Jin-Young Lee

Androgens inhibit breast cancer (BC) growth in estrogen receptor (ER)-positive BC and promote growth in ER-negative BC. Correlating intratumoral androgens, instead of circulating androgens, and their downstream transcriptome, a measure of free unbound androgen function, may offer a direct assessment of androgen action in BC. Intratumoral androgen androstenedione (A4) levels in BC specimens correlated with 1388 genes, which classified patients into low, intermediate, and high A4 levels. This A4-high patients’ transcriptome was associated with lower tumor cell proliferation, earlier stage and grade, and longer survival, while A4-low patients’ transcriptome was associated with the triple-negative subtype. We developed a 90-gene A4-associated transcriptional classifier that captures intratumoral A4-associated biology. The signature requires independent validation. snRNAseq analysis indicated that high A4 specimens were enriched for favorable cell lineage, while low A4 specimens were enriched for aggressive cell lineage and cancer hallmarks. Supporting in vitro evidence suggests that A4 can inhibit ER-positive AR-positive BC cells. Collectively, these data show that intratumoral A4 levels are associated with a transcriptional state linked to lower proliferation, more luminal features, and better BC outcome.

Motivation: Tumor viruses account for ∼10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as viral oncogene dose may impact the disease course. To our knowledge, no tool has been proposed to assess the intra-viral copy number alterations that define the gene dose of viral oncogenes and associated suppressive pathways native to the pathogen’s normal life cycle. Results: We propose an R package, “ELViS,” that analyzes viral copy number changes from DNA sequencing of whole viral genomes. The method adjusts for viral load with 2D transformation and segmentation to offer the relative viral gene doses. Availability and implementation: The ELViS R package is available from https://bioconductor.org/packages/ELViS. This article used controlled access data from dbGaP (phs001713.v1.p1).

Jin-Young Lee, Won Park, Hyunjoong Kim, Hong Seok Lee, Tae-Wook Kang, Dong-Hun Shin, Kyung Su Kim, Yoon Kyeong Lee, Seon-Young Kim, Ji Hwan Park & Young-Joon Kim. BMB Reports -0001;0:. https://doi.org/10.5483/BMBRep.2023-0155

Sejoon Lee, Kil-yong Lee, Ji-Hwan Park, Duck-Woo Kim, Heung-Kwon Oh, Seong-Taek Oh, Jongbum Jeon, Dongyoon Lee, Soobok Joe, Hoang Bao Khanh Chu, Jisun Kang, Jin-Young Lee, Sheehyun Cho, Hyeran Shim, Si-Cho Kim, Hong Seok Lee, Young-Joon Kim, Jin Ok Yang, Jaeim Lee & Sung-Bum Kang. BMB Reports 2024;57:161-6. https://doi.org/10.5483/BMBRep.2023-0103

Hyeran Shim, Kiwon Jang, Yeong Hak Bang, Hoang Bao Khanh Chu , Jisun Kang , Jin-Young Lee , Sheehyun Cho , Hong Seok Lee , Jongbum Jeon , Taeyeon Hwang , Soobok Joe , Jinyeong Lim , Ji-Hye Choi , Eun Hye Joo , Kyunghee Park , Ji Hwan Moon , Kyung Yeon Han , Yourae Hong , Woo Yong Lee , Hee Cheol Kim , Seong Hyeon Yun , Yong Beom Cho , Yoon Ah Park , Jung Wook Huh , Jung Kyong Shin , Dae Hee Pyo , Hyekyung Hong , Hae-Ock Lee, Woong-Yang Park, Jin Ok Yang & Young-Joon Kim. BMB Reports 2024;57:110-5. https://doi.org/10.5483/BMBRep.2023-0093

We aimed to predict postoperative prognosis of stage II/III colorectal cancer (CRC). Tumor-like normal microenvironment (tNME) and healthy normal microenvironment (hNME) groups were created using RNA sequencing (RNA-seq) data derived from 273 tumors and 273 paired normal tissues from margins of resected specimens. With a median follow-up of 58.2 months, the tNME group showed poor 5-year recurrence-free survival (54.7 vs. 73.0%, HR = 1.94, P = 0.002) and 5-year overall survival (78.2 vs. 83.0%, HR = 1.76, P = 0.033). Only the tNME group showed similar microbiome diversity between tumor and normal tissues. scRNA-seq revealed a positive co-occurrence of Th17, GZMK^highCD8+T cells, and IL1B^high neutrophils in the tumor and normal tissues of tNME. A high proportion of EMP1^high epithelial cells was observed in the tNME group, with upregulated epithelial-mesenchymal transition and leukocyte signaling pathways. In conclusion, the microenvironmental status of normal tissues offers a promising biomarker for stage II/III CRC.

Soobok Joe, Jinyong Kim, Jin-Young Lee, Jongbum Jeon, Iksu Byeon, Sae-Won Han, Seung-Bum Ryoo, Kyu Joo Park, Sang-Hyun Song, Sheehyun Cho, Hyeran Shim, Hoang Bao Khanh Chu, Jisun Kang, Hong Seok Lee, DongWoo Kim, Young-Joon Kim, Tae-You Kim & Seon-Young Kim. BMB Reports -0001;0:. https://doi.org/10.5483/BMBRep.2023-0096

Seok-Byung Lim, Soobok Joe, Hyo-Ju Kim, Jong Lyul Lee, In Ja Park, Yong Sik Yoon, Chan Wook Kim, Jong-Hwan Kim, Sangok Kim, Jin-Young Lee, Hyeran Shim, Hoang Bao Khanh Chu, Sheehyun Cho, Jisun Kang, Si-Cho Kim, Hong Seok Lee, Young-Joon Kim, Seon-Young Kim & Chang Sik Yu. BMB Reports 2023;56:569-74. https://doi.org/10.5483/BMBRep.2023-0106

Given the difficulties of obtaining diseased cells, differentiation of neurons from patient-specific human induced pluripotent stem cells (iPSCs) with neural progenitor cells (NPCs) as intermediate precursors is of great interest. While cellular and transcriptomic changes during the differentiation process have been tracked, little attention has been given to examining spatial re-organization, which has been revealed to control gene regulation in various cells. To address the regulatory mechanism by 3D chromatin structure during neuronal differentiation, we examined the changes that take place during differentiation process using two cell types that are highly valued in the study of neurodegenerative disease - iPSCs and NPCs. In our study, we used Hi-C, a derivative of chromosome conformation capture that enables unbiased, genome-wide analysis of interaction frequencies in chromatin. We showed that while topologically associated domains remained mostly the same during differentiation, the presence of differential interacting regions in both cell types suggested that spatial organization affects gene regulation of both pluripotency maintenance and neuroectodermal differentiation. Moreover, closer analysis of promoter–promoter pairs suggested that cell fate specification is under the control of cis-regulatory elements. Our results are thus a resourceful addition in benchmarking differentiation protocols and also provide a greater appreciation of NPCs, the common precursors from which required neurons for applications in neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, schizophrenia and spinal cord injuries are utilized.

In this study, we investigated the nutritional and functional constituents as well as quality characteristics and antioxidant activity of Korean cultivated wild ginseng (KG). The chemical compositions