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Li H, Shi Y, Li Y, Wu S, Yang R, Liu Q, Sun L. DNA damage response-related signatures characterize the immune landscape and predict the prognosis of HCC via integrating single-cell and bulk RNA-sequencing. Int Immunopharmacol 2024; 137:112475. [PMID: 38909498 DOI: 10.1016/j.intimp.2024.112475] [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: 04/28/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND The occurrence and progression of hepatocellular carcinoma (HCC) are significantly affected by DNA damage response (DDR). Exploring DDR-related biomarkers can help predict the prognosis and immune characteristics of HCC. METHODS First, the single-cell RNA sequencing (scRNA-seq) dataset GSE242889 was processed and performed manual annotation. Then we found the marker genes of DDR-active subgroups based on "AUCell" algorithm. The "Limma" R package was used to identify differentially expressed genes (DEGs) between tumor and normal samples of HCC. The risk prognostic model was constructed by filtering genes using univariate Cox and LASSO regression analyses. Finally, the signatures were analyzed for immune infiltration, gene mutation, and drug sensitivity. Last but not least, KPNA2, which had the largest coefficient in our model was validated by experiments including western blot, MTT, colony formation and γ-H2AX assays. RESULTS We constructed a prognostic model based on 5 DDR marker genes including KIF2C, CDC20, KPNA2, UBE2S and ADH1B for HCC. We also proved that the model had an excellent performance in both training and validation cohorts. Patients in the high-risk group had a poorer prognosis, different immune features, gene mutation frequency, immunotherapy response and drug sensitivity compared with the low-risk group. Besides, our experimental results proved that KPNA2 was up-regulated in liver cancer cells than in hepatocytes. More importantly, the knockdown of KPNA2 significantly inhibited cell variability, proliferation and promoted DNA damage. CONCLUSIONS We innovatively integrated scRNA-seq and bulk RNA sequencing to construct the DDR-related prognostic model. Our model could effectively predict the prognosis, immune landscape and therapy response of HCC.
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Affiliation(s)
- Hanqi Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yu Shi
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yue Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Shaobo Wu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, PR China
| | - Ruida Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Qingguang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China.
| | - Liankang Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China.
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Constantinides M, Robert N, Multrier C, Coënon L, Campos-Mora M, Jacquard C, Gao F, Zemiti S, Presumey J, Cartron G, Moreaux J, Villalba M. FCGR3A F158V alleles frequency differs in multiple myeloma patients from healthy population. Oncoimmunology 2024; 13:2388306. [PMID: 39175948 PMCID: PMC11340758 DOI: 10.1080/2162402x.2024.2388306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/28/2024] [Accepted: 07/31/2024] [Indexed: 08/24/2024] Open
Abstract
FCGR3A presents a single nucleotide polymorphism at location 158 (V/F), which affects its binding to the fragment crystallizable (Fc) of antibodies (Abs). FcγRIIIa-158 V allotype has the highest affinity and is associated with a better clinical response to IgG1 monoclonal Abs (mAb) treatment. We compared the allele frequency of FCGR3A-F158V polymorphism in cohorts of patients with B-cell lymphoproliferative disorders, including multiple myeloma (MM), monoclonal gammopathy of undetermined significance (MGUS), non-Hodgkin lymphoma (NHL), and B-cell chronic leukemia (B-CLL). FCGR3A-158F homozygous were enriched and tended to be in MM and MGUS patients, respectively; but neither in B-CLL nor in NHL patients. We identified a significantly lower concentration of CD8 T-cells and resting memory CD4 T-cells in MM patients bone marrow with the F/F genotype, associated with an increase in the macrophage percentage. In contrast, natural killer cells increased in V/V homozygous patients. This suggests a deregulation of the immune microenvironment in FCGR3A-F/F homozygous patients. However, we did not observe difference in response following treatment combining chemotherapy associated or not with daratumumab, an IgG1 mAb direct against CD38. Our findings suggest that FCGR3A F158V polymorphism can regulate the immune environment and affect the development of tumor plasma cells.
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Affiliation(s)
- Michaël Constantinides
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
- Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | - Caroline Multrier
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Loïs Coënon
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | | | - Carine Jacquard
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Fei Gao
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Sara Zemiti
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Jessy Presumey
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Guillaume Cartron
- Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Jérome Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- Institute of Human Genetics, UMR CNRS-UM 9002, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Martin Villalba
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
- IRMB, Univ Montpellier, INSERM, CNRS, CHRU de Montpellier, Montpellier, France
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3
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Fu D, Zhang T, Liu J, Chang B, Zhang Q, Tan Y, Chen X, Tan L. Identification of adipocyte infiltration-related gene subtypes for predicting colorectal cancer prognosis and responses of immunotherapy/chemotherapy. Heliyon 2024; 10:e33616. [PMID: 39050460 PMCID: PMC11266998 DOI: 10.1016/j.heliyon.2024.e33616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Colorectal cancer (CRC) is a prevalent and aggressive malignancy characterized by a complex tumor microenvironment (TME). Given the variations in the level of adipocyte infiltration in TME, the prognosis may differ among CRC patients. Thus, there is an urgent need to establish a reliable method for identifying adipocyte subtypes in CRC in order to elucidate the impact of adipocyte infiltration on CRC treatment and prognosis. Herein, 144 adipocyte-infiltration-related genes (AIRGs) were identified as predictive markers for the immune-associated features and prognosis of CRC patients. Based on the 144 genes, the unsupervised clustering algorithm identified two distinct clusters of CRC patients with variations in molecular and signaling pathways, clinicopathological characteristics and responses to CRC chemotherapy and immunotherapy. Furthermore, an AIRG prognostic signature was constructed and validated in independent datasets. Overall, this study developed a prognostic signature based on AIRGs in CRC, which may contribute to the development of personalized treatment strategies and enhance prognostic prediction for CRC patients.
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Affiliation(s)
- Daan Fu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Tianhao Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jia Liu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bingcheng Chang
- The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Qingqing Zhang
- Haiyan County Hospital of Traditional Chinese Medicine, JiaXing, 314399, China
| | - Yuyan Tan
- Department of Breast and Thyroid Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443000, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lulu Tan
- Department of Breast and Thyroid Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443000, China
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Li CX, Yue L. The Multifaceted Nature of Macrophages in Cardiovascular Disease. Biomedicines 2024; 12:1317. [PMID: 38927523 PMCID: PMC11201197 DOI: 10.3390/biomedicines12061317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/01/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
As the leading cause of mortality worldwide, cardiovascular disease (CVD) represents a variety of heart diseases and vascular disorders, including atherosclerosis, aneurysm, ischemic injury in the heart and brain, arrythmias, and heart failure. Macrophages, a diverse population of immune cells that can promote or suppress inflammation, have been increasingly recognized as a key regulator in various processes in both healthy and disease states. In healthy conditions, these cells promote the proper clearance of cellular debris, dead and dying cells, and provide a strong innate immune barrier to foreign pathogens. However, macrophages can play a detrimental role in the progression of disease as well, particularly those inflammatory in nature. This review will focus on the current knowledge regarding the role of macrophages in cardiovascular diseases.
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Affiliation(s)
- Cindy X. Li
- Department of Cell Biology, Pat and Jim Calhoun Cardiovascular Center, University of Connecticut Health Center, Farmington, CT 06030, USA;
- Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Lixia Yue
- Department of Cell Biology, Pat and Jim Calhoun Cardiovascular Center, University of Connecticut Health Center, Farmington, CT 06030, USA;
- Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT 06269, USA
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Xin S, Su J, Li R, Cao Q, Wang H, Wei Z, Wang C, Zhang C. Identification of a risk model for prognostic and therapeutic prediction in renal cell carcinoma based on infiltrating M0 cells. Sci Rep 2024; 14:13390. [PMID: 38862642 PMCID: PMC11166996 DOI: 10.1038/s41598-024-64207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The tumor microenvironment (TME) comprises immune-infiltrating cells that are closely linked to tumor development. By screening and analyzing genes associated with tumor-infiltrating M0 cells, we developed a risk model to provide therapeutic and prognostic guidance in clear cell renal cell carcinoma (ccRCC). First, the infiltration abundance of each immune cell type and its correlation with patient prognosis were analyzed. After assessing the potential link between the depth of immune cell infiltration and prognosis, we screened the infiltrating M0 cells to establish a risk model centered on three key genes (TMEN174, LRRC19, and SAA1). The correlation analysis indicated a positive correlation between the risk score and various stages of the tumor immune cycle, including B-cell recruitment. Furthermore, the risk score was positively correlated with CD8 expression and several popular immune checkpoints (ICs) (TIGIT, CTLA4, CD274, LAG3, and PDCD1). Additionally, the high-risk group (HRG) had higher scores for tumor immune dysfunction and exclusion (TIDE) and exclusion than the low-risk group (LRG). Importantly, the risk score was negatively correlated with the immunotherapy-related pathway enrichment scores, and the LRG showed a greater therapeutic benefit than the HRG. Differences in sensitivity to targeted drugs between the HRG and LRG were analyzed. For commonly used targeted drugs in RCC, including axitinib, pazopanib, temsirolimus, and sunitinib, LRG had lower IC50 values, indicating increased sensitivity. Finally, immunohistochemistry results of 66 paraffin-embedded specimens indicated that SAA1 was strongly expressed in the tumor samples and was associated with tumor metastasis, stage, and grade. SAA1 was found to have a significant pro-tumorigenic effect by experimental validation. In summary, these data confirmed that tumor-infiltrating M0 cells play a key role in the prognosis and treatment of patients with ccRCC. This discovery offers new insights and directions for the prognostic prediction and treatment of ccRCC.
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Affiliation(s)
- Shiyong Xin
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, No. 636, Guan-lin Rd, Luo-long District, Luoyang, China.
| | - Junjie Su
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, No. 636, Guan-lin Rd, Luo-long District, Luoyang, China
| | - Ruixin Li
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, No. 636, Guan-lin Rd, Luo-long District, Luoyang, China
| | - Qiong Cao
- Department of Pathology, The Third Affiliated Hospital of Henan University of Science and Technology, Luoyang, 471003, China
| | - Haojie Wang
- Department of Central Laboratory, Zhengzhou University, Luoyang Central Hospital, Luoyang, 471003, China
| | - Zhihao Wei
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, 471023, China
| | - Chengliang Wang
- Department of Urology, Shangcheng County People's Hospital, Xinyang, 464000, China
| | - Chengdong Zhang
- Department of Urology, Xinxiang First People's Hospital, Xinxiang, 453000, China
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Hu H, Xu Y, Zhang Q, Ai X, Wang T, Li H, Jin C, Ouyang C, Wu Z. Exploring prognostic and immunological characteristics of pancreatic ductal adenocarcinoma through comprehensive genomic analysis of tertiary lymphoid structures and CD8 + T-cells. J Cancer Res Clin Oncol 2024; 150:300. [PMID: 38850373 PMCID: PMC11162401 DOI: 10.1007/s00432-024-05824-0] [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: 04/07/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
PURPOSE Tertiary lymphoid structures (TLSs) and CD8 + T-cells are potential prognostic indicators for pancreatic ductal adenocarcinoma (PDAC). We established a novel scoring system for evaluating the risk for PDAC based on TLS- and CD8 + T-cell-related genes. METHODS We analyzed single-cell sequence data from PDAC patients in the Genome Sequence Archive. Bioinformatics and machine algorithms established and validated a scoring method (T-C score) based on PDAC survival-related genes highly expressed in TLSs and CD8 + T-cells. Patients were stratified into the low- and high-T-C score groups. Differences in survival, pathway enrichment, mutation status, immune cell infiltration, expression of immune checkpoint-associated genes, tumor stemness, and response to antitumor therapy were compared through computer simulation methods. RESULTS Overall survival differed significantly between the training and validation cohorts' low- and high-T-C score groups. The low-T-C score group correlated with lower tumor mutation burden and lower levels of tumor stemness compared with the high-T-C score group. Patients with lower T-C scores exhibited advantages in immunotherapeutic responses and might be more sensitive to the chemotherapeutic regimen and multi-kinase inhibitors. CONCLUSION The T-C score could serve as an effective model for predicting the survival and therapeutic responses of patients with PDAC.
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Affiliation(s)
- Hao Hu
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Yang Xu
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Qiang Zhang
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Xiangnan Ai
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Tengfei Wang
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Huixing Li
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Changguo Jin
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Caiguo Ouyang
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China
| | - Zhenyu Wu
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, No. 15, Yuquan Road, Haidian District, Beijing, 100049, China.
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Fei Y, Cao D, Dong R, Li Y, Wang Z, Gao P, Zhu M, Wang X, Zuo X, Cai J. The cuproptosis-related gene UBE2D2 functions as an immunotherapeutic and prognostic biomarker in pan-cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03495-4. [PMID: 38703335 DOI: 10.1007/s12094-024-03495-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Cuproptosis, as a unique modality of regulated cell death, requires the involvement of ubiquitin-binding enzyme UBE2D2. However, the prognostic and immunotherapeutic values of UBE2D2 in pan-cancer remain largely unknown. METHODS Using UCSC Xena, TIMER, Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Human Protein Atlas (HPA) databases, we aimed to explore the differential expression pattern of UBE2D2 across multiple cancer types and to evaluate its association with patient prognosis, clinical features, and genetic variations. The association between UBE2D2 and immunotherapy response was assessed by gene set enrichment analysis, tumor microenvironment, immune gene co-expression and drug half maximal inhibitory concentration (IC50) analysis. RESULTS The mRNA and protein levels of UBE2D2 were markedly elevated in most cancer types, and UBE2D2 exhibited prognostic significance in liver hepatocellular carcinoma (LIHC), kidney chromophobe (KICH), uveal melanomas (UVM), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), and kidney renal papillary cell carcinoma (KIRP). UBE2D2 expression was correlated with clinical features, tumor mutation burden, microsatellite instability, and anti-tumor drug resistance in several tumor types. Gene enrichment analysis showed that UBE2D2 was significantly associated with immune-related pathways. The expression level of UBE2D2 was correlated with immune cell infiltration, including CD4 + T cells、Macrophages M2、CD8 + T cells in pan-cancer. PDCD1, CD274 and CTLA4 expression levels were positively correlated with UBE2D2 level in multiple cancers. CONCLUSIONS We comprehensively investigated the potential value of UBE2D2 as a prognostic and immunotherapeutic predictor for pan-cancer, providing a novel insight for cancer immunotherapy.
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Affiliation(s)
- Yao Fei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Danping Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Runyu Dong
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Yanna Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Zhixiong Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Peng Gao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Menglin Zhu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Xiaoming Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Xueliang Zuo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China.
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China.
| | - Juan Cai
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China.
- Department of Oncology, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu, China.
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Gao X, Ren X, Wang F, Ren X, Liu M, Cui G, Liu X. Immunotherapy and drug sensitivity predictive roles of a novel prognostic model in hepatocellular carcinoma. Sci Rep 2024; 14:9509. [PMID: 38664521 PMCID: PMC11045740 DOI: 10.1038/s41598-024-59877-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most significant causes of cancer-related deaths in the worldwide. Currently, predicting the survival of patients with HCC and developing treatment drugs still remain a significant challenge. In this study, we employed prognosis-related genes to develop and externally validate a predictive risk model. Furthermore, the correlation between signaling pathways, immune cell infiltration, immunotherapy response, drug sensitivity, and risk score was investigated using different algorithm platforms in HCC. Our results showed that 11 differentially expressed genes including UBE2C, PTTG1, TOP2A, SPP1, FCN3, SLC22A1, ADH4, CYP2C8, SLC10A1, F9, and FBP1 were identified as being related to prognosis, which were integrated to construct a prediction model. Our model could accurately predict patients' overall survival using both internal and external datasets. Moreover, a strong correlation was revealed between the signaling pathway, immune cell infiltration, immunotherapy response, and risk score. Importantly, a novel potential drug candidate for HCC treatment was discovered based on the risk score and also validated through ex vivo experiments. Our finds offer a novel perspective on prognosis prediction and drug exploration for cancer patients.
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Affiliation(s)
- Xiaoge Gao
- Cancer Institute, Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, People's Republic of China
| | - Xin Ren
- Cancer Institute, Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, People's Republic of China
- Department of Oncology, Jiangyin Clinical College, Xuzhou Medical University, Jiangyin, 214400, Jiangsu Province, People's Republic of China
| | - Feitong Wang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, People's Republic of China
| | - Xinxin Ren
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Mengchen Liu
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519040, Guangdong Province, People's Republic of China
| | - Guozhen Cui
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519040, Guangdong Province, People's Republic of China
| | - Xiangye Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, People's Republic of China.
- National Demonstration Center for Experimental Basic Medical Science Education (Xuzhou Medical University), Xuzhou, 221002, Jiangsu Province, People's Republic of China.
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Yang R, Sun F, Shi Y, Wang H, Fan Y, Wu Y, Fan R, Wu S, Sun L. Machine Learning-based Development and Validation of a Cell Senescence Predictive and Prognostic Signature in Intrahepatic Cholangiocarcinoma. J Cancer 2024; 15:2810-2828. [PMID: 38577599 PMCID: PMC10988306 DOI: 10.7150/jca.92698] [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: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
Background: Previous studies have shown that cellular senescence is strongly associated with tumorigenesis and the tumor microenvironment. Accordingly, we developed a novel prognostic signature for intrahepatic cholangiocarcinoma (ICCA) based on senescence-associated long non-coding RNAs (SR-lncRNAs) and identified a lncRNA-miRNA-mRNA axis involving in ICCA. Methods: Based on the 197 senescence-associated genes (SRGs) from Genacards and their expression in Fu-ICCA cohort, we identified 20 lncRNAs as senescence-associated lncRNAs (SR-lncRNAs) through co-expression and cox-regression analysis. According to 20 SR-lncRNAs, patients with ICCA were classified into 2 molecular subtypes using unsupervised clustering machine learning approach and to explore the prognostic and functional heterogeneity between these two subtypes. Subsequently, we integrated 113 machine learning algorithms to develop senescence-related lncRNA signature, ultimately identifying 11 lncRNAs and constructing prognostic models and risk stratification. The correlation between the signature and the immune landscape, immunotherapy response as well as drug sensitivity are explored too. Results: We developed a novel senescence related signature. The predictive model and risk score calculated by the signature exhibited favorable prognostic predictive performance, which is a suitable independent risk factor for the prognosis of patients with ICCA based on Kaplan-Meier plotter, nomogram and receiving operating characteristic (ROC) curves. The results were validated using external datasets. Estimate, ssGSEA (single sample gene set enrichment analysis), IPS (immunophenotype score) and TIDE (tumor immune dysfunction and exclusion) algorithms revealed higher immune infiltration, higher immune scores, lower immune escape potential and better response to immunotherapy in the high-risk group. In addition, signature identifies eight chemotherapeutic agents, including cisplatin for patients with different risk levels, providing guidance for clinical treatment. Finally, we identified a set of lncRNA-miRNA-mRNA axes involved in ICCA through regulation of senescence. Conclusion: SR-lncRNAs signature can favorably predict the prognosis, risk stratification, immune landscape and immunotherapy response of patients with ICCA and consequently guide individualized treatment.
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Affiliation(s)
- Ruida Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Feidi Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yu Shi
- Department of Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Huanhuan Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yangwei Fan
- Department of Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yinying Wu
- Department of Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Ruihan Fan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Shaobo Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Liankang Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
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Zhang S, Qin O, Wu S, Xu H, Huang W, Hailiang S. A pyrimidine metabolism-related signature for prognostic and immunotherapeutic response prediction in hepatocellular carcinoma by integrating analyses. Aging (Albany NY) 2024; 16:5545-5566. [PMID: 38517376 PMCID: PMC11006494 DOI: 10.18632/aging.205663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC), with discouraging morbidity and mortality, ranks as one of the most prevalent tumors worldwide. Pyrimidine metabolism is a critical process that regulates DNA and RNA synthesis in cells. It is imperative to investigate the significance of pyrimidine metabolism in liver cancer. METHODS Transcriptome and clinical data were downloaded from the TCGA database and the GEO database. The genes related to pyrimidine metabolism were sourced from the MSigDB. The pyrimidine metabolism-related signature (PMRS) was constructed through Cox regression and Lasso regression and then verified in the external validation set from the ICGC database. Functional enrichment, immune infiltration analysis, drug sensitivity, and Immunophenoscore (IPS) were further implemented to predict the response to immunotherapy. The role of PMRS in the malignant phenotype of hepatocellular carcinoma was explored by conducting a series of in vitro experiments. RESULTS Our study developed a four-genes PMRS which demonstrates a substantial correlation with the prognosis of HCC patients, serving as an independent predictor in clinical practice. The result of risk-stratified analysis yielded evidence that low-risk patients experienced more favorable clinical outcomes. The nomogram exhibited remarkable prognostic predictive value. The subsequent results revealed that low-risk patients manifested a more promising response to immunotherapy. Moreover, the results of cell experiments demonstrated that the downregulation of DCK markedly inhibited the malignant phenotype of hepatocellular carcinoma. CONCLUSIONS Our pyrimidine metabolism-centered prognostic signature accurately predicts overall survival, immune status, and treatment response in hepatocellular carcinoma (HCC) patients, offering innovative insights for precise diagnosis, personalized treatment, and improved prognosis.
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Affiliation(s)
- Shihang Zhang
- Department of General Surgery, Dalang Hospital, Dongguan, Guangdong, P.R. China
| | - Ouyang Qin
- Department of General Surgery, Dalang Hospital, Dongguan, Guangdong, P.R. China
| | - Shu Wu
- Affiliated Dongguan Hospital Southern Medical University (Dongguan People’s Hospital) Dongguan Guangdong, Guangdong, P.R. China
| | - Huanming Xu
- Department of General Surgery, Dalang Hospital, Dongguan, Guangdong, P.R. China
| | - Wei Huang
- Department of Hepatic-Biliary-Pancreatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, P.R. China
| | - Song Hailiang
- Department of General Surgery, Dalang Hospital, Dongguan, Guangdong, P.R. China
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Javanmardi Z, Mahmoudi M, Rafatpanah H, Rezaieyazdi Z, Shapouri-Moghaddam A, Ahmadi P, Mollazadeh S, Tabasi NS, Esmaeili SA. Tolerogenic probiotics Lactobacillus delbrueckii and Lactobacillus rhamnosus promote anti-inflammatory profile of macrophages-derived monocytes of newly diagnosed patients with systemic lupus erythematosus. Cell Biochem Funct 2024; 42:e3981. [PMID: 38509733 DOI: 10.1002/cbf.3981] [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: 12/09/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Systemic lupus erythematosus (SLE) is known as an autoimmune disorder that is characterized by the breakdown of self-tolerance, resulting in disease onset and progression. Macrophages have been implicated as a factor in the development of SLE through faulty phagocytosis of dead cells or an imbalanced M1/M2 ratio. The study aimed to investigate the immunomodulatory effects of Lactobacillus delbrueckii and Lactobacillus rhamnosus on M1 and M2 macrophages in new case lupus patients. For this purpose, blood monocytes were collected from lupus patients and healthy people and were cultured for 5 days to produce macrophages. For 48 h, the macrophages were then cocultured with either probiotics or lipopolysaccharides (LPS). Flow cytometry and real-time polymerase chain reaction were then used to analyze the expression of cluster of differentiation (CD) 14, CD80, and human leukocyte antigen - DR (HLADR) markers, as well as cytokine expression (interleukin [IL]1-β, IL-12, tumor necrosis factor α [TNF-α], IL-10, and transforming growth factor beta [TGF-β]). The results indicated three distinct macrophage populations, M0, M1, and M2. In both control and patient-derived macrophage-derived monocytes (MDMs), the probiotic groups showed a decrease in CD14, CD80, and HLADR expression compared to the LPS group. This decrease was particularly evident in M0 and M2 macrophages from lupus patients and M1 macrophages from healthy subjects. In addition, the probiotic groups showed increased levels of IL-10 and TGF-β and decreased levels of IL-12, IL1-β, and TNF-α in MDMs from both healthy and lupus subjects compared to the LPS groups. Although there was a higher expression of pro-inflammatory cytokines in lupus patients, there was a higher expression of anti-inflammatory cytokines in healthy subjects. In general, L. delbrueckii and L. rhamnosus could induce anti-inflammatory effects on MDMs from both healthy and lupus subjects.
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Affiliation(s)
- Zahra Javanmardi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Mahmoudi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Immunology Research Centre, Division of Inflammation and Inflammatory Diseases, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Rezaieyazdi
- Rheumatic Diseases Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Nafiseh Sadat Tabasi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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12
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Pu L, Sun Y, Pu C, Zhang X, Wang D, Liu X, Guo P, Wang B, Xue L, Sun P. Machine learning-based disulfidptosis-related lncRNA signature predicts prognosis, immune infiltration and drug sensitivity in hepatocellular carcinoma. Sci Rep 2024; 14:4354. [PMID: 38388539 PMCID: PMC10883983 DOI: 10.1038/s41598-024-54115-8] [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: 09/05/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Disulfidptosis a new cell death mode, which can cause the death of Hepatocellular Carcinoma (HCC) cells. However, the significance of disulfidptosis-related Long non-coding RNAs (DRLs) in the prognosis and immunotherapy of HCC remains unclear. Based on The Cancer Genome Atlas (TCGA) database, we used Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression model to construct DRL Prognostic Signature (DRLPS)-based risk scores and performed Gene Expression Omnibus outside validation. Survival analysis was performed and a nomogram was constructed. Moreover, we performed functional enrichment annotation, immune infiltration and drug sensitivity analyses. Five DRLs (AL590705.3, AC072054.1, AC069307.1, AC107959.3 and ZNF232-AS1) were identified to construct prognostic signature. DRLPS-based risk scores exhibited better predictive efficacy of survival than conventional clinical features. The nomogram showed high congruence between the predicted survival and observed survival. Gene set were mainly enriched in cell proliferation, differentiation and growth function related pathways. Immune cell infiltration in the low-risk group was significantly higher than that in the high-risk group. Additionally, the high-risk group exhibited higher sensitivity to Afatinib, Fulvestrant, Gefitinib, Osimertinib, Sapitinib, and Taselisib. In conclusion, our study highlighted the potential utility of the constructed DRLPS in the prognosis prediction of HCC patients, which demonstrated promising clinical application value.
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Affiliation(s)
- Lei Pu
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention of the Ministry of Education, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Yan Sun
- Department of Veterinary Medicine, Shandong Vocational Animal Science and Veterinary College, Weifang, 261071, Shandong, People's Republic of China
| | - Cheng Pu
- School of Martial Arts, Shanghai University of Sport, Shanghai, 200438, People's Republic of China
| | - Xiaoyan Zhang
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention of the Ministry of Education, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Dong Wang
- Jiangsu Vocational Institute of Architectural Technology, Xuzhou, 221116, Jiangsu, People's Republic of China
| | - Xingning Liu
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention of the Ministry of Education, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Pin Guo
- Department of Veterinary Medicine, Shandong Vocational Animal Science and Veterinary College, Weifang, 261071, Shandong, People's Republic of China
| | - Bing Wang
- Department of Oncological Surgery, Minhang Branch of Shanghai Cancer Center, Fudan University, Shanghai, 200240, People's Republic of China.
| | - Liang Xue
- Zhejiang Institute of Sports Science, Hangzhou, 310004, Zhejiang, People's Republic of China.
| | - Peng Sun
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention of the Ministry of Education, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China.
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Murkar R, von Heckel C, Walles H, Moch TB, Arens C, Davaris N, Weber A, Zuschratter W, Baumann S, Reinhardt J, Kopp S. Establishment of a Human Immunocompetent 3D Tissue Model to Enable the Long-Term Examination of Biofilm-Tissue Interactions. Bioengineering (Basel) 2024; 11:187. [PMID: 38391673 PMCID: PMC10885984 DOI: 10.3390/bioengineering11020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Different studies suggest an impact of biofilms on carcinogenic lesion formation in varying human tissues. However, the mechanisms of cancer formation are difficult to examine in vivo as well as in vitro. Cell culture approaches, in most cases, are unable to keep a bacterial steady state without any overgrowth. In our approach, we aimed to develop an immunocompetent 3D tissue model which can mitigate bacterial outgrowth. We established a three-dimensional (3D) co-culture of human primary fibroblasts with pre-differentiated THP-1-derived macrophages on an SIS-muc scaffold which was derived by decellularisation of a porcine intestine. After establishment, we exposed the tissue models to define the biofilms of the Pseudomonas spec. and Staphylococcus spec. cultivated on implant mesh material. After 3 days of incubation, the cell culture medium in models with M0 and M2 pre-differentiated macrophages presented a noticeable turbidity, while models with M1 macrophages presented no noticeable bacterial growth. These results were validated by optical density measurements and a streak test. Immunohistology and immunofluorescent staining of the tissue presented a positive impact of the M1 macrophages on the structural integrity of the tissue model. Furthermore, multiplex ELISA highlighted the increased release of inflammatory cytokines for all the three model types, suggesting the immunocompetence of the developed model. Overall, in this proof-of-principle study, we were able to mitigate bacterial overgrowth and prepared a first step for the development of more complex 3D tissue models to understand the impact of biofilms on carcinogenic lesion formation.
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Affiliation(s)
- Rasika Murkar
- Core Facility Tissue Engineering, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Charlotte von Heckel
- Core Facility Tissue Engineering, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Heike Walles
- Core Facility Tissue Engineering, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Theresia Barbara Moch
- Core Facility Tissue Engineering, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Christoph Arens
- Department of Otorhinolaryngology, Head and Neck Surgery, University Clinic Giessen, 35392 Giessen, Germany
| | - Nikolaos Davaris
- Department of Otorhinolaryngology, Head and Neck Surgery, University Clinic Giessen, 35392 Giessen, Germany
| | - André Weber
- Photonscore GmbH, Brenneckestr. 20, 39118 Magdeburg, Germany
| | | | - Sönke Baumann
- Omicron-Laserage® Laserprodukte GmbH, Raiffeisenstr. 5e, 63110 Rodgau, Germany
| | - Jörg Reinhardt
- MedFact Engineering GmbH, Hammerstrasse 3, 79540 Lörrach, Germany
| | - Sascha Kopp
- Core Facility Tissue Engineering, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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Rath S, Jema JP, Kesavan K, Mallick S, Pradhan J, Chainy GBN, Nayak D, Kaushik S, Dandapat J. Arsenic album 30C exhibits crystalline nano structure of arsenic trioxide and modulates innate immune markers in murine macrophage cell lines. Sci Rep 2024; 14:745. [PMID: 38185726 PMCID: PMC10772077 DOI: 10.1038/s41598-024-51319-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: 06/01/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024] Open
Abstract
Macrophages are associated with innate immune response and M1-polarized macrophages exhibit pro-inflammatory functions. Nanoparticles of natural or synthetic compounds are potential triggers of innate immunity. As2O3 is the major component of the homeopathic drug, Arsenic album 30C.This has been claimed to have immune-boosting activities, however, has not been validated experimentally. Here we elucidated the underlying mechanism of Ars. alb 30C-mediated immune priming in murine macrophage cell line. Transmission Electron Microscopy (TEM) and X-ray diffraction (XRD) used for the structural analysis of the drug reveals the presence of crystalline As2O3 nanoparticles of cubic structure. Similarly, signatures of M1-macrophage polarization were observed by surface enhanced Raman scattering (SERS) in RAW 264.7 cells with concomitant over expression of M1 cell surface marker, CD80 and transcription factor, NF-κB, respectively. We also observed a significant increase in pro-inflammatory cytokines like iNOS, TNF-α, IL-6, and COX-2 expression with unaltered ROS and apoptosis in drug-treated cells. Enhanced expression of Toll-like receptors 3 and 7 were observed both in transcriptional and translational levels after the drug treatment. In sum, our findings for the first time indicated the presence of crystalline As2O3 cubic nanostructure in Ars. alb 30C which facilitates modulation of innate immunity by activating macrophage polarization.
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Affiliation(s)
- Suvasmita Rath
- Centre of Environment, Climate Change and Public Health, Utkal University, Vani Vihar, Bhubaneswar, Odisha, India
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | - Jyoti Prava Jema
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | - Kamali Kesavan
- CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, Odisha, India
| | - Sagar Mallick
- CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, Odisha, India
| | - Jyotsnarani Pradhan
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | | | - Debadatta Nayak
- Central Council for Research in Homeopathy, New Delhi, India
| | - Subhash Kaushik
- Central Council for Research in Homeopathy, New Delhi, India
| | - Jagneshwar Dandapat
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India.
- Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar, Odisha, 751004, India.
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15
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Zhang YJ, Yi DH. CDK1-SRC Interaction-Dependent Transcriptional Activation of HSP90AB1 Promotes Antitumor Immunity in Hepatocellular Carcinoma. J Proteome Res 2023; 22:3714-3729. [PMID: 37949475 DOI: 10.1021/acs.jproteome.3c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
This study aimed to analyze multiomics data and construct a regulatory network involving kinases, transcription factors, and immune genes in hepatocellular carcinoma (HCC) prognosis. The researchers used transcriptomic, proteomic, and clinical data from TCGA and GEO databases to identify immune genes associated with HCC. Statistical analysis, meta-analysis, and protein-protein interaction analyses were performed to identify key immune genes and their relationships. In vitro and in vivo experiments validated the CDK1-SRC-HSP90AB1 network's effects on HCC progression and antitumor immunity. A prognostic risk model was developed using clinicopathological features and immune infiltration. The immune genes LPA, BIRC5, HSP90AB1, ROBO1, and CCL20 were identified as the key prognostic factors. The CDK1-SRC-HSP90AB1 network promoted HCC cell proliferation and migration, with HSP90AB1 being transcriptionally activated by the CDK1-SRC interaction. Manipulating SRC or HSP90AB1 reversed the effects of CDK1 and SRC on HCC. The CDK1-SRC-HSP90AB1 network also influenced HCC tumor formation and antitumor immunity. Overall, this study highlights the importance of the CDK1-SRC-HSP90AB1 network as a crucial immune-regulatory network in the HCC prognosis.
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Affiliation(s)
- Yi-Jie Zhang
- Department of Hepatobiliary and Organ Transplantation, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
- The Key Laboratory of Organ Transplantation of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
| | - De-Hui Yi
- Department of Hepatobiliary and Organ Transplantation, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
- The Key Laboratory of Organ Transplantation of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
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16
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Wang W, Zhang Z, Li W, Wei D, Xu J, Qian Y, Cao S, Lei D. Characterization of the immune cell function landscape in head and neck squamous carcinoma to assist in prognosis prediction and immunotherapy. Aging (Albany NY) 2023; 15:12588-12617. [PMID: 37955651 PMCID: PMC10683602 DOI: 10.18632/aging.205201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND The malignant characteristics of cancer depend not only on intrinsic properties of cancer cells but also on the functions of infiltrating immune cells. In this study, we aimed to investigate the functional landscape of immune cells in head and neck squamous cell carcinoma (HNSCC). METHODS We employed single-sample gene set enrichment analysis to examine the immunophenotypes of HNSCC based on 29 immune cell functions (ICFs) in TCGA and GSE65858 datasets. We analyzed the clinical features, immune microenvironment, molecular profiles, and biological processes. Additionally, we developed and validated an ICF-based risk score for personalized prognosis prediction. We confirmed the value of the ICF score in our cohort using qRT-PCR and immunohistochemistry. Molecular docking was used to predict potential compounds for immunotherapy. RESULTS Three immunophenotypes (Immune-L, Immune-M, and Immune-H) were identified in 769 HNSCC samples. The characteristics of Immune-H were consistent with a "Hot" tumor, Immune-L was similar to a "Cold" tumor, and Immune-M exhibited intermediate features. The ICF risk score was associated with immune checkpoints, infiltrating immune cells, tumor mutation burden, and sensitivities to targeted/chemotherapeutic agents. Gene set variation analysis implicated the involvement of metabolic reprogramming pathways in the high-risk group. The combination of "Tumor Immune Dysfunction and Exclusion" and "Immunophenoscore" algorithms indicated that the low-risk group had a higher likelihood of benefiting from immunotherapy. Finally, we identified Eltrombopag and other compounds that may be beneficial for HNSCC immunotherapy. CONCLUSION Our study provides a novel perspective on the tumor microenvironment of HNSCC, aiding in the understanding of HNSCC heterogeneity and the development of personalized/precision medicine.
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Affiliation(s)
- Wenlun Wang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Zhouyi Zhang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Wenming Li
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Dongmin Wei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Jianing Xu
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Ye Qian
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
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Mi K, Zeng L, Chen Y, Yang S. Integrative Analysis of Single-Cell and Bulk RNA Sequencing Reveals Prognostic Characteristics of Macrophage Polarization-Related Genes in Lung Adenocarcinoma. Int J Gen Med 2023; 16:5031-5050. [PMID: 37942473 PMCID: PMC10629586 DOI: 10.2147/ijgm.s430408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a group of cancers with poor prognosis. The combination of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) can identify important genes involved in cancer development and progression from a broader perspective. Methods The scRNA-seq data and bulk RNA-seq data of LUAD were downloaded from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. Analyzing scRNA-seq for core cells in the GSE131907 dataset, and the uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Macrophage polarization-associated subtypes were acquired from the TCGA-LUAD dataset after analysis, followed by further identification of differentially expressed genes (DEGs) in the TCGA-LUAD dataset (normal/LUAD tissue samples, two subtypes). Venn diagrams were utilized to visualize differentially expressed and highly variable macrophage polarization-related genes. Subsequently, a prognostic risk model for LUAD patients was constructed by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO), and the model was investigated for stability in the external data GSE72094. After analyzing the correlation between the trait genes and significantly mutated genes, the immune infiltration between the high/low-risk groups was then examined. The Monocle package was applied to analyze the pseudo-temporal trajectory analysis of different cell clusters in macrophage clusters. Subsequently, cell clusters of data macrophages were selected as key cell clusters to explore the role of characteristic genes in different cell populations and to identify transcription factors (TFs) that affect signature genes. Finally, qPCR were employed to validate the expression levels of prognosis signature genes in LUAD. Results 424 macrophage highly variable genes, 3920 DEGs, and 9561 DEGs were obtained from macrophage clusters, the macrophage polarization-related subtypes, and normal/LUAD tissue samples, respectively. Twenty-eight differentially expressed and highly mutated MPRGs were obtained. A prognostic risk model with 7 DE-MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) was constructed. This prognostic model still has a good prediction effect in the GSE72094 dataset. ZNF536 and DNAH9 were mutated in the low-risk group, while COL11A1 was mutated in the high-risk group, and they were highly correlated with the characteristic genes. A total of 11 immune cells were significantly different in the high/low-risk groups. Five cell types were again identified in the macrophage cluster, and then NK cells: CD56hiCD62L+ differentiated earlier and were present mainly on 2 branches. While macrophages were present on 2 branches and differentiated later. It was found that the expression levels of BCLAF1 and MAX were higher in cluster 1, which might be the TFs affecting the expression of the characteristic genes. Moreover, qPCR confirmed that the expression of the prognosis genes was generally consistent with the results of the bioinformatic analysis. Conclusion Seven MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) were identified as prognostic genes for LUAD and revealed the mechanisms of MPRGs at the single-cell level.
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Affiliation(s)
- Ke Mi
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Lizhong Zeng
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
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18
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Gu J, Zhang X, Peng Z, Peng Z, Liao Z. A novel immune-related gene signature for predicting immunotherapy outcomes and survival in clear cell renal cell carcinoma. Sci Rep 2023; 13:18922. [PMID: 37919459 PMCID: PMC10622518 DOI: 10.1038/s41598-023-45966-8] [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: 05/09/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023] Open
Abstract
Clear cell renal carcinoma (ccRCC) is one of the most common cancers worldwide. In this study, a new model of immune-related genes was developed to predict the overall survival and immunotherapy efficacy in patients with ccRCC. Immune-related genes were obtained from the ImmPort database. Clinical data and transcriptomics of ccRCC samples were downloaded from GSE29609 and The Cancer Genome Atlas. An immune-related gene-based prognostic model (IRGPM) was developed using the least absolute shrinkage and selection operator regression algorithm and multivariate Cox regression. The reliability of the developed models was evaluated by Kaplan-Meier survival curves and time-dependent receiver operating characteristic curves. Furthermore, we constructed a nomogram based on the IRGPM and multiple clinicopathological factors, along with a calibration curve to examine the predictive power of the nomogram. Overall, this study investigated the association of IRGPM with immunotherapeutic efficacy, immune checkpoints, and immune cell infiltration. Eleven IRGs based on 528 ccRCC samples significantly associated with survival were used to construct the IRGPM. Remarkably, the IRGPM, which consists of 11 hub genes (SAA1, IL4, PLAUR, PLXNB3, ANGPTL3, AMH, KLRC2, NR3C2, KL, CSF2, and SEMA3G), was found to predict the survival of ccRCC patients accurately. The calibration curve revealed that the nomogram developed with the IRGPM showed high predictive performance for the survival probability of ccRCC patients. Moreover, the IRGPM subgroups showed different levels of immune checkpoints and immune cell infiltration in patients with ccRCC. IRGPM might be a promising biomarker of immunotherapeutic responses in patients with ccRCC. Overall, the established IRGPM was valuable for predicting survival, reflecting the immunotherapy response and immune microenvironment in patients with ccRCC.
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Affiliation(s)
- Jie Gu
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Hunan Province, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Xiaobo Zhang
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Hunan Province, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - ZhangZhe Peng
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Zhuoming Peng
- Department of Respiratory and Intensive Care Medicine, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, 518000, Guangdong Province, China
| | - Zhouning Liao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China.
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Zhang F, Luo H. Diosmetin inhibits the growth and invasion of gastric cancer by interfering with M2 phenotype macrophage polarization. J Biochem Mol Toxicol 2023; 37:e23431. [PMID: 37377034 DOI: 10.1002/jbt.23431] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Overturning M2 phenotype macrophage polarization is a promising therapeutic strategy for gastric cancer (GC). Diosmetin (DIO) is a natural flavonoid with antitumor effect. The aim of this study was to investigate the effect of DIO on polarization of M2 phenotype macrophages in GC. THP-1 cells were induced to M2 phenotype macrophages and co-cultured with AGS cells. The effects of DIO were determined by flow cytometry, qRT-PCR, CCK-8, Transwell, and western blot. To explore the mechanisms, THP-1 cells were transfected with adenoviral vectors containing tumor necrosis factor receptor-associated factor 2 (TRAF2) or si-TRAF2. DIO (0, 5, 10, and 20 μM) restrained the M2 phenotype macrophage polarization. In addition, DIO (20 μM) reversed the increased viability and invasion of AGS cells induced by the co-culture of M2 macrophages. Mechanistically, TRAF2 knockdown inhibited the effect of M2 phenotype macrophages on AGS cells' growth and invasion. Furthermore, DIO (20 μM) was found to decrease TRAF2/NF-κB activity in GC cells. However, TRAF2 overexpressed reversed the inhibitory effect of DIO on the co-culture system. The in vivo study confirmed that DIO treatment (50 mg/kg) could repress the growth of GC. DIO treatment markedly reduced the expressions of Ki-67 and N-cadherin, and decreased the protein levels of TRAF2 and p-NF-κB/NF-κB. In conclusion, DIO inhibited the growth and invasion of GC cells by interfering with M2 phenotype macrophage polarization through repression of the TRAF2/NF-κB signaling pathway.
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Affiliation(s)
- Faqiang Zhang
- Department of General Surgery, Zigong Fourth People's Hospital, Zigong, China
| | - Huan Luo
- Department of General Surgery, Yubei District Hospital of Traditional Chinese Medicine, Chongqing, China
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Chen Y, Pan Y, Gao H, Yi Y, Qin S, Ma F, Zhou X, Guan M. Mechanistic insights into super-enhancer-driven genes as prognostic signatures in patients with glioblastoma. J Cancer Res Clin Oncol 2023; 149:12315-12332. [PMID: 37432454 DOI: 10.1007/s00432-023-05121-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is one of the most common malignant brain tumors in adults and is characterized by high aggressiveness and rapid progression, poor treatment, high recurrence rate, and poor prognosis. Although super-enhancer (SE)-driven genes haven been recognized as prognostic markers for several cancers, whether it can be served as effective prognostic markers for patients with GBM has not been evaluated. METHODS We first combined histone modification data with transcriptome data to identify SE-driven genes associated with prognosis in patients with GBM. Second, we developed a SE-driven differentially expressed genes (SEDEGs) risk score prognostic model by univariate Cox analysis, KM survival analysis, multivariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression. Its reliability in predicting was verified by two external data sets. Third, through mutation analysis, immune infiltration, we explored the molecular mechanisms of prognostic genes. Next, Genomics of Drug Sensitivity in Cancer (GDSC) and the Connectivity Map (cMap) database were employed to assess different sensitivities to chemotherapeutic agents and small-molecule drug candidates between high- and low-risk patients. Finally, SEanalysis database was chosen to identify SE-driven transcription factors (TFs) regulating prognostic markers which will reveal a potential SE-driven transcriptional regulatory network. RESULTS First, we developed a 11-gene risk score prognostic model (NCF2, MTHFS, DUSP6, G6PC3, HOXB2, EN2, DLEU1, LBH, ZEB1-AS1, LINC01265, and AGAP2-AS1) selected from 1,154 SEDEGs, which is not only an independent prognostic factor for patients, but also can effectively predict the survival rate of patients. The model can effectively predict 1-, 2- and 3-year survival of patients and was validated in external Chinese Glioma Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) datasets. Second, the risk score was positively correlated with the infiltration of regulatory T cell, CD4 memory activated T cell, activated NK cell, neutrophil, resting mast cell, M0 macrophage, and memory B cell. Third, we found that high-risk patients showed higher sensitivity than low-risk patients to both 27 chemotherapeutic agents and 4 small-molecule drug candidates which might benefit further precision therapy for GBM patients. Finally, 13 potential SE-driven TFs imply how SE regulates GBM patient's prognosis. CONCLUSION The SEDEG risk model not only helps to elucidate the impact of SEs on the course of GBM, but also provides a bright future for prognosis determination and choice of treatment for GBM patients.
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Affiliation(s)
- Youran Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yi Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Hanyu Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yunmeng Yi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Shijie Qin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Fei Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Xue Zhou
- School of Chemistry and Biological Engineering, Nanjing Normal University Taizhou College, Taizhou, 225300, China.
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China.
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Fu C, Cheng C, Zhang Y. A novel signature of the ligand and receptor genes associated with disulfidoptosis for prediction of prognosis, immunologic therapy responses in hepatocellular carcinoma. Heliyon 2023; 9:e19502. [PMID: 37662746 PMCID: PMC10472309 DOI: 10.1016/j.heliyon.2023.e19502] [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: 05/19/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Backgroud We aimed to explore the prognostic features of ligand and receptor genes associated with disulfidoptosis in hepatocellular carcinoma (HCC) and establish a risk signature utilizing these genes to predict the prognosis of HCC patients. Methods We used scRNA-seq data from GSE166635 to differentiate malignant cells from normal cells using "copykat".The study thoroughly examined the disparities in disulfidoptosis scores and the associated gene expressions between malignant and normal cells.We identified key ligand and receptor genes that are specific to HCC cells.Subsequently, Correlation analysis was conducted to ascertain the ligand and receptor genes associated with disulfidoptosis.We performed univariate Cox regression analysis to identify prognostic ligand and receptor genes associated with disulfidoptosis.We employed LASSO to construct a risk signature using prognostic ligand and receptor genes associated with disulfidoptosis.Lastly, we developed a nomogram model that integrates the risk signature with clinicopathological characteristics. Results Malignant cells displayed a marked increase in disulfidoptosis scores and the expression of associated genes compared to normal cells.We identified 110 receptor and ligand genes significantly associated with disulfidoptosis, and narrowed them down to create a risk signature comprising eight genes.Multivariate analysis confirmed the risk signature as an independent prognostic factor for HCC and validated its predictive value for immunotherapy outcomes.A novel nomogram was developed, incorporating stage information and the risk signature derived from disulfidoptosis-related receptor and ligand genes, demonstrating excellent predictive accuracy and reliability in HCC prognosis prediction. Conclusion Risk signatures based on disulfidoptosis-associated ligand and receptor genes can effectively predict HCC prognosis and may inform immunotherapy strategies.
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Affiliation(s)
- Chong Fu
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
| | - Chang Cheng
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
| | - Yanping Zhang
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
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Chen X, Wang Z, Wu Y, Lan Y, Li Y. Typing and modeling of hepatocellular carcinoma based on disulfidptosis-related amino acid metabolism genes for predicting prognosis and guiding individualized treatment. Front Oncol 2023; 13:1204335. [PMID: 37637055 PMCID: PMC10454915 DOI: 10.3389/fonc.2023.1204335] [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: 04/12/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is the most common type of cancer worldwide and is a major public health problem in the 21st century. Disulfidopathy, a novel cystine-associated programmed cell death, plays complex roles in various tumors. However, the relationship between disulfidoptosis and prognosis in patients with HCC remains unclear. This study aimed to explore the relationship between disulfideptosis and the prognosis of liver cancer and to develop a prognostic model based on amino acid metabolism and disulfideptosis genes. Methods We downloaded the clinicopathological information and gene expression data of patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and classified them into different molecular subtypes based on the expression patterns of disulfidoptosis-associated amino acid metabolism genes (DRAGs). Patients were then classified into different gene subtypes using the differential genes between the molecular subtypes, and the predictive value of staging was assessed using survival and clinicopathological analyses. Subsequently, risk prognosis models were constructed based on Cox regression analysis to assess patient prognosis, receiver operating characteristic (ROC) curves, somatic mutations, microsatellite instability, tumor microenvironment, and sensitivity to antitumor therapeutic agents. Results Patients were classified into two subtypes based on differential DRAGs gene expression, with cluster B having a better survival outcome than cluster A. Three gene subtypes were identified based on the differential genes between the two DRAGs molecular subtypes. The patients in cluster B had the best prognosis, whereas those in cluster C had the worst prognosis. The heat map showed better consistency in the patient subtypes obtained using both typing methods. We screened six valuable genes and constructed a prognostic signature. By scoring, we found that patients in the low-risk group had a better prognosis, higher immune scores, and more abundant immune-related pathways compared to the high-risk group, which was consistent with the tumor subtype results. Discussion In conclusion, we developed a prognostic signature of disulfidptosis-related amino acid metabolism genes to assist clinicians in predicting the survival of patients with HCC and provide a reference value for targeted therapy and immunotherapy for HCC.
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Affiliation(s)
- Xuenuo Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhijian Wang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yilin Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yinghua Lan
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongguo Li
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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An J, Oh JH, Oh B, Oh YJ, Ju JS, Kim W, Kang HJ, Sung CO, Shim JH. Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination-deficient hepatocellular carcinoma. Hepatology 2023; 78:452-467. [PMID: 36177702 DOI: 10.1002/hep.32812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/20/2022] [Accepted: 09/24/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUNDS AND AIMS We performed an in-depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. APPROACH AND RESULTS We used a merged whole-exome or RNA sequencing data set derived from in-house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR-altered and found to be independently associated with poorer disease-free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication-related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP-ribose) polymerase inhibitors. CONCLUSIONS Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR-directed treatments in the affected patients are needed.
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Affiliation(s)
- Jihyun An
- Gastroenterology and Hepatology , Hanyang University College of Medicine , Guri , Republic of Korea
| | - Ji-Hye Oh
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
| | - Bora Oh
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Yoo-Jin Oh
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Jin-Sung Ju
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Wonkyung Kim
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
| | - Hyo Jung Kang
- Pathology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Asan Liver Center, Asan Medical Center , University of Ulsan College of Medicine , Seoul , South Korea
| | - Chang Ohk Sung
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
- Pathology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Center for Cancer Genome Discovery , Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center , Seoul , Republic of Korea
| | - Ju Hyun Shim
- Asan Liver Center, Asan Medical Center , University of Ulsan College of Medicine , Seoul , South Korea
- Gastroenterology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Digestive Diseases Research Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
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Devan AR, Nair B, Aryan MK, Liju VB, Koshy JJ, Mathew B, Valsan A, Kim H, Nath LR. Decoding Immune Signature to Detect the Risk for Early-Stage HCC Recurrence. Cancers (Basel) 2023; 15:2729. [PMID: 37345066 DOI: 10.3390/cancers15102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is often recognized as an inflammation-linked cancer, which possesses an immunosuppressive tumor microenvironment. Curative treatments such as surgical resection, liver transplantation, and percutaneous ablation are mainly applicable in the early stage and demonstrate significant improvement of survival rate in most patients. However, 70-80% of patients report HCC recurrence within 5 years of curative treatment, representing an important clinical issue. However, there is no effective recurrence marker after surgical and locoregional therapies, thus, tumor size, number, and histological features such as cancer cell differentiation are often considered as risk factors for HCC recurrence. Host immunity plays a critical role in regulating carcinogenesis, and the immune microenvironment characterized by its composition, functional status, and density undergoes significant alterations in each stage of cancer progression. Recent studies reported that analysis of immune contexture could yield valuable information regarding the treatment response, prognosis and recurrence. This review emphasizes the prognostic value of tumors associated with immune factors in HCC recurrence after curative treatment. In particular, we review the immune landscape and immunological factors contributing to early-stage HCC recurrence, and discuss the immunotherapeutic interventions to prevent tumor recurrence following curative treatments.
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Affiliation(s)
- Aswathy R Devan
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi 682041, Kerala, India
| | - Bhagyalakshmi Nair
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi 682041, Kerala, India
| | | | - Vijayastelar B Liju
- The Shraga Segal Department of Microbiology-Immunology and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Joel Joy Koshy
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi 682041, Kerala, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi 682041, Kerala, India
| | - Arun Valsan
- Department of Gastroenterology and Epatology, Amrita Institute of Medical Science, Kochi 682041, Kerala, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi 682041, Kerala, India
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Chen K, Gong W, Huang J, Yoshimura T, Ming Wang J. Developmental and homeostatic signaling transmitted by the G-protein coupled receptor FPR2. Int Immunopharmacol 2023; 118:110052. [PMID: 37003185 PMCID: PMC10149111 DOI: 10.1016/j.intimp.2023.110052] [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: 12/29/2022] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023]
Abstract
Formyl peptide receptor 2 (FPR2) and its mouse counterpart Fpr2 are the members of the G protein-coupled receptor (GPCR) family. FPR2 is the only member of the FPRs that interacts with ligands from different sources. FPR2 is expressed in myeloid cells as well as epithelial cells, endothelial cells, neurons, and hepatocytes. During the past years, some unusual properties of FPR2 have attracted intense attention because FPR2 appears to possess dual functions by activating or inhibiting intracellular signal pathways based on the nature, concentration of the ligands, and the temporal and spatial settings of the microenvironment in vivo, the cell types it interacts with. Therefore, FPR2 controls an abundant array of developmental and homeostatic signaling cascades, in addition to its "classical" capacity to mediate the migration of hematopoietic and non-hematopoietic cells including malignant cells. In this review, we summarize recent development in FPR2 research, particularly in its role in diseases, therefore helping to establish FPR2 as a potential target for therapeutic intervention.
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Affiliation(s)
- Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
| | - Wanghua Gong
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Jiaqiang Huang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA; College of Life Sciences, Beijing Jiaotong University, Beijing, PR China
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
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Constantin AM, Mihu CM, Boşca AB, Melincovici CS, Mărginean MV, Jianu EM, Onofrei MM, Micu CM, Alexandru BC, Sufleţel RT, Moldovan IM, Coneac A, Crintea A, Ştefan RA, Ştefan PA, Djouini A, Şovrea AS. Short histological kaleidoscope - recent findings in histology. Part III. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY = REVUE ROUMAINE DE MORPHOLOGIE ET EMBRYOLOGIE 2023; 64:115-133. [PMID: 37518868 PMCID: PMC10520383 DOI: 10.47162/rjme.64.2.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
The paper provides an overview of the current understanding of different cells' biology (e.g., keratinocytes, Paneth cells, myoepithelial cells, myofibroblasts, chondroclasts, monocytes, atrial cardiomyocytes), including their origin, structure, function, and role in disease pathogenesis, and of the latest findings in the medical literature concerning the brown adipose tissue and the juxtaoral organ of Chievitz.
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Affiliation(s)
- Anne Marie Constantin
- Discipline of Histology, Department of Morphological Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania;
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Xiang J, Liu C, He Q, He P, Dong W. Comprehensive analysis of immunogenic cell death associated genes expression, tumor microenvironment, and prognosis in hepatocellular carcinoma. Front Pharmacol 2023; 14:1122011. [PMID: 36998605 PMCID: PMC10045985 DOI: 10.3389/fphar.2023.1122011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/06/2023] [Indexed: 03/15/2023] Open
Abstract
Background: Immunogenic cell death (ICD) plays an important role in the development of cancers. This study attempted to explore the role of ICD in the prognosis of hepatocellular carcinoma (HCC).Methods: Gene expression and clinical data were downloaded from The Cancer Genome Alas and Gene Expression Omnibus dataset. The immune/stromal/Estimate scores of the tumor microenvironment (TME) were calculated by ESTIMATE and CIBERSORT algorithms. Kaplan-Meier analysis, functional enrichment analysis, least absolute shrinkage and selection operator (LASSO) analysis, and univariate and multivariate Cox regression analysis were used for prognostic gene screening and prognostic model construction. The correlation of immune cell infiltration and risk scores was analyzed as well. Molecular docking was used to explore the relevance of related genes to anti-cancer drugs.Results: Ten ICD associated differentially expressed genes in HCC were found, and all of them had good predictive ability for HCC. ICD gene high amount of expression group was associated with poor prognosis (p = 0.015). The TME, immune cell infiltration and gene expression were different between ICD high and low groups (all p < 0.05). Six ICD associated genes (BAX, CASP8, IFNB1, LY96, NT5E and PIK3CA) which could predict the survival status were identified and used to construct the prognostic model for HCC. A risk score was calculated and it could be used as an independent prognostic factor in HCC patients (p < 0.001). In addition, the risk score had a positive correlation with macrophage M0 (r = 0.33, p = 0.0086). Molecular docking indicated that sorafenib could bind strongly to the target protein, representing that sorafenib may exert anticancer effects through these six ICD associated genes.Conclusion: This study established a prognostic model including six ICD associated genes for HCC, which may deepen our understanding of ICD and guide therapy for HCC patients.
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Affiliation(s)
- Jiankang Xiang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuan Liu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qingmin He
- Henan Key Laboratory of Helicobacter Pylori and Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, the Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pengzhan He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Weiguo Dong,
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Deng S, Shen S, Liu K, El-Ashram S, Alouffi A, Cenci-Goga BT, Ye G, Cao C, Luo T, Zhang H, Li W, Li S, Zhang W, Wu J, Chen C. Integrated bioinformatic analyses investigate macrophage-M1-related biomarkers and tuberculosis therapeutic drugs. Front Genet 2023; 14:1041892. [PMID: 36845395 PMCID: PMC9945105 DOI: 10.3389/fgene.2023.1041892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Tuberculosis (TB) is a common infectious disease linked to host genetics and the innate immune response. It is vital to investigate new molecular mechanisms and efficient biomarkers for Tuberculosis because the pathophysiology of the disease is still unclear, and there aren't any precise diagnostic tools. This study downloaded three blood datasets from the GEO database, two of which (GSE19435 and 83456) were used to build a weighted gene co-expression network for searching hub genes associated with macrophage M1 by the CIBERSORT and WGCNA algorithms. Furthermore, 994 differentially expressed genes (DEGs) were extracted from healthy and TB samples, four of which were associated with macrophage M1, naming RTP4, CXCL10, CD38, and IFI44. They were confirmed as upregulation in TB samples by external dataset validation (GSE34608) and quantitative real-time PCR analysis (qRT-PCR). CMap was used to predict potential therapeutic compounds for tuberculosis using 300 differentially expressed genes (150 downregulated and 150 upregulated genes), and six small molecules (RWJ-21757, phenamil, benzanthrone, TG-101348, metyrapone, and WT-161) with a higher confidence value were extracted. We used in-depth bioinformatics analysis to investigate significant macrophage M1-related genes and promising anti-Tuberculosis therapeutic compounds. However, more clinical trials were necessary to determine their effect on Tuberculosis.
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Affiliation(s)
- Siqi Deng
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Shijie Shen
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Keyu Liu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Saeed El-Ashram
- Faculty of Science, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | - Guomin Ye
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Chengzhang Cao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Tingting Luo
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Hui Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Siyuan Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Wanjiang Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Jiangdong Wu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China,*Correspondence: Jiangdong Wu, ; Chuangfu Chen,
| | - Chuangfu Chen
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China,*Correspondence: Jiangdong Wu, ; Chuangfu Chen,
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Identification of Aging and Young Subtypes for Predicting Colorectal Cancer Prognosis and Immunotherapy Responses. Int J Mol Sci 2023; 24:ijms24021516. [PMID: 36675039 PMCID: PMC9862647 DOI: 10.3390/ijms24021516] [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: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is critically related to aging and severely threatens human lives. To better explore the effects of aging on CRC progression and therapy outcome, a reliable aging subtypes identification of CRC is urgently desired. Here, 28 aging-related genes associated with the CRC prognosis were selected by univariate Cox analyses. Based on these 28 genes, CRC patients were divided into the aging subtype and young subtype by non-negative matrix factorization clustering. Aging subtype and young subtype of CRC were identified with distinct molecular features and clinical prognosis. The aging subtype was characterized by upregulation of senescence-associated secretory phenotype, higher frequencies of TP53 and immune checkpoint molecules, and high sensitivity to protein kinase and angiogenesis inhibitors. Furthermore, 14 genes were selected by LASSO penalized Cox regression analyses for aging-related risk signature construction. The constructed aging risk signature exhibited good prediction and the nomogram showed robust discrimination power over the traditional CRC staging system. In conclusion, this study successfully established aging subtype and young subtype of CRC, which is helpful to identify patients with aging characteristics to evaluate prognosis and treatment outcomes. Introducing aging-based subtypes into clinical concern and patient prognostication provides new opportunities for personalized CRC treatment.
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Liu C, Wu S, Lai L, Liu J, Guo Z, Ye Z, Chen X. Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma. BMC Bioinformatics 2023; 24:4. [PMID: 36597032 PMCID: PMC9811804 DOI: 10.1186/s12859-022-05091-1] [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: 08/31/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Being among the most common malignancies worldwide, hepatocellular carcinoma (HCC) accounting for the third cause of cancer mortality. The regulation of cell death is the most crucial step in tumor progression and has become a crucial target for nearly all therapeutic options. Cuproptosis, a copper-induced cell death, was recently reported in Science. However, its primary function in carcinogenesis is still unclear. METHODS Cuproptosis-related lncRNAs significantly associated with overall survival (OS) were screened by stepwise univariate Cox regression. The signature of cuproptosis-related lncRNAs for HCC prognosis was constructed by the LASSO algorithm and multivariate Cox regression. Further Kaplan-Meier analysis, proportional hazards model, and ROC analysis were performed. Functional annotation was performed using gene set enrichment analysis (GSEA). The relationship between prognostic cuproptosis-related lncRNAs and HCC prognosis was further explored by GEPIA( http://gepia.cancer-pku.cn/ ) online analysis tool. Finally, we used the ESTIMATE and XCELL algorithms to estimate stromal and immune cells in tumor tissue and cast each sample to infer the underlying mechanism of cuproptosis-related lncRNAs in the tumor immune microenvironment (TIME) of HCC patients. RESULTS Four cuproptosis-related lncRNAs were used to construct a prognostic lncRNA signature, which was an independent factor in predicting OS in HCC patients. Kaplan-Meier curves showed significant differences in survival rates between risk subgroups (p = 0.002). At the same time, we found that the expression levels of most immune checkpoint genes increased with increasing risk scores. Tumorigenesis and immunological-related pathways were primarily enhanced in the high-risk group, as determined by GSEA. The results of drug sensitivity analysis showed that compared with patients in the high-risk group, the IC50 values of erlotinib and lapatinib were lower in patients in the low-risk group, while the opposite was true for sunitinib, paclitaxel, gemcitabine, and imatinib. We also found that elevated AL133243.2 expression was significantly associated with worse OS and disease-free survival (DFS), more advanced T stage and higher tumor grade, and reduced immune cell infiltration, suggesting that HCC patients with low AL133243.2 expression in tumor tissues may have a better response to immunotherapy. CONCLUSION Collectively, the cuproptosis-associated lncRNA signature can serve as an independent predictor to guide individual treatment strategies. Furthermore, AL133243.2 is a promising marker for predicting immunotherapy response in HCC patients. This data may facilitate further exploration of more effective immunotherapy strategies for HCC.
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Affiliation(s)
- Chunhua Liu
- grid.417384.d0000 0004 1764 2632Rehabilitation Center, The Second Affiliated Hospital of Wenzhou Medical University, 108 Xueyuan West Road, Wenzhou, Zhejiang China
| | - Simin Wu
- grid.417384.d0000 0004 1764 2632Rehabilitation Center, The Second Affiliated Hospital of Wenzhou Medical University, 108 Xueyuan West Road, Wenzhou, Zhejiang China
| | - Liying Lai
- grid.13402.340000 0004 1759 700XDepartment of Cancer Rehabilitation, Lishui Hospital of Traditional Chinese Medicine Affiliated to the Zhejiang University of Chinese Medicine, Lishui, Zhejiang China
| | - Jinyu Liu
- grid.13402.340000 0004 1759 700XDepartment of Cancer Rehabilitation, Lishui Hospital of Traditional Chinese Medicine Affiliated to the Zhejiang University of Chinese Medicine, Lishui, Zhejiang China
| | - Zhaofu Guo
- grid.13402.340000 0004 1759 700XDepartment of Cancer Rehabilitation, Lishui Hospital of Traditional Chinese Medicine Affiliated to the Zhejiang University of Chinese Medicine, Lishui, Zhejiang China
| | - Zegen Ye
- grid.13402.340000 0004 1759 700XDepartment of Cancer Rehabilitation, Lishui Hospital of Traditional Chinese Medicine Affiliated to the Zhejiang University of Chinese Medicine, Lishui, Zhejiang China
| | - Xiang Chen
- Rehabilitation Center, The Second Affiliated Hospital of Wenzhou Medical University, 108 Xueyuan West Road, Wenzhou, Zhejiang, China.
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Xu X, Wang J. Prognostic prediction and multidimensional dissections of a macrophages M0-related gene signature in liver cancer. Front Endocrinol (Lausanne) 2023; 14:1153562. [PMID: 37033261 PMCID: PMC10080084 DOI: 10.3389/fendo.2023.1153562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) is the seventh most commonly diagnosed malignancy and the third leading cause of all cancer death worldwide. The undifferentiated macrophages M0 can be induced into polarized M1 and M2 to exert opposite effects in tumor microenvironment. However, the prognostic value of macrophages M0 phenotype remains obscure in LIHC. METHODS The transcriptome data of LIHC was obtained from TCGA database and ICGC database. 365 LIHC samples from TCGA database and 231 LIHC samples from ICGC database were finally included. Macrophages M0-related genes (MRGs) were screened by Pearson correlation analysis and univariate Cox regression analysis based on the infiltration level of Macrophages M0. LASSO regression analysis was employed to construct a prognostic signature based on MRGs, and risk scores were accordingly calculated. Then we investigated the MRGs-based prognostic signature with respects to prognostic value, clinical significance, strengthened pathways, immune infiltration, gene mutation and drug sensitivity. Furthermore, the expression pattern of MRGs in the tumor microenvironment were also detected in LIHC. RESULTS A ten-MRG signature was developed and clarified as independent prognostic predictors in LIHC. The risk score-based nomogram showed favorable capability in survival prediction. Several substance metabolism activities like fatty acid/amino acid metabolism were strengthened in low-risk group. Low risk group was deciphered to harbor TTN mutation-driven tumorigenesis, while TP53 mutation was dominant in high-risk group. We also ascertained that the infiltration levels of immune cells and expressions of immune checkpoints are significantly influenced by the risk score. Besides, we implied that patients in low-risk group may be more sensitive to several anti-cancer drugs. What's more important, single-cell analysis verified the expression of MRGs in the tumor microenvironment of LIHC. CONCLUSION Multidimensional evaluations verified the clinical utility of the macrophages M0-related gene signature to predict prognosis, assist risk decision and guide treatment strategy for patients with LIHC.
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Affiliation(s)
- Xiaoming Xu
- Department of Gastroenterology, Jining First People’s Hospital, Jining, China
| | - Jingzhi Wang
- Department of Radiotherapy Oncology, The Affiliated Yancheng First Hospital of Nanjing University Medical School, The First People’s Hospital of Yancheng, Yancheng, China
- *Correspondence: Jingzhi Wang,
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