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Karunakara SH, Mehtani R, Kabekkodu SP, Kumar DP, Santhekadur PK. Genes of DLK1-DIO3 Locus and miR-379/656 Cluster is a Potential Diagnostic and Prognostic Marker in Patients With Hepatocellular Carcinoma: A Systems Biology Study. J Clin Exp Hepatol 2025; 15:102450. [PMID: 39698049 PMCID: PMC11650283 DOI: 10.1016/j.jceh.2024.102450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 11/05/2024] [Indexed: 12/20/2024] Open
Abstract
Background Hepatocellular carcinoma is the sixth most common malignancy reported globally. This highlights the need for reliable biomarkers that can be employed for diagnostic and prognostic applications. The present study aimed to classify and characterize the clinical potential of delta like non-canonical Notch ligand 1-type III iodothyronine deiodinase (DLK1-DIO3) and miR-379/656 cluster genes in hepatocellular carcinoma. Methods We extensively studied the clinical potential of DLK1-DIO3 genes through a comprehensive systems biology approach and assessed the diagnostic and prognostic potential of the genes associated with the region. Additionally, we have predicted the gene targets of the miR-379/656 cluster associated with the locus and have identified the gene ontology, pathway, and disease associations. Results We report this region as a potential biomarker for hepatocellular carcinoma. About thirty clustered miRNAs, a long-non-coding RNA, and two coding genes of the region were underexpressed in tumors. The receiver operating characteristic analysis identified 11 clustered miRNAs with diagnostic potential. Survival analyses identified maternally expressed gene 3 and the miR-379/656 cluster as prognostically significant. Further, the random forest model predicted that the miRNA cluster classifies patients according to Tumor, Node, Metastasis (TNM) staging. Furthermore, overrepresentation analysis identified several key pathways, molecular functions, and biological processes associated with the cluster gene targets. Conclusion Our study suggests that DLK1-DIO3 genes, miR-379/656 cluster, and its target gene network might be potential diagnostic and prognostic markers for hepatocellular carcinoma management and therapy.
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Affiliation(s)
- Shreyas H. Karunakara
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, Mysuru, India
| | - Rohit Mehtani
- Department of Hepatology, Amrita Institute of Medical Sciences and Research, Faridabad, India
| | - Shama P. Kabekkodu
- Department of Cell and Molecular Biology, Manipal Academy of Higher Education, Manipal, India
| | - Divya P. Kumar
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, Mysuru, India
| | - Prasanna K. Santhekadur
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, Mysuru, India
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Li JD, He RQ, Dang YW, Huang ZG, Xiong DD, Zhang L, Du XF, Chen G. Unveiling expression patterns, mechanisms, and therapeutic opportunities of transmembrane protein 106C: From pan-cancers to hepatocellular carcinoma. World J Gastrointest Oncol 2025; 17:92437. [DOI: 10.4251/wjgo.v17.i2.92437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 09/30/2024] [Accepted: 11/22/2024] [Indexed: 01/18/2025] Open
Abstract
BACKGROUND Although transmembrane protein 106C (TMEM106C) has been elucidated to be overexpressed in cancers, its underlying mechanisms have not yet been fully understood.
AIM To investigate the expression levels and molecular mechanisms of TMEM106C across 34 different cancer types, including liver hepatocellular carcinoma (LIHC).
METHODS We analyzed TMEM106C expression patterns in pan-cancers using microenvironment cell populations counter to evaluate its association with the tumor microenvironment. Gene set enrichment analysis was conducted to identify molecular pathways related to TMEM106C. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis was conducted to identify upstream transcriptional regulators of TMEM106C. In LIHC, we examined mRNA profiles, performed in-house quantitative polymerase chain reaction, immunohistochemistry, and constructed a co-expression gene network. Functional assays, including cell counting kit-8, cell cycle, apoptosis, migration, and invasion, were conducted. The effect of nitidine chloride (NC) on LIHC xenograft was evaluated through RNA sequencing and molecular docking. Finally, potential therapeutic agents targeting TMEM106C were predicted.
RESULTS TMEM106C was significantly overexpressed in 27 different cancer types and presaged poor prognosis in four of these types, including LIHC. Across pan-cancers, TMEM106C was inversely correlated to the abundances of immune and stromal cells. Furthermore, TMEM106C was significantly linked to cell cycle and DNA replication pathways in pan-cancers. ChIP-seq analysis predicted CCCTC-binding factor as a pivotal transcriptional factor targeting the TMEM106C gene in pan-cancers. Integrated analysis showed that TMEM106C was upregulated in 4657 LIHC compared with 3652 normal liver tissue [combined standardized mean difference = 1.31 (1.09, 1.52)]. In-house LIHC samples verified the expression status of TMEM106C. Higher TMEM106C expression signified worse survival conditions in LIHC patients treated with sorafenib, a tyrosine kinase inhibitor (TKI). Co-expressed analysis revealed that TMEM106C were significantly enriched in the cell cycle pathway. Knockout experiments demonstrated that TMEM106C plays a crucial role in LIHC cell proliferation, migration, and invasion, with cell cycle arrest occurring at the DNA synthesis phase, and increased apoptosis. Notably, TMEM106C upregulation was attenuated by NC treatment. Finally, TMEM106C expression levels were significantly correlated with the drug sensitivity of anti-hepatocellular carcinoma agents, including JNJ-42756493, a TKI agent.
CONCLUSION Overexpressed TMEM106C was predicted as an oncogene in pan-cancers, which may serve as a promising therapeutic target for various cancers, including LIHC. Targeting TMEM106C could potentially offer a novel direction in overcoming TKI resistance specifically in LIHC. Future research directions include in-depth experimental validation and exploration of TMEM106C’s role in other cancer types.
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Affiliation(s)
- Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Dan-Dan Xiong
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Lu Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiu-Fang Du
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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3
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Ba L, Zhao Z, Zhang C, Chu Y, Wu C. Expression and prognostic impact of hypoxia- and immune escape-related genes in triple-negative breast cancer: A comprehensive analysis. Int Immunopharmacol 2025; 146:113810. [PMID: 39689602 DOI: 10.1016/j.intimp.2024.113810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 11/23/2024] [Accepted: 12/04/2024] [Indexed: 12/19/2024]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that lacks effective therapeutic options. Hypoxia and immune escape are critical factors that contribute to the progression of and resistance to therapy in patients with TNBC. Nevertheless, few studies have comprehensively analyzed hypoxia and immune escape in patients with TNBC. This study aimed to examine the expression of hypoxia- and immune escape-related genes in TNBC and their influence on prognosis. TNBC datasets were downloaded and processed from The Cancer Genome Atlas and Gene Expression Omnibus. Differential expression analysis identified 4949 differentially expressed genes, between TNBC and normal tissues. The intersection yielded 116 hypoxia- and immune escape-related differentially expressed genes (H&IERDEGs), including KIF4A, BIRC5, and BUB1. Enrichment analyses indicated that H&IERDEGs were significantly enriched in biological processes, including cell chemotaxis, leukocyte migration, and cytokine-cytokine receptor interaction. Subsequently, weighted gene co-expression network analysis identified 43 module genes that were found to define two TNBC subtypes. We constructed a prognostic risk model consisting of eight signature genes, which demonstrated a high predictive performance to predict the overall survival (OS) of patients with TNBC with an area under the curve (AUC) exceeding 0.9 at 1 year survival. This indicates that the model effectively differentiates between outcomes, reflecting its robust performance. This study investigated the roles and potential mechanisms of hypoxia- and immune escape-related genes in TNBC and constructed a prognostic risk model with a high predictive performance. These findings offer novel molecular markers and potential therapeutic targets for TNBC.
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Affiliation(s)
- Li Ba
- Department of Ultrasound, First Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China
| | - Zhiyu Zhao
- Department of Ultrasound, First Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150001, PR China
| | - Chunmei Zhang
- Department of Ultrasound, First Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China
| | - Yinzhu Chu
- Department of Ultrasound, First Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China
| | - Changjun Wu
- Department of Ultrasound, First Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China.
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Chen G, Shi X, Jiao R, Qian J, Du X, Liu J, Zeng X. Expression and prognostic value of ferritinophagy-related NCOA4 gene in low-grade glioma: integration of bioinformatics and experimental validation. BMC Neurol 2025; 25:26. [PMID: 39825225 DOI: 10.1186/s12883-025-04036-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 01/14/2025] [Indexed: 01/20/2025] Open
Abstract
BACKGROUND Low-grade glioma (LGG) is a primary brain tumor with relatively low malignancy. NCOA4 is a key regulator of ferritinophagy-related processes and is involved in the occurrence and development of many cancers. However, the role of NCOA4 in LGG remains poorly understood. METHODS This study comprehensively analyzed several mainstream bioinformatics databases to explore the expression, diagnostic efficacy, clinical pathological features, immune infiltration, prognostic value, and biological functions of NCOA4 in LGG. Immunohistochemistry experiments were conducted using LGG tissue samples collected from our hospital to validate the bioinformatics analysis results. RESULTS NCOA4 expression was significantly elevated in LGG (p < 0.05), with an Area Under the Receiver Operating Characteristic Curve (AUC) of 0.973, suggesting it as a potential diagnostic marker. High NCOA4 expression was associated with younger age (21-40 years), lower malignancy (oligodendroglioma), and better prognosis (IDHmut-non-codel and IDHmut-codel subtypes) (all p < 0.05) in LGG. Kaplan-Meier survival curves from three databases showed that high NCOA4-expressing LGG patients had better prognosis (all p < 0.05). NCOA4 correlated weakly with B cells, CD8 + T cells, macrophages, and dendritic cells infiltration (all with correlation coefficients r < 0.3, and p < 0.05) in LGG. Multivariate Cox regression identified NCOA4, age, CD8 T cells, and macrophages as LGG independent prognostic factors (all p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that NCOA4's primary function in LGG is related to autophagy processes (all p < 0.05). CONCLUSION Our findings suggest that NCOA4 could be a potential prognostic marker and therapeutic target in LGG.
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Affiliation(s)
- Guangtang Chen
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xueping Shi
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Rukai Jiao
- Department of Neurosurgery, The Affiliated Jinyang Hospital of Guizhou Medical University, Guiyang, 550081, Guizhou, China
| | - Jiacai Qian
- Department of Neurosurgery, The Affiliated Jinyang Hospital of Guizhou Medical University, Guiyang, 550081, Guizhou, China
| | - Xiaolin Du
- Department of Neurosurgery, The Affiliated Jinyang Hospital of Guizhou Medical University, Guiyang, 550081, Guizhou, China
| | - Jian Liu
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, 550499, Guizhou, China.
| | - Xi Zeng
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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Li B, Zeng T, Chen C, Wu Y, Huang S, Deng J, Pang J, Cai X, Lin Y, Sun Y, Chong Y, Li X, Gong J, Tang G. Unraveling the potential mechanism and prognostic value of pentose phosphate pathway in hepatocellular carcinoma: a comprehensive analysis integrating bulk transcriptomics and single-cell sequencing data. Funct Integr Genomics 2025; 25:11. [PMID: 39798003 DOI: 10.1007/s10142-024-01521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 11/25/2024] [Accepted: 12/28/2024] [Indexed: 01/13/2025]
Abstract
Hepatocellular carcinoma (HCC) remains a malignant and life-threatening tumor with an extremely poor prognosis, posing a significant global health challenge. Despite the continuous emergence of novel therapeutic agents, patients exhibit substantial heterogeneity in their responses to anti-tumor drugs and overall prognosis. The pentose phosphate pathway (PPP) is highly activated in various tumor cells and plays a pivotal role in tumor metabolic reprogramming. This study aimed to construct a model based on PPP-related Genes for risk assessment and prognosis prediction in HCC patients. We integrated RNA-seq and microarray data from TCGA, GEO, and ICGC databases, along with single-cell RNA sequencing (scRNA-seq) data obtained from HCC patients via GEO. Based on the "Seurat" R package, we identified distinct gene clusters related to the PPP within the scRNA-seq data. Using a penalized Cox regression model with least absolute shrinkage and selection operator (LASSO) penalties, we constructed a risk prognosis model. The validity of our risk prognosis model was further confirmed in external cohorts. Additionally, we developed a nomogram capable of accurately predicting overall survival in HCC patients. Furthermore, we explored the predictive potential of our risk model within the immune microenvironment and assessed its relevance to biological function, particularly in the context of immunotherapy. Subsequently, we performed in vitro functional validation of the key genes (ATAD2 and SPP1) in our model. A ten-gene signature associated with the PPP was formulated to enhance the prediction of HCC prognosis and anti-tumor treatment response. Following this, the ROC curve, nomogram, and calibration curve outcomes corroborated the model's robust clinical predictive capability. Functional enrichment analysis unveiled the engagement of the immune system and notable variances in the immune infiltration landscape across the high and low-risk groups. Additionally, tumor mutation frequencies were observed to be elevated in the high-risk group. Based on our analyses, the IC50 values of most identified anticancer agents demonstrated a correlation with the RiskScore. Additionally, the high-risk and low-risk groups exhibited differential sensitivity to various drugs. Cytological experiments revealed that silencing ATAD2 or SPP1 suppresses malignant phenotypes, including viability and migration, in liver cancer cells. In this study, a novel gene signature related to the PPP was developed, demonstrating favorable predictive performance. This signature holds significant guiding value for assessing the prognosis of HCC patients and directing individualized treatment strategies.
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Affiliation(s)
- Bin Li
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Tao Zeng
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Cui Chen
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yuankai Wu
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Shuying Huang
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jing Deng
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jiahui Pang
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xiang Cai
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yuxi Lin
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yina Sun
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yutian Chong
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xinhua Li
- Department of Infectious Diseases, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Jiao Gong
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Guofang Tang
- Institute of Infectious Diseases, Guangdong Province, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China.
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6
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Takano EA, Jana MK, Lara Gonzalez LE, Pang JMB, Salgado R, Loi S, Fox SB. Preliminary characterisation of the spatial immune and vascular environment in triple negative basal breast carcinomas using multiplex fluorescent immunohistochemistry. PLoS One 2025; 20:e0317331. [PMID: 39792888 PMCID: PMC11723538 DOI: 10.1371/journal.pone.0317331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 12/27/2024] [Indexed: 01/12/2025] Open
Abstract
Triple negative breast cancers often contain higher numbers of tumour-infiltrating lymphocytes compared with other breast cancer subtypes, with their number correlating with prolonged survival. Since little is known about tumour-infiltrating lymphocyte trafficking in triple negative breast cancers, we investigated the relationship between tumour-infiltrating lymphocytes and the vascular compartment to better understand the immune tumour microenvironment in this aggressive cancer type. We aimed to identify mechanisms and signaling pathways responsible for immune cell trafficking in triple negative breast cancers, specifically of basal type, that could potentially be manipulated to change such tumours from immune "cold" to "hot" thereby increasing the likelihood of successful immunotherapy in this challenging patient population. We characterised the spatial immune environment in 10 basal breast cancers showing a range of tumour-infiltrating lymphocytes using multiplex fluorescent immunohistochemistry and quantitative digital analysis of CD3+ T cells. We examined their relationship to blood vessels and their activation status as defined by VCAM-1, ICAM-1 and PD-L1. Confirmation of the relationship between tumour-infiltrating lymphocytes and endothelial activation was performed through in silico analysis on TCGA BRCA RNA-seq data (N = 808). Significantly higher CD3+ T cell densities were observed in the stromal compartment compared with the neoplastic cell compartment (P = 0.003). ICAM-1 activated blood vessels were spatially associated with higher CD3+ T cell densities only within 30 microns of blood vessels compared with more distal activated and non-activated blood vessels (P = 0.041). In silico analysis confirmed higher numbers of tumour-infiltrating lymphocytes in basal breast cancers and that higher numbers were significantly associated with endothelial cell activation molecules, co-clustering with upregulated ICAM-1 and VCAM-1 amongst others. PD-L1 was also identified in a subset of blood vessels, suggesting an additional immune regulatory mechanism in endothelial cells. Regulating the activation status of tumour-associated vascular endothelial cells may improve T cell trafficking into basal breast tumours and enhance immunotherapeutic response.
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Affiliation(s)
- Elena A. Takano
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Metta K. Jana
- Centre for Advanced Histology and Microscopy, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Luis E. Lara Gonzalez
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jia-Min B. Pang
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Roberto Salgado
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- GZA-ZNA-Hospitals, Antwerp, Belgium
| | - Sherene Loi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen B. Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
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7
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Bai W, Xu J, Gu W, Wang D, Cui Y, Rong W, Du X, Li X, Xia C, Gan Q, He G, Guo H, Deng J, Wu Y, Yen RWC, Yegnasubramanian S, Rothbart SB, Luo C, Wu L, Liu J, Baylin SB, Kong X. Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy. Nat Commun 2025; 16:474. [PMID: 39774694 PMCID: PMC11707192 DOI: 10.1038/s41467-024-55481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
UHRF1 maintains DNA methylation by recruiting DNA methyltransferases to chromatin. In mouse, these dynamics are potently antagonized by a natural UHRF1 inhibitory protein STELLA, while the comparable effects of its human ortholog are insufficiently characterized, especially in cancer cells. Herein, we demonstrate that human STELLA (hSTELLA) is inadequate, while mouse STELLA (mSTELLA) is fully proficient in inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. Structural studies reveal a region of low sequence homology between these STELLA orthologs that allows mSTELLA but not hSTELLA to bind tightly and cooperatively to the essential histone-binding, linked tandem Tudor domain and plant homeodomain (TTD-PHD) of UHRF1, thus mediating ortholog-specific UHRF1 inhibition. For translating these findings to cancer therapy, we use a lipid nanoparticle (LNP)-mediated mRNA delivery approach in which the short mSTELLA, but not hSTELLA regions are required to reverse cancer-specific DNA hypermethylation and impair colorectal cancer tumorigenicity.
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Affiliation(s)
- Wenjing Bai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Wenbin Gu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Danyang Wang
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ying Cui
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Weidong Rong
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoan Du
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxia Li
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cuicui Xia
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qingqing Gan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Guantao He
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huahui Guo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinfeng Deng
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yuqiong Wu
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ray-Whay Chiu Yen
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Linping Wu
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA.
| | - Xiangqian Kong
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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8
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Furth N, Cohen N, Spitzer A, Salame TM, Dassa B, Mehlman T, Brandis A, Moussaieff A, Friedmann-Morvinski D, Castro MG, Fortin J, Suvà ML, Tirosh I, Erez A, Ron G, Shema E. Oncogenic IDH1 mut drives robust loss of histone acetylation and increases chromatin heterogeneity. Proc Natl Acad Sci U S A 2025; 122:e2403862122. [PMID: 39793065 PMCID: PMC11725805 DOI: 10.1073/pnas.2403862122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 11/15/2024] [Indexed: 01/12/2025] Open
Abstract
Malignant gliomas are heterogeneous tumors, mostly incurable, arising in the central nervous system (CNS) driven by genetic, epigenetic, and metabolic aberrations. Mutations in isocitrate dehydrogenase (IDH1/2mut) enzymes are predominantly found in low-grade gliomas and secondary high-grade gliomas, with IDH1 mutations being more prevalent. Mutant-IDH1/2 confers a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), resulting in an aberrant hypermethylation phenotype. Yet, the complete depiction of the epigenetic alterations in IDHmut cells has not been thoroughly explored. Here, we applied an unbiased approach, leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, to systematically profile the effect of mutant-IDH1 expression on a broad panel of histone modifications at single-cell resolution. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH1, with the most prominent being deregulation of histone acetylation marks. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Notably, the changes in acetylation are not predominantly driven by 2-HG, can be rescued by pharmacological inhibition of mutant-IDH1, and reversed by acetate supplementations. Furthermore, cells expressing mutant-IDH1 show higher epigenetic and transcriptional heterogeneity and upregulation of oncogenes such as KRAS and MYC, highlighting its tumorigenic potential. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma and highlights epigenetic and oncogenic pathways affected by mutant-IDH1-driven metabolic rewiring.
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Affiliation(s)
- Noa Furth
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Niv Cohen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
- Oncology Institute, Tel Aviv Sourasky Medical Center, Tel Aviv6423906, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tomer-Meir Salame
- Mass Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Tevie Mehlman
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Alexander Brandis
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Arieh Moussaieff
- The Institute for Drug Research, Faculty of Medicine, Hebrew University, Jerusalem9112102, Israel
| | - Dinorah Friedmann-Morvinski
- Sagol School of Neurobiology, Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI48109
| | - Jerome Fortin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QCH3A 2B4, Canada
| | - Mario L. Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Broad Institute of Harvard and MIT, Cambridge, MA02142
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Guy Ron
- Racah Institute of Physics, Hebrew University, Jerusalem9190401, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
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9
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Verma RK, Srivastava PK, Singh A. Comprehensive analysis of inhibin-β A as a potential biomarker for gastrointestinal tract cancers through bioinformatics approaches. Sci Rep 2025; 15:1090. [PMID: 39774945 PMCID: PMC11707248 DOI: 10.1038/s41598-024-72679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 09/10/2024] [Indexed: 01/11/2025] Open
Abstract
Inhibin, β, which is also known as INHBA, encodes a protein that belongs to the Transforming Growth factor-β (TGF-β) superfamily, which plays a pivotal role in cancer. Gastrointestinal tract (GI tract) cancer refers to the cancers that develop in the colon, liver, esophagus, stomach, rectum, pancreas, and bile ducts of the digestive system. The role of INHBA in all GI tract cancers remains understudied. By utilizing GEPIA2, which uses transcriptomic data from TCGA, we examined the expression of INHBA across different GI tract cancers. The results revealed consistent upregulation of INHBA in all TCGA GI tract cancers, except for liver hepatocellular carcinoma, where it showed downregulation compared to normal tissues, along with GTEx normal samples. Significant differences in INHBA expression were noted in adenocarcinomas of the colon, pancreas, rectum, and stomach, while no such differences were observed in cholangiocarcinoma and liver cancer. Moreover, a comprehensive bioinformatics analysis has been done to demonstrate that the differences in expression levels are significantly related to pathological tumor stages and prognosis in different GI tract cancers. Mucinous adenocarcinoma, esophageal squamous cell carcinoma, and stomach adenocarcinoma show a higher frequency of INHBA alteration and are primarily linked to mutations and amplifications. DNA methylation, immune infiltration, functional enrichment analysis, the genes associated with INHBA, and survival analysis in all TCGA GI tract cancers have been extensively analyzed. In colon and stomach cancers, increased INHBA expression significantly correlates with poorer overall survival (OS). However, in colon and pancreatic adenocarcinoma, higher expression is significantly associated with worse disease-free survival (DFS). Additionally, INHBA expression exhibited a positive correlation with cancer-associated fibroblasts across all gastrointestinal (GI) tract cancers. The KEGG pathway analysis revealed that INHBA and its interacting proteins are involved in several pathways, including TGF-beta signaling, Signalling pathways regulating pluripotency of stem cells, colorectal cancer, pancreatic cancer, AGE-RAGE signaling, and so on as major pathways. These findings demonstrate that INHBA could serve as a potential biomarker therapeutic target for GI tract cancer.
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Affiliation(s)
- Rohit Kumar Verma
- Department of Life Sciences, School of Natural Sciences (SONS), Shiv Nadar Institution of Eminence, Delhi NCR, India
| | | | - Ashutosh Singh
- Department of Life Sciences, School of Natural Sciences (SONS), Shiv Nadar Institution of Eminence, Delhi NCR, India.
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10
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Qiu Z, Guo C, Liu X, Gao S, Xiao W, Cheng H, Yin L. Exploring the relationship between MGAT2 and glioblastoma: A Mendelian Randomization and bioinformatics approach. Brain Res 2025; 1850:149449. [PMID: 39788365 DOI: 10.1016/j.brainres.2025.149449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 12/15/2024] [Accepted: 01/06/2025] [Indexed: 01/12/2025]
Abstract
BACKGROUND Mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase 2 (MGAT2) and tumors' relevant research was in full swing recently. Therefore, we employed Mendelian Randomization (MR) alongside bioinformatics to thoroughly investigate the possible relationship between MGAT2 and glioblastoma (GBM). METHODS We utilized the summary statistics of genome-wide association studies (GWAS) for MGAT2 (N = 35,559 from deCODE) and glioblastoma (N = 379,155 from FinnGen). MR was used to assess the causal relationship between MGAT2 and GBM. Bioinformatics was used for a more in-depth exploration of the relationship between MGAT2 and GBM. RESULTS MR analysis demonstrated a causal relationship, showing that elevated levels of MGAT2 are associated with an increased risk of GBM (OR = 2.59, 95 % CI: 1.13-5.91, p = 0.023). Further investigation revealed significant differences in MGAT2 expression across normal tissue, tumor tissue, and gliomas of different types. Additionally, we found that MGAT2 may influence GBM through immune-related pathways, particularly through the role of macrophages. Proteins associated with MGAT2 were also identified in the PPI network. CONCLUSION This study first validated the causal relationship between MGAT2 and glioblastoma, and used bioinformatics to explore the relationship from multiple perspectives. Additionally, we proposed hypotheses for further research to investigate the potential mechanisms underlying this connection.
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Affiliation(s)
- Zili Qiu
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China
| | - Chengcheng Guo
- Department of Intensive Care Unit, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xuejiao Liu
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China
| | - Shangfeng Gao
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China
| | - Weihan Xiao
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China
| | - Hai Cheng
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China
| | - Luxin Yin
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China; Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou 221002, China.
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11
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Yang J, Cao Z, Yu C, Cui W, Zhou J. Identification of a mitophagy-related gene signature for predicting overall survival and response to immunotherapy in rectal cancer. BMC Cancer 2025; 25:15. [PMID: 39762799 PMCID: PMC11706142 DOI: 10.1186/s12885-024-13412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Accepted: 12/30/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Rectal cancer is a highly heterogeneous gastrointestinal tumor, and the prognosis for patients with treatment-resistant and metastatic rectal cancer remains poor. Mitophagy, a type of selective autophagy that targets mitochondria, plays a role in promoting or inhibiting tumors; however, the importance of mitophagy-related genes (MRGs) in the prognosis and treatment of rectal cancer is unclear. METHODS In this study, we used the differentially expressed genes (DEGs) and MRGs from the TCGA-READ dataset to identify differentially expressed mitophagy-related genes (MRDEGs). The mitophagy scores were then analyzed for differential expression and ROC. Seven module genes were identified using the weighted gene coexpression network analysis (WGCNA) approach and subsequently validated in the merged datasets GSE87211 and GSE90627. The model genes were obtained based on prognostic features, and the subgroups were distinguished by risk score. Gene enrichment, immune infiltration and immunotherapy response were also evaluated. Finally, validation of prognostic gene expression in rectal cancer was carried out using clinical samples, employing Immunohistochemistry (IHC). RESULTS We demonstrated that 22 MRGs were differentially expressed between normal and rectal cancer tissues. A prognostic model for rectal cancer MRGs was constructed using WGCNA and Cox regression, which exhibited good diagnostic performance. In this study, we identified four molecular markers (MYLK, FLNC, MYH11, and NEXN) as potential prognostic biomarkers for rectal cancer for the first time. Moreover, our findings indicate that the risk scores derived from the four MRGs are associated with tumor immunity. To further validate our findings, IHC analyses suggested that the expression of MYH11 in rectal cancer tissues was lower than in nontumorous rectal tissues. CONCLUSION MRGs could predict the prognosis and response to immunotherapy in patients with rectal cancer and might be able to personalize treatment for patients.
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Affiliation(s)
- Jian Yang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Zhifei Cao
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Chengqing Yu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Wenxu Cui
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Jian Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China.
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12
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Zhang Y, Liu K, Xu Z, Li B, Wu X, Fan R, Yao X, Wu H, Duan C, Gong Y, Chen K, Zeng J, Li L, Xu H. OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers. Nucleic Acids Res 2025; 53:D1460-D1466. [PMID: 39558172 PMCID: PMC11701682 DOI: 10.1093/nar/gkae1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 10/06/2024] [Accepted: 11/04/2024] [Indexed: 11/20/2024] Open
Abstract
Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event. We have developed the OncoSplicing database for integrative analysis of clinically relevant alternative splicing events in TCGA cancers. Here, we further updated the OncoSplicing database by performing correlation analysis between the splicing and mRNA expression data from the TCGA cancers or GTEx tissues, mapping known RNA-binding motifs and eCLIP-seq peaks to all AS events, conducting splicing analysis for RNA-seq data from RBP perturbation experiments in the ENCODE project, and integrating exon and intron sequences for each AS event. With this updated database, users can easily identify potential RBPs responsible for the queried AS event and obtain sequences to design AS-specific primers and minigene constructs for experiment validation. Overall, compared to the previous version, the substantially updated OncoSplicing database (www.oncosplicing.com) offers a more valuable resource for users to identify RBPs responsible for regulating alternative splicing events in cancers.
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Affiliation(s)
- Yangjun Zhang
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
- Department of Biological Repositories, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
- Department of Urology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Kai Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Zhenzhen Xu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Bo Li
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Ruixin Fan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Huahui Wu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
| | - Chen Duan
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
| | - Yan Gong
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Jin Zeng
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330000, China
| | - Lu Li
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Hua Xu
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
- Department of Biological Repositories, Zhongnan Hospital, Wuhan University, Wuhan 430000, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430000, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430000, China
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13
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Nakano T, Okita K, Okazaki S, Yoshimoto S, Masuko S, Yagi H, Kato K, Tomioka Y, Imai K, Hamada Y, Masuko K, Shimada-Takaura K, Nagai N, Saya H, Arai T, Ishiwata T, Masuko T. CD44v, S1PR1, HER3, MET and cancer-associated amino acid transporters are promising targets for the pancreatic cancers characterized using mAb. FEBS Open Bio 2025. [PMID: 39757718 DOI: 10.1002/2211-5463.13963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 11/09/2024] [Accepted: 12/18/2024] [Indexed: 01/07/2025] Open
Abstract
Effective therapies have yet to be established for pancreatic ductal adenocarcinomas (PDAC) even though it is the most aggressive cancer. In the present study, PDAC was analyzed using novel rat mAbs against membrane proteins in conjunction with flow cytometry and immunohistochemistry. Human epidermal growth receptor (HER)1-4, mesenchymal to epithelial transition factor (MET), sphingosine-1-phospahate receptor 1 (S1PR1), l-type amino acid transporter 1 (LAT1), system x- c transporter (xCT), alanine-serine-cysteine transporter (ASCT2), cationic amino acid transporter 1 (CAT1) and variant CD44 (CD44v) were expressed at high frequencies in both in vitro and in vivo PDAC. Internalization of membrane proteins by mAbs and growth inhibition by toxin-linked mAbs were demonstrated in many PDAC cell lines, and mAbs against S1PR1, ASCT2, HER3 and CD44v inhibited the growth of xenografted MIA PaCa-2 PDAC cells. Furthermore, CD44v-high PDAC showed high mRNA expression of HER1-3, MET and CD44v, and was correlated with poor prognosis. Taken together, our results suggest that CD44v, S1PR1, HER3, MET and the above-mentioned cancer-associated amino acid transporters might be promising targets for the diagnosis and treatment of PDAC.
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Affiliation(s)
- Takashi Nakano
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Faculty of Health and Sports Sciences, Toyo University, Kita-ku, Japan
| | - Kouki Okita
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Advanced Design for Pharmaceuticals, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
| | - Shogo Okazaki
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Department of Microbiology, Division of Immunology and Pathobiology, School of Dentistry, Nihon University, Chiyoda-ku, Japan
| | - Soshi Yoshimoto
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- PIERAS Co., Ltd, Osaka-shi, Japan
| | - Sachiko Masuko
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- PIERAS Co., Ltd, Osaka-shi, Japan
| | - Hideki Yagi
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Department of Pharmaceuticals, Faculty of Pharmacy, International University of Health and Welfare, Otawara-shi, Japan
| | - Kazunori Kato
- Faculty of Health and Sports Sciences, Toyo University, Kita-ku, Japan
| | - Yoshihisa Tomioka
- Oncology Pharmacy Practice and Science, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai-shi, Japan
| | - Kenichi Imai
- Department of Microbiology, Division of Immunology and Pathobiology, School of Dentistry, Nihon University, Chiyoda-ku, Japan
| | | | - Kazue Masuko
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
| | | | - Noriaki Nagai
- Advanced Design for Pharmaceuticals, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
| | - Hideyuki Saya
- Oncology Innovation Center, Fujita Health University, Toyoake-shi, Japan
| | - Tomio Arai
- Division of Aging and Carcinogenesis, Research Team for Geriatric Pathology, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Japan
| | - Toshiyuki Ishiwata
- Division of Aging and Carcinogenesis, Research Team for Geriatric Pathology, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Japan
| | - Takashi Masuko
- Cell Biology Laboratory, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Advanced Design for Pharmaceuticals, School of Pharmacy, Kindai University, Higashiosaka-shi, Japan
- Oncology Innovation Center, Fujita Health University, Toyoake-shi, Japan
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14
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Hu X, Wang Y, Zhang S, Gu X, Zhang X, Li L. LncRNA HOXA10-AS as a novel biomarker and therapeutic target in human cancers. Front Mol Biosci 2025; 11:1520498. [PMID: 39830983 PMCID: PMC11738949 DOI: 10.3389/fmolb.2024.1520498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Accepted: 12/06/2024] [Indexed: 01/22/2025] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial regulatory molecules that participate in numerous cellular development processes, and they have gathered much interest recently. HOXA10 antisense RNA (HOXA10-AS, also known as HOXA-AS4) is a novel lncRNA that was identified to be dysregulated in some prevalent malignancies. In this review, the clinical significance of HOXA10-AS for the prognosis of various cancers is analyzed. In addition, the major advances in our understanding of the cellular biological functions and mechanisms of HOXA10-AS in different human cancers are summarized. These cancers include esophageal carcinoma (ESCA), gastric cancer (GC), glioma, laryngeal squamous cell carcinoma (LSCC), acute myeloid leukemia (AML), lung adenocarcinoma (LUAD), nasopharyngeal carcinoma (NPC), oral squamous cell carcinoma (OSCC), and pancreatic cancer. We also note that the aberrant expression of HOXA10-AS promotes malignant progression through various underlying mechanisms. In conclusion, HOXA10-AS is expected to serve as an ideal clinical biomarker and an effective cancer therapy target.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Yong Wang
- Shandong Provincial Engineering Research Center for Bacterial Oncolysis and Cell Treatment, Jinan, Shandong, China
| | - Sijia Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Xiaosi Gu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Lianlian Li
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong, China
- Laboratory of Metabolism and Gastrointestinal Tumor, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
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15
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Zhou T, Zhang DD, Jin J, Xie J, Yu J, Zhu C, Wan R. Multiomic characterization, immunological and prognostic potential of SMAD3 in pan-cancer and validation in LIHC. Sci Rep 2025; 15:657. [PMID: 39753728 PMCID: PMC11698864 DOI: 10.1038/s41598-024-84553-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 12/24/2024] [Indexed: 01/06/2025] Open
Abstract
SMAD3, a protein-coding gene, assumes a pivotal role within the transforming growth factor-beta (TGF-β) signaling pathway. Notably, aberrant SMAD3 expression has been linked to various malignancies. Nevertheless, an extensive examination of the comprehensive pan-cancer impact on SMAD3's diagnostic, prognostic, and immunological predictive utility has yet to be undertaken. Bioinformatics methods were employed to systematically investigate the potential carcinogenic impact of SMAD3. We extensively harnessed data from authoritative sources, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), cBioPortal, Human Protein Atlas (HPA), UALCAN, and various other databases. Our study encompassed a comprehensive analysis of the following aspects: differential SMAD3 expression and its association with prognosis across diverse cancer types, gene mutations, immune cell infiltration, single-cell sequencing analysis, DNA methylation patterns, and drug sensitivity profiles. In vitro experiments were conducted with the primary objective of appraising both the expression profile and the precise functional attributes of SMAD3 within the milieu of Liver Hepatocellular Carcinoma (LIHC). Our findings revealed significant variations in SMAD3 expression between cancerous and adjacent normal tissues. High levels of SMAD3 expression were consistently associated with unfavorable prognoses across multiple cancer types,. Additionally, our analysis of SMAD3 methylation patterns in human cancers unveiled a favorable prognosis linked to elevated DNA methylation levels in pan-cancer. Furthermore, we identified positive associations between SMAD3 expression and RNAm6A methylation-related genes in the majority of cancers. Moreover, SMAD3 expression displayed substantial correlations with immune cell infiltration. Notably, immune checkpoint genes exhibited significant associations with SMAD3 expression across diverse cancers. Single-cell sequencing results elucidated the pan-cancer single-cell expression landscape of SMAD3. Within specific cancer subtypes, SMAD3 expression exhibited a noteworthy positive association with distinctive facets of malignancy. Finally, in our comprehensive analysis of drug sensitivity, we discerned a catalog of prospective therapeutic agents. In our comprehensive analysis across multiple cancer types, we observed a significant disparity in SMAD3 expression compared to normal tissues, and this findings suggest that SMAD3 holds promise as both a prognostic biomarker and a therapeutic target against various cancers. Difference displayed a noteworthy association with patient prognosis.
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Affiliation(s)
- Tao Zhou
- Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China
| | - Dan Dan Zhang
- Department of General Surgery, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China
| | - Jiejing Jin
- Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China
| | - Jinyang Xie
- Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China
| | - Jianhua Yu
- Department of Cardiovascular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China
| | - Chao Zhu
- Department of Pharmacology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Rong Wan
- Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China.
- Department of Pharmacology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
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Takao S, Fukushima H, Furusawa A, Kato T, Okuyama S, Kano M, Yamamoto H, Suzuki M, Kano M, Choyke PL, Kobayashi H. Tissue factor targeted near-infrared photoimmunotherapy: a versatile therapeutic approach for malignancies. Cancer Immunol Immunother 2025; 74:48. [PMID: 39751657 PMCID: PMC11699179 DOI: 10.1007/s00262-024-03903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 11/20/2024] [Indexed: 01/04/2025]
Abstract
Tissue factor (TF) is a cell surface protein that plays a role in blood clotting but is also commonly expressed in many cancers. Recent research implicated TF in cancer proliferation, metastasis, angiogenesis, and immune escape. Therefore, TF can be considered a viable therapeutic target against cancer. Herein, we developed and tested a TF-targeted near-infrared photoimmunotherapy (NIR-PIT) as a potential treatment for several types of cancer. Tisotumab, a TF antibody, was conjugated to IR700. The efficacy of TF-targeted NIR-PIT was investigated using multiple cancer cell lines (A431; epidermoid carcinoma, HPAF-II; pancreatic adenocarcinoma, HSC-2; oral carcinoma, HT1376-luc; bladder carcinoma, MDAMB231; breast adenocarcinoma, and SKOV3-luc; ovarian serous cystadenocarcinoma) in vitro. In vivo, the efficacy of TF-targeted NIR-PIT was evaluated in HPAF-II and A431 xenograft mouse models. Pathologic changes in these tumors after NIR-PIT were evaluated in these tumor models. All cancer lines demonstrated TF expression in vitro and in vivo. Additionally, TF expression was documented to localize to cancer cells in tumors. In vitro, TF-targeted NIR-PIT caused cell death in a light dose-dependent manner. In vivo, TF-targeted NIR-PIT suppressed tumor growth and improved survival rates compared to controls. Furthermore, in vivo NIR-PIT showed histological signs of cancer cell damage, such as cytoplasmic vacuolation, nuclear dysmorphism, and extracellular leakage of LDHA consistent with cell death. In conclusion, TF-targeted NIR-PIT holds promise as a treatment for multiple cancer models expressing TF, spanning multiple cancer types.
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Affiliation(s)
- Seiichiro Takao
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Hiroshi Fukushima
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Aki Furusawa
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Takuya Kato
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Shuhei Okuyama
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Makoto Kano
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Hiroshi Yamamoto
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Motofumi Suzuki
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Miyu Kano
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Peter L Choyke
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Hisataka Kobayashi
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA.
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17
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Jiang Y, Li Y, Zheng D, Du X, Yang H, Wang C, Zhao M, Xiao H, Zhang L, Li X, Shi S. Nano-polymeric platinum activates PAR2 gene editing to suppress tumor metastasis. Biomaterials 2025; 317:123090. [PMID: 39799696 DOI: 10.1016/j.biomaterials.2025.123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 11/18/2024] [Accepted: 01/02/2025] [Indexed: 01/15/2025]
Abstract
Metastasis as the hallmark of cancer preferentially contributes to tumor recurrence and therapy resistance, aggrandizing the lethality of patients with cancer. Despite their robust suppressions of tumor progression, chemotherapeutics failed to attenuate cancer cell migration and even triggered pro-metastatic effects. In parallel, protease-activated receptor 2 (PAR2), a member of the G protein-coupled receptor subfamily, actively participates in cancer metastasis via multiple signal transduction pathways. CRISPR/Cas9 that is a dominating genome editing tool can evoke PAR2 knockout to inhibit cancer metastasis. However, the absence of valid delivery systems largely limits its efficacy. Herein, we nanosized polymeric platinum (NanoPt) as therapeutical drug carries to deliver CRISPR/Cas9 to elicit genome editing of PAR2, which drastically augmented anti-metastatic effects and alleviated systematic toxicity of platinum-based treatment in vitro and in vivo. More importantly, the NanoPt@Cas9-PAR2 initiated PAR2 deficiency to mechanistically attenuate EMT process and ferroptosis via RAGE/ERK signalling, consequently preventing cancer cell migration. Our findings indicate that NanoPt@Cas9-PAR2 that mitigated PAR2 signalling and cytotoxic effects of platinum could be a safe and powerful all-in-one combinatorial strategy for cancer treatment.
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Affiliation(s)
- Yuhong Jiang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Dongmei Zheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xin Du
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Huan Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Chuan Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Science and Education Division, Public Health Clinical Center of Chengdu& Public Health Clinical Center of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, China
| | - Lingpu Zhang
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, China.
| | - Xiaofang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Beijing Institute of Technology Chongqing Innovation Center, Chongqing, 401120, China.
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18
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Mills JN, Gunchick V, McGue J, Qin Z, Kumar-Sinha C, Bednar F, Brown N, Shi J, Udager AM, Frankel T, Zalupski MM, Sahai V. Characterization of undifferentiated carcinomas of the pancreas with and without osteoclast-like giant cells. JNCI Cancer Spectr 2025; 9:pkae097. [PMID: 39363498 DOI: 10.1093/jncics/pkae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 09/03/2024] [Accepted: 09/22/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Undifferentiated carcinoma (UC) is a rare subtype of pancreatic cancer distinguished from UC with osteoclast-like giant cells (UC-OGC) in 2019, affecting interpretation of literature that does not distinguish these subtypes. We sought to identify translationally relevant differences between these 2 variants and compared with pancreatic ductal adenocarcinoma. METHODS We characterized clinical and multiomic differences between UC (n = 32) and UC-OGC (n = 15) using DNA sequencing, RNA sequencing, and multiplex immunofluorescence and compared these findings with pancreatic ductal adenocarcinoma. RESULTS Characteristics at diagnosis were similar between UC and UC-OGC, though the latter was more resectable (P = .009). Across all stages, median overall survival was shorter for UC than for UC-OGC (0.4 years vs 10.8 years, respectively; P = .003). This shorter survival was retained after stratification by resection, albeit without statistical significance (1.8 years vs 11.9 years, respectively; P = .08). In a subset of patients with available tissue, the genomic landscape was similar among UC (n = 9), UC-OGC (n = 5), and pancreatic ductal adenocarcinoma (n = 159). Bulk RNA sequencing was deconvoluted and, along with multiplex immunofluorescence in UC (n = 13), UC-OGC (n = 5), and pancreatic ductal adenocarcinoma (n = 16), demonstrated statistically significantly increased antigen-presenting cells, including M2 macrophages and natural killer cells, and decreased cytotoxic and regulatory T cells in UC and UC-OGC vs pancreatic ductal adenocarcinoma. Findings were similar between UC and UC-OGC , except for decreased regulatory T cells in UC-OGC (P = .04). CONCLUSIONS In this series, UC was more aggressive than UC-OGC, with these variants having more antigen-presenting cells and fewer regulatory T cells than pancreatic ductal adenocarcinoma, suggesting potential for immune-modulating therapies in the treatment of these pancreatic cancer subtypes.
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Affiliation(s)
- Jamie N Mills
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Valerie Gunchick
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Current affiliation:Department of Medicine, Division of Epidemiology, Vanderbilt University, Nashville, TN, USA
| | - Jake McGue
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Zhaoping Qin
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Filip Bednar
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Noah Brown
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jiaqi Shi
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Timothy Frankel
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Mark M Zalupski
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Vaibhav Sahai
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
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19
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Zafar S, Bai Y, Muhammad SA, Guo J, Khurram H, Zafar S, Muqaddas I, Shaikh RS, Bai B. Molecular dynamics simulation based prediction of T-cell epitopes for the production of effector molecules for liver cancer immunotherapy. PLoS One 2025; 20:e0309049. [PMID: 39752339 PMCID: PMC11698456 DOI: 10.1371/journal.pone.0309049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/05/2024] [Indexed: 01/06/2025] Open
Abstract
Liver cancer is the sixth most frequent malignancy and the fourth major cause of deaths worldwide. The current treatments are only effective in early stages of cancer. To overcome the therapeutic challenges and exploration of immunotherapeutic options, broad spectral therapeutic vaccines could have significant impact. Based on immunoinformatic and integrated machine learning tools, we predicted the potential therapeutic vaccine candidates of liver cancer. In this study, machine learning and MD simulation-based approach are effectively used to design T-cell epitopes that aid the immune system against liver cancer. Antigenicity, molecular weight, subcellular localization and expression site predictions were used to shortlist liver cancer associated proteins including AMBP, CFB, CDHR5, VTN, APOBR, AFP, SERPINA1 and APOE. We predicted CD8+ T-cell epitopes of these proteins containing LGEGATEAE, LLYIGKDRK, EDIGTEADV, QVDAAMAGR, HLEARKKSK, HLCIRHEMT, LKLSKAVHK, EQGRVRAAT and CD4+ T-cell epitopes of VLGEGATEA, WVTKQLNEI, VEEDTKVNS, FTRINCQGK, WGILGREEA, LQDGEKIMS, VKFNKPFVF, VRAATVGSL. We observed the substantial physicochemical properties of these epitopes with a significant binding affinity with MHC molecules. A polyvalent construct of these epitopes was designed using suitable linkers and adjuvant indicated significant binding energy (>-10.5 kcal/mol) with MHC class-I and II molecule. Based on in silico cloning, we found the considerable compatibility of this polyvalent construct with the E. coli expression system and the efficiency of its translation in host. The system-level and machine learning based cross validations showed the possible effect of these T-cell epitopes as potential vaccine candidates for the treatment of liver cancer.
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Affiliation(s)
- Sidra Zafar
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Punjab, Pakistan
| | - Yuhe Bai
- Department of Computer Science, Sorbonne University, Paris, France
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Punjab, Pakistan
| | - Jinlei Guo
- School of Intelligent Medical Engineering, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Haris Khurram
- Department of Mathematics and Computer Science, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Pattani, Thailand
- Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Chiniot, Punjab, Pakistan
| | - Saba Zafar
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
| | - Iraj Muqaddas
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Punjab, Pakistan
| | - Rehan Sadiq Shaikh
- Center for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Punjab, Pakistan
| | - Baogang Bai
- School of Information and Technology, Wenzhou Business College, Wenzhou, Zhejiang, China
- Zhejiang Province Engineering Research Center of Intelligent Medicine, Wenzhou, China
- The 1 School of Medical, School of Information and Engineering, The 1st Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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20
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Xiao J, Wang J, Li J, Xiao J, Liu C, Tan L, Tu Y, Yang R, Pei Y, Wang M, Wong J, Zhou BP, Li J, Feng J. L3MBTL3 and STAT3 collaboratively upregulate SNAIL expression to promote metastasis in female breast cancer. Nat Commun 2025; 16:231. [PMID: 39747894 PMCID: PMC11696420 DOI: 10.1038/s41467-024-55617-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 12/18/2024] [Indexed: 01/04/2025] Open
Abstract
The STAT3 pathway promotes epithelial-mesenchymal transition, migration, invasion and metastasis in cancer. STAT3 upregulates the transcription of the key epithelial-mesenchymal transition transcription factor SNAIL in a DNA binding-independent manner. However, the mechanism by which STAT3 is recruited to the SNAIL promoter to upregulate its expression is still elusive. In our study, the lysine methylation binding protein L3MBTL3 is positively associated with metastasis and poor prognosis in female patients with breast cancer. L3MBTL3 also promotes epithelial-mesenchymal transition and metastasis in breast cancer. Mechanistic analysis reveals that L3MBTL3 interacts with STAT3 and recruits STAT3 to the SNAIL promoter to increase SNAIL transcription levels. The interaction between L3MBTL3 and STAT3 is required for SNAIL transcription upregulation and metastasis in breast cancer, while the methylated lysine binding activity of L3MBTL3 is not required for these functions. In conclusion, L3MBTL3 and STAT3 synergistically upregulate SNAIL expression to promote breast cancer metastasis.
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Affiliation(s)
- Jianpeng Xiao
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
- The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China
| | - Jie Wang
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jie Xiao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - CuiCui Liu
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
| | - Libi Tan
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yanhong Tu
- The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China
| | - Ruifang Yang
- Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Yujie Pei
- Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Minghua Wang
- The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Binhua P Zhou
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Jing Li
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China.
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.
| | - Jing Feng
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China.
- The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China.
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.
- The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.
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21
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Chung TT, Piao Z, Lee SJ. Identification of ferroptosis-related signature predicting prognosis and therapeutic responses in pancreatic cancer. Sci Rep 2025; 15:75. [PMID: 39748113 PMCID: PMC11695983 DOI: 10.1038/s41598-024-84607-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 12/24/2024] [Indexed: 01/04/2025] Open
Abstract
Ferroptosis plays a role in tumorigenesis by affecting lipid peroxidation and metabolic pathways; however, its prognostic or therapeutic relevance in pancreatic adenocarcinoma (PAAD) remains poorly understood. In this study, we developed a prognostic ferroptosis-related gene (FRG)-based risk model using cohorts of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), proposing plausible therapeutics. Differentially expressed FRGs between tumors from TCGA-PAAD and normal pancreatic tissues from Genotype-Tissue Expression were analyzed to construct a prognostic risk model using univariate and multivariate Cox regression and LASSO analyses. A model incorporating AURKA, CAV1, and PML gene expression effectively distinguished survival differences between high- and low-risk groups among TCGA-PAAD patients, with validation in two ICGC cohorts. The high-risk group was enriched in gene sets involving mTOR, MAPK, and E2F signaling. The immune and stromal cells infiltration score did not differ between the groups. Analysis of PRISM datasets using our risk model to classify pancreatic cell lines suggested the dasatinib's efficacy in the high-risk group, which was experimentally confirmed in four cell lines with a high- or low-risk signature. In conclusion, this study proposed a robust FRG-based prognostic model that may help stratify PAAD patients with poor prognoses and select potential therapeutic avenues.
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Affiliation(s)
- Ting Ting Chung
- College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Zanyue Piao
- College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Seung Jin Lee
- College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
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22
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Lian Z, Liu X, Li X. Elucidating the expression and role of cGAS in pan-cancer using integrated bioinformatics and experimental approaches. BMC Cancer 2025; 25:5. [PMID: 39748320 PMCID: PMC11697830 DOI: 10.1186/s12885-024-13379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 12/20/2024] [Indexed: 01/04/2025] Open
Abstract
cGAS plays an important role in regulating both tumor immune responses and DNA damage repair. Nevertheless, there was little research that comprehensively analyzed the correlation between cGAS and the tumor microenvironment, immune cell infiltration, and DNA damage repair in different cancers. In this study, The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) data were used to analyze the mRNA expression and genomic alterations of cGAS in pan-cancer. The HPA database was used to explore the protein levels of cGAS in normal tissues and cancers. Correlation analysis were performed to explore the role of cGAS in interferon expression, immune cell infiltrations, DNA damage repair, and predictive immune markers. The prognostic value of cGAS was analyzed using survival data from the TCGA, Kaplan-Meier plotter database, and PrognoScan database. Lastly, the role of cGAS in DNA damage repair signaling and interferon signaling was validated in NSCLC cell lines. The results showed that cGAS was widely expressed in human normal tissues and various cancers, and the expression of cGAS was significantly upregulated in almost all of the solid cancers. Genomic analysis indicated that the expression of cGAS was positively correlated with copy number levels, while negatively correlated with the methylation levels of cGAS promoter. In addition, the level of cGAS was positively correlated with type I interferons expression, infiltration levels of most immune cell types, TMB and MSI levels, stromal and immune scores, and DNA damage repair gene sets including nonhomologous end joining and homologous recombination pathway. Survival analysis indicated that cGAS levels were associated with patient prognosis in several cancers. Lastly, in vitro study showed knockdown of cGAS expression inhibits the DNA damage repair signaling pathway and interferon signaling in NSCLC. In conclusions, cGAS is wildly activated in human cancers, which might participate in regulating cancer immunity and DNA damage repair. cGAS could be used as an effective target for cancer treatment and might be a potential predictive immune marker.
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Affiliation(s)
- Zhen Lian
- Department of Emergency, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Xue Liu
- Department of Comprehensive Treatment Ward, Mudan People's Hospital of Heze, Heze, 274000, China
| | - Xue Li
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
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23
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Nasier-Hussain M, Samanje JN, Mokhtari K, Nabi-Afjadi M, Fathi Z, Hoseini A, Bahreini E. Serum levels of oxidative stress, IL-8, and pepsinogen I/II ratio in Helicobacter pylori and gastric cancer patients: potential diagnostic biomarkers. BMC Gastroenterol 2025; 25:2. [PMID: 39748276 PMCID: PMC11697901 DOI: 10.1186/s12876-024-03564-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 12/13/2024] [Indexed: 01/04/2025] Open
Abstract
BACKGROUND AND AIM Helicobacter pylori (H.pylori), a gram-negative bacterial pathogen associated with an increased risk of gastric cancer. This study investigates potential factors in the incidence of gastric cancer in patients with H.pylori, including oxidative stress, inflammatory biomarkers, serum pepsinogens (PG) of I and II, and PG-I/PG-II ratio. METHODS The study comprised individuals with Helicobacter pylori (H.pylori) infection, gastric cancer patients, and healthy individuals. Biochemical parameters such as FBS (fasting blood sugar), lipid profile, and liver and kidney functional factors were evaluated using colorimetric techniques. Oxidative markers such as total oxidant status (TOS) and malondialdehyde (MDA) were quantified through colorimetric methods. IL-8, PG-II, and PG-II levels were also determined using the ELISA technique. RESULTS Individuals with H. pylori infection exhibited elevated levels of IL-8 (940.5 ± 249.7 vs. 603.4 ± 89.1 pg/ml, P < 0.0001) and oxidative species (5.47 ± 0.7 vs. 1.64 ± 0.7 nM, P < 0.05) compared to gastric cancer patients, who, despite having lower levels of IL-8 and oxidative species, showed higher levels of MDA. H.pylori patients exhibited significantly higher levels of PG-I (7.28 ± 2.1 vs. 2.61 ± 1.4 ng/ml, P < 0.001), PG-II (3.21 ± 1 vs. 2.6 ± 0.6 ng/ml, P < 0.001), and the PG-I/PG-II ratio (2.27 ± 1.2 vs. 1 ± 0.4, P < 0.001) compared to gastric cancer patients. The findings were substantiated using various data analysis platforms such as Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN (The University of ALabama at Birmingham CANcer data analysis), cBioPortal, and TIMER (Tumor IMmune Estimation Resource). These parameters could serve as potential diagnostic biomarkers for screening and therapeutic interventions based on the cut-off values derived from ROC (receiver operating characteristic) curves for IL-8, PGI, PGII, and PGI/PGII across the three groups. CONCLUSIONS IL-8, PGI, PGII, and PGI/PGII parameters could serve as potential diagnostic markers for the screening and treatment of gastric conditions.
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Affiliation(s)
- Marwa Nasier-Hussain
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614525, Tehran, Iran
| | - Jaleel Najah Samanje
- Collage of Health and Medical Technology, Middle Technical University, Baghdad, Iraq
| | - Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zeinab Fathi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Asieh Hoseini
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Elham Bahreini
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614525, Tehran, Iran.
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24
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Wang Y, Zhou B, Lian X, Yu S, Huang B, Wu X, Wen L, Zhu C. KIF18A Is a Novel Target of JNK1/c-Jun Signaling Pathway Involved in Cervical Tumorigenesis. J Cell Physiol 2025; 240:e31516. [PMID: 39749722 DOI: 10.1002/jcp.31516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 11/21/2024] [Accepted: 12/13/2024] [Indexed: 01/04/2025]
Abstract
Cervical cancer remains a significant global health concern. KIF18A, a kinesin motor protein regulating microtubule dynamics during mitosis, is frequently overexpressed in various cancers, but its regulatory mechanisms are poorly understood. This study investigates KIF18A's role in cervical cancer and its regulation by the JNK1/c-Jun signaling pathway. Cell growth was assessed in vitro using MTT and colony formation assays, and in vivo using a nude mouse xenograft model with KIF18A knockdown HeLa cells. The Genomic Data Commons (GDC) data portal was used to identify KIF18A-related protein kinases in cervical cancer. Western blot analysis was employed to analyze phosphor-c-Jun, c-Jun, and KIF18A expression levels following JNK1 inhibition, c-Jun knockdown/overexpression, and KIF18A knockdown in cervical cancer cells. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were performed to assess c-Jun binding and transcriptional activity of the KIF18A promoter. KIF18A knockdown significantly impaired cervical cancer cell growth both in vitro and in vivo. A strong positive correlation was observed between JNK1 and KIF18A expression in cervical and other cancers. JNK1 inhibition decreased both KIF18A expression and c-Jun phosphorylation. c-Jun was found to directly bind to and activate the KIF18A promoter. Furthermore, c-Jun knockdown inhibited cervical cancer cell growth, and this effect was partially rescued by KIF18A overexpression. This study demonstrates that the JNK1/c-Jun pathway activates KIF18A expression, which is essential for cervical cancer cell growth. Targeting the JNK/c-Jun/KIF18A axis may represent a promising novel therapeutic strategy for cancer treatment.
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Affiliation(s)
- Yajie Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Bowen Zhou
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xiaoying Lian
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Siqi Yu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Baihai Huang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xinyue Wu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Lianpu Wen
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Changjun Zhu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
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Zhong Y, Wang R, Huang Z, Hu Z, Peng B, Chen B, Sun L. Identification of SETD4 as an Onco-Immunological Biomarker Encompassing the Tumor Microenvironment, Prognoses, and Therapeutic Responses in Various Human Cancers. Immun Inflamm Dis 2025; 13:e70126. [PMID: 39817582 PMCID: PMC11736640 DOI: 10.1002/iid3.70126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 11/24/2024] [Accepted: 01/03/2025] [Indexed: 01/18/2025] Open
Abstract
BACKGROUND SET domain-containing protein 4 (SETD4) is a histone methyltransferase that has been shown to modulate cell proliferation, differentiation, and inflammatory responses by regulating histone H4 trimethylation (H4K20me3). Previous reports have demonstrated its function in the quiescence of cancer stem cells as well as drug resistance in several cancers. A limited number of systematic studies have examined SETD4's role in the tumor microenvironment, pathogenesis, prognosis, and therapeutic response. METHODS Utilizing The Cancer Genome Atlas database, and other publicly accessible platforms, we comprehensively analyzed SETD4 gene expression, methylation patterns, and prognostic significance. Furthermore, we investigated its association with cancer-related pathways, the immune microenvironment, immunotherapy markers, and drug resistance signatures of chemotherapy. Additionally, qRT-PCR was performed to validate SETD4 expression in clinical specimens. RESULTS The expression of SETD4 was abnormal across a variety of cancer types and the expression of SETD4 in colorectal cancer tissues was verified in clinical specimens. The upregulation of SETD4 may be a prognostic risk factor predicting poor overall survival and progression-free survival. The analysis revealed that the mRNA level of SETD4 was modulated by promoter methylation, and patients with lower methylation levels showed shorter survival times. Pathway analysis showed that SETD4 influenced several key cell cycle pathways, including the G2M checkpoint, and mitotic spindle pathways. In addition, SETD4 negatively affects immune cell infiltration in most cancers, including B cells, CD8 T cells, and macrophages. The correlation between SETD4 and cancer stemness as well as homologous recombination deficiency varied across tumor types, suggesting that SETD4 may play a multifaceted role in tumor resistance. Notably, we identified several potential agents targeting SETD4. CONCLUSIONS This study demonstrates that SETD4 is an immune-oncogenic molecule in multiple cancers, with the potential to be a diagnosis, prognosis, and targeted therapy marker.
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Affiliation(s)
- Yuyun Zhong
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
- The Guangzhou Bay Area Institute of BiomedicineGuangzhouChina
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's HospitalZhuhai Hospital Affiliated With Jinan UniversityZhuhaiChina
| | - Zijie Huang
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Zhaoting Hu
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
| | - Bin Peng
- Department of Thoracic SurgeryThe First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's HospitalShenzhenChina
| | - Bin Chen
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
- The Guangzhou Bay Area Institute of BiomedicineGuangzhouChina
| | - Liyue Sun
- Second Department of OncologyGuangdong Second Provincial General HospitalGuangzhouChina
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Zhao X, Wu J, Lai J, Pan B, Ji M, Li X, He Y, Han J. CITMIC: Comprehensive Estimation of Cell Infiltration in Tumor Microenvironment based on Individualized Intercellular Crosstalk. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2408007. [PMID: 39498855 PMCID: PMC11714168 DOI: 10.1002/advs.202408007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 09/27/2024] [Indexed: 11/07/2024]
Abstract
The tumor microenvironment (TME) cells interact with each other and play a pivotal role in tumor progression and treatment response. A comprehensive characterization of cell and intercellular crosstalk in the TME is essential for understanding tumor biology and developing effective therapies. However, current cell infiltration analysis methods only partially describe the TME's cellular landscape and overlook cell-cell crosstalk. Here, this approach, CITMIC, can infer the cell infiltration of TME by simultaneously measuring 86 different cell types, constructing an individualized cell-cell crosstalk network based on functional similarities between cells, and using only gene transcription data. This is a novel approach to estimating the relative cell infiltration levels, which are shown to be superior to the current methods. The TME cell-based features generated by analyzing melanoma data are effective in predicting prognosis and treatment response. Interestingly, these features are found to be particularly effective in assessing the prognosis of high-stage patients, and this method is applied to multiple high-stage adenocarcinomas, where more significant prognostic performance is also observed. In conclusion, CITMIC offers a more comprehensive description of TME cell composition by considering cell-cell crosstalk, providing an important reference for the discovery of predictive biomarkers and the development of new therapeutic strategies.
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Affiliation(s)
- Xilong Zhao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Jiashuo Wu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Jiyin Lai
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Bingyue Pan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Miao Ji
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Xiangmei Li
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yalan He
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Junwei Han
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
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Okamoto H, Mizutani S, Tsukamoto T, Katsuragawa-Taminishi Y, Kawaji-Kanayama Y, Mizuhara K, Muramatsu A, Isa R, Fujino T, Shimura Y, Ichikawa K, Kuroda J. Robust anti-myeloma effect of TAS0612, an RSK/AKT/S6K inhibitor, with venetoclax regardless of cytogenetic abnormalities. Leukemia 2025; 39:211-221. [PMID: 39438587 DOI: 10.1038/s41375-024-02439-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/08/2024] [Accepted: 10/10/2024] [Indexed: 10/25/2024]
Abstract
Multiple myeloma (MM) remains a difficult-to-treat disease even with the latest therapeutic advances due to the complex, overlapping, and heterogeneous cytogenetic, genetic, and molecular abnormalities. To address this challenging problem, we previously identified the universal and critical roles of RSK2 and AKT, the effector signaling molecules downstream of PDPK1, regardless of cytogenetic and genetic profiles. Based on this, in this study, we investigated the anti-myeloma potency of TAS0612, a triple inhibitor against RSK, including RSK2, AKT, and S6K. Treatment with TAS0612 exerted the anti-proliferative effect via cell cycle blockade and the induction of apoptosis in human myeloma-derived cell lines (HMCLs) with diverse cytogenetic and genetic profiles. Ex vivo treatment with TAS0612 also significantly reduced the viability of patient-derived primary myeloma cells with diverse cytogenetic profiles. TAS0612 simultaneously caused the upregulation of several tumor suppressor genes, modulated prognostic genes according to the MMRF CoMMpass data, and downregulated a series of Myc- and mTOR-related genes. Moreover, the combination of TAS0612 with venetoclax (VEN) showed the synergy in inducing apoptosis in HMCLs irrespective of the t(11;14) translocation status. TAS0612 alone and combined with VEN are new potent candidate therapeutic strategies for MM, regardless of cytogenetic/genetic profiles, facilitating its future clinical development.
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Affiliation(s)
- Haruya Okamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Yoko Katsuragawa-Taminishi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Yuka Kawaji-Kanayama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Kentaro Mizuhara
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Ayako Muramatsu
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Reiko Isa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Takahiro Fujino
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
- Department of Blood Transfusion, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koji Ichikawa
- Taiho Pharmaceutical Co. Ltd., Tsukuba, Ibaraki, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan.
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28
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Cui Y, Zhou X, Zheng D, Zhu Y. Validation of endoplasmic reticulum stress-related gene signature to predict prognosis and immune landscape of patients with non-small cell lung cancer. Technol Health Care 2025; 33:363-393. [PMID: 39331119 DOI: 10.3233/thc-241059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
BACKGROUND Lung cancer is one of the most common cancers worldwide, with the incidence increasing each year. It is crucial to improve the prognosis of patients who have lung cancer. Non-Small Cell Lung Cancer (NSCLC) accounts for the majority of lung cancer. Though its prognostic significance in NSCLC has not been often documented, Endoplasmic Reticulum (ER) stress has been identified to be implicated in tumour malignant behaviours and resistance to treatment. OBJECTIVE This work aimed to develop a gene profile linked to ER stress that could be applied to predictive and risk assessment for non-small cell lung cancer. METHODS Data from 1014 NSCLC patients were sourced from The Cancer Genome Atlas (TCGA) database, integrating clinical and Ribonucleic Acid (RNA) information. Diverse analytical techniques were utilized to identify ERS-associated genes associated with patients' prognoses. These techniques included Kaplan-Meier analysis, univariate Cox regression, Least Absolute Shrinkage and Selection Operator regression analysis (LASSO) regression, and Pearson correlation analysis. Using a risk score model obtained from multivariate Cox analysis, a nomogram was created and validated to classify patients into high- and low-risk groups. The study employed the CIBERSORT algorithm and Single-Sample Gene Set Eenrichment Analysis (ssGSEA) to investigate the tumour immune microenvironment. We used the Genomics of Drug Sensitivity in Cancer (GDSC) database and R tools to identify medicines that could be responsive. RESULTS Four genes - FABP5, C5AR1, CTSL, and LTA4H - were chosen to create the risk model. Overall Survival (OS) was considerably lower (P< 0.05) in the high-risk group. When it came to predictive accuracy, the risk model outperformed clinical considerations. Several medication types that are sensitive to high-risk groups were chosen. CONCLUSION Our study has produced a gene signature associated with ER stress that may be employed to forecast the prognosis and therapeutic response of non-small cell lung cancer patients.
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Affiliation(s)
- Yingying Cui
- College of Basic Medicine, Zhengzhou University, Henan, China
- Charité-Universitäts Medizin Berlin, Berlin, Germany
| | - Xiaoli Zhou
- College of Basic Medicine, Zhengzhou University, Henan, China
| | - Dan Zheng
- College of Basic Medicine, Zhengzhou University, Henan, China
| | - Yumei Zhu
- College of Basic Medicine, Zhengzhou University, Henan, China
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29
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Ye B, Jiang A, Liang F, Wang C, Liang X, Zhang P. Navigating the immune landscape with plasma cells: A pan-cancer signature for precision immunotherapy. Biofactors 2025; 51:e2142. [PMID: 39495620 DOI: 10.1002/biof.2142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 10/22/2024] [Indexed: 11/06/2024]
Abstract
Immunotherapy has revolutionized cancer treatment; however, predicting patient response remains a significant challenge. Our study identified a novel plasma cell signature, Plasma cell.Sig, through a pan-cancer single-cell RNA sequencing analysis, which predicts patient outcomes to immunotherapy with remarkable accuracy. The signature was developed using rigorous machine learning algorithms and validated across multiple cohorts, demonstrating superior predictive power with an area under the curve (AUC) exceeding 0.7. Notably, the low-risk group, as classified by Plasma cell.Sig, exhibited enriched immune cell infiltration and heightened tumor immunogenicity, indicating an enhanced responsiveness to immunotherapy. Conversely, the high-risk group showed reduced immune activity and potential mechanisms of immune evasion. These findings not only enhance understanding of the intrinsic and extrinsic immune landscapes within the tumor microenvironment but also pave the way for more precise, biomarker-guided immunotherapy approaches in oncology.
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Affiliation(s)
- Bicheng Ye
- School of Clinical Medicine, Yangzhou Polytechnic College, Yangzhou, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Feng Liang
- Department of Gastroenterology, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Changcheng Wang
- Department of Gastroenterology, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Xiaoqing Liang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pengpeng Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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30
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Zu F, Chen C, Geng Q, Li H, Chan B, Luo G, Wu M, Ilmer M, Renz BW, Bentum-Ennin L, Gu H, Sheng W. Smad2 Cooperating with TGIF2 Contributes to EMT and Cancer Stem Cells Properties in Pancreatic Cancer via Co-Targeting SOX2. Int J Biol Sci 2025; 21:524-543. [PMID: 39781447 PMCID: PMC11705628 DOI: 10.7150/ijbs.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 11/18/2024] [Indexed: 01/12/2025] Open
Abstract
The underlying mechanisms between cancer stem cells (CSC) and epithelial-mesenchymal transition (EMT) in pancreatic cancer (PC) remain unclear. In this study, we identified TGIF2 as a target gene of CSC using sncRNA and machine learning. TGIF2 is closely related to the expression of SOX2, EGFR, and E-cadherin, indicating poor prognosis. Mechanistically, TGIF2 promoted the EMT phenotype and CSC properties following the activation of SOX2, Slug, CD44, and ERGF/MAPK signaling, which were rescued by SOX2 silencing. TGIF2 silencing contributes to the opposite phenotype via SOX2. Notably, Smad2 cooperates with TGIF2 to co-regulate the SOX2 promoter, which in turn promotes EMT and CSC signaling by transactivating Slug and EGFR, respectively. The transactivation of EGFR/MAPK signaling by SOX2 promotes TGIF2 nuclear translocation, forming a positive feedback loop in vitro. Moreover, the interaction of TGIF2 and SOX2 with EGFR inhibitors promoted subcutaneous tumors and liver metastasis in vivo. Thus, the TGIF2/SOX2 axis contributes to CSC, EMT, and chemoresistance, providing a promising target for PC therapy.
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Affiliation(s)
- Fuqiang Zu
- Department of General Surgery, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - ChuanPing Chen
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Qilong Geng
- Department of Clinical Medicine, Anhui Medical University, Hefei, 230022, China
| | - Haoyu Li
- Department of Clinical Medicine, Anhui Medical University, Hefei, 230022, China
| | - Boyuan Chan
- Department of Clinical Medicine, Anhui Medical University, Hefei, 230022, China
| | - Guopei Luo
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Mengcheng Wu
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Matthias Ilmer
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernhard W Renz
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lutterodt Bentum-Ennin
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Hao Gu
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Weiwei Sheng
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
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Xu X, Lin J, Wang J, Wang Y, Zhu Y, Wang J, Guo J. SPP1 expression indicates outcome of immunotherapy plus tyrosine kinase inhibition in advanced renal cell carcinoma. Hum Vaccin Immunother 2024; 20:2350101. [PMID: 38738709 PMCID: PMC11093034 DOI: 10.1080/21645515.2024.2350101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Clinical guidelines have recently advised combination therapy involving immunotherapy (IO) and tyrosine kinase inhibitors (TKI) as the first-line therapy approach for advanced renal cell carcinoma (RCC). Nevertheless, there is currently no available biomarker that can effectively distinguish the progression-free survival (PFS). RNA-sequencing and immunohistochemistry were conducted on our cohort of metastatic RCC patients, namely ZS-MRCC, who received combination therapy consisting of IO and TKI. We further applied RNA-sequencing, immunohistochemistry, and flow cytometry to examine the immune cell infiltration and functionality inside the tumor microenvironment of high-risk localized RCC samples. SPP1 expression was significantly higher in non-responders to IO-TKI therapy. Elevated levels of SPP1 were associated with poor PFS in both the ZS-MRCC cohort (HR = 2.73, p = .018) and validated in the JAVELIN Renal 101 cohort (HR = 1.61, p = .004). By multivariate Cox analysis, SPP1 was identified as a significant independent prognosticator. Furthermore, there existed a negative correlation between elevated levels of SPP1 and the presence of GZMB+CD8+ T cells (Spearman's ρ= -0.48, p < .001). Conversely, SPP1 expression is associated with T cell exhaustion markers. A significant increase in the abundance of Tregs was observed in tumors with high levels of SPP1. Additionally, a machine-learning-based model was constructed to predict the benefit of IO-TKI treatment. High SPP1 is associated with therapeutic resistance and unfavorable PFS in IO-TKI therapy. SPP1 expression have also been observed to be indicative of malfunction and exhaustion in T cells. Increased SPP1 expression has the potential to serve as a potential biomarker for treatment selection of metastatic RCC.
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Affiliation(s)
- Xianglai Xu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Jinglai Lin
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Jiahao Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying Wang
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanjun Zhu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
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Yu Y, Jin B, Jia R, Shi L, Chen Y, Ge J, Xu C. Exosomes loaded with the anti-cancer molecule mir-1-3p inhibit intrapulmonary colonization and growth of human esophageal squamous carcinoma cells. J Transl Med 2024; 22:1166. [PMID: 39741298 DOI: 10.1186/s12967-024-05997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 12/15/2024] [Indexed: 01/02/2025] Open
Abstract
BACKGROUND The overall prognosis of patients with esophageal cancer (EC) is extremely poor. There is an urgent need to develop innovative therapeutic strategies. This study will investigate the anti-cancer effects of exosomes loaded with specific anti-cancer microRNAs in vivo and in vitro. METHODS Specific miRNAs that were significantly down-regulated in EC tissues were screened using the miRNAs profiling data of human EC tissue samples in TCGA, and the role of their exogenous expression in the proliferation and migration of human EC cell lines, KYSE150 and Eca109, were detected using CCK-8 and Transwell assays. Exosomes were loaded with miRNAs using electroporation. RESULTS The expression of miR-1-3p was significantly down-regulated in human EC tissues with potential anti-cancer effects. Exosomes loaded with miR-1-3p significantly inhibited the proliferation, migration and invasion of KYSE150 and Eca109 cells in vitro, as well as the intrapulmonary colonization and growth of KYSE150 cells in vivo. In addition, miR-1-3p could directly bind to the 3'UTR of the transcription factor E2F5 mRNA, down-regulate the protein expression of E2F5, and inhibit the activation of the MAPK/ERK signaling pathway. CONCLUSION Exosomes loaded with miR-1-3p may be applicable to the treatment of EC.
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Affiliation(s)
- Yanmei Yu
- Ultrasonography Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Bingjie Jin
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China
| | - Ruzhen Jia
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China
| | - Lei Shi
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China
| | - Yong Chen
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China
| | - Jian Ge
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China
| | - Changqin Xu
- Gastroenterology Department, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 JingwuWeiqi Road, Jinan, Shandong, 250021, China.
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Xiao J, Cao Y, Li X, Xu L, Wang Z, Huang Z, Mu X, Qu Y, Xu Y. Elucidation of Factors Affecting the Age-Dependent Cancer Occurrence Rates. Int J Mol Sci 2024; 26:275. [PMID: 39796131 PMCID: PMC11720044 DOI: 10.3390/ijms26010275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 12/24/2024] [Accepted: 12/29/2024] [Indexed: 01/13/2025] Open
Abstract
Cancer occurrence rates exhibit diverse age-related patterns, and understanding them may shed new and important light on the drivers of cancer evolution. This study systematically analyzes the age-dependent occurrence rates of 23 carcinoma types, focusing on their age-dependent distribution patterns, the determinants of peak occurrence ages, and the significant difference between the two genders. According to the SEER reports, these cancer types have two types of age-dependent occurrence rate (ADOR) distributions, with most having a unimodal distribution and a few having a bimodal distribution. Our modeling analyses have revealed that (1) the first type can be naturally and simply explained using two age-dependent parameters: the total number of stem cell divisions in an organ from birth to the current age and the availability levels of bloodborne growth factors specifically needed by the cancer (sub)type, and (2) for the second type, the first peak is due to viral infection, while the second peak can be explained as in (1) for each cancer type. Further analyses indicate that (i) the iron level in an organ makes the difference between the male and female cancer occurrence rates, and (ii) the levels of sex hormones are the key determinants in the onset age of multiple cancer types. This analysis deepens our understanding of the dynamics of cancer evolution shared by diverse cancer types and provides new insights that are useful for cancer prevention and therapeutic strategies, thereby addressing critical gaps in the current paradigm of oncological research.
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Affiliation(s)
- Jun Xiao
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (J.X.); (X.L.); (Z.W.); (Z.H.)
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Yangkun Cao
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Xuan Li
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (J.X.); (X.L.); (Z.W.); (Z.H.)
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Long Xu
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Zhihang Wang
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (J.X.); (X.L.); (Z.W.); (Z.H.)
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Zhenyu Huang
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (J.X.); (X.L.); (Z.W.); (Z.H.)
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Xuechen Mu
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
- School of Mathematics, Jilin University, Changchun 130012, China
| | - Yinwei Qu
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (J.X.); (X.L.); (Z.W.); (Z.H.)
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
| | - Ying Xu
- Systems Biology Laboratory for Metabolic Reprogramming, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.C.); (L.X.); (X.M.)
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Waas M, Karamboulas C, Wu BZ, Khan S, Poon S, Meens J, Govindarajan M, Khoo A, Mejia-Guerrero S, Ha A, Liu LY, Nixon KCJ, Walton J, Bratman SV, Huang SH, Goldstein D, Gaiti F, Ailles L, Kislinger T. Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes. Nat Commun 2024; 15:10869. [PMID: 39738080 DOI: 10.1038/s41467-024-55203-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 11/29/2024] [Indexed: 01/01/2025] Open
Abstract
There is a pressing need to improve risk stratification and treatment selection for HPV-negative head and neck squamous cell carcinoma (HNSCC) due to the adverse side effects of treatment. One of the most important prognostic features is lymph nodes involvement. Previously, we demonstrated that tumor formation in patient-derived xenografts (i.e. engraftment) was associated with poor clinical outcomes in patients with HPV-negative HNSCC. However, assessing engraftment is challenging in clinical settings. Here, we perform transcriptomic and proteomic profiling of 88 HNSCC patients and find the relationship between engraftment and clinical outcomes is recapitulated by molecular phenotype. We identify LAMC2 and TGM3 as candidate prognostic biomarkers and validated their utility in an independent cohort containing 404 HPV-negative HNSCC patients. Strikingly, these markers significantly improve prediction of outcomes beyond nodal status alone and can significantly stratify patients without any nodal involvement. Overall, our study demonstrates how the molecular characteristics of engraftment can inform patient prognostication.
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Affiliation(s)
- Matthew Waas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Christina Karamboulas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Benson Z Wu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephanie Poon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Meinusha Govindarajan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Amanda Khoo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Annie Ha
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lydia Y Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kevin C J Nixon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Walton
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, and Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Shao Hui Huang
- Radiation Medicine Program, Princess Margaret Cancer Centre, and Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, and University of Toronto, Toronto, ON, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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35
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Xu X, Jané P, Taelman V, Jané E, Dumont RA, Garama Y, Kim F, Del Val Gómez M, Gariani K, Walter MA. The Theranostic Genome. Nat Commun 2024; 15:10904. [PMID: 39738156 DOI: 10.1038/s41467-024-55291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 12/05/2024] [Indexed: 01/01/2025] Open
Abstract
Theranostic drugs represent an emerging path to deliver on the promise of precision medicine. However, bottlenecks remain in characterizing theranostic targets, identifying theranostic lead compounds, and tailoring theranostic drugs. To overcome these bottlenecks, we present the Theranostic Genome, the part of the human genome whose expression can be utilized to combine therapeutic and diagnostic applications. Using a deep learning-based hybrid human-AI pipeline that cross-references PubMed, the Gene Expression Omnibus, DisGeNET, The Cancer Genome Atlas and the NIH Molecular Imaging and Contrast Agent Database, we bridge individual genes in human cancers with respective theranostic compounds. Cross-referencing the Theranostic Genome with RNAseq data from over 17'000 human tissues identifies theranostic targets and lead compounds for various human cancers, and allows tailoring targeted theranostics to relevant cancer subpopulations. We expect the Theranostic Genome to facilitate the development of new targeted theranostics to better diagnose, understand, treat, and monitor a variety of human cancers.
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Affiliation(s)
- Xiaoying Xu
- University of Lucerne, Lucerne, LU, Switzerland
| | - Pablo Jané
- University of Geneva, Geneva, GE, Switzerland
- Nuclear Medicine and Molecular Imaging Division, Geneva University Hospitals, Geneva, GE, Switzerland
| | | | - Eduardo Jané
- Departamento de Matemática Aplicada a la Ingeniería Aeroespacial - ETSIAE, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | | | | | | | - María Del Val Gómez
- Servicio de Medicina Nuclear, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Karim Gariani
- Division of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Geneva University Hospitals, Geneva, GE, Switzerland
| | - Martin A Walter
- University of Lucerne, Lucerne, LU, Switzerland.
- St. Anna Hospital, University of Lucerne, Lucerne, LU, Switzerland.
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36
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Guan L, Zeng R, Chen Y, He G, Yao W, Liu Z, Liu H. Pan-cancer analysis of the potential of PEA3 subfamily genes as tumor markers. Sci Rep 2024; 14:31518. [PMID: 39732961 DOI: 10.1038/s41598-024-82973-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 12/10/2024] [Indexed: 12/30/2024] Open
Abstract
Polyomavirus enhancer activator 3 (PEA3), an ETS transcription factor, has been documented to regulate the development and metastasis of human cancers. Nonetheless, a thorough analysis examining the relationship between the PEA3 subfamily members and tumour development, prognosis, and the tumour microenvironment (TME) across various cancer types has not yet been conducted. The expression profiles and prognostic significance of the PEA3 subfamily were evaluated using data from the GEO, TCGA, and PrognoScan databases, in conjunction with COX regression analyses and the Kaplan-Meier Plotter. Furthermore, the relationships between PEA3 subfamily expression, stemness scores, tumor microenvironments, immune subtypes, and drug susceptibility across multiple cancer types were explored. We found that ETV1, ETV4 and ETV5 are highly expressed in cancer, and their biological functions are synergistic. In the prognostic analysis of the Cancer Genome Atlas, the PEA3 subfamily genes were found to be associated with the prognosis of multiple cancers such as Lung adenocarcinoma (LUAD), Liver hepatocellular carcinoma (LIHC), etc., and marked a worse prognosis at different endpoints. In addition, it was significantly correlated with the stromal and immune scores of pan-cancer, and also significantly associated with the RNA stemness score and DNA stemness score of pan-cancer. Expression levels of the PEA3 subfamily genes correlate with immune subtypes of LIHC, LUAD, and Lung squamous cell carcinoma. We also found a variety of drugs with positive and negative associations of ETV1, ETV4 and ETV5. These findings elucidate the role of the PEA3 subfamily gene as a biomarker for carcinogenesis and cancer progression, offering valuable insights for future research into the PEA3 subfamily gene as a potential therapeutic target across various cancer types.
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Affiliation(s)
- Lingling Guan
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
- The State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Runhao Zeng
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
| | - Yi Chen
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
| | - Guohua He
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
| | - Wenxia Yao
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China.
| | - Zhaoyu Liu
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China.
| | - Hui Liu
- Precision Medicine Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China.
- The State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, Guangzhou, China.
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37
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Li Y, Zeng M, Qin Y, Feng F, Wei H. The role of KRT18 in lung adenocarcinoma development: integrative bioinformatics and experimental validation. Discov Oncol 2024; 15:841. [PMID: 39729139 DOI: 10.1007/s12672-024-01728-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024] Open
Abstract
Lung adenocarcinoma (LUAD) represents one of the most common subtypes of lung cancer with high rates of incidence and mortality, which contributes to substantial health and economic demand across the globe. Treatment today mainly consists of surgery, radiotherapy, and chemotherapy, but their efficacy in advanced stages is often suboptimal and emphasizes the clear need for new biomarkers and therapeutic targets. Using comprehensive bioinformatics analyses consisting of the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Human Protein Atlas (HPA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), immune infiltration analysis and functional enrichment analysis, and single-cell analysis, we examined the potential of keratin 18 (KRT18) as a candidate biomarker in advanced LUAD. KRT18 was significantly elevated in LUAD tissue relative to normal adjacent tissue (p < 0.05), and its expression was correlated with poor clinical-pathological features and inferior prognostic outcome. Furthermore, KRT18 expression was associated with several populations of immune cells, suggesting KRT18 may contribute to the local tumor microenvironment and potentially pathways of immune evasion. Survival analysis indicated that elevated KRT18 expression correlated with poor overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI), reinforcing its legitimacy as a prognostic tool (AUC = 0.846). Importantly, gene enrichment analysis found KRT18-associated genes enriched for pathways associated with lymphocyte differentiation and immune response pathways, which provides mechanistic insight into biological effects attributed to KRT18. Notably, NU.1025 has demonstrated the capability of reversing KRT18-modulated oncogenic features, and targeted therapeutic strategies can be developed moving forward. In conclusion, our data demonstrate that KRT18 has utility as a potential biomarker but may also serve as a therapeutic target in LUAD and merit further investigation into underlying mechanistic functions and potential therapeutic roles in the clinic.
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Affiliation(s)
- Yongjie Li
- School of Pharmacy, Shaoyang University, Shaoyang, 422000, Hunan, China
- Southwest Hunan Research Center of Engineering for Development and Utilization of Traditional Chinese Medicine, Shaoyang, 422000, Hunan, China
| | - Min Zeng
- Department of Respiratory and Critical Care Medicine, The Affiliated Shaoyang Hospital, Hengyang Medical School, University of South China, Shaoyang, 422000, Hunan, China.
| | - Yinan Qin
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310005, Zhejiang, China
| | - Fen Feng
- School of Pharmacy, Shaoyang University, Shaoyang, 422000, Hunan, China
| | - Hailiang Wei
- School of Pharmacy, Shaoyang University, Shaoyang, 422000, Hunan, China
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38
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Hermán-Sánchez N, G-García ME, Jiménez-Vacas JM, Yubero-Serrano EM, López-Sánchez LM, Romero-Martín S, Raya-Povedano JL, Álvarez-Benito M, Castaño JP, Luque RM, Gahete MD. The splicing machinery is dysregulated and represents a therapeutic vulnerability in breast cancer. Cell Mol Life Sci 2024; 82:18. [PMID: 39725737 DOI: 10.1007/s00018-024-05515-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/27/2024] [Accepted: 11/15/2024] [Indexed: 12/28/2024]
Abstract
Breast cancer (BCa) is a highly prevalent pathological condition (̴30% in women) with limited and subtype-dependent prognosis and therapeutic options. Therefore, BCa management might benefit from the identification of novel molecular elements with clinical potential. Since splicing process is gaining a great relevance in cancer, this work analysed the expression of multiple Spliceosome Components (SCs = 17) and Splicing Factors (SFs = 26) and found a drastic dysregulation in BCa (n = 69) vs. control (negative biopsies; n = 50) samples. Among all the components analysed, we highlight the upregulation of ESRP1 and down-regulation of PRPF8 and NOVA1 in BCa vs. control samples. Indeed, ESRP1 was specially overexpressed in triple-negative BCa (TNBCa) and associated with worse prognosis (i.e., higher BCa grade and lower overall survival), suggesting an association of ESRP1 with BCa aggressiveness. On the other hand, PRPF8 expression was generally downregulated in BCa with no associations to clinical characteristics, while NOVA1 expression was lower in TNBCa patients and highly aggressive tumours. Consistently, NOVA1 overexpression in vitro reduced functional parameters of aggressiveness in ER-/PR- cell lines (MDA-MB-231 and BT-549) but not in ER+/PR+ cells (MCF7), suggesting a critical role of NOVA1 in subtype-specific BCa. Finally, the in vitro pharmacological inhibition of splicing machinery using pladienolide B decreased aggressiveness features in all the BCa cell lines, showing a subtype-independent inhibitory potential, but being relatively innocuous in normal-like breast cells. These results demonstrate the profound dysregulation of the splicing machinery in BCa and their potential as source of promising diagnosis/prognosis markers, as well as valuable therapeutic targets for BCa.
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Affiliation(s)
- Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain
| | - Miguel E G-García
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain
| | - Juan M Jiménez-Vacas
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain
| | - Elena M Yubero-Serrano
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain
- Lipids and Atherosclerosis Unit, Reina Sofía University Hospital, Córdoba, Spain
| | - Laura M López-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain
| | - Sara Romero-Martín
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- Mammary Gland Unit, Reina Sofía University Hospital, Córdoba, Spain
| | - Jose L Raya-Povedano
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- Mammary Gland Unit, Reina Sofía University Hospital, Córdoba, Spain
| | - Marina Álvarez-Benito
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain
- Reina Sofía University Hospital, Córdoba, 14004, Spain
- Mammary Gland Unit, Reina Sofía University Hospital, Córdoba, Spain
| | - Justo P Castaño
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain.
- Reina Sofía University Hospital, Córdoba, 14004, Spain.
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain.
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain.
- Reina Sofía University Hospital, Córdoba, 14004, Spain.
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain.
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), IMIBIC building. Av. Menéndez Pidal s/n, Córdoba, 14004, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, 14004, Spain.
- Reina Sofía University Hospital, Córdoba, 14004, Spain.
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, 14004, Spain.
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Gu Y, Fang Y, Guo Y, Yang R, Ma J, Zhang C, Deng M, Wen Q, Gao N, Qiao H. Cytochrome P450 2E1 inhibitor Q11 is effective on hepatocellular carcinoma by promoting peritumor neutrophil chemotaxis. Int J Biol Macromol 2024; 293:139189. [PMID: 39732257 DOI: 10.1016/j.ijbiomac.2024.139189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 12/04/2024] [Accepted: 12/23/2024] [Indexed: 12/30/2024]
Abstract
Current studies found that the peritumoral tissue of hepatocellular carcinoma (HCC) may be different from normal liver tissue based on proteomics, and related to progression, recurrence and metastasis of HCC. Our previous study proposed "peritumor microenvironment (PME)" to summarize the influence of peritumor tissue on occurrence and progression of HCC. Peritumor CYP2E1 activity was significantly elevated in HCC, and related to occurrence and progression of HCC. However, the effectiveness and mechanism of inhibiting CYP2E1 against HCC remain unclear. In this study, by integrating the advantages of proteomics and transcriptomics, we reanalyzed the various influencing factors in PME. Although there were large differences in the occurrence and progression, the immunity and inflammation still played crucial roles. Peritumor neutrophil were "pro-tumor" phenotype in the stage of progression, while it showed cytotoxicity for tumor cell in the occurrence stage. CYP2E1 activity is associated with peritumor neutrophil infiltration and occurrence of HCC. CYP2E1 inhibitor Q11 showed anti-tumor effects in an orthotopic HCC mouse model by promoting secretion of chemokines and infiltration of neutrophils in peritumor tissue. Overall, these findings provided a reasonable mechanism of anti-tumor effects of CYP2E1 inhibitors, which may be a new strategy for the prevention and treatment of HCC.
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Affiliation(s)
- Yuhan Gu
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Department of Clinical Pharmacy, Nanyang Central Hospital, Nanyang, China
| | - Yan Fang
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuanyuan Guo
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Rui Yang
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun Ma
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cunzhen Zhang
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Mengyan Deng
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiang Wen
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Na Gao
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hailing Qiao
- Institute of Clinical Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
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40
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Gao L, Jing X, Hua Q, Li Z, Lei P, Song P, Zhou L, Tian Y, Liu J, Cai Q. Complement C1S is a potential prognostic biomarker and associated with M2 macrophage infiltration in gliomas: From bioinformatics to comprehensive experimental validation. Int Immunopharmacol 2024; 143:113573. [PMID: 39515040 DOI: 10.1016/j.intimp.2024.113573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 11/02/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024]
Abstract
Glioma is the most common malignant tumor of the central nervous system, and the ability of traditional clinical treatment to prolong the survival of glioma patients is limited. A substantial body of evidence underscores the pivotal role of the immune system in eradicating malignant cells and impeding tumor metastasis. Consequently, tumor immunotherapy has become a promising avenue to address the clinical conundrum faced by glioma patients. The complement system is a natural immune system that is an important line of defense in the immune response. C1S plays a key role in activating the classical complement system. Nevertheless, few studies have focused on the role of C1S in glioma tumorigenesis and progression. In this study, we demonstrated that C1S was upregulated in GBM (Grade IV) and low-grade gliomas (LGG, Grade II-III) by combining glioma cohorts from multiple public databases with our internal independent cohorts and that increased C1S expression levels predict a poor prognosis for gliomas. Cox regression analysis identified C1S as an important prognostic indicator for glioma patients. In addition, gene functional enrichment analysis demonstrated that C1S was involved in cellular immunity, T-cell activation, macrophage differentiation, and cell proliferation. Further experiments demonstrated that C1S facilitates tumor cell proliferation, cell migration and intracranial tumor growth in nude mice. More importantly, we evaluated the role of C1S in immune infiltration. These results suggested that C1S was closely related to a variety of immune cell types in glioma, especially M2 macrophages. Our findings were further validated via glioma tissue microarray immunohistochemical analysis and an M2 macrophage infiltration assay. Together, these findings revealed the underlying critical role of C1S in glioma tumorigenesis, progression, and the tumor immune microenvironment, contributing to further understanding of glioma pathogenesis and guiding immunotherapy.
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Affiliation(s)
- Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Xiongfei Jing
- Department of Neurosurgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City 433000, PR China
| | - Qiuwei Hua
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Zhiyang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Pan Lei
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Ping Song
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Long Zhou
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Yihao Tian
- Department of Human Anatomy, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, PR China.
| | - Junhui Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China.
| | - Qiang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China.
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Yang L, Fang A, Zhou S, Liu H. -RAMP3 promotes hepatocellular carcinoma tumor cell-mediated CCL2 degradation by supporting membrane distribution of ACKR2. Int Immunopharmacol 2024; 143:113419. [PMID: 39437486 DOI: 10.1016/j.intimp.2024.113419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 10/12/2024] [Accepted: 10/13/2024] [Indexed: 10/25/2024]
Abstract
This study aimed to explore the potential bind of Receptor Activity-Modifying Protein 3 (RAMP3) with atypical chemokine receptor 2 (ACKR2), and their cooperative regulation on the degradation of the immunosuppressive chemokine CCL2 in the tumor microenvironment of HCC. Bioinformatic analysis was conducted using available bulk-tissue RNA-seq, single-cell RNA-seq, and protein-protein interaction datasets. Human HCC cell line Huh7 and HepG2 and mouse HCC cell line Hepa1-6 were utilized for experiments. Results showed that RAMP3 binds with ACKR2 in HCC tumor cells and promotes the membrane distribution of ACKR2 through RAB4-positive vesicles. RAMP3 promotes CCL2 scavenging through ACKR2 in HCC cells. Mouse RAMP3 inhibited the proliferation of mouse liver cancer cell line (Hepa1-6)-derived syngeneic tumors through ACKR2, reduced the intratumoral concentration of CCL2 in the tumor, and inhibited the phosphorylation of Signal Transducer and Activator of Transcription 3 (STAT3) and protein kinase B (AKT). In addition, mouse RAMP3 inhibited CD11b+/Gr-1 + myeloid cell infiltration and neovascularization in the tumors through ACKR2. In TCGA-LIHC, RAMP3low/ACKR2low group had the worst progression-free interval (PFI), while the RAMP3high/ACKR2high group had the best overall survival (OS). In summary, restoring RAMP3 expression in HCC cells may generate synergistic support for the anticancer effect of ACKR2.
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Affiliation(s)
- Lan Yang
- Department of Oncology Centre, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Aiping Fang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 610072 Chengdu, China
| | - Shijie Zhou
- Jinruijie Biotechnology Center, Chengdu 610041, China.
| | - Hao Liu
- Department of Oncology Centre, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China.
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Gao T, Zhou R, Huang D, Wu D, Gao Y, Yuan Y, Li J, Huang S, Xian Y, Tang Y, Lin Z, Zhou D, Wang S. Pharmacological Effects of a Ginseng-Containing Chinese Medicine Formula in Treating Hepatocellular Carcinoma Based on Comprehensive Bioinformatics and Experimental Validation. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2024; 52:2511-2529. [PMID: 39721956 DOI: 10.1142/s0192415x24500964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2024]
Abstract
Ginseng-containing Shentao Ruangan granules (STR) have been a well-known Chinese medicine prescription for the treatment of hepatocellular carcinoma (HCC) in China for decades. This study aimed to establish an in silico experimental framework to decipher the underlying mechanism of STR in the treatment of HCC. Microarray analysis, network pharmacology, RNA-sequencing (RNA-seq), bioinformatics analysis, and in vivo and in vitro experiments were used as integrated approaches to uncover the effects and mechanisms of action of STR. The introduction of STR significantly suppresses the proliferation and metastasis of HepG2 and Huh7 cells. STR treatment notably suppressed the growth of transplanted Huh7 tumors. Furthermore, STR administration reduced the expression of various epithelial-to-mesenchymal transition (EMT)-related proteins including N-cadherin, vimentin, and [Formula: see text]-catenin. By employing a systems biology approach, 21 common genes were identified across RNA-seq data, TCGA-HCC dataset, and network pharmacology analysis. Finally, of these genes nine were found to be associated with both OS and PFS in patients with HCC within the TCGA cohort. Validation of candidate genes by qPCR and WB identified a significant downregulation in the expression of pGSK3[Formula: see text] and RELA protein with increasing concentrations of STR. These results elucidated the mechanism by which STR inhibits tumor growth and EMT of HCC may be related to the GSK3[Formula: see text]/RELA pathway.
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Affiliation(s)
- Tianqi Gao
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Ruisheng Zhou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Dan Huang
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Dailin Wu
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Yong Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Yi Yuan
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Jing Li
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Shangyi Huang
- Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Yanfang Xian
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P. R. China
| | - Ying Tang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Zhixiu Lin
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P. R. China
| | - Daihan Zhou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
| | - Shutang Wang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, P. R. China
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Du J, Zhao Y, Dong J, Li P, Hu Y, Fan H, Zhang F, Sun L, Zhang D, Zhang Y. Single-cell transcriptomics reveal the prognostic roles of epithelial and T cells and DNA methylation-based prognostic models in pancreatic cancer. Clin Epigenetics 2024; 16:188. [PMID: 39709423 DOI: 10.1186/s13148-024-01800-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 12/02/2024] [Indexed: 12/23/2024] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PDAC) exhibits a complex microenvironment with diverse cell populations influencing patient prognosis. Single-cell RNA sequencing (scRNA-seq) was used to identify prognosis-related cell types, and DNA methylation (DNAm)-based models were developed to predict outcomes based on their cellular characteristics. METHODS We integrated scRNA-seq, bulk data, and clinical information to identify key cell populations associated with prognosis. The TCGA dataset was used for validation, and cell composition was inferred from DNAm data. Prognostic models were constructed based on cell-type-specific DNAm markers, and genomic features were compared across risk groups. Nomograms were created to assess treatment responses in different risk levels. RESULTS Epithelial and T cells were major prognostic factors. Genomic analysis showed that epithelial cells in PDAC followed a malignant trajectory. DNAm data from TCGA confirmed the association of higher epithelial and T cell proportions with worse prognosis. Prognostic models based on DNAm markers of these cells effectively predicted patient survival, especially 5-year overall survival (AUC = 0.834). High-risk group with epithelial cell model showed altered pathways (tight junctions, NOTCH, and P53 signaling), while high-risk group with T cell model had changes in glycolysis, hypoxia, and NOTCH signaling, with more KRAS or TP53 mutations. Low-risk groups in the T cell model displayed stronger antitumor immune responses. Treatment predictions and nomograms were developed for clinical use. CONCLUSIONS scRNA-seq and DNAm data integration enabled the creation of predictive models based on epithelial and T cell-specific methylation patterns, offering robust prognosis prediction for PDAC patients.
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Affiliation(s)
- Jing Du
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Jie Dong
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Peng Li
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yan Hu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Feifan Zhang
- Department of Computer Science, University College London, London, UK
| | - Lanlan Sun
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Yuhua Zhang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
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Calaf GM, Roy D, Jara L, Romero C, Crispin LA. Genes Associated with the Immune System Affected by Ionizing Radiation and Estrogen in an Experimental Breast Cancer Model. BIOLOGY 2024; 13:1078. [PMID: 39765744 PMCID: PMC11673214 DOI: 10.3390/biology13121078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 12/06/2024] [Accepted: 12/17/2024] [Indexed: 01/11/2025]
Abstract
Breast cancer is a global health issue that, when in the metastasis stage, is characterized by the lack of estrogen receptor-α, the progesterone receptor, and human epidermal growth receptor expressions. The present study analyzed the differential gene expression related to the immune system affected by ionizing radiation and estrogen in cell lines derived from an experimental breast cancer model that was previously developed; where the immortalized human breast epithelial cell line MCF-10F, a triple-negative breast cancer cell line, was exposed to low doses of high linear energy transfer α particle radiation (150 keV/μm), it subsequently grew in the presence or absence of 17β-estradiol. Results indicated that interferon-related developmental regulator 1 gene expression was affected in the estrogen-treated cell line; this interferon, as well as the Interferon-Induced Transmembrane protein 2, and the TNF alpha-induced Protein 6 gene expression levels were higher than the control in the Alpha3 cell line. Furthermore, the interferon-related developmental regulator 1, the Interferon-Induced Transmembrane protein 2, the TNF alpha-induced Protein 6, the Nuclear Factor Interleukin 3-regulated, and the Interferon-Gamma Receptor 1 showed high expression levels in the Alpha5 cell line, and the Interferon Regulatory Factor 6 was high in the Tumor2 cell line. Additionally, to further strengthen these data, publicly available datasets were analyzed. This analysis was conducted to assess the correlation between estrogen receptor alpha expression and the genes mentioned above in breast cancer patients, the differential gene expression between tumor and normal tissues, the immune infiltration level, the ER status, and the survival outcome adjusted by the clinical stage factor. It can be concluded that the genes of the interferon family and Tumor Necrosis factors can be potential therapeutic targets for breast cancer, since they are active before tumor formation as a defense of the body under radiation or estrogen effects.
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Affiliation(s)
- Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile;
| | - Debasish Roy
- Department of Natural Sciences, Hostos College of the City University of New York, Bronx, NY 10451, USA;
| | - Lilian Jara
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile;
| | - Carmen Romero
- Laboratorio de Endocrinología, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile;
| | - Leodan A. Crispin
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile;
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Wang W, Li J, He Q, Liu C, Zheng Z, Zhang B, Mou S, Sun W, Zhao J. Crosstalk between CD180-overexpression macrophages and glioma cells worsens patient survival through malignant phenotype promotion and immunosuppressive regulation. Mol Med 2024; 30:264. [PMID: 39707188 DOI: 10.1186/s10020-024-01029-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 12/04/2024] [Indexed: 12/23/2024] Open
Abstract
BACKGROUND Understanding the molecular mechanisms in immunosuppressive regulation is crucial for improving immunotherapeutic strategies. Macrophages, the major immune cells in tumor microenvironment (TME), play a dual role in tumor progression. CD180, primarily expressed in macrophages, remains unclear and requires further investigation. METHODS RNA-seq data were obtained to analyze CD180 expression in gliomas and assess its prognostic value. The comprehensive immune infiltration analysis was performed. Single-cell RNA-seq (scRNA-seq) data were used to examine CD180 expression distribution at the cellular level. CD180-overexpression macrophages were co-cultured with three glioma cell lines. The effects on glioma cell behavior were evaluated through qRT-PCR, Western blot, CCK-8 assay, EdU assay, Transwell assay, TUNEL assay, and flow cytometry. Differentially expressed genes (DEGs) and their potential biological functions were analyzed between different CD180 expression groups. Consensus clustering was used to identify CD180-related glioma subtypes. RESULTS CD180 was significantly upregulated in glioma samples and associated with poor prognosis. High CD180 expression was correlated with increased immune cell infiltration, particularly macrophages, and elevated levels of immune checkpoints. Analysis of scRNA-seq data revealed the predominant expression of CD180 in macrophages within the glioma TME. In vitro experiments demonstrated that CD180-overexpression macrophages promoted glioma cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT), while decreasing apoptosis. Mutations in TP53 and PTEN were significantly more prevalent in the high CD180 expression group. We identified nine chemotherapeutic agents that were more effective in glioma patients with high CD180 expression. Additionally, two CD180-related glioma subtypes with distinct prognosis were identified. CONCLUSIONS This study confirmed the prognostic role of CD180 in glioma and its involvement in immunosuppressive regulation and malignant phenotype promotion. Therefore, CD180 was considered as a promising target for immunotherapeutic strategies in glioma treatment.
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Affiliation(s)
- Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Qiheng He
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chenglong Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zhiyao Zheng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Bojian Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Siqi Mou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wei Sun
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
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Zhai Z, Cui Z, Zhang Y, Song P, Wu J, Tan Z, Lin S, Ma X, Guan F, Kang H. Integrated pan-cancer analysis and experimental verification of the roles of meiotic nuclear divisions 1 in breast cancer. Biochem Biophys Res Commun 2024; 739:150600. [PMID: 39191147 DOI: 10.1016/j.bbrc.2024.150600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/08/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION The aberrant up-regulation of meiotic nuclear division 1 (MND1) in somatic cells is considered as one of the driving factors of oncogenesis, whereas its expression and role in breast invasive cancer (BRCA) remain unclear. Hence, this study embarked on a comprehensive evaluation of MND1 across various cancers and identified its roles in BRCA. METHODS Based on publicly available databases, including but not limited to UCSC Xena, TCGA, GTEx, GEO, STRING, GeneMANIA, and CancerSEA, we evaluated the expression patterns, genomic features, and biological functions of MND1 from a pan-cancer viewpoint and delved into the implications of MND1 in the prognosis and treatment of BRCA. Further molecular biology experiments were undertaken to identify the role of MND1 in proliferation, migration, and apoptosis in BRCA cells. RESULTS Elevated levels of MND1 were notably observed in a wide array of tumor types, especially in BRCA, COAD, HNSC, LIHC, LUAD, LUSC, STAD, and UCEC. Elevated MND1 expression was markedly associated with shortened OS in several tumors, including BRCA (HR = 1.52 [95%CI, 1.10-2.09], P = 0.011). The up-regulation of MND1 in BRCA was validated in external cohorts and clinical samples. Survival analyses demonstrated that elevated MND1 expression was associated with decreased survival for patients with BRCA. Co-expressed genes of MND1 were identified, and subsequent pathway analyses based on significantly associated genes indicated that MND1 plays key roles in DNA replication, cell cycle regulation, and DNA damage repair. The observed abnormal elevation and activation of MND1 led to increased proliferation and migration, along with decreased apoptosis in BRCA cells. CONCLUSIONS MND1 emerges as a promising biomarker for diagnostic and therapeutic targeting in various cancers, including BRCA. The abnormal up-regulation and activation of MND1 are linked to carcinogenesis and poor prognosis among BRCA patients, which may be attributed to its involvement in HR-dependent ALT, warranting further scrutiny.
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Affiliation(s)
- Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi' an, China
| | - Yu Zhang
- Department of Infectious Diseases, Honghui-hospital, Xi'an Jiaotong University, Shanghua Road, Xi'an, China
| | - Ping Song
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 157, West Fifth Road, Xi'an, China
| | - Jinpeng Wu
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Zengqi Tan
- Institute of Hematology, Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Feng Guan
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China.
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China.
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Dong X, Zhang K, Yi S, Wang L, Wang X, Li M, Liang S, Wang Y, Zeng Y. Multi-omics profiling combined with molecular docking reveals immune-inflammatory proteins as potential drug targets in colorectal cancer. Biochem Biophys Res Commun 2024; 739:150598. [PMID: 39213754 DOI: 10.1016/j.bbrc.2024.150598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Colorectal cancer is globally ranked as the third most common malignant tumor. Its development involves a complex biological process driven by various genetic and epigenetic alterations. To elucidate the biological significance of the extensive omics data, we conducted comparative multi-omics studies on colorectal cancer patients at different clinical stages. Bioinformatics methods were applied to analyze multi-omics datasets and explore the molecular landscape. Drug prediction and molecular docking also were conducted to assess potential therapeutic interventions. In vitro experiments were used to validate the inhibitory effect on the migration and proliferation of cell lines. The results indicate up-regulated proteins involved in immune-inflammatory related pathways, while biomarkers related to muscular contraction and cell adhesion are significantly down-regulated. Drug prediction, coupled with in vitro experiments, suggests that AZ-628 may act as a potential drug to inhibit the proliferation and migration of CRC cell lines HCT-116 and HT-29 by regulating the aforementioned key biological pathways or proteins. Complementing these findings, metabolomics analysis unveiled a down-regulation of key carbon metabolism pathways, alongside an up-regulation in amino acid metabolism, particularly proline metabolism. This metabolic shift may reflect an adaptive response in cancer cells, favoring specific amino acids to support their growth. Together, these integrated results provide valuable insights into the intricate landscape of tumor development, highlighting the crossroads of immune regulation, cellular structure, and metabolic reprogramming in the tumorigenic process and providing valuable insights into cancer pathology.
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Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Siwei Yi
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Lingxiang Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China; The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xingyao Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Mengtuo Li
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - YongJun Wang
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China; The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
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Zhang X, Ma J, Chen Y, Deng X, Zhang Y, Han Y, Tan J, Deng G, Ouyang Y, Zhou Y, Cai C, Zeng S, Shen H. FOS + B cells: Key mediators of immunotherapy resistance in diverse cancer types. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200895. [PMID: 39583007 PMCID: PMC11584611 DOI: 10.1016/j.omton.2024.200895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 10/02/2024] [Accepted: 10/16/2024] [Indexed: 11/26/2024]
Abstract
While immunotherapy has marked significant advances in cancer treatment, resistance remains a challenge. The complexity of the tumor microenvironment, particularly the role of B cell subpopulations, is a critical factor affecting treatment efficacy. In this study, we conducted analyses of single-cell RNA sequencing data from immunotherapy patients (n = 25) to explore the biomarker of immunotherapy resistance. Spatial transcriptome analysis, immunofluorescence analysis, and multi-cancer immunotherapy transcriptome analysis (n = 1,253) were used to validate our finding, and the potential mechanisms were explored. FOS+ B cells, identified across multiple cancer types, were associated with poor response to immunotherapy. FOS may form AP-1 (activator protein 1) with JUNB, thereby promoting the expression of Blimp-1 and subsequently facilitating the differentiation of B cells into immunosuppressive plasma cells. Furthermore, FOS+ B cells were linked to altered tumor necrosis factor signaling pathways, suggesting a mechanism for their immunosuppressive effects. Our findings highlight FOS+ B cells as important players in immunotherapy resistance, providing a novel biomarker for predicting treatment response. This study not only deepens our understanding of the immunological landscape influencing immunotherapy efficacy but also opens avenues for targeted interventions to overcome resistance.
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Affiliation(s)
- Xiangyang Zhang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong 518057, China
| | - Jiayao Ma
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiangying Deng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yan Zhang
- Department of Oncology, Yueyang People’s Hospital, Yueyang Hospital Affiliated to Hunan Normal University, Yueyang 414022, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Gongping Deng
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311 China
| | - Yanhong Ouyang
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311 China
| | - Yulai Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008 China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008 China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008 China
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Zhang X, Zhang L, Cui M, Ji S, Zhang Y, Li Q, Zhang M. SPAG5 is a potential therapeutic target affecting proliferation, apoptosis, and invasion of esophageal cancer cells. Eur J Med Res 2024; 29:596. [PMID: 39696708 DOI: 10.1186/s40001-024-02182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 11/28/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND Sperm-associated antigen 5 (SPAG5) is a mitotic spindle protein crucial for coordinating the separation of sister chromatids into daughter cells. Increasing evidence suggests that SPAG5 is overexpressed in various malignancies, functioning as an oncogene. However, research specifically examining SPAG5 in esophageal cancer remains limited. METHODS In this research, we leveraged bioinformatics techniques to evaluate the expression and prognostic significance of SPAG5 in a variety of cancer types. We conducted Gene Set Enrichment Analysis (GSEA) to elucidate the relationship between SPAG5 and cancer characteristics. Additionally, we investigated the correlation between SPAG5 expression and immune cell infiltration utilizing the TIMER2.0 platform. The TIDE platform was used to assess the impact of SPAG5 on the effectiveness of immunotherapy and to screen for potential therapeutic drugs. We employed qRT-PCR and immunohistochemistry staining to ascertain the expression of SPAG5 in esophageal cancer tissue. Through cellular functional experiments, we examined the influence of SPAG5 expression on the proliferation, apoptosis, invasion, and migration of esophageal cancer cells. The Pathscan Stress Signaling Antibody Array was utilized to probe the potential molecular mechanisms of SPAG5. RESULTS SPAG5 exhibits high levels of expression in various cancers, encompassing esophageal cancer, and its presence indicates an unfavorable prognosis. SPAG5 is primarily enriched in pathways associated with cellular proliferation and demonstrates a correlation with immune gene expression as well as the infiltration of immune cells. Suppression of SPAG5 expression in esophageal cancer cells not only inhibits cell proliferation, but also attenuates cell invasion and migration while inducing cellular apoptosis. The depletion of SPAG5 results in a decline in the levels of critical signaling proteins. CONCLUSION SPAG5 plays a pivotal role in esophageal cancer cell proliferation, apoptosis, and metastasis within the tumor microenvironment, making it a promising therapeutic target.
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Affiliation(s)
- Xiaohui Zhang
- Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, 710021, Shaanxi, China
| | - Lingmin Zhang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Manli Cui
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
- Engineering Research Center of Shaanxi Universities for Innovative Services of Chronic Disease Prevention and Control and Transformation of Nutritional Functional Food, Xi'an, 710077, Shaanxi, China
| | - Shiyu Ji
- Jingbian County People's Hospital of Shaanxi Province, Yulin Shi, 718500, Shaanxi, China
| | - Yanan Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Qian Li
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China.
- Engineering Research Center of Shaanxi Universities for Innovative Services of Chronic Disease Prevention and Control and Transformation of Nutritional Functional Food, Xi'an, 710077, Shaanxi, China.
| | - Mingxin Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China.
- Engineering Research Center of Shaanxi Universities for Innovative Services of Chronic Disease Prevention and Control and Transformation of Nutritional Functional Food, Xi'an, 710077, Shaanxi, China.
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50
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Wu J, Chen Z, Xiao S, Liu G, Wu W, Wang S. DeepMoIC: multi-omics data integration via deep graph convolutional networks for cancer subtype classification. BMC Genomics 2024; 25:1209. [PMID: 39695368 DOI: 10.1186/s12864-024-11112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 12/02/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND Achieving precise cancer subtype classification is imperative for effective prognosis and treatment. Multi-omics studies, encompassing diverse data modalities, have emerged as powerful tools for unraveling the complexities of cancer. However, owing to the intricacies of biological data, multi-omics datasets generally show variations in data types, scales, and distributions. These intractable problems lead to challenges in exploring intact representations from heterogeneous data, which often result in inaccuracies in multi-omics information analysis. RESULTS To address the challenges of multi-omics research, our approach DeepMoIC presents a novel framework derived from deep Graph Convolutional Network (GCN). Leveraging autoencoder modules, DeepMoIC extracts compact representations from omics data and incorporates a patient similarity network through the similarity network fusion algorithm. To handle non-Euclidean data and explore high-order omics information effectively, we design a Deep GCN module with two strategies: residual connection and identity mapping. With extracted higher-order representations, our approach consistently outperforms state-of-the-art models on a pan-cancer dataset and 3 cancer subtype datasets. CONCLUSION The introduction of Deep GCN shows encouraging performance in terms of supervised multi-omics feature learning, offering promising insights for precision medicine in cancer research. DeepMoIC can potentially be an important tool in the field of cancer subtype classification because of its capacity to handle complex multi-omics data and produce reliable classification findings.
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Affiliation(s)
- Jiecheng Wu
- College of Computer and Data Science, Fuzhou University, Fuzhou, 350108, China
| | - Zhaoliang Chen
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Shunxin Xiao
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, 361024, China
| | - Genggeng Liu
- College of Computer and Data Science, Fuzhou University, Fuzhou, 350108, China
| | - Wenjie Wu
- Department of Ophthalmology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, 350001, China
| | - Shiping Wang
- College of Computer and Data Science, Fuzhou University, Fuzhou, 350108, China.
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