 using Korean and Chinese characters in combination. This book, an adaptation of the original text, explained the responsibilities and roles of nurses to guide them in serving patients as well as assisting in treatment or directly performing emergency medical treatment when necessary, with a focus on the treatment of the war wounded. It would have been partially used in actual nursing education among the missionary community.
Conclusion
Textbook on Nursing in 1918 was published not only for the nursing students of missionary nursing schools but also for other nursing trainees of diverse hospitals, nurses and missionary volunteers and to help them to acquire the licenses. It reflects the enforcement on nursing education by GGK and the reality and resistance in terms of the content of education of nursing in Korea during that period.

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