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3. Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Published
2023
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4. Integrated proteogenomic characterization of glioblastoma evolution

Author

Kim, Kyung-Hee, Migliozzi, Simona, Koo, Harim, Hong, Jun-Hee, Park, Seung Min, Kim, Sooheon, Kwon, Hyung Joon, Ha, Seokjun, Garofano, Luciano, Oh, Young Taek, D'Angelo, Fulvio, Kim, Chan Il, Kim, Seongsoo, Lee, Ji Yoon, Kim, Jiwon, Hong, Jisoo, Jang, Eun-Hae, Mathon, Bertrand, Di Stefano, Anna-Luisa, Bielle, Franck, Laurenge, Alice, Nesvizhskii, Alexey I., Hur, Eun-Mi, Yin, Jinlong, Shi, Bingyang, Kim, Youngwook, Moon, Kyung-Sub, Kwon, Jeong Taik, Lee, Shin Heon, Lee, Seung Hoon, Gwak, Ho Shin, Lasorella, Anna, Yoo, Heon, Sanson, Marc, Sa, Jason K., Park, Chul-Kee, Nam, Do-Hyun, Iavarone, Antonio, and Park, Jong Bae

Published
2024
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5. Age and ethnic-driven molecular and clinical disparity of East Asian breast cancers

Author

Lee, Ji Yoon, primary, Chung, Min Sung, additional, Choi, Jong Gwon, additional, Sim, Sung Hoon, additional, Kim, Hyo Jeong, additional, Kim, Jeong Eun, additional, Lee, Kyoung Eun, additional, Park, Yeon Hee, additional, Kang, Myoung Joo, additional, Ahn, Mi Sun, additional, Chae, Yee Soo, additional, Park, Ji Hyun, additional, Kim, Jee Hyun, additional, Kim, Gun Min, additional, Byun, Jae Ho, additional, Park, Keon Uk, additional, Kim, Ju Won, additional, Jung, Seung Pil, additional, Lee, Jung Hyun, additional, An, Jung Seok, additional, Jang, Byunghyun, additional, Yoon, Dayoung, additional, Kim, Jiwon, additional, Hong, Jisoo, additional, Koo, Harim, additional, Cho, Kyu Ran, additional, Kim, Cheol Yong, additional, Sa, Jason K., additional, Park, Kyong Hwa, additional, and Lee, Ji Won, additional

Published
2024
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7. Comprehensive pharmacogenomic characterization of gastric cancer

Author

Sa, Jason K., Hong, Jung Yong, Lee, In-Kyoung, Kim, Ju-sun, Sim, Moon-Hee, Kim, Ha Jung, An, Ji Yeong, Sohn, Tae Sung, Lee, Joon Ho, Bae, Jae Moon, Kim, Sung, Kim, Kyoung-Mee, Kim, Seung Tae, Park, Se Hoon, Park, Joon Oh, Lim, Ho Yeong, Kang, Won Ki, Her, Nam-Gu, Lee, Yeri, Cho, Hee Jin, Shin, Yong Jae, Kim, Misuk, Koo, Harim, Kim, Mirinae, Seo, Yun Jee, Kim, Ja Yeon, Choi, Min-Gew, Nam, Do-Hyun, and Lee, Jeeyun

Published
2020
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8. Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers

Author

Sa, Jason K., Hwang, Jae Ryoung, Cho, Young-Jae, Ryu, Ji-Yoon, Choi, Jung-Joo, Jeong, Soo Young, Kim, Jihye, Kim, Myeong Seon, Paik, E. Sun, Lee, Yoo-Young, Choi, Chel Hun, Kim, Tae-Joong, Kim, Byoung-Gie, Bae, Duk-Soo, Lee, Yeri, Her, Nam-Gu, Shin, Yong Jae, Cho, Hee Jin, Kim, Ja Yeon, Seo, Yun Jee, Koo, Harim, Oh, Jeong-Woo, Lee, Taebum, Kim, Hyun-Soo, Song, Sang Yong, Bae, Joon Seol, Park, Woong-Yang, Han, Hee Dong, Ahn, Hyung Jun, Sood, Anil K., Rabadan, Raul, Lee, Jin-Ku, Nam, Do-Hyun, and Lee, Jeong-Won

Published
2019
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9. Additional file 2 of Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Abstract

Additional file 2: Fig. S1. Timeline of sample acquisition, sequencing, in vitro culture and TMZ screening. Fig. S2. Gaussian Mixture Model used to identify genes with the same expression profile between patient-derived cells (PDCs) and tumor tissues. Fig. S3. Principal Component Analysis and differentially expressed gene analysis on 34 tissue RNA-seq samples. Fig. S4. Association of MGMT promoter methylation status to survival and in vitro TMZ screening in the main cohort. Fig. S5. Copy number estimation by GliomaSCAN. Fig. S6. Copy number estimation by RNA-seq. Fig. S7. Machine learning model feature importance. Fig. S8. Correlations between GBM subtypes and TMZ response. Fig. S9. Comparison of survival prediction in TCGA cohort. Fig. S10. Genomic landscape of multi-sector samples. Fig. S11. TMZ-resistant marker expression and CNV comparison in patient M13 and M14. Fig. S12. Progression free survival difference in patients with multi-sector samples.

Published
2023
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10. Additional file 3 of Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Abstract

Additional file 3. Supplementary methods.

Published
2023
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11. Modulation of Nogo receptor 1 expression orchestrates myelin-associated infiltration of glioblastoma

Author

Hong, Jun-Hee, primary, Kang, Sangjo, additional, Sa, Jason K, additional, Park, Gunwoo, additional, Oh, Young Taek, additional, Kim, Tae Hoon, additional, Yin, Jinlong, additional, Kim, Sung Soo, additional, D’Angelo, Fulvio, additional, Koo, Harim, additional, You, Yeonhee, additional, Park, Saewhan, additional, Kwon, Hyung Joon, additional, Kim, Chan Il, additional, Ryu, Haseo, additional, Lin, Weiwei, additional, Park, Eun Jung, additional, Kim, Youn-Jae, additional, Park, Myung-Jin, additional, Kim, Hyunggee, additional, Kim, Mi-Suk, additional, Chung, Seok, additional, Park, Chul-Kee, additional, Park, Sung-Hye, additional, Kang, Yun Hee, additional, Kim, Jong Heon, additional, Saya, Hideyuki, additional, Nakano, Ichiro, additional, Gwak, Ho-Shin, additional, Yoo, Heon, additional, Lee, Jeongwu, additional, Hur, Eun-Mi, additional, Shi, Bingyang, additional, Nam, Do-Hyun, additional, Iavarone, Antonio, additional, Lee, Seung-Hoon, additional, and Park, Jong Bae, additional

Published
2021
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12. NIMG-20. MULTI-HABITAT RADIOMICS UNRAVELS DISTINCT PHENOTYPIC SUBTYPES OF GLIOBLASTOMA WITH CLINICAL AND GENOMIC SIGNIFICANCE

Author

Won Choi, Seung, primary, Cho, Hwan-ho, additional, Koo, Harim, additional, Cho, Kyung rae, additional, Nenning, Karl-Heinz, additional, Langs, Georg, additional, Furtner, Julia, additional, Baumann, Bernhard, additional, Woehrer, Adelheid, additional, Cho, Hee Jin, additional, Kong, Doo-Sik, additional, Seol, Ho Jun, additional, Lee, Jung-il, additional, Nam, Do-Hyun, additional, and Park, Hyunjin, additional

Published
2020
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14. Ethnic delineation of primary glioblastoma genome

Author

Koo, Harim, primary, Choi, Seung Won, additional, Cho, Hee Jin, additional, Lee, In‐Hee, additional, Kong, Doo‐Sik, additional, Seol, Ho Jun, additional, Lee, Jung‐Il, additional, Choi, Jung‐Won, additional, Sa, Jason K., additional, and Nam, Do‐Hyun, additional

Published
2020
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15. Multi-Habitat Radiomics Unravels Distinct Phenotypic Subtypes of Glioblastoma with Clinical and Genomic Significance

Author

Choi, Seung Won, primary, Cho, Hwan-Ho, additional, Koo, Harim, additional, Cho, Kyung Rae, additional, Nenning, Karl-Heinz, additional, Langs, Georg, additional, Furtner, Julia, additional, Baumann, Bernhard, additional, Woehrer, Adelheid, additional, Cho, Hee Jin, additional, Sa, Jason K., additional, Kong, Doo-Sik, additional, Seol, Ho Jun, additional, Lee, Jung-Il, additional, Nam, Do-Hyun, additional, and Park, Hyunjin, additional

Published
2020
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16. Sphere-Forming Culture for Expanding Genetically Distinct Patient-Derived Glioma Stem Cells by Cellular Growth Rate Screening

Author

Shin, Kayoung, primary, Shin, Hyemi, additional, Cho, Hee Jin, additional, Kang, Hyunju, additional, Lee, Jin-Ku, additional, Seo, Yun Jee, additional, Shin, Yong Jae, additional, Kim, Donggeon, additional, Koo, Harim, additional, Kong, Doo-Sik, additional, Seol, Ho Jun, additional, Lee, Jung-Il, additional, Lee, Hye Won, additional, and Nam, Do-Hyun, additional

Published
2020
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17. Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas

Author

Shin, Hyemi, primary, Sa, Jason K., additional, Bae, Joon Seol, additional, Koo, Harim, additional, Jin, Seonwhee, additional, Cho, Hee Jin, additional, Choi, Seung Won, additional, Kyoung, Jong Min, additional, Kim, Ja Yeon, additional, Seo, Yun Jee, additional, Joung, Je-Gun, additional, Kim, Nayoung K. D., additional, Son, Dae-Soon, additional, Chung, Jongsuk, additional, Lee, Taeseob, additional, Kong, Doo-Sik, additional, Choi, Jung Won, additional, Seol, Ho Jun, additional, Lee, Jung-Il, additional, Suh, Yeon-Lim, additional, Park, Woong-Yang, additional, and Nam, Do-Hyun, additional

Published
2020
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20. Phenotypic Plasticity of Invasive Edge Glioma Stem-like Cells in Response to Ionizing Radiation

Author

Minata, Mutsuko, primary, Audia, Alessandra, additional, Shi, Junfeng, additional, Lu, Songjian, additional, Bernstock, Joshua, additional, Pavlyukov, Marat S., additional, Das, Arvid, additional, Kim, Sung-Hak, additional, Shin, Yong Jae, additional, Lee, Yeri, additional, Koo, Harim, additional, Snigdha, Kirti, additional, Waghmare, Indrayani, additional, Guo, Xing, additional, Mohyeldin, Ahmed, additional, Gallego-Perez, Daniel, additional, Wang, Jia, additional, Chen, Dongquan, additional, Cheng, Peng, additional, Mukheef, Farah, additional, Contreras, Minerva, additional, Reyes, Joel F., additional, Vaillant, Brian, additional, Sulman, Erik P., additional, Cheng, Shi-Yuan, additional, Markert, James M., additional, Tannous, Bakhos A., additional, Lu, Xinghua, additional, Kango-Singh, Madhuri, additional, Lee, L. James, additional, Nam, Do-Hyun, additional, Nakano, Ichiro, additional, and Bhat, Krishna P., additional

Published
2019
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21. Identification of genomic and molecular traits that present therapeutic vulnerability to HGF-targeted therapy in glioblastoma

Author

Sa, Jason K, primary, Kim, Sung Heon, additional, Lee, Jin-Ku, additional, Cho, Hee Jin, additional, Shin, Yong Jae, additional, Shin, Hyemi, additional, Koo, Harim, additional, Kim, Donggeon, additional, Lee, Mijeong, additional, Kang, Wonyoung, additional, Hong, Sung Hee, additional, Kim, Jung Yong, additional, Park, Young-Whan, additional, Song, Seong-Won, additional, Lee, Song-Jae, additional, Joo, Kyeung Min, additional, and Nam, Do-Hyun, additional

Published
2018
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24. Novel Semi-Replicative Retroviral Vector Mediated Double Suicide Gene Transfer Enhances Antitumor Effects in Patient-Derived Glioblastoma Models.

Author

Lee, Mijeong, Kim, Yeon-Soo, Lee, Kyoungmin, Kang, Moonkyung, Shin, Hyemi, Oh, Jeong-Woo, Koo, Harim, Kim, Donggeon, Kim, Yejin, Kong, Doo-Sik, Nam, Do-Hyun, and Lee, Hye Won

Subjects
GANCICLOVIR, PRODRUGS, CELL proliferation, APOPTOSIS, CELL adhesion molecules, CELL lines, FLOW cytometry, GENE therapy, GLIOMAS, HERPES simplex, MACROPHAGES, RETROVIRUSES, STEM cells, XENOGRAFTS, YEAST, TREATMENT effectiveness, GENE expression profiling, CELL migration inhibition, PATHOLOGIC neovascularization, IN vitro studies, THERAPEUTICS
Abstract

As glioblastomas are mostly localized infiltrative lesions, gene therapy based on the retroviral replicating vector (RRV) system is considered an attractive strategy. Combinations of multiple suicide genes can circumvent the limitations associated with each gene, achieving direct and synergistic cytotoxic effects, along with bystander cell killing. In this study, we constructed a semi-and pseudotyped-RRV (sp-RRV) system harboring two suicide genes—herpes simplex virus type 1 thymidine kinase (TK) and yeast cytosine deaminase (CD)—to verify the dissemination and antitumor efficacy of our sp-RRV system (spRRVe-sEF1α-TK/sRRVgp-sEF1α-CD) in seven patient-derived glioblastoma stem-like cells (GSCs). Flow cytometry and high-content analysis revealed a wide range of transduction efficiency and good correlation between the delivery of therapeutic genes and susceptibility to the prodrugs ganciclovir and 5-fluorocytosine in patient-derived GSCs in vitro. Intra-tumoral delivery of spRRVe-sEF1α-TK/sRRVgp-sEF1α-CD, combined with prodrug treatment, synergistically inhibited cell proliferation and angiogenesis while increasing apoptosis and the depletion of tumor-associated macrophages in orthotopic glioblastoma xenografts. Genomic profiling of patient-derived GSCs revealed that the key genes preventing sp-RRV infection and transmission were associated with cell adhesion, migration, development, differentiation, and proliferation. This is the first report demonstrating that a novel sp-RRV-mediated TK/CD double suicide gene transfer system has high oncolytic power against extremely heterogeneous and treatment-refractory glioblastomas. [ABSTRACT FROM AUTHOR]

Published
2019
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25. Elucidation of Novel Therapeutic Targets for Acute Myeloid Leukemias with RUNX1-RUNX1T1 Fusion.

Author

Koo, Harim, Yun, Jae Won, Bae, Yoon Kyung, Joo, Kyeung Min, Nam, Do-Hyun, Park, Woong-Yang, Kim, Hee-Jin, Kim, Sun-Hee, Cho, So Yeong, and Chun, Sejong

Subjects
*CHROMOSOME abnormalities, *ACUTE myeloid leukemia, *CHIMERIC proteins, *CYCLOOXYGENASES, *VASCULAR endothelial growth factors, *PLATELET-derived growth factor receptors
Abstract

The RUNX1-RUNX1T1 fusion is a frequent chromosomal alteration in acute myeloid leukemias (AMLs). Although RUNX1-RUNX1T1 fusion protein has pivotal roles in the development of AMLs with the fusion, RUNX1-RUNX1T1, fusion protein is difficult to target, as it lacks kinase activities. Here, we used bioinformatic tools to elucidate targetable signaling pathways in AMLs with RUNX1-RUNX1T1 fusion. After analysis of 93 AML cases from The Cancer Genome Atlas (TCGA) database, we found expression of 293 genes that correlated to the expression of the RUNX1-RUNX1T1 fusion gene. Based on these 293 genes, the cyclooxygenase (COX), vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), and fibroblast growth factor receptor (FGFR) pathways were predicted to be specifically activated in AMLs with RUNX1-RUNX1T1 fusion. Moreover, the in vitro proliferation of AML cells with RUNX1-RUNX1T1 fusion decreased significantly more than that of AML cells without the fusion, when the pathways were inhibited pharmacologically. The results indicate that novel targetable signaling pathways could be identified by the analysis of the gene expression features of AMLs with non-targetable genetic alterations. The elucidation of specific molecular targets for AMLs that have a specific genetic alteration would promote personalized treatment of AMLs and improve clinical outcomes. [ABSTRACT FROM AUTHOR]

Published
2019
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