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Rong D, Su Y, Jia D, Zeng Z, Yang Y, Wei D, Lu H, Cao Y. Experimentally validated oxidative stress -associated prognostic signatures describe the immune landscape and predict the drug response and prognosis of SKCM. Front Immunol 2024; 15:1387316. [PMID: 38660305 PMCID: PMC11039952 DOI: 10.3389/fimmu.2024.1387316] [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: 02/17/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Background Skin Cutaneous Melanoma (SKCM) incidence is continually increasing, with chemotherapy and immunotherapy being among the most common cancer treatment modalities. This study aims to identify novel biomarkers for chemotherapy and immunotherapy response in SKCM and explore their association with oxidative stress. Methods Utilizing TCGA-SKCM RNA-seq data, we employed Weighted Gene Co-expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) networks to identify six core genes. Gene co-expression analysis and immune-related analysis were conducted, and specific markers associated with oxidative stress were identified using Gene Set Variation Analysis (GSVA). Single-cell analysis revealed the expression patterns of Oxidative Stress-Associated Genes (OSAG) in the tumor microenvironment. TIDE analysis was employed to explore the association between immune therapy response and OSAG, while CIBERSORT was used to analyze the tumor immune microenvironment. The BEST database demonstrated the impact of the Oxidative Stress signaling pathway on chemotherapy drug resistance. Immunohistochemical staining and ROC curve evaluation were performed to assess the protein expression levels of core genes in SKCM and normal samples, with survival analysis utilized to determine their diagnostic value. Results We identified six central genes associated with SKCM metastasis, among which the expression of DSC2 and DSC3 involved in the oxidative stress pathway was closely related to immune cell infiltration. DSC2 influenced drug resistance in SKMC patients. Furthermore, downregulation of DSC2 and DSC3 expression enhanced the response of SKCM patients to immunotherapy. Conclusion This study identified two Oxidative Stress-Associated genes as novel biomarkers for SKCM. Additionally, targeting the oxidative stress pathway may serve as a new strategy in clinical practice to enhance SKCM chemotherapy and sensitivity.
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Affiliation(s)
- Dongyun Rong
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yushen Su
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dechao Jia
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhirui Zeng
- Department of anorectal surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
- School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Yang
- Department of Internal Medicine, The Third Affiliated Hospital of Guizhou Medical University, Duyun, Guizhou, China
| | - Dalong Wei
- Department of Burns, Plastic Surgery and Wound Repair, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Key Laboratory of Tumor Molecular Pathology of Baise, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Honguan Lu
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu Cao
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
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Lv H, Liu L, He Y, Yang K, Fu Y, Bao Y. Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma. Front Pharmacol 2024; 15:1344755. [PMID: 38515849 PMCID: PMC10955143 DOI: 10.3389/fphar.2024.1344755] [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: 11/26/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Melanoma is the most lethal type of skin cancer with an increasing incidence. Cuproptosis is the most recently identified copper-dependent form of cell death that relies on mitochondrial respiration. The hippocampal (Hippo) pathway functions as a tumor suppressor by regulating Yes-associated protein/transcriptional coactivator with PDZ-binding motif (YAP/TAZ) activity. However, its role in cuproptosis remains unknown. In addition, the correlation of cuproptosis-related genes and Hippo pathway-related genes with tumor prognosis warrants further investigation. In the present study, we explored the correlation of cuproptosis-related genes and Hippo pathway-related genes with the prognosis of melanoma through analysis of data from a public database and experimental verification. We found eight Hippo pathway-related genes that were downregulated in melanoma and exhibited predictive value for prognosis. There was a significant positive correlation between cuproptosis-related genes and Hippo pathway-related genes in skin cutaneous melanoma. YAP1 expression was positively correlated with ferredoxin 1 (FDX1) expression in the GSE68599 dataset and A2058 cells. Moreover, YAP1 was positively and negatively correlated with M2 macrophages and regulatory T cell infiltration, respectively. In conclusion, the present study demonstrated the prognostic value of Hippo pathway-related genes (particularly YAP1) in melanoma, revealing the correlation between the expression of Hippo pathway-related genes and immune infiltration. Thus, the present findings may provide new clues on the prognostic assessment of patients with melanoma and a new target for the immunotherapy of this disease.
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Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Liu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yuexi He
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Kun Yang
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Fu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yingqiu Bao
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Chen F, Lei L, Chen S, Zhao Z, Huang Y, Jiang G, Guo X, Li Z, Zheng Z, Wang J. Serglycin secreted by late-stage nucleus pulposus cells is a biomarker of intervertebral disc degeneration. Nat Commun 2024; 15:47. [PMID: 38167807 PMCID: PMC10761730 DOI: 10.1038/s41467-023-44313-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Intervertebral disc degeneration is a natural process during aging and a leading cause of lower back pain. Here, we generate a comprehensive atlas of nucleus pulposus cells using single-cell RNA-seq analysis of human nucleus pulposus tissues (three males and four females, age 41.14 ± 18.01 years). We identify fibrotic late-stage nucleus pulposus cells characterized by upregulation of serglycin expression which facilitate the local inflammatory response by promoting the infiltration of inflammatory cytokines and macrophages. Finally, we discover that daphnetin, a potential serglycin ligand, substantially mitigates the local inflammatory response by downregulating serglycin expression in an in vivo mouse model, thus alleviating intervertebral disc degeneration. Taken together, we identify late-stage nucleus pulposus cells and confirm the potential mechanism by which serglycin regulates intervertebral disc degeneration. Our findings indicate that serglycin is a latent biomarker of intervertebral disc degeneration and may contribute to development of diagnostic and therapeutic strategies.
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Affiliation(s)
- Fan Chen
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Linchuan Lei
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shunlun Chen
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
| | - Zhuoyang Zhao
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuming Huang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
| | - Guowei Jiang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xingyu Guo
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
| | - Zemin Li
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China
| | - Zhaomin Zheng
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China.
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China.
| | - Jianru Wang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, P.R. China.
- Guangdong Province Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, P.R. China.
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Abbasi EY, Deng Z, Magsi AH, Ali Q, Kumar K, Zubedi A. Optimizing Skin Cancer Survival Prediction with Ensemble Techniques. Bioengineering (Basel) 2023; 11:43. [PMID: 38247920 PMCID: PMC10813432 DOI: 10.3390/bioengineering11010043] [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: 12/05/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
The advancement in cancer research using high throughput technology and artificial intelligence (AI) is gaining momentum to improve disease diagnosis and targeted therapy. However, the complex and imbalanced data with high dimensionality pose significant challenges for computational approaches and multi-omics data analysis. This study focuses on predicting skin cancer and analyzing overall survival probability. We employ the Kaplan-Meier estimator and Cox proportional hazards regression model, utilizing high-throughput machine learning (ML)-based ensemble methods. Our proposed ML-based ensemble techniques are applied to a publicly available dataset from the ICGC Data Portal, specifically targeting skin cutaneous melanoma cancers (SKCM). We used eight baseline classifiers, namely, random forest (RF), decision tree (DT), gradient boosting (GB), AdaBoost, Gaussian naïve Bayes (GNB), extra tree (ET), logistic regression (LR), and light gradient boosting machine (Light GBM or LGBM). The study evaluated the performance of the proposed ensemble methods and survival analysis on SKCM. The proposed methods demonstrated promising results, outperforming other algorithms and models in terms of accuracy compared to traditional methods. Specifically, the RF classifier exhibited outstanding precision results. Additionally, four different ensemble methods (stacking, bagging, boosting, and voting) were created and trained to achieve optimal results. The performance was evaluated and interpreted using accuracy, precision, recall, F1 score, confusion matrix, and ROC curves, where the voting method achieved a promising accuracy of 99%. On the other hand, the RF classifier achieved an outstanding accuracy of 99%, which exhibits the best performance. We compared our proposed study with the existing state-of-the-art techniques and found significant improvements in several key aspects. Our approach not only demonstrated superior performance in terms of accuracy but also showcased remarkable efficiency. Thus, this research work contributes to diagnosing SKCM with high accuracy.
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Affiliation(s)
- Erum Yousef Abbasi
- State Key Laboratory of Wireless Network Positioning and Communication Engineering Integration Research, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China;
| | - Zhongliang Deng
- State Key Laboratory of Wireless Network Positioning and Communication Engineering Integration Research, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China;
| | - Arif Hussain Magsi
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China;
| | - Qasim Ali
- Department of Software Engineering, Mehran University of Engineering and Technology, Jamshoro 76062, Pakistan;
| | - Kamlesh Kumar
- School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China;
| | - Asma Zubedi
- School of Economics and Management, Beijing University of Posts and Telecommunications, Beijing 100876, China;
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Torres GM, Jarnagin HC, Park C, Yang H, Kosarek NN, Bhandari R, Wang CY, Kolling FW, Whitfield ML, Turk MJ, Liby KT, Pioli PA. CDDO-Methyl Ester Inhibits BRAF Inhibitor Resistance and Remodels the Myeloid Compartment in BRAF-mutant Melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551524. [PMID: 37577680 PMCID: PMC10418171 DOI: 10.1101/2023.08.01.551524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Approximately 50% of advanced melanomas harbor activating BRAF V600E mutations that are sensitive to BRAF inhibition. However, the duration of the response to BRAF inhibitors (BRAFi) has been limited due to the development of acquired resistance, which is preceded by recruitment of immunosuppressive myeloid cells and regulatory T cells (T regs ). While the addition of MAPK/ERK kinase 1 inhibitors (MEKi) prolongs therapeutic response to BRAF inhibition, most patients still develop resistance. Using a Braf V600E/+ /Pten -/- graft mouse model of melanoma, we now show that the addition of the methyl ester of the synthetic triterpenoid 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (C-Me) to the BRAFi vemurafenib analog PLX4720 at resistance significantly reduces tumor burden. Dual treatment remodels the BRAFi resistant-tumor microenvironment (TME), reducing infiltration of T regs and tumor associated macrophages (TAMs), and attenuates immunosuppressive cytokine production. For the first time, we characterize myeloid populations using scRNA-seq in BRAFi-resistant tumors and demonstrate that restoration of therapeutic response is associated with significant changes in immune-activated myeloid subset representation. Collectively, these studies suggest that C-Me inhibits acquired resistance to BRAFi. Use of C-Me in combination with other therapies may both inhibit melanoma growth and enhance therapeutic responsiveness more broadly.
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Xue L, Zhang W, Ju Y, Xu X, Bo H, Zhong X, Hu Z, Zheng C, Fang B, Tang S. TNFSF10, an autophagy related gene, was a prognostic and immune infiltration marker in skin cutaneous melanoma. J Cancer 2023; 14:2417-2430. [PMID: 37670976 PMCID: PMC10475358 DOI: 10.7150/jca.86735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/07/2023] Open
Abstract
Autophagy exerts a pivotal effect on skin cutaneous melanoma (SKCM). This study was aimed to investigate the expression of autophagy related genes (ARGs) in SKCM as well as its clinical value. Differentially expressed (DE) ARGs were downloaded from the intersection of SKCM data in GEPIA2 database and ARGs in Human Autophagy Database (HADB) database, and were verified in SKCM datasets GSE46517 and GSE15605. DE ARGs were enriched by Metascape online tools. According to GEPIA2 database, tumor necrosis factor-related apoptosis-inducing ligand (TNFSF10) was identified as a closely related factor and prognostic marker of SKCM. Then the correlation analysis of clinicopathological characteristics between TNFSF10 and SKCM was completed by several online tools such as TISCH, HPA, BEST and qRT-PCR. Subsequently, we investigated TNFSF10 related functions and signal pathways with LinkedOmics online tool, and immune infiltration using Assistant for Clinical Bioinformatics online tool. Furthermore, correlation analysis between TNFSF10 expression and immunotherapy response was performed by TIDE algorithm and BEST online tool. And Kaplan-Meier Plotter was used to assessing the prognosis of SKCM patients receiving immunotherapy. Finally, the correlation analysis among TNFSF10 methylation, TNFSF10 expression and patient prognosis was completed by the DiseaseMeth version 2.0, UCSC XENA and qRT-PCR. ARGs are DE in SKCM and participate in the ERBB signaling pathway, as well as the processing and presentation of antigens. Moreover, TNFSF10's expression along with methylation expression were significantly associated with the prognosis. Low expression of TNFSF10 was associated with malignant clinicopathological features, lower immune signal activity and lower immunocytes abundance in patients with SKCM. As an ARG, TNFSF10 has a potential capacity in predicting the prognosis of SKCM patients, meanwhile, may be a novel immunotherapy marker for SKCM.
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Affiliation(s)
- Lei Xue
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wancong Zhang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuezheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xiaoping Zhong
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhexiao Hu
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Congyuan Zheng
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
- Plastic Surgery Institute of Shantou University Medical College, Shantou, Guangdong, China
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Huang J, Chen Y, Guo Z, Yu Y, Zhang Y, Li P, Shi L, Lv G, Sun B. Prospective study and validation of early warning marker discovery based on integrating multi-omics analysis in severe burn patients with sepsis. BURNS & TRAUMA 2023; 11:tkac050. [PMID: 36659877 PMCID: PMC9840905 DOI: 10.1093/burnst/tkac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/22/2022] [Indexed: 01/17/2023]
Abstract
Background Early detection, timely diagnosis and rapid response are essential for case management and precautions of burn-associated sepsis. However, studies on indicators for early warning and intervention have rarely been conducted. This study was performed to better understand the pathophysiological changes and targets for prevention of severe burn injuries. Methods We conducted a multi-center, prospective multi-omics study, including genomics, microRNAomics, proteomics and single-cell transcriptomics, in 60 patients with severe burn injuries. A mouse model of severe burn injuries was also constructed to verify the early warning ability and therapeutic effects of potential markers. Results Through genomic analysis, we identified seven important susceptibility genes (DNAH11, LAMA2, ABCA2, ZFAND4, CEP290, MUC20 and ENTPD1) in patients with severe burn injuries complicated with sepsis. Through plasma miRNAomics studies, we identified four miRNAs (hsa-miR-16-5p, hsa-miR-185-5p, hsa-miR-451a and hsa-miR-423-5p) that may serve as early warning markers of burn-associated sepsis. A proteomic study indicated the changes in abundance of major proteins at different time points after severe burn injury and revealed the candidate early warning markers S100A8 and SERPINA10. In addition, the proteomic analysis indicated that neutrophils play an important role in the pathogenesis of severe burn injuries, as also supported by findings from single-cell transcriptome sequencing of neutrophils. Through further studies on severely burned mice, we determined that S100A8 is also a potential early therapeutic target for severe burn injuries, beyond being an early warning indicator. Conclusions Our multi-omics study identified seven susceptibility genes, four miRNAs and two proteins as early warning markers for severe burn-associated sepsis. In severe burn-associated sepsis, the protein S100A8 has both warning and therapeutic effects.
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Affiliation(s)
| | | | | | - Yanzhen Yu
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, Jiangsu Province, China
| | - Yi Zhang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu, China
| | - Pingsong Li
- Department of Burns and Plastic Surgery, Northern Jiangsu People’s Hospital, Yangzhou 225001, Jiangsu, China
| | - Lei Shi
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, Jiangsu, China
| | - Guozhong Lv
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangnan University, Wuxi 214041, Jiangsu, China
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Yang LK, Lin CX, Li SH, Liang JJ, Xiao LL, Xie GH, Liu HW, Liao X. Novel IKZF3 transcriptomic signature correlates with positive outcomes of skin cutaneous melanoma: A pan-cancer analysis. Front Genet 2022; 13:1036402. [PMID: 36353107 PMCID: PMC9638148 DOI: 10.3389/fgene.2022.1036402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022] Open
Abstract
To investigate the potential relationship between Ikaros family genes and skin cutaneous melanoma (SKCM), we undertook a pan-cancer analysis of the transcriptional signature and clinical data of melanoma through multiple databases. First, 10,327 transcriptomic samples from different cancers were included to determine the overall characteristics and clinical prognoses associated with Ikaros gene expression across cancer types. Second, differentially expressed genes analysis, prognostic evaluation, and gene set enrichment analysis were employed to investigate the role of Ikaros (IKZF) genes in SKCM. Third, we evaluated the relationship between Ikaros family genes and SKCM immune infiltrates and verified the findings using the GEO single-cell sequencing dataset. The results show that Ikaros genes were widely expressed among different cancer types with independently similar patterns as follows: 1. IKZF1 and IKZF3, and 2. IKZF2 and IKZF4–5. IKZF2 and IKZF5 were downregulated in the primary tumor, and IKZF1–3 expression decreased significantly as the T-stage or metastasis increased in SKCM. Moreover, high IKZF1–3 expression was associated with better overall survival, disease-specific survival, and progression-free interval. IKZF3 is an independent prognostic factor of SKCM. Among Ikaros genes, the expression of IKZF1 and IKZF3 positively correlated with the infiltration level of CD4+ T cells and CD8+ T cells, B cells, and Tregs in SKCM and negatively correlated with the infiltration level of M0 and M1 macrophages. Moreover, single-cell sequencing data analysis revealed that IKZF1 and IKZF3 were mainly expressed by immune cells. Correlation analysis shows the immune factors and drug responses associated with IKZF3 expression. In conclusion, the present study is the first, to our knowledge, to identify a pan-cancer genomic signature of the Ikaros gene family among different cancers. Expression of these family members, particularly high levels of IKZF3, indicate positive immunological status and beneficial clinical outcomes of SKCM. IKZF3 may therefore serve as potential targets for immunotherapy of melanoma.
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Affiliation(s)
| | | | | | | | | | | | | | - Xuan Liao
- *Correspondence: Hong-Wei Liu, ; Xuan Liao,
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Liu JY, Liu LP, Li Z, Luo YW, Liang F. The role of cuproptosis-related gene in the classification and prognosis of melanoma. Front Immunol 2022; 13:986214. [PMID: 36341437 PMCID: PMC9632664 DOI: 10.3389/fimmu.2022.986214] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background Melanoma, as one of the most aggressive and malignant cancers, ranks first in the lethality rate of skin cancers. Cuproptosis has been shown to paly a role in tumorigenesis, However, the role of cuproptosis in melanoma metastasis are not clear. Studying the correlation beteen the molecular subtypes of cuproptosis-related genes (CRGs) and metastasis of melanoma may provide some guidance for the prognosis of melanoma. Methods We collected 1085 melanoma samples in The Cancer Genome Atlas(TCGA) and Gene Expression Omnibus(GEO) databases, constructed CRGs molecular subtypes and gene subtypes according to clinical characteristics, and investigated the role of CRGs in melanoma metastasis. We randomly divide the samples into train set and validation set according to the ratio of 1:1. A prognostic model was constructed using data from the train set and then validated on the validation set. We performed tumor microenvironment analysis and drug sensitivity analyses for high and low risk groups based on the outcome of the prognostic model risk score. Finally, we established a metastatic model of melanoma. Results According to the expression levels of 12 cuproptosis-related genes, we obtained three subtypes of A1, B1, and C1. Among them, C1 subtype had the best survival outcome. Based on the differentially expressed genes shared by A1, B1, and C1 genotypes, we obtained the results of three gene subtypes of A2, B2, and C2. Among them, the B2 group had the best survival outcome. Then, we constructed a prognostic model consisting of 6 key variable genes, which could more accurately predict the 1-, 3-, and 5-year overall survival rates of melanoma patients. Besides, 98 drugs were screened out. Finally, we explored the role of cuproptosis-related genes in melanoma metastasis and established a metastasis model using seven key genes. Conclusions In conclusion, CRGs play a role in the metastasis and prognosis of melanoma, and also provide new insights into the underlying pathogenesis of melanoma.
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Affiliation(s)
- Jin-Ya Liu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Le-Ping Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Li
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Wei Luo
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
| | - Fang Liang
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
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Zhang S, Chen K, Zhao Z, Zhang X, Xu L, Liu T, Yu S. Lower Expression of GBP2 Associated With Less Immune Cell Infiltration and Poor Prognosis in Skin Cutaneous Melanoma (SKCM). J Immunother 2022; 45:274-283. [PMID: 35543550 DOI: 10.1097/cji.0000000000000421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 11/26/2022]
Abstract
Guanylate binding protein 2 (GBP2) could bind to guanine nucleotides (GMP, GDP, and GTP) and exhibits antiviral activity against influenza virus through the innate immune response. Some researchers have demonstrated that the value of GBP2 in predicting the prognosis of multiple cancers and the complex correlation with immune response. However, the correlation of GBP2 to prognosis and immune cell infiltration level were unknown in skin cutaneous melanoma (SKCM). The GBP2 expression in multiple cancers were evaluated through Tumor Immune Estimation Resource (TIMER) and Oncomine. We also evaluated the influence of GBP2 on overall survival in multiple caners through GEPIA, TIMER, and tissue microarray. The correlation between GBP2 expression level and immune cell or gene markers of immune infiltration level was explored on TIMER and GEPIA. Gene set enrichment analysis was performed using the TCGA dataset. The GBP2 expression level represented a significant reduction and the GBP2 expression was lower compared with the SKCM-Metastasis with P<0.01. Lower GBP2 expression was significantly correlated with the poor overall survival of SKCM patients. Simultaneously, higher GBP2 expression predicted the better SKCM-free survival with P=0.019. GBP2 expression was positively correlated with the infiltration cells of B-cell, CD8+ T-cell, CD4+ T-cell, macrophage, neutrophil, and dendritic cell in SKCM. And there was a significant negative correlation between the expression of GBP2 and DNA methylation in the cBioPortal database (P=3.39e-42). Gene set enrichment analysis revealed that GBP2 was closely correlated with multiple pathways of immune response in cancer. In conclusion, Lower expression of GBP2 associated with less immune cell infiltration and poor prognosis in SKCM and the high promoter methylation of GBP2 represented a promising biomarker for poor prognostication in SKCM.
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Affiliation(s)
| | - Kun Chen
- State Key Lab of Molecular Oncology and Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Chen J, Hu S, Wang H, Zhao T, Song Y, Zhong X, Luo Q, Xu M, He L, Chen Q, Du B, Xiao J, Wang K. Integrated analysis reveals the pivotal interactions between immune cells in the melanoma tumor microenvironment. Sci Rep 2022; 12:10040. [PMID: 35710862 PMCID: PMC9203818 DOI: 10.1038/s41598-022-14319-2] [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: 02/24/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
Melanoma is the most lethal type of skin cancer. Despite the breakthroughs in the clinical treatment of melanoma using tumor immunotherapy, many patients do not benefit from these immunotherapies because of multiple immunosuppressive mechanisms. Therefore, there is an urgent need to determine the mechanisms of tumor-immune system interactions and their molecular determinants to improve cancer immunotherapy. In this study, combined analysis of microarray data and single-cell RNA sequencing data revealed the key interactions between immune cells in the melanoma microenvironment. First, differentially expressed genes (DEGs) between normal and malignant tissues were obtained using GEO2R. The DEGs were then subjected to downstream analyses, including enrichment analysis and protein–protein interaction analysis, indicating that these genes were associated with the immune response of melanoma. Then, the GEPIA and TIMER databases were used to verify the differential expression and prognostic significance of hub genes, and the relationship between the hub genes and immune infiltration. In addition, we combined single cell analysis from GSE123139 to identify immune cell types, and validated the expression of the hub genes in these immune cells. Finally, cell-to-cell communication analysis of the proteins encoded by the hub genes and their interactions was performed using CellChat. We found that the CCL5-CCR1, SELPLG-SELL, CXCL10-CXCR3, and CXCL9-CXCR3 pathways might play important roles in the communication between the immune cells in tumor microenvironment. This discovery may reveal the communication basis of immune cells in the tumor microenvironment and provide a new idea for melanoma immunotherapy.
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Affiliation(s)
- Jiawei Chen
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Shan Hu
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.,Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Huiqi Wang
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Tingxiu Zhao
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yue Song
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.,Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xueying Zhong
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Qingling Luo
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Mansi Xu
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Lina He
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Qiugu Chen
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.,Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Biaoyan Du
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Jianyong Xiao
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China. .,Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Kun Wang
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China. .,Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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12
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Zhang S, Chen K, Liu H, Jing C, Zhang X, Qu C, Yu S. PMEL as a Prognostic Biomarker and Negatively Associated With Immune Infiltration in Skin Cutaneous Melanoma (SKCM). J Immunother 2021; 44:214-223. [PMID: 34028390 PMCID: PMC8225232 DOI: 10.1097/cji.0000000000000374] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/19/2021] [Indexed: 11/25/2022]
Abstract
Premelanosome protein (PMEL) is crucial for the formation of melanosomal fibrils through the transition from stage I to stage II melanosomes. It was used as a target antigen in some adoptive T-cell therapy of melanoma. The correlation of PMEL to prognosis and immune cell infiltration level are unknown in melanoma. The PMEL expression was evaluated via Tumor Immune Estimation Resource, Oncomine and Gene Expression Profiling Interactive Analysis (GEPIA). We also evaluate the influence of PMEL on overall survival via GEPIA, PrognoScan, and immunohistochemistry in human tissue microarray. The correlation between PMEL expression level and immune cell or gene markers of immune infiltration level was explored on Tumor Immune Estimation Resource and GEPIA. PMEL expression was significantly higher in skin cutaneous melanoma (SKCM) and SKCM-metastasis in comparison with the other cancers. In SKCM, PMEL expression in high levels was associated with poor overall survival. In both SKCM and SKCM-metastasis patients, PMEL expression is negatively correlated with the infiltration cells of CD8+ T cells, macrophages, and neutrophils. Programmed cell-death protein 1 just showed response rates ranging from 20% to 40% in patients with melanoma, so it is critical to discover a new therapeutic target. PMEL is negatively associated with immune cell infiltration and can be as a negative prognosis marker or new immunotherapy target in SKCM and SKCM-metastasis.
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Affiliation(s)
| | - Kun Chen
- State Key Laboratory of Molecular Oncology and Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | - Chunfeng Qu
- State Key Laboratory of Molecular Oncology and Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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13
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Xiong D, Zhang Z, Wang T, Wang X. A comparative study of multiple instance learning methods for cancer detection using T-cell receptor sequences. Comput Struct Biotechnol J 2021; 19:3255-3268. [PMID: 34141144 PMCID: PMC8192570 DOI: 10.1016/j.csbj.2021.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/02/2022] Open
Abstract
As a branch of machine learning, multiple instance learning (MIL) learns from a collection of labeled bags, each containing a set of instances. The learning process is weakly supervised due to ambiguous instance labels. Since its emergence, MIL has been applied to solve various problems including content-based image retrieval, object tracking/detection, and computer-aided diagnosis. In biomedical research, the use of MIL has been focused on medical image analysis and molecule activity prediction. We review and apply 16 methods to investigate the applicability of MIL to a novel biomedical application, cancer detection using T-cell receptor (TCR) sequences. This important application can be a viable approach for large-scale cancer screening, as TCRs can be easily profiled from a subject's peripheral blood. We consider two feasible data-generating mechanisms, and for the purpose of performance evaluation, we simulate data under each mechanism, where we vary potentially important factors to mimic realistic situations. We also apply the methods to sequencing data of ten cancer types from The Cancer Genome Atlas, as an early proof of concept for distinguishing tumor patients from healthy individuals via TCR sequencing of peripheral blood. We find that given an appropriate MIL method is used, satisfactory performance with Area Under the Receiver Operating Characteristic Curve above 80% can be achieved for five in the ten cancers. Based on our numerical results, we make suggestions about selection of a proper method and avoidance of any method with poor performance. We further point out directions of future research as well as identify a pressing need of new MIL methodologies for improved performance (for some cancer types) and more explainable outcomes.
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Affiliation(s)
- Danyi Xiong
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, Dallas 75275, TX, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas 75390, TX, USA
| | - Ze Zhang
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas 75390, TX, USA
| | - Tao Wang
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas 75390, TX, USA
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, Dallas 75275, TX, USA
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