Seobin Park, Yubin Lee, Minseo Kwak, Yoonha Kim, Junhyung Ryu, Kyung Bo Kim, Dong-Eun Kim
{"title":"Immunoproteasome inhibition protects the retina from Alzheimer's-associated degeneration.","authors":"Seobin Park, Yubin Lee, Minseo Kwak, Yoonha Kim, Junhyung Ryu, Kyung Bo Kim, Dong-Eun Kim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is marked by progressive cognitive decline and retinal abnormalities, including degeneration of the retinal pigment epithelium (RPE). In models of AD, the accumulation of amyloid-β (Aβ) peptides triggers chronic inflammation and activates the immunoproteasome (iP), primarily driven by tumor necrosis factor-alpha (TNFα) from glial cells. Although pharmacological inhibition of iP has demonstrated protective effects against retinal damage, the precise molecular mechanisms involved remain unclear. In this study, we reveal that Aβ stimulation initiates a signaling cascade from glia to RPE, mediated by TNFα, which in turn promotes iP activation and upregulation of the NLRP3 inflammasome in RPE cells. Aβ exposure significantly increased TNFα secretion in Müller glia, whereas RPE cells exhibited only a minimal intrinsic response to TNFα secretion in response to Aβ. Inhibition of iP reduced TNFα release from glial cells. Additionally, neutralizing gliaderived TNFα decreased iP activity and mitigated epithelialmesenchymal transition (EMT) in RPE cells, highlighting TNFα's crucial role in glial-induced retinal inflammation. These findings position glia-derived TNFα as a central factor in Aβ-induced RPE degeneration through the TNFα-iP-NLRP3 pathway, supporting the use of iP inhibition as a potential therapeutic approach to maintain retinal integrity in AD.</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148306958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yu Kyung Jun, Jibin Jeong, Byoung Mok Kim, Jinho Kim, Jong-Ho Park, Yonghoon Choi, Cheol Min Shin, Young Soo Park, Nayoung Kim, Dong Ho Lee, Sejoon Lee, Hyuk Yoon
{"title":"Whole genome-based polygenic risk score and structural variation analysis in Korean patients with inflammatory bowel disease.","authors":"Yu Kyung Jun, Jibin Jeong, Byoung Mok Kim, Jinho Kim, Jong-Ho Park, Yonghoon Choi, Cheol Min Shin, Young Soo Park, Nayoung Kim, Dong Ho Lee, Sejoon Lee, Hyuk Yoon","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The specific roles of single-nucleotide polymorphisms and structural variants (SVs) in Korean patients with inflammatory bowel disease (IBD) susceptibility remain unclear; hence this study aimed to evaluate polygenic risk scores (PRS) for IBD and identify IBD-associated SVs in a Korean IBD cohort. Whole genome sequencing data from 75 Korean patients with IBD were analyzed, and compared with individuals from the general Korean population cohort. The PRS models significantly distinguished patients with IBD from the general Korean population, confirming the predictive power of PRS in Korean patients with IBD. SV analysis revealed IBD-associated deletions, with candidate loci including PLA2R1, PTPN2, LINC00484, CCND3, COMMD7, and ERAP2. Of these, DEL5948 in ERAP2 overlapped multiple IBD-associated SNP loci and disrupted key regulatory and coding regions, potentially influencing immune regulation. This study provides a comprehensive genome-wide analysis of PRS and SVs in Korean patients with IBD, highlighting novel genetic factors in IBD pathogenesis.</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinseon Yoo, Jinyong Kim, Hoang Bao Khanh Chu, Soobok Joe, Sae-Won Han, Sheehyun Cho, Hyeran Shim, Jisun Kang, Hong Seok Lee, DongWoo Kim, Jisu Kim, Jong-Hwan Kim, Jongbum Jeon, Jin Ok Yang, Seon-Young Kim, Young-Joon Kim, Seung-Bum Ryoo
{"title":"Immune phenotype-based stratification of colorectal cancer reveals subtype-specific immunotherapeutic opportunities: insights from a Korean patient cohort.","authors":"Jinseon Yoo, Jinyong Kim, Hoang Bao Khanh Chu, Soobok Joe, Sae-Won Han, Sheehyun Cho, Hyeran Shim, Jisun Kang, Hong Seok Lee, DongWoo Kim, Jisu Kim, Jong-Hwan Kim, Jongbum Jeon, Jin Ok Yang, Seon-Young Kim, Young-Joon Kim, Seung-Bum Ryoo","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Colorectal cancer (CRC) poses major clinical challenges, and deeper molecular and immunological insights are essential for precision oncology. We integrated RNA sequencing (RNA-seq) and clinical data from a Korean CRC cohort to profile tumor biology and immune heterogeneity. Differential expression analysis revealed 1,652 upregulated and 1,372 downregulated genes in tumors, with enrichment of DNA damage response (DDR), WNT signaling, and extracellular matrix (ECM)- receptor pathways, whereas normal tissues were enriched for metabolic processes. Consensus Molecular Subtype (CMS) classification identified canonical subtype-specific features, with unclassified tumors resembling CMS2. Immune phenotyping stratified tumors into hot, intermediate, and cold groups, showing distinct associations with microsatellite instability (MSI) and CMS subtypes. Tumor Immune Dysfunction and Exclusion (TIDE) analysis predicted responders across all phenotypes, unexpectedly including intermediate and cold tumors. Notably, interferon-STAT3-PIM1 signaling characterized non-responders, implicating oncogenic drivers of immune resistance. Immunehot tumors displayed strong antigen presentation (HLA-C, B2M) and apoptosis (FAS) signatures, supporting sensitivity to PD-1 blockade with potential benefit from apoptosis-targeting agents. Intermediate tumors showed partial CD8+ T cell activation, suggesting combinatorial strategies such as CTLA-4 blockade or oncolytic priming. Cold tumors with IRF1 expression exhibited latent immune potential, indicating opportunities for epigenetic modulation plus checkpoint inhibition. These findings highlight the immune transcriptomic diversity of CRC and demonstrate that immune phenotype-based stratification provides actionable insights beyond MSI or CMS classification. This framework may guide personalized immunotherapy strategies for Korean CRC patients and inform future integration with spatial transcriptomic profiling.</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Da-Young Eum, Cong So Tran, Jisu Kim, Mi-So Jeong, Soon Yong Park, Jeyun Jo, Chaeyoung Lee, Yeo Jin Lee, Seyeon Jung, Goeun Lee, Seoung Rak Lee, Si Ho Choi, Kyu Heo, Hwayoung Yun, Yoo-Jin Choi
{"title":"EK-16005, a 2-anilinopyrimidine derivative, inhibits breast cancer progression by regulating myeloid-derived suppressor cells.","authors":"Da-Young Eum, Cong So Tran, Jisu Kim, Mi-So Jeong, Soon Yong Park, Jeyun Jo, Chaeyoung Lee, Yeo Jin Lee, Seyeon Jung, Goeun Lee, Seoung Rak Lee, Si Ho Choi, Kyu Heo, Hwayoung Yun, Yoo-Jin Choi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Targeting the behavior of myeloid-derived suppressor cells (MDSCs), either by decreasing their population or inhibiting their immunosuppressive activity, has become a promising approach in breast cancer therapy. As pivotal mediators within the tumor microenvironment (TME), MDSCs facilitate tumor progression via diverse mechanisms, including T-cell suppression, epithelial-mesenchymal transition (EMT), and the preservation of cancer cell stemness. EK-16005, a novel 2-anilinopyrimidine derivative, has shown robust inhibitory activity against breast cancer cells. In this investigation, we examined the impact of EK-16005 on the reciprocal interactions between MDSCs and cancer cells that modulate cytokine production and signaling pathway activation. EK-16005 downregulated the secretion of critical cytokines such as G-CSF, VEGF, and CXCL1/2, leading to blockade of STAT3 and Notch signaling cascades in vitro and in vivo. As a result, EK-16005 decreased MDSC expansion, tumor growth, and cancer stemness properties. Collectively, these results establish EK-16005 as a potential therapeutic candidate for interrupting MDSC-mediated tumor progression and improving outcomes in breast cancer treatment.</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multifaceted roles of casein kinase 1 in health and disease: beyond cancer.","authors":"Semi Kim, Ji Hoon Oh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Casein kinase 1 (CK1) enzymes, a family of serine/threoninespecific protein kinases, are remarkably conserved throughout evolution and exhibit diverse functionalities across eukaryotic species. While initially characterized by their role in casein (a type of milk protein) phosphorylation, subsequent investigations have unveiled their extensive involvement in fundamental biological processes, including cell division, maintenance of DNA integrity, programmed cell death, and the intricate regulation of gene transcription. Furthermore, CK1 significantly influences circadian rhythm mechanisms, highlighting its systemic regulatory importance. In mammals, multiple CK1 isoforms have been identified, each contributing to both physiological functions and various disease states. Dysregulation of CK1 activity is consistently associated with oncogenesis, where it promotes tumor cell proliferation, survival, metastasis, and resistance to therapeutic interventions. Emerging evidence also points to the critical relevance of CK1 in non-malignant conditions, such as neurodegenerative diseases, metabolic syndromes, and immune dysfunctions. In these conditions, CK1 often mediates pathogenic signaling through aberrant phosphorylation and the disruption of temporal gene expression. This review aims to re-examine the CK1 family as a versatile regulator that interacts with various pathological conditions, extending beyond its traditional classification as merely a signaling kinase. We provide an overview of the structural and functional properties of CK1 isoforms, summarize their relevance across a range of diseases, and explore novel possibilities for therapeutic interventions targeting this kinase family. Moreover, by reviewing the current understanding of CK1, we search for a new perspective on its role in maintaining cellular balance and its contribution to disease mechanisms, thereby proposing novel avenues for future research. [BMB Reports 2026; 59(6): 299-312].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"299-312"},"PeriodicalIF":4.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13311417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146141324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prime editing updates: technological evolution, methodological expansion, and delivery strategies for in vivo applications.","authors":"Uijin Jong, Dongjae Lim, Seung Hwan Lee","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Prime editing is a next-generation genome editing technology that enables precise base substitutions, insertions, and deletions at target genomic loci without inducing double-strand breaks or requiring exogenous donor DNA. This system operates through a fusion protein composed of Cas9 nickase and reverse transcriptase together with prime editing guide RNA; it has emerged as a precise genome editing platform that overcomes the limitations of conventional double-strand break-inducing CRISPR-Cas9 systems. Since first reported in 2019, diverse methodological improvements from PE1 to PE7 have been achieved, leading to rapid advances in editing efficiency, expansion of the editable target range, correction of large genomic regions, and development of in vivo delivery technologies. In this review, we comprehensively discuss the fundamental working mechanism of prime editing, its methodological evolution, recent expansion strategies, and delivery platforms for therapeutic applications, and provide perspectives for future development. [BMB Reports 2026; 59(6): 313-320].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"313-320"},"PeriodicalIF":4.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13311412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hoang Bao Khanh Chu, Ji Hye Choi, Jongbum Jeon, Soobok Joe, Hyeran Shim, Jisun Kang, Sheehyun Cho, Hong Seok Lee, Yeong Hak Bang, Jinyeong Lim, Eun Hye Joo, Kyunghee Park, Ji Hwan Moon, Kyung Yeon Han, 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, Yourae Hong, Hae-Ock Lee, Jong-Hwan Kim, Jinseon Yoo, Jaeeun Jung, Jin Ok Yang, Woong-Yang Park, Young-Joon Kim
{"title":"Transcriptomic analysis of colorectal carcinoma tissues from a Korean population.","authors":"Hoang Bao Khanh Chu, Ji Hye Choi, Jongbum Jeon, Soobok Joe, Hyeran Shim, Jisun Kang, Sheehyun Cho, Hong Seok Lee, Yeong Hak Bang, Jinyeong Lim, Eun Hye Joo, Kyunghee Park, Ji Hwan Moon, Kyung Yeon Han, 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, Yourae Hong, Hae-Ock Lee, Jong-Hwan Kim, Jinseon Yoo, Jaeeun Jung, Jin Ok Yang, Woong-Yang Park, Young-Joon Kim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>As a disease with a high mortality rate, colorectal cancer (CRC) highlights the importance of comprehending its molecular mechanisms to develop effective therapies. In this study, we conducted RNA sequencing (RNA-seq) analysis on 476 samples consisting of fresh-frozen CRC tissues and adjacent normal tissues obtained from Samsung Medical Center (SMC) in South Korea. By analyzing gene expression differences, we identified that upregulated genes in tumor samples were significantly associated with pathways related to the cell cycle, extracellular matrix (ECM)-receptor interaction, and DNA damage response (DDR). Conversely, genes exhibiting high expression in normal samples were primarily related to metabolic pathways. Tumor samples were found to be enriched in various DDR pathways, prompting an investigation into the enrichment of related genes. Additionally, the analysis focused on the Homologous recombination (HR) pathway, for which the Homologous recombination deficiency (HRD) score was calculated. Furthermore, we categorized colorectal tumor samples into four subgroups using in silico methods to identify the biological and clinical characteristics of each subgroup and compared our results with those of the widely used existing subgrouping methods. Majority of our fibroblast and immune enriched/fibroblast samples aligned with CMS4, characterized by stromal invasion and mesenchymal differentiation, whereas the immune enriched subtype aligned with CMS1, known for its immune-centric profile. To investigate the clinical implications, the composition of the tumor microenvironment (TME) by cell type was examined across four subgroups, along with an immunological analysis. In particular, the calculated HRD score and the expression levels of immune-related genes associated with CRC were analyzed to provide evidence for personalized therapeutic strategies for each subgroup. Our findings provide valuable insights into the molecular mechanisms underlying CRC in Korean patients, particularly in the SMC patient group, and offer opportunities for personalized therapeutic strategies. [BMB Reports 2026; 59(6): 321-328].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"321-328"},"PeriodicalIF":4.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13311885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"AQP1/4, CLIC5 dysregulation and lipid metabolism alterations in lung cancer.","authors":"Heung-Seok Bae, Je-Yoel Cho","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>To advance the development of novel therapies for lung cancer, we investigated tumor-associated molecules implicated in tumorigenesis. RNA-seq data were generated from paired tumors and adjacent normal tissues of four patients with lung squamous cell carcinoma (LUSC) and five patients with lung adenocarcinoma (LUAD). Additional analyses utilized RNA-seq data from The Cancer Genome Atlas (TCGA), including paired tumor and adjacent normal samples (51 LUSC, 57 LUAD) and tumor-only samples (450 LUSC, 461 LUAD). Adjacent normal tissues served as controls. Our RNA-seq results showed strong concordance with TCGA data. Ion channels Aqp1, Aqp4, and Clic5 were significantly downregulated in lung tumors, whereas enzymes involved in membrane lipid metabolism, including phosphatidylcholine (PC), sphingomyelin (SM), and cholesterol (Cho), were upregulated in lung tumors. Cardiolipin (CL), a mitochondrial inner membrane lipid, was downregulated in lung tumors. These changes might have impaired oxygen permeability and mitochondrial function, promoting hypoxia and reactive oxygen species (ROS) production. Hif1α expression was elevated in both LUSC and LUAD, along with a hypoxia-responsive protein kinase Csnk2a1 and its downstream targets Hdac1 and Hdac2. ROS-responsive transcription factors Yy1, Foxm1, E2f1, and E2f8 were also significantly upregulated in both LUSC and LUAD. Notably, the master epigenetic regulator Uhrf1 activated by these transcription factors showed marked overexpression in tumors compared to that in normal tissues. TCGA data corroborated these findings. Our study identified tumor cell membrane-associated molecules, including ion channels (Aqp1, Aqp4, Clic5) and membrane lipid metabolism enzymes (PC, SM, Cho, and CL), as critical contributors to lung tumorigenesis. These molecules represent promising targets for developing innovative anti-cancer therapies. [BMB Reports 2026; 59(6): 329-340].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"329-340"},"PeriodicalIF":4.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13311888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"SLC39 and SLC30 zinc transporters: functions and potential mechanisms in cancer.","authors":"Sung Eun Kim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Solute carrier (SLC) transporters are membrane proteins that facilitate the movement of various substrates, such as nutrients and organic or inorganic ions, across cellular membranes. Recent studies underscore the critical roles of SLC transporters in regulating cancer metabolism, immune evasion, and the tumor microenvironment. Increasing evidence suggests that the SLC39 and SLC30 families of zinc transporters, responsible for importing and exporting zinc into and out of the cytoplasm, respectively, modulate intracellular zinc distribution and signaling and may play a role in cancer initiation or progression. In this review, we discuss the functional roles of these zinc transporters in different cancer types and examine potential mechanisms linking zinc metabolism with oncogenic pathways that contribute to malignancy. [BMB Reports 2026; 59(5): 262-272].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"262-272"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147353770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinseon Yoo, Jong Lyul Lee, Hyeran Shim, Soobok Joe, Jong-Hwan Kim, Jongbum Jeon, Jisu Kim, Chan Wook Kim, Seok-Byung Lim, In Ja Park, Yong Sik Yoon, Hoang Bao Khanh Chu, Jisun Kang, Sheehyun Cho, Hong Seok Lee, Young-Joon Kim, Chang Sik Yu, Seon-Young Kim
{"title":"Integrated analysis of RNA-sequencing data and clinical data for the molecular insights and applicability of immunotherapy in the Korean colorectal cancer patients.","authors":"Jinseon Yoo, Jong Lyul Lee, Hyeran Shim, Soobok Joe, Jong-Hwan Kim, Jongbum Jeon, Jisu Kim, Chan Wook Kim, Seok-Byung Lim, In Ja Park, Yong Sik Yoon, Hoang Bao Khanh Chu, Jisun Kang, Sheehyun Cho, Hong Seok Lee, Young-Joon Kim, Chang Sik Yu, Seon-Young Kim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Colorectal cancer (CRC) is a major health concern and understanding its molecular characteristics is crucial for improving its diagnosis and treatment. Here, we present a comprehensive analysis utilizing RNA-sequencing (RNA-seq) data and clinical information from Korean patients with CRC. Differential gene expression analysis identified significant changes in gene expression between tumor and normal tissues. Gene Set Enrichment Analysis (GSEA) revealed dysregulated pathways associated with tumor progression. Furthermore, using CMScaller, we successfully stratified CRC tissues into distinct molecular subtypes. Upon reviewing the public consensus molecular subtype (CMS) signature, it was confirmed that it shares similar biological characteristics with the existing CRC. Additionally, biological characteristics of the group that could not be classified using CMScaller were found to resemble those of CMS2. Finally, distinguishing characteristics were observed between the tumor and normal groups when analyzed from an immunological perspective. Patients with CRC were checked for immunotherapy responsiveness, and those who clinically responded to immunotherapy were identified. Survival analysis confirmed that certain microsatellite stable (MSS) samples were responsive to immunotherapy and showed a relatively better prognosis. Furthermore, analysis of various immune cell types to identify genes involved in the response to immunotherapy revealed that RORC, NOS2, and KLRK1 are potential candidate genes. Our findings provide valuable insights into the molecular landscape of CRC in the Korean population and underscore the potential for integrating RNA-seq data with clinical information to improve cancer research and patient care. Immunotherapy was found to be effective in Korean patients with CRC. [BMB Reports 2026; 59(5): 273-282].</p>","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"273-282"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}