https://scholar.dgist.ac.kr/handle/20.500.11750/9954 2026-04-04T12:02:43Z 2026-04-04T12:02:43Z Lee, Ju-yeon Yang, Jiyoul Kim, Jinyoung Do, YeJi Kim, Min-Sik Kye, Dong-eun Min, Geonhui Jeon, In-sook Kim, Eung-gook Choi, Joong-kook Choi, Minjae Lee, Hyun Yang, Bumhee https://scholar.dgist.ac.kr/handle/20.500.11750/59936 2026-02-05T18:01:21Z 2025-09-30T15:00:00Z

Title: Bronchoalveolar lavage proteomics in exacerbation of bronchiectasis Author(s): Lee, Ju-yeon; Yang, Jiyoul; Kim, Jinyoung; Do, YeJi; Kim, Min-Sik; Kye, Dong-eun; Min, Geonhui; Jeon, In-sook; Kim, Eung-gook; Choi, Joong-kook; Choi, Minjae; Lee, Hyun; Yang, Bumhee Abstract: Background: The molecular pathophysiology underlying the development of bronchiectasis with exacerbation at the proteomic level has not been clarified using bronchoalveolar lavage fluid samples. This study aimed to evaluate the bronchoalveolar lavage fluid inflammatory profiles associated with exacerbation of bronchiectasis. Methods: We analyzed the bronchoalveolar lavage fluid specimens from 4 patients in the exacerbation status and 4 patients in a stable status using liquid chromatography-tandem mass spectrometry. Results: A total of 1,577 proteins were identified using proteomic analysis, with 127 differentially expressed proteins. Of 127 differentially expressed proteins, 23 proteins showed more than 2-fold differences between exacerbation and stable status groups. The exacerbation status was associated with 18 upregulated proteins (TPI1, CRP, BPI, ORM1, PTPRE, S100A9, BPY2, TPM4, ERVFC1-1, CYS1, CLEC3B, S100A8, PSAT1, NDUFA10, MDGA1, SPRR3, ALDOA, and PSMB2) and five downregulated proteins (MUC5B, HSPE1, KLK13, IGHA1, and MUC5AC). Pathway analysis revealed that the neutrophil degranulation pathway (R-HSA-6798695) was the most enriched pathway in these proteins, followed by the C-type lectin receptor pathway (R-HSA-5621481). Conclusion: The bronchoalveolar lavage fluid protein expression in patients in the exacerbation status of bronchiectasis was significantly different from that in patients in the stable status, indicating that neutrophil degranulation and C-type lectin receptor pathways are the most enriched pathways during exacerbation.

2025-09-30T15:00:00Z Karuppiah, Chelladurai Kim, Seongyeop Lee, So Yeon Lee, Gyudong Ahmed, Imteaz Jhung, Sung Hwa Baek, Song-Yee Yim, Yong-Hyeon Alam, Rafiqul Kim, Min-Sik Lee, Hye Jin https://scholar.dgist.ac.kr/handle/20.500.11750/59932 2026-02-08T16:10:21Z 2025-11-30T15:00:00Z

Title: Synergistic NH2-MIL-101(Fe)/thermally reduced graphene oxide composite integrated voltammetric sensor for carcinogenic chrysene in particulate matter Author(s): Karuppiah, Chelladurai; Kim, Seongyeop; Lee, So Yeon; Lee, Gyudong; Ahmed, Imteaz; Jhung, Sung Hwa; Baek, Song-Yee; Yim, Yong-Hyeon; Alam, Rafiqul; Kim, Min-Sik; Lee, Hye Jin Abstract: Atmospheric particulate matter (PM) containing polycyclic aromatic hydrocarbons (PAHs) poses serious health risks due to its carcinogenic nature. Chrysene (CHR), a priority pollutant known for its toxicity and persistence, necessitates the development of sensitive and cost-effective detection methods. In this study, we report, for the first time, a highly sensitive voltammetric sensor for CHR detection using a composite of NH2-MIL-101(Fe) and thermally reduced graphene oxide (TRGO) modified glassy carbon electrode (NH2-MIL-101(Fe)/TRGO/GCE). The composite was prepared via ultrasonication of TRGO with NH2-MIL-101(Fe) and synthesized using a microwave-assisted method. Comprehensive physicochemical characterization, including various spectroscopic and electrochemical measurements alongside thermogravimetry and N2 adsorption isotherms, confirmed the composite’s crystallinity, high porosity, and conductivity. Under optimal conditions, the NH2-MIL-101(Fe)/ TRGO/GCE sensor achieved a low limit of detection (0.037 µM), high sensitivity (0.345 µA µM− 1 ), and a wide linear detection range (0.1–240 μM). The sensor demonstrated superior selectivity for CHR, even in the presence of other carcinogenic PAHs, including naphthalene, phenanthrene, fluorene, pyrene, and benzo[a]pyrene. These impressive attributes were primarily due to the synergistic effects of the composite, including strong π-π interaction and rapid electron transfer. Furthermore, the sensor showed excellent selectivity, reproducibility, and high recovery rates when applied to CHR detection in complex PM samples and other contaminant sources such as soil and river water. These results demonstrate the NH2-MIL-101(Fe)/TRGO/GCE sensor as a promising technology for pollutant analysis and environmental monitoring in practical applications.

2025-11-30T15:00:00Z Mun, Dong-Gi Madugundu, Anil K. Renuse, Santosh Nirujogi, Raja Sekhar Na, Chan Hyun Kim, Min-Sik Saraswat, Mayank Singh, Smrita Ramarajan, Madan G. Tiwary, Shivani Cox, Jurgen Prakash, Amol Halushka, Marc K. Burns, Kathleen H. Kandasamy, Richard k Pandey, Akhilesh https://scholar.dgist.ac.kr/handle/20.500.11750/59923 2026-02-05T18:01:17Z 2025-12-31T15:00:00Z

Title: A transcriptomic and proteomic map of primary human cell types Author(s): Mun, Dong-Gi; Madugundu, Anil K.; Renuse, Santosh; Nirujogi, Raja Sekhar; Na, Chan Hyun; Kim, Min-Sik; Saraswat, Mayank; Singh, Smrita; Ramarajan, Madan G.; Tiwary, Shivani; Cox, Jurgen; Prakash, Amol; Halushka, Marc K.; Burns, Kathleen H.; Kandasamy, Richard k; Pandey, Akhilesh Abstract: Molecular profiling of human primary cell types is essential for understanding human biology. We present a transcriptome and proteome map of 28 primary human cell types. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed in both the transcriptome and proteome levels along with the discovery of cell type enriched molecules including GRAP and C1orf116. The epithelial cell specific protein C1orf116 was further validated using immunohistochemistry across various human tissues. An exhaustive protein database search considering 39 post-translational modifications (PTMs) revealed novel insights into the PTM landscape including identification of understudied PTMs such as serine O-acetylation and histidine methylation. This also enabled comprehensive characterization of proteins with diverse PTMs. Interestingly, an unexpectedly higher frequency of dioxidation on tryptophan compared to methionine led to the identification of oxidative mitochondria complex subunit proteins. Further, a search strategy accounting for alternative translational start sites, splice junctions and translational readthrough refined genome annotation using proteomic evidence. For example, peptides from translational readthrough including extended sequence of LDHB and MDH1 were detected representing the first peptide-level evidence of these protein readthrough isoforms. Our comprehensive transcriptome and proteome data revealed cell type-specific molecular cues and heterogeneity, offering new insights into disease mechanisms often overlooked by tissue proteomics.

2025-12-31T15:00:00Z Song, Kyu Jin Kim, Minsuh Heo, Yong Jin Cho, Kyung-Cho Oh, Jae-Won Kim, Dae Ho Hwa, Chanwoong Do, Yeji Choi, Seunghyuk Hwang, Hee Sang Kim, Kwoneel Kim, Kyunggon Na, Seungjin Paek, Eunok An, Joon-Yong Jang, Se Jin Kim, Min-Sik Kim, Kwang Pyo https://scholar.dgist.ac.kr/handle/20.500.11750/59226 2025-11-27T02:40:10Z 2025-08-31T15:00:00Z

Title: Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability Author(s): Song, Kyu Jin; Kim, Minsuh; Heo, Yong Jin; Cho, Kyung-Cho; Oh, Jae-Won; Kim, Dae Ho; Hwa, Chanwoong; Do, Yeji; Choi, Seunghyuk; Hwang, Hee Sang; Kim, Kwoneel; Kim, Kyunggon; Na, Seungjin; Paek, Eunok; An, Joon-Yong; Jang, Se Jin; Kim, Min-Sik; Kim, Kwang Pyo Abstract: As research into cancer biology progresses, multiomics analyses have become essential for unraveling its molecular complexities. However, sample availability remains a challenge due to factors such as collection procedures and long-term storage effects. Archived samples present an opportunity to expand multiomics studies, but concerns persist regarding storage duration's impact on data reliability. This study examines the genomic, transcriptomic, and proteomic profiles of samples stored for over a decade. Transcriptomic analysis revealed a decline in read counts for protein-coding genes but preserved core gene expression patterns. Proteomic measurements remained stable, with minimal changes in post-translational modifications. While phosphorylation and acetylation rates were largely unaffected, a slight increase in modification frequencies was observed. Housekeeping genes and proteins exhibited consistent expression across samples, yet proteomic differences between the tumor and normal tissues were distinct. Despite technical variations in transcriptomic data, essential transcription factors and kinases retained functionality. These findings underscore the viability of archived samples for multiomics research, enabling broader investigations into cancer biology and providing insights into molecular mechanisms. By leveraging archived specimens, researchers can overcome sample limitations and advance precision oncology efforts, ultimately deepening our understanding of cancer at the systems level.

2025-08-31T15:00:00Z