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Cao L, Ba Y, Chen F, Zhang S, Zhang H. Exploration of bacterial lipopolysaccharide-related genes signature based on T cells for predicting prognosis in colorectal cancer. Aging (Albany NY) 2024; 16:11606-11625. [PMID: 39115879 DOI: 10.18632/aging.206041] [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: 04/03/2024] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
PURPOSE The intratumoral microorganisms participates in the progression and immunotherapy of colorectal cancer (CRC). However, due to technical limitations, the impact of microorganisms on CRC has not been fully understood. Therefore, we conducted a systematic analysis of relationship between bacterial lipopolysaccharide (LPS)-associated genes and immune cells to explore new biomarkers for predicting the prognosis of CRC. METHODS The single-cell RNA sequencing data and the Comparative Toxicogenomics Database were used to screen T cells-associated LPS-related genes (TALRGs). Then, we established and validated the TALRGs risk signature in The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) cohort and GSE39582 cohort. Besides, we compared the differences in tumor-infiltrating immune cell types, immunotherapeutic response, somatic mutation profiles, and tumor mutation burden (TMB) between high-risk group and low-risk group. In addition, the immunotherapeutic cohort (Imvigor210) treated with an anti-PD-L1 agent was performed to explore the potential value of the TALRGs signature on immunotherapy. RESULTS Five prognostic TALRGs were identified and selected to build the prognostic model. The high-risk group had poor prognosis in both TCGA-COAD cohort (P < 0.0001) and GSE39582 cohort (P = 0.00019). The areas under the curves (AUCs) of TALRGs signature were calculated (TCGA-COAD cohort: 0.624 at 1 years, 0.639 at 3 years, 0.648 at 5 years; anti-PD-L1 cohort was 0.59). The high-risk group had advanced pathological stages and higher TMN stages in both TCGA-COAD cohort and GSE39582 cohort. The high-risk group had the higher infiltration of immunosuppressive cells, the expressions of immune checkpoint molecules, the IC50 values of chemotherapy drugs, and TP53 mutation rate (P < 0.05). In addition, patients with high TMB had worse prognosis (P < 0.05). Furthermore, the Imvigor210 also showed patients with high-risk scores had poor prognosis (platinum-treated cohort: P = 0.0032; non-platinum-treated cohort: P = 0.00017). CONCLUSIONS Microorganisms are closely related to the tumor microenvironment to influence the progression and immune response of CRC via stimulating T cells through LPS-related genes. The TALRGs signature contributed to predict the prognosis and immunotherapy of CRC, and became new therapeutic targets and biomarkers of CRC.
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Affiliation(s)
- Lichao Cao
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Ying Ba
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Fang Chen
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Shenrui Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Hezi Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
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Wang J, Tan Z, Huang Y, Li C, Zhan P, Wang H, Li H. Integrating single-cell RNA-seq to identify fibroblast-based molecular subtypes for predicting prognosis and therapeutic response in bladder cancer. Aging (Albany NY) 2024; 16:11385-11408. [PMID: 39033778 PMCID: PMC11315389 DOI: 10.18632/aging.206021] [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: 01/09/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Bladder cancer (BLCA) is a highly aggressive and heterogeneous disease, posing challenges for diagnosis and treatment. Cancer immunotherapy has recently emerged as a promising option for patients with advanced and drug-resistant cancers. Fibroblasts, a significant component of the tumor microenvironment, play a crucial role in tumor progression, but their precise function in BLCA remains uncertain. METHODS Single-cell RNA sequencing (scRNA-seq) data for BLCA were obtained from the Gene Expression Omnibus database. The R package "Seurat" was used for processing scRNA-seq data, with uniform manifold approximation and projection (UMAP) for downscaling and cluster identification. The FindAllMarkers function identified marker genes for each cluster. Differentially expressed genes influencing overall survival (OS) of BLCA patients were identified using the limma package. Differences in clinicopathological characteristics, immune microenvironment, immune checkpoints, and chemotherapeutic drug sensitivity between high- and low-risk groups were investigated. RT-qPCR and immunohistochemistry validated the expression of prognostic genes. RESULTS Fibroblast marker genes identified three molecular subtypes in the testing set. A prognostic signature comprising ten genes stratified BLCA patients into high- and low-score groups. This signature was validated in one internal and two external validation sets. High-score patients exhibited increased immune cell infiltration, elevated chemokine expression, and enhanced immune checkpoint expression but had poorer OS and a reduced response to immunotherapy. Six sensitive anti-tumor drugs were identified for the high-score group. RT-qPCR and immunohistochemistry showed that CERCAM, TM4SF1, FN1, ANXA1, and LOX were highly expressed, while EMP1, HEYL, FBN1, and SLC2A3 were downregulated in BLCA. CONCLUSION A novel fibroblast marker gene-based signature was established, providing robust predictions of survival and immunotherapeutic response in BLCA patients.
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Affiliation(s)
- Jia Wang
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Endocrinology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhiyong Tan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yinglong Huang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Charles Li
- Core Facility for Protein Research, Chinese Academy of Sciences, Beijing, China
- Zhongke Jianlan Medical Research Institute, Beijing, China
- Zhejiang Institute of Integrated Traditional and Western Medicine, Hangzhou, China
| | - Peiqin Zhan
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haifeng Wang
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haihao Li
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Yang Y, Qiu YT, Li WK, Cui ZL, Teng S, Wang YD, Wu J. Multi-Omics analysis elucidates tumor microenvironment and intratumor microbes of angiogenesis subtypes in colon cancer. World J Gastrointest Oncol 2024; 16:3169-3192. [PMID: 39072166 PMCID: PMC11271793 DOI: 10.4251/wjgo.v16.i7.3169] [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: 01/19/2024] [Revised: 02/13/2024] [Accepted: 05/06/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Angiogenesis plays an important role in colon cancer (CC) progression. AIM To investigate the tumor microenvironment (TME) and intratumor microbes of angiogenesis subtypes (AGSs) and explore potential targets for antiangiogenic therapy in CC. METHODS The data were obtained from The Cancer Genome Atlas database and Gene Expression Omnibus database. K-means clustering was used to construct the AGSs. The prognostic model was constructed based on the differential genes between two subtypes. Single-cell analysis was used to analyze the expression level of SLC2A3 on different cells in CC, which was validated by immunofluorescence. Its biological functions were further explored in HUVECs. RESULTS CC samples were grouped into two AGSs (AGS-A and AGS-B) groups and patients in the AGS-B group had poor prognosis. Further analysis revealed that the AGS-B group had high infiltration of TME immune cells, but also exhibited high immune escape. The intratumor microbes were also different between the two subtypes. A convenient 6-gene angiogenesis-related signature (ARS), was established to identify AGSs and predict the prognosis in CC patients. SLC2A3 was selected as the representative gene of ARS, which was higher expressed in endothelial cells and promoted the migration of HUVECs. CONCLUSION Our study identified two AGSs with distinct prognoses, TME, and intratumor microbial compositions, which could provide potential explanations for the impact on the prognosis of CC. The reliable ARS model was further constructed, which could guide the personalized treatment. The SLC2A3 might be a potential target for antiangiogenic therapy.
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Affiliation(s)
- Yi Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
| | - Yu-Ting Qiu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
| | - Wen-Kun Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
| | - Zi-Lu Cui
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
| | - Shuo Teng
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100050, China
| | - Ya-Dan Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100050, China
| | - Jing Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, China
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Yu J, Gong Y, Xu Z, Chen L, Li S, Cui Y. Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling. PeerJ 2024; 12:e17629. [PMID: 38938617 PMCID: PMC11210462 DOI: 10.7717/peerj.17629] [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: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model's accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a "hot" immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment.
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Affiliation(s)
- Jinglu Yu
- PuDong Traditional Chinese Medicine Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China, Shanghai, Pudong, China
| | - Yabin Gong
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Zhenye Xu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Lei Chen
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Shuang Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongkang Cui
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Wu Z, Yu W, Luo J, Shen G, Cui Z, Ni W, Wang H. Comprehensive transcriptomic analysis unveils macrophage-associated genes for establishing an abdominal aortic aneurysm diagnostic model and molecular therapeutic framework. Eur J Med Res 2024; 29:323. [PMID: 38867262 PMCID: PMC11167832 DOI: 10.1186/s40001-024-01900-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: 10/09/2023] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a highly lethal cardiovascular disease. The aim of this research is to identify new biomarkers and therapeutic targets for the treatment of such deadly diseases. METHODS Single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT algorithms were used to identify distinct immune cell infiltration types between AAA and normal abdominal aortas. Single-cell RNA sequencing data were used to analyse the hallmark genes of AAA-associated macrophage cell subsets. Six macrophage-related hub genes were identified through weighted gene co-expression network analysis (WGCNA) and validated for expression in clinical samples and AAA mouse models. We screened potential therapeutic drugs for AAA through online Connectivity Map databases (CMap). A network-based approach was used to explore the relationships between the candidate genes and transcription factors (TFs), lncRNAs, and miRNAs. Additionally, we also identified hub genes that can effectively identify AAA and atherosclerosis (AS) through a variety of machine learning algorithms. RESULTS We obtained six macrophage hub genes (IL-1B, CXCL1, SOCS3, SLC2A3, G0S2, and CCL3) that can effectively diagnose abdominal aortic aneurysm. The ROC curves and decision curve analysis (DCA) were combined to further confirm the good diagnostic efficacy of the hub genes. Further analysis revealed that the expression of the six hub genes mentioned above was significantly increased in AAA patients and mice. We also constructed TF regulatory networks and competing endogenous RNA networks (ceRNA) to reveal potential mechanisms of disease occurrence. We also obtained two key genes (ZNF652 and UBR5) through a variety of machine learning algorithms, which can effectively distinguish abdominal aortic aneurysm and atherosclerosis. CONCLUSION Our findings depict the molecular pharmaceutical network in AAA, providing new ideas for effective diagnosis and treatment of diseases.
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Affiliation(s)
- Zhen Wu
- Department of Vascular and Interventional Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Weiming Yu
- Department of Vascular and Interventional Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
- General Surgery, Thyroid Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, Guangdong, China
| | - Jie Luo
- Department of Vascular and Interventional Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Guanghui Shen
- Department of Vascular and Interventional Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zhongqi Cui
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Wenxuan Ni
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
| | - Haiyang Wang
- Department of Vascular and Interventional Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China.
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Hu S, Xiao Q, Gao R, Qin J, Nie J, Chen Y, Lou J, Ding M, Pan Y, Wang S. Identification of BGN positive fibroblasts as a driving factor for colorectal cancer and development of its related prognostic model combined with machine learning. BMC Cancer 2024; 24:516. [PMID: 38654221 PMCID: PMC11041013 DOI: 10.1186/s12885-024-12251-4] [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: 12/29/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Numerous studies have indicated that cancer-associated fibroblasts (CAFs) play a crucial role in the progression of colorectal cancer (CRC). However, there are still many unknowns regarding the exact role of CAF subtypes in CRC. METHODS The data for this study were obtained from bulk, single-cell, and spatial transcriptomic sequencing data. Bioinformatics analysis, in vitro experiments, and machine learning methods were employed to investigate the functional characteristics of CAF subtypes and construct prognostic models. RESULTS Our study demonstrates that Biglycan (BGN) positive cancer-associated fibroblasts (BGN + Fib) serve as a driver in colorectal cancer (CRC). The proportion of BGN + Fib increases gradually with the progression of CRC, and high infiltration of BGN + Fib is associated with poor prognosis in terms of overall survival (OS) and recurrence-free survival (RFS) in CRC. Downregulation of BGN expression in cancer-associated fibroblasts (CAFs) significantly reduces migration and proliferation of CRC cells. Among 101 combinations of 10 machine learning algorithms, the StepCox[both] + plsRcox combination was utilized to develop a BGN + Fib derived risk signature (BGNFRS). BGNFRS was identified as an independent adverse prognostic factor for CRC OS and RFS, outperforming 92 previously published risk signatures. A Nomogram model constructed based on BGNFRS and clinical-pathological features proved to be a valuable tool for predicting CRC prognosis. CONCLUSION In summary, our study identified BGN + Fib as drivers of CRC, and the derived BGNFRS was effective in predicting the OS and RFS of CRC patients.
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Affiliation(s)
- Shangshang Hu
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Qianni Xiao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Rui Gao
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Junjie Nie
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China
| | - Yuhan Chen
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Jinwei Lou
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Muzi Ding
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
| | - Shukui Wang
- School of Medicine, Southeast University, 210009, Nanjing, Jiangsu, China.
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, 210006, Nanjing, Jiangsu, China.
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211122, Nanjing, Jiangsu, China.
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211100, Nanjing, Jiangsu, China.
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Wang S, Wang L, Qiu M, Lin Z, Qi W, Lv J, Wang Y, Lu Y, Li X, Chen W, Qiu W. Constructing and validating a risk model based on neutrophil-related genes for evaluating prognosis and guiding immunotherapy in colon cancer. J Gene Med 2024; 26:e3684. [PMID: 38618694 DOI: 10.1002/jgm.3684] [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: 01/09/2024] [Revised: 02/25/2024] [Accepted: 03/03/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND Colon cancer is one of the most common digestive tract malignancies. Although immunotherapy has brought new hope to colon cancer patients, there is still a large proportion of patients who do not benefit from immunotherapy. Studies have shown that neutrophils can interact with immune cells and immune factors to affect the prognosis of patients. METHODS We first determined the infiltration level of neutrophils in tumors using the CIBERSORT algorithm and identified key genes in the final risk model by Spearman correlation analysis and subsequent Cox analysis. The risk score of each patient was obtained by multiplying the Cox regression coefficient and the gene expression level, and patients were divided into two groups based on the median of risk score. Differences in overall survival (OS) and progression-free survival (PFS) were assessed by Kaplan-Meier survival analysis, and model accuracy was validated in independent dataset. Differences in immune infiltration and immunotherapy were evaluated by immunoassay. Finally, immunohistochemistry and western blotting were performed to verify the expression of the three genes in the colon normal and tumor tissues. RESULTS We established and validated a risk scoring model based on neutrophil-related genes in two independent datasets, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, with SLC11A1 and SLC2A3 as risk factors and MMP3 as a protective factor. A new nomogram was constructed and validated by combining clinical characteristics and the risk score model to better predict patients OS and PFS. Immune analysis showed that patients in the high-risk group had immune cell infiltration level, immune checkpoint level and tumor mutational burden, and were more likely to benefit from immunotherapy. CONCLUSIONS The low-risk group showed better OS and PFS than the high-risk group in the neutrophil-related gene-based risk model. Patients in the high-risk group presented higher immune infiltration levels and tumor mutational burden and thus may be more responsive to immunotherapy.
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Affiliation(s)
- Shasha Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lili Wang
- Department of Oncology, Rizhao Central Hospital, Rizhao, China
| | - Mingxiu Qiu
- Department Second of Respiratory and Critical Care, Qingdao Municipal Hospital, Qingdao, China
| | - Zhongkun Lin
- Department of Oncology, Shandong Provincial Third Hospital, Shandong University, Jinan, China
| | - Weiwei Qi
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing Lv
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yan Wang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yangyang Lu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoxuan Li
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenzhi Chen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Wensheng Qiu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
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Yang X, Tao Y, Xu Y, Cai W, Shao Q. SLC35A2 expression drives breast cancer progression via ERK pathway activation. FEBS J 2024; 291:1483-1505. [PMID: 38143314 DOI: 10.1111/febs.17044] [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: 12/31/2022] [Revised: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023]
Abstract
Alterations in glycosylation are associated with breast tumor formation and progression. Nevertheless, the specific functions and mechanisms of the human major UDP-galactose transporter-encoding gene solute carrier family 35 member A2 (SLC35A2) in breast invasive carcinoma (BRCA) have not been fully determined. Here, we report that SLC35A2 promotes BRCA progression by activating extracellular signal regulated kinase (ERK). SLC35A2 expression and prognosis-predictive significance in pan-cancer were evaluated using public databases. The upstream non-coding RNAs (ncRNAs) of SLC35A2 were analyzed, and their expression and regulations were validated in breast tissues and cell lines by a quantitative PCR and dual-luciferase assays. We used bioinformatic tools to assess the link between SLC35A2 expression and immune infiltration and performed immunohistochemistry for validation. Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine, transwell, flow cytometer and western blotting were used to assess the proliferation, motility, cell cycle and apoptosis of BRCA cells in vitro. The xenograft models were constructed to assess the effect of SLC35A2 on BRCA tumor growth in vivo. The results indicated that SLC35A2 expression was upregulated and linked to an unfavorable prognosis in BRCA. The most likely upstream ncRNA-associated pathway of SLC35A2 in BRCA was the AC074117.1/hsa-let-7b-5p axis. SLC35A2 expression had positive correlations with the presence of Th2 cells, regulatory T cells and immune checkpoints. Knockdown of SLC35A2 could reduce BRCA cell proliferation, motility, and cause G2/M arrest and cell apoptosis via ERK signaling. Moreover, ERK activation can rescue the inhibitory effects of knockdown SLC35A2 in BRCA. In conclusion, AC074117.1/hsa-let-7b-5p axis-mediated high expression of SLC35A2 acts as a tumor promoter in BRCA via ERK signaling, which provides a potential target for BRCA treatment.
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Affiliation(s)
- Xiaochen Yang
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Yukai Tao
- Clinical Research & Lab Center, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Yan Xu
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, The Digestive and Reproductive System Cancers Precise Prevention Engineering Research Center of Jiangsu Province, Jiangsu College of Nursing, Huai'an, China
| | - Qixiang Shao
- Clinical Research & Lab Center, Affiliated Kunshan Hospital of Jiangsu University, China
- Institute of Medical Genetics and Reproductive Immunity, The Digestive and Reproductive System Cancers Precise Prevention Engineering Research Center of Jiangsu Province, Jiangsu College of Nursing, Huai'an, China
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Chen H, Fang X, Shao J, Zhang Q, Xu L, Chen J, Mei Y, Jiang M, Wang Y, Li Z, Chen Z, Chen Y, Yu C, Ma L, Zhang P, Zhang T, Liao Y, Lv Y, Wang X, Yang L, Fu Y, Chen D, Jiang L, Yan F, Lu W, Chen G, Shen H, Wang J, Wang C, Liang T, Han X, Wang Y, Guo G. Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304755. [PMID: 38010945 PMCID: PMC10837386 DOI: 10.1002/advs.202304755] [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: 07/13/2023] [Revised: 10/11/2023] [Indexed: 11/29/2023]
Abstract
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
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Affiliation(s)
- Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- M20 Genomics, Hangzhou, 311121, China
| | - Xiunan Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Jikai Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Xu
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | | | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Yuting Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhouyang Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Yang Chen
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
- The Second Clinical Medical College of Zhejiang Chinese Medical University Hangzhou, Hangzhou, 310053, China
| | - Chengxuan Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
| | | | - Yuan Liao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- M20 Genomics, Hangzhou, 311121, China
| | | | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Liming Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongcheng Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310006, China
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10
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Liu B, Zhang J, Wang X, Ye W, Yao J. Exploration of the Mechanisms Underlying Yu's Enema Formula in Treating Ulcerative Colitis by Blocking the RhoA/ROCK Pathway based on Network Pharmacology, High-performance Liquid Chromatography Analysis, and Experimental Verification. Curr Pharm Des 2024; 30:1085-1102. [PMID: 38523541 DOI: 10.2174/0113816128290586240315071044] [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: 11/28/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND The traditional Chinese medicine formula, Yu's Enema Formula (YEF), has demonstrated potential in the treatment of Ulcerative Colitis (UC). OBJECTIVE This study aimed to unveil the anti-UC mechanisms of YEF. METHODS Utilizing public databases, we obtained YEF and UC-related targets. GO and KEGG analyses were conducted via clusterProfiler and Reactome. The STRING database facilitated the construction of the PPI network, and hub targets were selected using cytoHubba. We used R software for differential expression and correlation analyses, and molecular docking was performed with PyMOL and AutoDock. HPLC analysis identified the compounds in YEF. For in vivo validation, a UC rat model was employed. RESULTS AND DISCUSSION 495 YEF-UC overlapping targets were identified. GO and KEGG analyses indicated enrichment in exogenous stimuli response, peptide response, positive MAPK cascade regulation, interleukin- related signaling, and the TLR4 cascade. Hub targets included CTNNB1, JUN, MAPK1, MAPK3, SRC, STAT3, TLR4, TP53, and RELA, which were often interconnected. Molecular docking revealed quercetin's strong binding affinity with CTNNB1, MAPK1, MAPK3, SRC, STAT3, TLR4, and TP53, consistent with HPLC analysis. In vivo experiments suggested that YEF has the potential to alleviate UC symptoms and protect the intestinal mucosal barrier by inhibiting the RhoA/ROCK pathway. CONCLUSION YEF may safeguard the intestinal mucosal barrier in UC by targeting CTNNB1, MAPK1, MAPK3, SRC, STAT3, TLR4, and TP53, while blocking the RhoA/ROCK pathway.
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Affiliation(s)
- Binbin Liu
- Department of Digestion, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jie Zhang
- Department of Digestion, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiaoqi Wang
- Department of Digestion, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wei Ye
- Department of Digestion, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiaming Yao
- Department of Digestion, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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11
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Chai F, Zhang J, Fu T, Jiang P, Huang Y, Wang L, Yan S, Yan X, Yu L, Xu Z, Wang R, Xu B, Du X, Jiang Y, Zhang J. Identification of SLC2A3 as a prognostic indicator correlated with the NF-κB/EMT axis and immune response in head and neck squamous cell carcinoma. Channels (Austin) 2023; 17:2208928. [PMID: 37134043 PMCID: PMC10158547 DOI: 10.1080/19336950.2023.2208928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
SLC2A3 is an important member of the glucose transporter superfamily. It has been recently suggested that upregulation of SLC2A3 is associated with poor survival and acts as a prognostic marker in a variety of tumors. Unfortunately, the prognostic role of SLC2A3 in head and neck squamous cell carcinoma (HNSC) is less known. In the present study, we analyzed SLC2A3 expression in HNSC and its correlation with prognosis using TCGA and GEO databases. The results showed that SLC2A3 mRNA expression was higher in HNSC compared with adjacent normal tissues, which was validated with our 9 pairs of HNSC specimens. Moreover, high SLC2A3 expression predicted poor prognosis in HNSC patients. Mechanistically, GSEA revealed that high expression of SLC2A3 was enriched in epithelial-mesenchymal transition (EMT) and NF-κB signaling. In HNSC cell lines, SLC2A3 knockdown inhibited cell proliferation and migration. In addition, NF-κB P65 and EMT-related gene expression was suppressed upon SLC2A3 knockdown, indicating that SLC2A3 may play a preeminent role in the progression of HNSC through the NF-κB/EMT axis. Meanwhile, the expression of SLC2A3 was negatively correlated with immune cells, suggesting that SLC2A3 may be involved in the immune response in HNSC. The correlation between SLC2A3 expression and drug sensitivity was further assessed. In conclusion, our study demonstrated that SLC2A3 could predict the prognosis of HNSC patients and mediate the progression of HNSC via the NF-κB/EMT axis and immune responses.
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Affiliation(s)
- Fangyu Chai
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jingfang Zhang
- Department of Pathology, Shandong First Medical University, Jinan, Shandong, China
| | - Tao Fu
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peng Jiang
- Organ Transplantation Center, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yichuan Huang
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lin Wang
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Shu Yan
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xudong Yan
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Longgang Yu
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Zhen Xu
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Ruohuang Wang
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Bingqing Xu
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xiaoyun Du
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yan Jiang
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Key Laboratory of Otolaryngology-Head and Neck Surgery, Medical Research Center, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jisheng Zhang
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Key Laboratory of Otolaryngology-Head and Neck Surgery, Medical Research Center, the Affiliated Hospital of Qingdao University, Qingdao, China
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12
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Aaes TL, Burgoa Cardás J, Ravichandran KS. Defining solute carrier transporter signatures of murine immune cell subsets. Front Immunol 2023; 14:1276196. [PMID: 38077407 PMCID: PMC10704505 DOI: 10.3389/fimmu.2023.1276196] [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: 08/11/2023] [Accepted: 10/13/2023] [Indexed: 12/18/2023] Open
Abstract
Solute carrier (SLC) transporters are membrane-bound proteins that facilitate nutrient transport, and the movement across cellular membranes of various substrates ranging from ions to amino acids, metabolites and drugs. Recently, SLCs have gained increased attention due to their functional linkage to innate immunological processes such as the clearance of dead cells and anti-microbial defense. Further, the druggable nature of these transporters provides unique opportunities for improving outcomes in different immunological diseases. Although the SLCs represent the largest group of transporters and are often identified as significant hits in omics data sets, their role in immunology has been insufficiently explored. This is partly due to the absence of tools that allow identification of SLC expression in particular immune cell types and enable their comparison before embarking on functional studies. In this study, we used publicly available RNA-Seq data sets to analyze the transcriptome in adaptive and innate immune cells, focusing on differentially and highly expressed SLCs. This revealed several new insights: first, we identify differentially expressed SLC transcripts in phagocytes (macrophages, dendritic cells, and neutrophils) compared to adaptive immune cells; second, we identify new potential immune cell markers based on SLC expression; and third, we provide user-friendly online tools for researchers to explore SLC genes of interest (and the rest of the genes as well), in three-way comparative dot plots among immune cells. We expect this work to facilitate SLC research and comparative transcriptomic studies across different immune cells.
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Affiliation(s)
- Tania Løve Aaes
- Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Javier Burgoa Cardás
- Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Kodi S. Ravichandran
- Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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13
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Li M, Song J, Wang L, Wang Q, Huang Q, Mo D. Natural killer cell-related prognosis signature predicts immune response in colon cancer patients. Front Pharmacol 2023; 14:1253169. [PMID: 38026928 PMCID: PMC10679416 DOI: 10.3389/fphar.2023.1253169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Natural killer (NK) cells are crucial components of the innate immune system that fight tumors and viral infections. Patients with colorectal cancer (CRC) have a poor prognosis, and immunotherapeutic tools play a key role in the treatment of CRC. Methods: Public data on CRC patients was collected from the TCGA and the GEO databases. Tissue data of CRC patients were collected from Guangxi Medical University Affiliated Cancer Hospital. An NK-related prognostic model was developed by the least absolute shrinkage and selection operator (LASSO) and Cox regression method. Validation data were collected from different clinical subgroups and an external independent validation cohort to verify the model's accuracy. In addition, multiple external independent immunotherapy datasets were collected to further examine the value of NK-related risk scores (NKRS) in the prediction of immunotherapy response. Potential biological functions of key genes were examined by methods of cell proliferation, apoptosis and Western blotting. Results: A novel prognostic model for CRC patients based on NK-related genes was developed and NKRS was generated. There was a significantly poorer prognosis among the high-NKRS group. Based on immune response prediction, patients with low NKRS may be more suitable for immunotherapy and they are more sensitive to immunotherapy. The proliferation rate of CRC cells was significantly reduced and apoptosis of CRC cells was increased after SLC2A3 was knocked down. SLC2A3 was also found to be associated with the TGF-β signaling pathway. Conclusion: NKRS has potential applications for predicting prognostic status and response to immunotherapy in CRC patients. SLC2A3 has potential as a therapeutic target for CRC.
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Affiliation(s)
- Meiqin Li
- Department of Clinical Laboratory, Guang Xi Medical University Cancer Hospital, Nanning, China
| | - Jingqing Song
- Department of Gastrointestinal Surgery, Guang Xi Medical University Cancer Hospital, Nanning, China
| | - Lin Wang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Qi Wang
- Department of Basic Medicine, Guangxi Health Science College, Nanning, China
| | - Qinghua Huang
- Department of Breast Surgery, Wuzhou Red Cross Hospital, Wuzhou, China
| | - Dan Mo
- Department of Breast, Maternal and Child Healthcare Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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14
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Barraza-Vergara LF, Carmona-Sarabia L, Torres-García W, Domenech-García M, Mendez-Vega J, Torres-Lugo M. In vitro assessment of inflammatory skin potential of poly(methyl methacrylate) at non-cytotoxic concentrations. J Biomed Mater Res A 2023; 111:1822-1832. [PMID: 37589190 DOI: 10.1002/jbm.a.37591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/10/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Poly(methyl methacrylate) (PMMA) is considered an attractive substrate material for fabricating wearable skin sensors such as fitness bands and microfluidic devices. Despite its widespread use, inflammatory and allergic responses have been attributed to the use of this material. Therefore, the main objective of this study was to obtain a comprehensive understanding of potential biological effects triggered by PMMA at non-cytotoxic concentrations using in vitro models of NIH3T3 fibroblasts and reconstructed human epidermis (RhE). It was hypothesized that concentrations that do not reduce cell viability are sufficient to activate pathways of inflammatory processes in the skin. The study included cytotoxicity, cell metabolism, cytokine quantification, histopathological, and gene expression analyses. The NIH3T3 cell line was used as a testbed for screening cell toxicity levels associated with the concentration of PMMA with different molecular weights (MWs) (i.e., MW ~5,000 and ~15,000 g/mol). The lower MW of PMMA had a half-maximal inhibitory concentration (IC50 ) value of 5.7 mg/cm2 , indicating greater detrimental effects than the higher MW (IC50 = 14.0 mg/cm2 ). Non-cytotoxic concentrations of 3.0 mg/cm2 for MW ~15,000 g/mol and 0.9 mg/cm2 for MW ~5,000 g/mol) induced negative metabolic changes in NIH3T3 cells. Cell viability was severely reduced to 7% after the exposure to degradation by-products generated after thermal and photodegradation degradation of PMMA. PMMA at non-cytotoxic concentrations still induced overexpression of pro-inflammatory cytokines, chemokines, and growth factors (IL1B, CXCL10, CCL5, IL1R1, IL7, IL17A, VEGFA, FGF2, IFNG, IL15) on the RhE model. The inflammatory response was also supported by histopathological and gene expression analyses of PMMA-treated RhE, indicating tissue damage and gene overexpression. Results suggested that non-cytotoxic concentrations of PMMA (3.0 to 5.6 mg/cm2 for MW ~15,000 g/mol and 0.9 to 2.1 mg/cm2 for MW ~5,000 g/mol) were sufficient to negatively alter NIH3T3 cells metabolism and activate inflammatory events in the RhE skin.
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Affiliation(s)
- Luisa F Barraza-Vergara
- Department of Chemical Engineering, University of Puerto Rico at Mayagüez, Mayaguez, Puerto Rico, USA
| | - Lesly Carmona-Sarabia
- Department of Chemistry, University of Puerto Rico at Río Piedras, San Juan, Puerto Rico, USA
| | - Wandaliz Torres-García
- Department of Industrial Engineering, University of Puerto Rico at Mayagüez, Mayaguez, Puerto Rico, USA
| | - Maribella Domenech-García
- Department of Chemical Engineering, University of Puerto Rico at Mayagüez, Mayaguez, Puerto Rico, USA
| | - Janet Mendez-Vega
- Department of Chemical Engineering, University of Puerto Rico at Mayagüez, Mayaguez, Puerto Rico, USA
| | - Madeline Torres-Lugo
- Department of Chemical Engineering, University of Puerto Rico at Mayagüez, Mayaguez, Puerto Rico, USA
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15
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Li Y, Tang M, Dang W, Zhu S, Wang Y. Identification of disulfidptosis-related subtypes, characterization of tumor microenvironment infiltration, and development of a prognosis model in colorectal cancer. J Cancer Res Clin Oncol 2023; 149:13995-14014. [PMID: 37543978 DOI: 10.1007/s00432-023-05211-1] [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: 07/09/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND Colorectal cancer is the second leading cause of cancer-related deaths, which imposes a significant societal burden. Regular screening and emerging molecular tumor markers have important implications for detecting the progression and development of colorectal cancer. Disulfidptosis is a newly defined type of programmed cell death triggered by abnormal accumulation of disulfide compounds in cells that stimulate disulfide stress. Currently, there is no relevant discussion on this mechanism and colorectal cancer. METHODS We classified the disulfidptosis-related subtypes of colorectal cancer using bioinformatics methods. Through secondary clustering of differentially expressed genes between subtypes, we identified characteristic genes of the disulfidptosis subtype, constructed a prognostic model, and searched for potential biomarkers through clinical validation. RESULTS Using disulfidptosis-related genes collected from the literature, we classified colorectal cancer patients from public databases into three subtypes. The differentially expressed genes between subtypes were clustered into three gene subtypes, and eight characteristic genes were screened to construct a prognostic model. CONCLUSION The disulfidptosis mechanism has important value in the classification of colorectal cancer patients, and characteristic genes selected based on this mechanism can serve as a new potential biological marker for colorectal cancer.
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Affiliation(s)
- Ying Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Mengyao Tang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wei Dang
- The First College for Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shu Zhu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
- Department of Gastroenterology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jingshi Street, Lixia District, Jinan, Shandong, China.
| | - Yunpeng Wang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
- Department of Gastroenterology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jingshi Street, Lixia District, Jinan, Shandong, China.
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16
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Huang L, Sha Y, Liang W, Mo C, Li C, Deng Y, Gong W, Hou X, Ou M. High-throughput sequencing reveals Jatrorrhizine inhibits colorectal cancer growth by ferroptosis-related genes. BMC Med Genomics 2023; 16:217. [PMID: 37710311 PMCID: PMC10500743 DOI: 10.1186/s12920-023-01619-3] [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: 05/16/2023] [Accepted: 07/30/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Colorectal cancer is a malignant tumor that poses a serious threat to human health. The main objective of this study is to investigate the mechanism by which Jatrorrhizine (JAT), a root extract from Stephania Epigaea Lo, exerts its anticancer effects in colorectal cancer. METHODS We initially assessed the inhibitory properties of JAT on SW480 cells using MTT and cell scratch assays. Flow cytometry was employed to detect cell apoptosis. Differentially expressed genes were identified through high-throughput sequencing, and they were subjected to functional enrichment and signaling pathway analysis and PPI network construction. RT-qPCR was used to evaluate gene expression and identify critical differentially expressed genes. Finally, the function and role of differentially expressed genes produced by JAT-treated SW480 cells in colorectal cancer will be further analyzed using the TCGA database. RESULTS Our study demonstrated that JAT exhibits inhibitory effects on SW480 cells at concentrations of 12.5µM, 25µM, 50µM, and 75µM without inducing cell apoptosis. Through high-throughput sequencing, we identified 244 differentially expressed genes. KEGG and GO analysis of high-throughput sequencing results showed that differentially expressed genes were significantly enriched in MAPK, Wnt, and P53 signaling pathways. Notably, JAT significantly altered the expression of genes associated with ferroptosis. Subsequent RT-qPCR showed that the expression of ferroptosis genes SLC2A3 and ASNS was significantly lower in JAT-treated SW480 cells than in the control group. Analysis by TCGA data also showed that ferroptosis genes SLC2A3 and ASNS were significantly highly expressed in COAD. The prognosis of SLC2A3 was significantly worse in COAD compared to the normal group. SLC2A3 may be a core target of JAT for the treatment of COAD. CONCLUSIONS JAT can inhibit COAD growth by ferroptosis-related genes. And it is a potential natural substance for the treatment of COAD.
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Affiliation(s)
- Lingyu Huang
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Ministry of Education of China, Guangxi Normal University, Guilin, 541000 China
| | - Yu Sha
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
| | - Wenken Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Ministry of Education of China, Guangxi Normal University, Guilin, 541000 China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
| | - Chunhong Li
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
| | - Yecheng Deng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Ministry of Education of China, Guangxi Normal University, Guilin, 541000 China
| | - Weiwei Gong
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
| | - Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000 China
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Chen W, Chen Y, Wu L, Gao Y, Zhu H, Li Y, Ji X, Wang Z, Wang W, Han L, Zhu B, Wang H, Xu M. Identification of cell death-related biomarkers and immune infiltration in ischemic stroke between male and female patients. Front Immunol 2023; 14:1164742. [PMID: 37435058 PMCID: PMC10332266 DOI: 10.3389/fimmu.2023.1164742] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/17/2023] [Indexed: 07/13/2023] Open
Abstract
Background Stroke is the second leading cause of death and the third leading cause of disability worldwide, with ischemic stroke (IS) being the most prevalent. A substantial number of irreversible brain cell death occur in the short term, leading to impairment or death in IS. Limiting the loss of brain cells is the primary therapy target and a significant clinical issue for IS therapy. Our study aims to establish the gender specificity pattern from immune cell infiltration and four kinds of cell-death perspectives to improve IS diagnosis and therapy. Methods Combining and standardizing two IS datasets (GSE16561 and GSE22255) from the GEO database, we used the CIBERSORT algorithm to investigate and compare the immune cell infiltration in different groups and genders. Then, ferroptosis-related differently expressed genes (FRDEGs), pyroptosis-related DEGs (PRDEGs), anoikis-related DEGs (ARDEGs), and cuproptosis-related DEGs (CRDEGs) between the IS patient group and the healthy control group were identified in men and women, respectively. Machine learning (ML) was finally used to generate the disease prediction model for cell death-related DEGs (CDRDEGs) and to screen biomarkers related to cell death involved in IS. Results Significant changes were observed in 4 types of immune cells in male IS patients and 10 types in female IS patients compared with healthy controls. In total, 10 FRDEGs, 11 PRDEGs, 3 ARDEGs, and 1 CRDEG were present in male IS patients, while 6 FRDEGs, 16 PRDEGs, 4 ARDEGs, and 1 CRDEG existed in female IS patients. ML techniques indicated that the best diagnostic model for both male and female patients was the support vector machine (SVM) for CDRDEG genes. SVM's feature importance analysis demonstrated that SLC2A3, MMP9, C5AR1, ACSL1, and NLRP3 were the top five feature-important CDRDEGs in male IS patients. Meanwhile, the PDK4, SCL40A1, FAR1, CD163, and CD96 displayed their overwhelming influence on female IS patients. Conclusion These findings contribute to a better knowledge of immune cell infiltration and their corresponding molecular mechanisms of cell death and offer distinct clinically relevant biological targets for IS patients of different genders.
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Affiliation(s)
- Wenli Chen
- Department of Rehabilitation Medicine, ZhongDa Hospital Southeast University, Nanjing, China
| | - Yuanfang Chen
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
| | - Liting Wu
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yue Gao
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Hangju Zhu
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- Jiangsu Cancer Center, Jiangsu Cancer Hospital, Nanjing, China
| | - Ye Li
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xinyu Ji
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
| | - Ziyi Wang
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen Wang
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Han
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Baoli Zhu
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxing Wang
- Department of Rehabilitation Medicine, ZhongDa Hospital Southeast University, Nanjing, China
| | - Ming Xu
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
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Liu Y, Zhang M, Liao Y, Chen H, Su D, Tao Y, Li J, Luo K, Wu L, Zhang X, Yang R. Human umbilical cord mesenchymal stem cell-derived exosomes promote murine skin wound healing by neutrophil and macrophage modulations revealed by single-cell RNA sequencing. Front Immunol 2023; 14:1142088. [PMID: 36999022 PMCID: PMC10044346 DOI: 10.3389/fimmu.2023.1142088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
IntroductionFull-thickness skin wound healing remains a serious undertaking for patients. While stem cell-derived exosomes have been proposed as a potential therapeutic approach, the underlying mechanism of action has yet to be fully elucidated. The current study aimed to investigate the impact of exosomes derived from human umbilical cord mesenchymal stem cells (hucMSC-Exosomes) on the single-cell transcriptome of neutrophils and macrophages in the context of wound healing.MethodsUtilizing single-cell RNA sequencing, the transcriptomic diversity of neutrophils and macrophages was analyzed in order to predict the cellular fate of these immune cells under the influence of hucMSC-Exosomes and to identify alterations of ligand-receptor interactions that may influence the wound microenvironment. The validity of the findings obtained from this analysis was subsequently corroborated by immunofluorescence, ELISA, and qRT-PCR. Neutrophil origins were characterized based on RNA velocity profiles.ResultsThe expression of RETNLG and SLC2A3 was associated with migrating neutrophils, while BCL2A1B was linked to proliferating neutrophils. The hucMSC-Exosomes group exhibited significantly higher levels of M1 macrophages (215 vs 76, p < 0.00001), M2 macrophages (1231 vs 670, p < 0.00001), and neutrophils (930 vs 157, p < 0.00001) when compared to control group. Additionally, it was observed that hucMSC-Exosomes elicit alterations in the differentiation trajectories of macrophages towards more anti-inflammatory phenotypes, concomitant with changes in ligand-receptor interactions, thereby facilitating healing.DiscussionThis study has revealed the transcriptomic heterogeneity of neutrophils and macrophages in the context of skin wound repair following hucMSC-Exosomes interventions, providing a deeper understanding of cellular responses to hucMSC-Exosomes, a rising target of wound healing intervention.
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Affiliation(s)
- Yuanyuan Liu
- Medical School of Chinese People’s Liberation Army, Beijing, China
- Department of Dermatology, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Mingwang Zhang
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yong Liao
- Department of Dermatology, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Hongbo Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Shenzhen, China
| | - Dandan Su
- School of Pharmaceutical Sciences, Sun Yat-sen University, Shenzhen, China
| | - Yuandong Tao
- Department of Pediatric Urology, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jiangbo Li
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing, China
| | - Kai Luo
- Biomedical Treatment Center, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lihua Wu
- Biomedical Treatment Center, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xingyue Zhang
- Department of Dermatology, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Rongya Yang
- Department of Dermatology, the Seventh Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Rongya Yang,
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Identification of Gene Signature-Related Oxidative Stress for Predicting Prognosis of Colorectal Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:5385742. [PMID: 36819776 PMCID: PMC9936508 DOI: 10.1155/2023/5385742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/25/2022] [Accepted: 11/24/2022] [Indexed: 02/10/2023]
Abstract
Background Colorectal cancer (CRC) is the third most common cancer. Nearly a decade of studies had shown that cancer regimens tailored to molecular and pathological features lead to improved overall survival. Oxidative stress (OS) refers to a state in which oxidation and antioxidant effects are unbalanced in the body. However, the molecular mechanism of OS-related CRC remains unclear. Methods Univariate Cox regression analysis gained OS signature genes related to CRC prognosis, and then, different CRC molecular subtypes were obtained by consensus clustering analysis. Differential expression analysis and least absolute shrinkage and selection operator (LASSO) algorithm were used to obtain prognostic-related signature genes. Significantly, risk score was calculated by RiskScore = Σβi × Expi. Moreover, the Kaplan-Meier survival analysis, immune cell infiltration, and sensitivity to treatment regimens were performed to assess the model's validity and adaptability. Finally, RiskScore incorporated clinicopathological features to further improve prognostic models and survival prediction. Results 63 OS-related prognostic genes were obtained, and four distinct molecular subtypes of CRC were identified based on the expression characteristics. 230 differentially expressed genes (DEGs) between different molecular subtypes were compressed by LASSO algorithm, and finally, 6 OS-related genes were obtained. The Kaplan-Meier survival analysis indicated that the high RiskScore groups had poorer prognosis and the RiskScore model showed better predictive performance in all three other independent datasets. Moreover, immunotherapy/chemosensitivity analysis found that the low-risk group was more sensitive to different treatment options and could achieve better treatment outcomes. Conclusion Oxidative stress-related RiskScore model built in this work has good predictive performance for CRC.
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Pan S, Li Y, He H, Cheng S, Li J, Pathak JL. Identification of ferroptosis, necroptosis, and pyroptosis-associated genes in periodontitis-affected human periodontal tissue using integrated bioinformatic analysis. Front Pharmacol 2023; 13:1098851. [PMID: 36686646 PMCID: PMC9852864 DOI: 10.3389/fphar.2022.1098851] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction: Periodontitis is a chronic inflammatory oral disease that destroys soft and hard periodontal support tissues. Multiple cell death modes including apoptosis, necroptosis, pyroptosis, and ferroptosis play a crucial role in the pathogenicity of inflammatory diseases. This study aimed to identify genes associated with ferroptosis, necroptosis, and pyroptosis in different cells present in the periodontium of periodontitis patients. Methods: Gingival tissues' mRNA sequencing dataset GSE173078 of 12 healthy control and 12 periodontitis patients' and the microarray dataset GSE10334 of 63 healthy controls and 64 periodontitis patients' were obtained from Gene Expression Omnibus (GEO) database. A total of 910 differentially expressed genes (DEGs) obtained in GSE173078 were intersected with necroptosis, pyroptosis, and ferroptosis-related genes to obtain the differential genes associated with cell death (DCDEGs), and the expression levels of 21 differential genes associated with cell death were verified with dataset GSE10334. Results: Bioinformatic analysis revealed 21 differential genes associated with cell death attributed to ferroptosis, pyroptosis, and necroptosis in periodontitis patients compared with healthy controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that 21 differential genes associated with cell death were related to various cellular and immunological pathways including inflammatory responses, necroptosis, and osteoclast differentiation. Additionally, the single-cell RNA (scRNA) sequencing data GSE171213 of 4 healthy controls and 5 periodontitis patients' periodontal tissue was analyzed to obtain cell clustering and cell types attributed to differential genes associated with cell death. We found that among 21 DCDEGs, SLC2A3, FPR2, TREM1, and IL1B were mainly upregulated in neutrophils present in the periodontium of periodontitis patients. Gene overlapping analysis revealed that IL-1B is related to necroptosis and pyroptosis, TREM1 and FPR2 are related to pyroptosis, and SLC2A3 is related to ferroptosis. Finally, we utilized the CIBERSORT algorithm to assess the association between DCDEGs and immune infiltration phenotypes, based on the gene expression profile of GSE10334. The results revealed that the upregulated SLC2A3, FPR2, TREM1, and IL1B were positively correlated with neutrophil infiltration in the periodontium. Discussion: The findings provide upregulated SLC2A3, FPR2, TREM1, and IL1B in neutrophils as a future research direction on the mode and mechanism of cell death in periodontitis and their role in disease pathogenicity.
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Affiliation(s)
| | | | | | | | - Jiang Li
- *Correspondence: Janak L. Pathak, ; Jiang Li,
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Liu M, Xiao Q, Yu X, Zhao Y, Qu C. Characterization of lung adenocarcinoma based on immunophenotyping and constructing an immune scoring model to predict prognosis. Front Pharmacol 2022; 13:1081244. [PMID: 36601052 PMCID: PMC9806149 DOI: 10.3389/fphar.2022.1081244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Lung cancer poses great threat to human health, and lung adenocarcinoma (LUAD) is the main subtype. Immunotherapy has become first line therapy for LUAD. However, the pathogenic mechanism of LUAD is still unclear. Methods: We scored immune-related pathways in LUAD patients using single sample gene set enrichment analysis (ssGSEA) algorithm, and further identified distinct immune-related subtypes through consistent clustering analysis. Next, immune signatures, Kaplan-Meier survival analysis, copy number variation (CNV) analysis, gene methylation analysis, mutational analysis were used to reveal differences between subtypes. pRRophetic method was used to predict the response to chemotherapeutic drugs (half maximal inhibitory concentration). Then, weighted gene co-expression network analysis (WGCNA) was performed to screen hub genes. Significantly, we built an immune score (IMscore) model to predict prognosis of LUAD. Results: Consensus clustering analysis identified three LUAD subtypes, namely immune-Enrich subtype (Immune-E), stromal-Enrich subtype (Stromal-E) and immune-Deprived subtype (Immune-D). Stromal-E subtype had a better prognosis, as shown by Kaplan-Meier survival analysis. Higher tumor purity and lower immune cell scores were found in the Immune-D subtype. CNV analysis showed that homologous recombination deficiency was lower in Stromal-E and higher in Immune-D. Likewise, mutational analysis found that the Stromal-E subtype had a lower mutation frequency in TP53 mutations. Difference in gene methylation (ZEB2, TWIST1, CDH2, CDH1 and CLDN1) among three subtypes was also observed. Moreover, Immune-E was more sensitive to traditional chemotherapy drugs Cisplatin, Sunitinib, Crizotinib, Dasatinib, Bortezomib, and Midostaurin in both the TCGA and GSE cohorts. Furthermore, a 6-gene signature was constructed to predicting prognosis, which performed better than TIDE score. The performance of IMscore model was successfully validated in three independent datasets and pan-cancer.
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Affiliation(s)
- Mengfeng Liu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin Medical Sciences University, Harbin, China
| | - Qifan Xiao
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin Medical Sciences University, Harbin, China
| | - Xiran Yu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin Medical Sciences University, Harbin, China
| | - Yujie Zhao
- Regional Marketing Department, YuceBio Technology Co., Shenzhen, China
| | - Changfa Qu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin Medical Sciences University, Harbin, China,*Correspondence: Changfa Qu,
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De Palma FDE, Carbonnier V, Salvatore F, Kroemer G, Pol JG, Maiuri MC. Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers. Cancers (Basel) 2022; 14:cancers14235980. [PMID: 36497462 PMCID: PMC9738797 DOI: 10.3390/cancers14235980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Long non-coding RNAs may constitute epigenetic biomarkers for the diagnosis, prognosis, and therapeutic response of a variety of tumors. In this context, we aimed at assessing the diagnostic and prognostic value of the recently described long intergenic non-coding RNA 01087 (LINC01087) in human cancers. (2) Methods: We studied the expression of LINC01087 across 30 oncological indications by interrogating public resources. Data extracted from the TCGA and GTEx databases were exploited to plot receiver operating characteristic curves (ROC) and determine the diagnostic performance of LINC01087. Survival data from TCGA and KM-Plotter directories allowed us to graph Kaplan-Meier curves and evaluate the prognostic value of LINC01087. To investigate the function of LINC01087, gene ontology (GO) annotation and Kyoto Encyclopedia of Gene and Genomes (KEGG) enrichment analyses were performed. Furthermore, interactions between LINC01087 and both miRNA and mRNA were studied by means of bioinformatics tools. (3) Results: LINC01087 was significantly deregulated in 7 out of 30 cancers, showing a predominant upregulation. Notably, it was overexpressed in breast (BC), esophageal (ESCA), and ovarian (OV) cancers, as well as lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD), and uterine carcinosarcoma (UCS). By contrast, LINC01087 displayed downregulation in testicular germ cell tumors (TGCT). ROC curve analyses identified LINC01087 as a potential diagnostic indicator in BC, ESCA, OV, STAD, and TGCT. Moreover, high and low expression of LINC01087 predicted a favorable prognosis in BC and papillary cell carcinoma, respectively. In silico analyses indicated that deregulation of LINC01087 in cancer was associated with a modulation of genes related to ion channel, transporter, and peptide receptor activity. (4) Conclusions: the quantification of an altered abundance of LINC01087 in tissue specimens might be clinically useful for the diagnosis and prognosis of some hormone-related tumors, including BC, OV, and TGCT, as well as other cancer types such as ESCA and STAD. Moreover, our study revealed the potential of LINC01087 (and perhaps other lncRNAs) to regulate neuroactive molecules in cancer.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Vincent Carbonnier
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Centro Interuniversitario per Malattie Multigeniche e Multifattoriali e Loro Modelli Animali (Federico II, 80131, Napoli, Tor Vergata, Rome and “G. D’Annunzio”, Chieti-Pescara), 80131 Napoli, Italy
| | - Guido Kroemer
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, 75004 Paris, France
| | - Jonathan G. Pol
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
| | - Maria Chiara Maiuri
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
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Jiang HZ, Yang B, Jiang YL, Liu X, Chen DL, Long FX, Yang Z, Tang DX. Development and validation of prognostic models for colon adenocarcinoma based on combined immune-and metabolism-related genes. Front Oncol 2022; 12:1025397. [PMID: 36387195 PMCID: PMC9661394 DOI: 10.3389/fonc.2022.1025397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/30/2022] [Indexed: 11/02/2023] Open
Abstract
Background The heterogeneity of tumor tissue is one of the reasons for the poor effect of tumor treatment, which is mainly affected by the tumor immune microenvironment and metabolic reprogramming. But more research is needed to find out how the tumor microenvironment (TME) and metabolic features of colon adenocarcinoma (COAD) are related. Methods We obtained the transcriptomic and clinical data information of COAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Consensus clustering analysis was used to identify different molecular subtypes, identify differentially expressed genes (DEGs) associated with immune-and metabolism-related genes (IMRGs) prognosis. Univariate and multivariable Cox regression analysis and Lasso regression analysis were applied to construct the prognostic models based on the IMRG risk score. The correlations between risk scores and TME, immune cell infiltration, and immune checkpoint genes were investigated. Lastly, potential appropriate drugs related to the risk score were screened by drug sensitivity analysis. Results By consensus clustering analysis, we identified two distinct molecular subtypes. It was also found that the multilayered IMRG subtypes were associated with the patient's clinicopathological characteristics, prognosis, and TME cell infiltration characteristics. Meanwhile, a prognostic model based on the risk score of IMRGs was constructed and its predictive power was verified internally and externally. Clinicopathological analysis and nomogram give it better clinical guidance. The IMRG risk score plays a key role in immune microenvironment infiltration. Patients in the high-risk groups of microsatellite instability (MSI) and tumor mutational burden (TMB) were found to, although with poor prognosis, actively respond to immunotherapy. Furthermore, IMRG risk scores were significantly associated with immune checkpoint gene expression. The potential drug sensitivity study helps come up with and choose a chemotherapy treatment plan. Conclusion Our comprehensive analysis of IMRG signatures revealed a broad range of regulatory mechanisms affecting the tumor immune microenvironment (TIME), immune landscape, clinicopathological features, and prognosis. And to explore the potential drugs for immunotherapy. It will help to better understand the molecular mechanisms of COAD and provide new directions for disease treatment.
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Affiliation(s)
- Hui-zhong Jiang
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Bing Yang
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Ya-li Jiang
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Xun Liu
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Da-lin Chen
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Feng-xi Long
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhu Yang
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dong-xin Tang
- College of Graduate, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Zhu H, Tan J, Wang Z, Wu Z, Zhou W, Zhang Z, Li M, Zhao Y. Bioinformatics analysis constructs potential ferroptosis-related ceRNA network involved in the formation of intracranial aneurysm. Front Cell Neurosci 2022; 16:1016682. [PMCID: PMC9612944 DOI: 10.3389/fncel.2022.1016682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundIntracranial aneurysm (IA) causes more than 80% of nontraumatic subarachnoid hemorrhages (SAHs). The mechanism of ferroptosis involved in IA formation remains unclear. The roles played by competitive endogenous RNA (ceRNA) regulation networks in many diseases are becoming clearer. The goal of this study was to understand more fully the ferroptosis-related ceRNA regulation network in IA.Materials and methodsTo identify differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs), and differentially expressed lncRNAs (DELs) across IA and control samples, the GEO datasets GSE122897 and GSE66239 were downloaded and analyzed with the aid of R. Ferroptosis DEGs were discovered by exploring the DEGs of ferroptosis-related genes of the ferroptosis database. Potentially interacting miRNAs and lncRNAs were predicted using miRWalk and StarBase. Enrichment analysis was also performed. We utilized the STRING database and Cytoscape software to identify protein-protein interactions and networks. DAB-enhanced Prussian blue staining was used to detect iron in IA tissues.ResultsIron deposition was evident in IA tissue. In all, 30 ferroptosis DEGs, 5 key DEMs, and 17 key DELs were screened out for constructing a triple regulatory network. According to expression regulation of DELs, DEMs, and DEGs, a hub triple regulatory network was built. As the functions of lncRNAs are determined by their cellular location, PVT1-hsa-miR-4644-SLC39A14 ceRNA and DUXAP8-hsa-miR-378e/378f-SLC2A3 ceRNA networks were constructed.ConclusionCeRNA (PVT1-hsa-miR-4644-SLC39A14 and DUXAP8-hsa-miR-378e/378f-SLC2A3) overexpression networks associated with ferroptosis in IA were established.
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Su X, Ma G, Bai X, Zhang J, Li M, Zhang F, Sun T, Ma D, Lu F, Ji C. The prognostic marker FLVCR2 associated with tumor progression and immune infiltration for acute myeloid leukemia. Front Cell Dev Biol 2022; 10:978786. [DOI: 10.3389/fcell.2022.978786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is one of the most common hematopoietic malignancies in adults. The tumor microenvironment (TME) has a critical effect on AML occurrence, recurrence, and progression. The gene feline leukemia virus subgroup C cellular receptor family member 2 (FLVCR2) belongs to the major facilitator superfamily of transporter protein members, which is primarily involved in transporting small molecules. The potential role of FLVCR2 in the TME in AML has not been investigated. To clarify the expression and role of FLVCR2 in AML, we analyzed the Gene Expression Omnibus and The Cancer Genome Atlas databases and found that FLVCR2 mRNA expression significantly increased among patients with AML. Furthermore, based on an analysis of the Gene Expression Profiling Interactive Analysis database, FLVCR2 upregulation predicted dismal overall survival of patients with AML. Our validation analysis revealed the significant upregulation of FLVCR2 within the bone marrow of AML relative to healthy controls by western blotting and qPCR assays. Gene set enrichment analysis was conducted to explore FLVCR2’s related mechanism in AML. We found that high FLVCR2 expression was related to infiltration degrees of immune cells and immune scores among AML cases, indicating that FLVCR2 possibly had a crucial effect on AML progression through the immune response. Specifically, FLVCR2 upregulation was negatively related to the immune infiltration degrees of activated natural killer cells, activated memory CD4+ T cells, activated dendritic cells, and CD8+ T cells using CIBERSORT analysis. According to the in vitro research, FLVCR2 silencing suppressed AML cell growth and promoted their apoptosis. This study provides insights into FLVCR2’s effect on tumor immunity, indicating that it might serve as an independent prognostic biomarker and was related to immune infiltration within AML.
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Comprehensive Analysis of the Role of SLC2A3 on Prognosis and Immune Infiltration in Head and Neck Squamous Cell Carcinoma. Anal Cell Pathol (Amst) 2022; 2022:2371057. [PMID: 36247875 PMCID: PMC9553684 DOI: 10.1155/2022/2371057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/01/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Background. SLC2A3 is upregulated in various cancer types and promotes proliferation, invasion, and metabolism. However, its role in the prognosis and immune regulation of head and neck squamous cell carcinoma (HNSCC) is still obscure. This study is aimed at exploring the prognostic and immunotherapeutic potential of SLC2A3 in HNSCC. Methods. All data were downloaded from TCGA database and integrated via R software. SLC2A3 expression was evaluated using R software, TIMER, CPTAC, and HPA databases. The association between SLC2A3 expression and clinicopathologic characteristics was assessed by R software. The effect of SLC2A3 on survival was analyzed by R software and Kaplan-Meier Plotter. Genomic alterations in SLC2A3 were investigated using the cBioPortal database. Coexpression of SLC2A3 was studied using LinkedOmics and STRING, and enrichment analyses were performed with R software. The relationship between SLC2A3 expression and immune infiltration was determined using TIMER and TISIDB databases. Immune checkpoints and ESTIMATE score were analyzed via the SangerBox database. Results. SLC2A3 expression was upregulated in HNSCC tissues compared to normal tissues. It was significantly related to TNM stage, histological grade, and alcohol history. High SLC2A3 expression was associated with poor prognosis in HNSCC. Coexpression analysis indicated that SLC2A3 mostly participated in the HIF-1 signaling pathway and glycolysis. Furthermore, SLC2A3 expression strongly correlated with tumor-infiltrating lymphocytes in HNSCC. Conclusion. SLC2A3 could serve as a potential prognostic biomarker for tumor immune infiltration in HNSCC.
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Lin L, Que R, Wang J, Zhu Y, Liu X, Xu R. Prognostic value of the ferroptosis-related gene SLC2A3 in gastric cancer and related immune mechanisms. Front Genet 2022; 13:919313. [PMID: 35957685 PMCID: PMC9358142 DOI: 10.3389/fgene.2022.919313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
SLC2A3 is a ferroptosis marker engaged in transmembrane glucose transport. However, the effect of SLC2A3 on the prognosis of patients with cancer remains unclear. This study aimed to explore the prognostic implications of SLC2A3 and its underlying immune mechanisms in gastric cancer. The mRNA expression profiles and corresponding clinical data of patients with gastric cancer were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. Differentially expressed genes related to SLC2A3 were identified using the R package “limma.” Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, gene set enrichment analysis, and gene set variation analysis were used to explore the underlying mechanisms. The protein–protein and miRNA interaction networks were analyzed using Cytoscape software. Immune cell infiltration was assessed using single-sample gene set enrichment analysis. Univariate and multivariate Cox regression analyses revealed the relationship between SLC2A3 expression and prognosis. SLC2A3 was found to be highly expressed in tumor tissues and was associated with an unfavorable prognosis in patients with gastric cancer. Functional enrichment analysis showed that SLC2A3 is related to cytokine–cytokine receptor interaction, epithelial–mesenchymal transition, T cell receptor signaling pathway, B cell receptor signaling pathway, and immune checkpoints. SLC2A3 is also involved in immune response regulation and is regulated by multiple miRNAs, including miR-195-5p, miR-106a-5p, miR-424-5p, and miR-16-5p. Univariate and multivariate Cox regression analyses indicated that SLC2A3 can be used as an independent prognostic factor for predicting the outcome in patients with gastric cancer. SLC2A3 and related miRNAs are potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Liubing Lin
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Renye Que
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Gastroenterology, Shanghai TCM Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian Wang
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Zhu
- Department of Internal Medicine I, Shanghai Jiading District Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Xiaolin Liu
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Xiaolin Liu, ; Rongzhong Xu,
| | - Rongzhong Xu
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Xiaolin Liu, ; Rongzhong Xu,
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Gao G, Deng A, Liang S, Liu S, Fu X, Zhao X, Yu Z. Integration of Bulk RNA Sequencing and Single-Cell RNA Sequencing to Reveal Uveal Melanoma Tumor Heterogeneity and Cells Related to Survival. Front Immunol 2022; 13:898925. [PMID: 35865532 PMCID: PMC9294459 DOI: 10.3389/fimmu.2022.898925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular classification based on transcriptional characteristics is often used to study tumor heterogeneity. Human cancer has different cell populations with distinct transcription in tumors, and their heterogeneity is the focus of tumor therapy. Our purpose was to explore the tumor heterogeneity of uveal melanoma (UM) through RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq). Based on the consensus clustering assays of the prognosis-related immune gene set, the immune subtype (IS) of UM and its corresponding immune characteristics were comprehensively analyzed. The heterogeneous cell groups and corresponding marker genes of UM were identified from GSE138433 using scRNA-seq analysis. Pseudotime trajectory analysis and SCENIC analysis were conducted to explore the trajectory of cell differentiation and the regulatory network of single-cell transcription factors (TFs). Based on 37 immune gene sets, UM was divided into two different immune subtypes (IS1 and IS2). The two kinds of ISs have different characteristics in prognosis, immune-related molecules, immune score, and immune cell infiltration. According to 11,988 cells of scRNA-seq data from six UM samples, 11 cell clusters and 10 cell types were identified. The subsets of C1, C4, C5, C8, and C9 were related to the prognosis of UM, and different TF–target gene regulatory networks were involved. These five cell subsets differentiated into 3 different states. Our results provided valuable information about the heterogeneity of UM tumors and the expression patterns of TFs in different cell types.
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Gu I, Gregory E, Atwood C, Lee SO, Song YH. Exploring the Role of Metabolites in Cancer and the Associated Nerve Crosstalk. Nutrients 2022; 14:nu14091722. [PMID: 35565690 PMCID: PMC9103817 DOI: 10.3390/nu14091722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
Since Otto Warburg's first report on the increased uptake of glucose and lactate release by cancer cells, dysregulated metabolism has been acknowledged as a hallmark of cancer that promotes proliferation and metastasis. Over the last century, studies have shown that cancer metabolism is complex, and by-products of glucose and glutamine catabolism induce a cascade of both pro- and antitumorigenic processes. Some vitamins, which have traditionally been praised for preventing and inhibiting the proliferation of cancer cells, have also been proven to cause cancer progression in a dose-dependent manner. Importantly, recent findings have shown that the nervous system is a key player in tumor growth and metastasis via perineural invasion and tumor innervation. However, the link between cancer-nerve crosstalk and tumor metabolism remains unclear. Here, we discuss the roles of relatively underappreciated metabolites in cancer-nerve crosstalk, including lactate, vitamins, and amino acids, and propose the investigation of nutrients in cancer-nerve crosstalk based on their tumorigenicity and neuroregulatory capabilities. Continued research into the metabolic regulation of cancer-nerve crosstalk will provide a more comprehensive understanding of tumor mechanisms and may lead to the identification of potential targets for future cancer therapies.
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Affiliation(s)
- Inah Gu
- Department of Food Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72704, USA
| | - Emory Gregory
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Casey Atwood
- Department of Food Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72704, USA
| | - Sun-Ok Lee
- Department of Food Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72704, USA
| | - Young Hye Song
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA
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Kang N, Xie X, Zhou X, Wang Y, Chen S, Qi R, Liu T, Jiang H. Identification and validation of EMT-immune-related prognostic biomarkers CDKN2A, CMTM8 and ILK in colon cancer. BMC Gastroenterol 2022; 22:190. [PMID: 35429970 PMCID: PMC9013447 DOI: 10.1186/s12876-022-02257-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/31/2022] [Indexed: 12/26/2022] Open
Abstract
Colon cancer (CC) is a disease with high incidence and mortality rate. The interaction between epithelial-mesenchymal transition (EMT) and immune status has important clinical significance. We aim to identify EMT-immune-related prognostic biomarkers in colon cancer. The GEO2R and GEPIA 2.0 were utilized to calculate the differential expression genes between CC and normal mucosa. Immport, InnateDB and EMTome databases were used to define EMT-immune-related genes. We conducted batch prognostic analysis by TCGA data. The expression patterns were verified by multiple datasets and lab experiments. GEPIA 2.0 and TIMER 2.0 were utilized to analyze the correlation of the hub genes with EMT markers and immune infiltration. GeneMANIA, STRING, and Metascape were used for co-expression and pathway enrichment analysis. Finally, we established a signature by the method of multivariate Cox regression analysis. CDKN2A, CMTM8 and ILK were filtered out as prognostic genes. CDKN2A and CMTM8 were up-regulated, while ILK was down-regulated in CC. CDKN2A was positively correlated with infiltration of macrophages, Th2 cells, Treg cells, and negatively correlated with NK cells. CMTM8 was negatively correlated with CD8+ T cells, dendritic cells, and NK cells. ILK was positively correlated with CD8+ T cells and dendritic cells. Moreover, CDKN2A, CMTM8 and ILK were significantly correlated with EMT markers. The three genes could participate in the TGF-β pathway. The prognosis model established by the three hub genes was an independent prognosis factor, which can better predict the prognosis. CDKN2A, CMTM8 and ILK are promising prognostic biomarkers and may be potential therapeutic targets in colon cancer.
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Lu M, Li J, Fan X, Xie F, Fan J, Xiong Y. Novel Immune-Related Ferroptosis Signature in Esophageal Cancer: An Informatics Exploration of Biological Processes Related to the TMEM161B-AS1/hsa-miR-27a-3p/GCH1 Regulatory Network. Front Genet 2022; 13:829384. [PMID: 35281840 PMCID: PMC8908453 DOI: 10.3389/fgene.2022.829384] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Considering the role of immunity and ferroptosis in the invasion, proliferation and treatment of cancer, it is of interest to construct a model of prognostic-related differential expressed immune-related ferroptosis genes (PR-DE-IRFeGs), and explore the ferroptosis-related biological processes in esophageal cancer (ESCA).Methods: Four ESCA datasets were used to identify three PR-DE-IRFeGs for constructing the prognostic model. Validation of our model was based on analyses of internal and external data sets, and comparisons with past models. With the biological-based enrichment analysis as a guide, exploration for ESCA-related biological processes was undertaken with respect to the immune microenvironment, mutations, competing endogenous RNAs (ceRNA), and copy number variation (CNV). The model’s clinical applicability was measured by nomogram and correlation analysis between risk score and gene expression, and also immune-based and chemotherapeutic sensitivity.Results: Three PR-DE-IRFeGs (DDIT3, SLC2A3, and GCH1), risk factors for prognosis of ESCA patients, were the basis for constructing the prognostic model. Validation of our model shows a meaningful capability for prognosis prediction. Furthermore, many biological functions and pathways related to immunity and ferroptosis were enriched in the high-risk group, and the role of the TMEM161B-AS1/hsa-miR-27a-3p/GCH1 network in ESCA is supported. Also, the KMT2D mutation is associated with our risk score and SLC2A3 expression. Overall, the prognostic model was associated with treatment sensitivity and levels of gene expression.Conclusion: A novel, prognostic model was shown to have high predictive value. Biological processes related to immune functions, KMT2D mutation, CNV and the TMEM161B-AS1/hsa-miR-27a-3p/GCH1 network were involved in ESCA progression.
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Affiliation(s)
- Min Lu
- Department of Emergency, Shangrao People’s Hospital, Shangrao Hospital Affiliated to Nanchang University, Shangrao, China
| | - Jiaqi Li
- School of Stomatology, Nanchang University, Nanchang, China
| | - Xin Fan
- School of Stomatology, Nanchang University, Nanchang, China
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Xin Fan,
| | - Fei Xie
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jie Fan
- Shangrao Municipal Hospital, Shangrao, China
| | - Yuanping Xiong
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
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