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Sun J, Feng Q, Xu Y, Liu P, Wu Y. Analysis of prognostic value of lactate metabolism-related genes in ovarian cancer based on bioinformatics. J Ovarian Res 2024; 17:110. [PMID: 38778371 PMCID: PMC11110319 DOI: 10.1186/s13048-024-01426-z] [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: 04/18/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Recent studies have provided evidence supporting the functional role and mechanism of lactate in suppressing anticancer immunity. However, there is no systematic analysis of lactate metabolism-related genes (LMRGs) and ovarian cancer (OV) prognosis. RESULTS Six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) were selected as prognostic genes and a prognostic model was utilized. Kaplan-Meier (K-M) and Receiver Operating Characteristic (ROC) analyses were further performed and indicated that the prognostic model was effective. Subsequently, the neoplasm_cancer_status and RiskScore were determined as independent prognostic factors, and a nomogram was established with relatively accurate forecasting ability. Additionally, 2 types of immune cells (Central memory CD8 T cell and Immature B cell), 4 types of immune functions (APC co inhibition, DCs, Tfh and Th1 cells), 9 immune checkpoints (BTLA, CTLA4, IDO1, LAG3, VTCN1, CXCL10, CXCL9, IFNG, CD27) and tumor immune dysfunction and exclusion (TIDE) scores were significantly different between risk groups. The expression of 6 genes were verified by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and the expression of 6 genes were higher in the high-grade serous carcinoma (HGSC) samples. CONCLUSION A prognostic model related to lactate metabolism was established for OV based on six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) that could provide new insights into therapy.
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Affiliation(s)
- Jinrui Sun
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
- Department of Gynecology, Shanxi Provincial People's Hospital, Taiyuan, 030001, Shanxi Province, China
| | - Qinmei Feng
- Department of Gynecology, Shanxi Provincial People's Hospital, Taiyuan, 030001, Shanxi Province, China
| | - Yingying Xu
- Department of Gynecology, Shanxi Provincial People's Hospital, Taiyuan, 030001, Shanxi Province, China
| | - Ping Liu
- Department of Gynecology, Shanxi Provincial People's Hospital, Taiyuan, 030001, Shanxi Province, China
| | - Yumei Wu
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China.
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Wang B, Du Z, Lin C, Liu D, Guo J, Shi J, Wang X. Comprehensive analysis of INTS family related to expression, prognosis, diagnosis and immune features in hepatocellular carcinoma. Heliyon 2024; 10:e30244. [PMID: 38720706 PMCID: PMC11076979 DOI: 10.1016/j.heliyon.2024.e30244] [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: 02/29/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Purpose The integrator subunit (INTS) family, a group exclusive to metazoans, participates in various biologic processes. However, their roles in hepatocellular carcinoma (HCC) remain largely unexplored. Methods Public databases were utilized to investigate the transcriptional and protein expression, and clinical relevance of the INTS family in HCC. Meanwhile, the effects of INTS13 knockdown and overexpression on cell proliferation and apoptosis were studied using HCC cell lines. Results The mRNA expression of most INTSs were higher in tumor than normal tissues. Higher expression of INTS1/2/3/4/7/8/9/11/12/13 were correlated with poorer overall survival (OS) in Kaplan-Meier Survival Analysis. Multivariate analysis revealed higher level of INTS13 was an independent prognostic factor for shorter OS. Furthermore, genetic alteration of INTS3/6/7/8/9/10 were found in HCC patients and was associated with shorter disease-free survival and progression-free survival. INTS1/2/3/5/7/11/13/14 were associated with activation of tumor-induced immune response and immune infiltration in HCC. Knockdown of INTS13 inhibited cell proliferation and induced apoptosis in HCC cell lines, while overexpression of INTS13 had the opposite effect. Conclusion Our results indicate that INTS13 is an independent prognostic biomarker in HCC. Furthermore, INTS13 enhances cell proliferation and decreases cell apoptosis in HCC cell lines leading to a poorer OS in HCC patients.
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Affiliation(s)
- Bingyu Wang
- Department of Science and Education, The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zifei Du
- Department of Science and Education, The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - ChongSen Lin
- Department of Orthopedics, Huizhou Hospital of Guangzhou University of Chinese Medicine, Huicheng, Guangdong, China
| | - Dandan Liu
- Department of Respiratory Medicine, Taixing Hospital of TCM, Taixing, Jiangsu, China
| | - Jiewen Guo
- Department of Science and Education, The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiawei Shi
- Department of Spinal Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaobo Wang
- Department of Spinal Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Liu W, Li HM, Bai G. Integrated bioinformatics analysis of ferroptosis-related gene signature in inflammation and immunity in intervertebral disc degeneration. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-21. [PMID: 38531048 DOI: 10.1080/15257770.2024.2332403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Ferroptosis has recently been shown to play a significant role in the progression of intervertebral disk degeneration (IDD), although the underlying mechanism is still unknown. The objective of this work was to use stringent bioinformatic techniques to clarify the crucial roles played by genes associated with ferroptosis in the emergence of IDD. For additional study, the microarray data pertinent to the IDD were acquired from the Gene Expression Omnibus database. The ferroptosis-related and IDD-related genes (FIDDRGs) were identified using a variety of bioinformatic techniques, which were also used to carry out function enrichment analysis, protein-protein correlation analysis, build the correlation regulatory network, and examine the potential connections between ferroptosis and immune abnormalities and inflammatory responses in IDD. A total of 16 FIDDRGs were eliminated for the further function enrichment analysis, and 10 hub FIDDRGs were chosen to build the correlation regulatory network. Hub FIDDRGs were shown to be highly associated with M2 macrophages and hub inflammatory response-related genes in IDD. When seen as a whole, our findings can give fresh perspectives on the mechanistic studies of ferroptosis in the emergence of IDD and new prospective targets for the therapeutic approaches.
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Affiliation(s)
- Wei Liu
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
| | - Hui-Min Li
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
| | - Guangchao Bai
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
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Zhao Q, Ye Y, Zhang Q, Wu Y, Wang G, Gui Z, Zhang M. PANoptosis-related long non-coding RNA signature to predict the prognosis and immune landscapes of pancreatic adenocarcinoma. Biochem Biophys Rep 2024; 37:101600. [PMID: 38371527 PMCID: PMC10873882 DOI: 10.1016/j.bbrep.2023.101600] [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: 09/11/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 02/20/2024] Open
Abstract
Background Cancer growth is significantly influenced by processes such as pyroptosis, apoptosis, and necroptosis that underlie PANoptosis, a proinflammatory programmed cell death. Several studies have examined the long non-coding RNAs (lncRNAs) associated with pancreatic adenocarcinoma (PAAD). However, the predictive value of lncRNAs related to PANoptosis for PAAD has not been established. Methods The Clinical Genome Atlas database was used to obtain the transcriptome 、clinical data and the corresponding mutation data of the patients with PAAD in this study. The least absolute shrinkage and selection operator regression analysis was employed to obtain prognosis-related lncRNAs for constructing a risk signature. According to the median risk score of the signature, patients with PAAD were grouped into low- and high-risk groups to further compare the survival prognosis of different risk groups. Time-dependent receiver operating characteristic curves, c-index analysis, nomograms, principal component analysis and univariate Cox and multivariate Cox regression were performed for the internal validation of the signature. In addition, enrichment analysis of different genes was performed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Lastly, differences in tumor mutation burden (TMB), immune function, tumor immune dysfunction and rejection (TIDE), and drug response were determined for the two risk groups. Results The signature was constructed with six PANoptosis-related lncRNAs (AC067817.2、LINC02004、AC243829.1、AC092171.5、AP005233.2、AC004687.1) that predicted the prognosis of the patients with PAAD. Survival curves showed that patients in the two risk groups had statistically significant differences in prognosis (P < 0.05), and multi-cox regression analysis identified risk score as an independent risk factor for PAAD prognosis, and internal validation of nomograms showed high confidence in the signature. GO and KEGG enrichment analysis showed functional and pathway differences between the high- and low-risk groups. TMB evaluation demonstrated that patients in the high-risk group had a higher frequency of mutations. The TIDE score indicated that the high-risk group had a lower risk of immunotherapy escape and better immunotherapy outcomes. Additionally, the two risk groups revealed significantly different responses to 11 anticancer drugs. Conclusion We identified a novel risk signature for PANoptosis-related lncRNAs, which is a standalone prognostic indicator for PAAD. The PANoptosis-related lncRNA risk signature may be relevant for immunotherapy and a therapeutic target for PAAD.
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Affiliation(s)
- Qinying Zhao
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Yingquan Ye
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Quan Zhang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Yue Wu
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Gaoxiang Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Zhongxuan Gui
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Mei Zhang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
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Zhang D, Xiang KF, Xiang C, Wu Y, Wang L. Construction of novel 7 integrin-related gene signatures in thyroid cancer construction of model based on integrin genes. Medicine (Baltimore) 2023; 102:e36412. [PMID: 38115319 PMCID: PMC10727611 DOI: 10.1097/md.0000000000036412] [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: 04/13/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Advanced and metastatic THCA patients usually have a poor prognosis. Thus, this study aimed to establish a risk model to discriminate the high risk population. The expression and clinical data were obtained from TCGA database. The cluster analysis, lasso, univariate and multivariate cox analyses were used to construct risk model. K-M, ROC and DCA were applied to validate the efficiency and stability of the model. GO, KEGG, and ssGSEA analysis were performed to identify the potential mechanism of signatures. The 7-gene prognosis model was constructed, including FAM27E3, FIGN, GSTM4, BEX5, RBPMS2, PHF13, and DCSTAMP. ROC and DCA results showed our model had a better prognosis prediction performance than other risk models. The high risk score was associated with the poor prognosis of THCA patients with different clinical characteristics. The risk score was closely related to cell cycle. Further, we found that the expressions of signatures were significantly dysregulated in THCA and associated with prognosis. These gene expressions were affected by some clinical characteristics, methylation and CNV. Some signatures played a role in drug sensitivity and pathway activation. We constructed a 7-gene signature model based on the integrin-related genes, which showed a great prognostic value in THCA.
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Affiliation(s)
- Dong Zhang
- Department of General Surgery, Kong Jiang Hosptal of Yangpu District, Shanghai, China
| | - Kai-fang Xiang
- Department of Thyroid and Breast Surgery, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Cheng Xiang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Wu
- Department of Oncology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Ling Wang
- Department of Thyroid and Breast Surgery, The First People’s Hospital of Jiangxia, Wuhan, China
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Zhou S, Zhao X, Zhang S, Tian X, Wang X, Mu Y, Li F, Zhao AZ, Zhao Z. Prognosis prediction based on methionine metabolism genes signature in gliomas. BMC Med Genomics 2023; 16:317. [PMID: 38057821 PMCID: PMC10699061 DOI: 10.1186/s12920-023-01754-x] [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: 03/31/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Glioma cells have increased intake and metabolism of methionine, which can be monitored with 11 C-L-methionine. However, a short half-life of 11 C (~ 20 min) limits its application in clinical practice. It is necessary to develop a methionine metabolism genes-based prediction model for a more convenient prediction of glioma survival. METHODS We evaluated the patterns of 29 methionine metabolism genes in glioma from the Cancer Genome Atlas (TCGA). A risk model was established using Lasso regression analysis and Cox regression. The reliability of the prognostic model was validated in derivation and validation cohorts (Chinese Glioma Genome Atlas; CGGA). GO, KEGG, GSEA and ESTIMATE analyses were performed for biological functions and immune characterization. RESULTS Our results showed that a majority of the methionine metabolism genes (25 genes) were involved in the overall survival of glioma (logrank p and Cox p < 0.05). A 7-methionine metabolism prognostic signature was significantly related to a poor clinical prognosis and overall survival of glioma patients (C-index = 0.83). Functional analysis revealed that the risk model was correlated with immune responses and with epithelial-mesenchymal transition. Furthermore, the nomogram integrating the signature of methionine metabolism genes manifested a strong prognostic ability in the training and validation groups. CONCLUSIONS The current model had the potential to improve the understanding of methionine metabolism in gliomas and contributed to the development of precise treatment for glioma patients, showing a promising application in clinical practice.
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Affiliation(s)
- Sujin Zhou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Xianan Zhao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Shiwei Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Xue Tian
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Xuepeng Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Yunping Mu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Fanghong Li
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Allan Z Zhao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China
| | - Zhenggang Zhao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 510006, Guangzhou, Guangdong Province, China.
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Wang D, Ding D, Ying J, Qin Y. Bioinformatics identification of a T-cell-related signature for predicting prognosis and drug sensitivity in hepatocellular carcinoma. IET Syst Biol 2023; 17:366-377. [PMID: 37935646 PMCID: PMC10725711 DOI: 10.1049/syb2.12082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal disease with poor clinical outcomes. T cells play a vital role in the crosstalk between the tumour microenvironment and HCC. Single-cell RNA sequencing data were downloaded from the GSE149614 dataset. The T-cell-related prognostic signature (TRPS) was developed with the integrative procedure including 10 machine learning algorithms. The TRPS was established using 7 T-cell-related markers in the Cancer Genome Atlas cohort with 1-, 2- and 3-year area under curve values of 0.820, 0.725 and 0.678, respectively. TRPS acted as an independent risk factor for HCC patients. HCC patients with a high TRPS-based risk score had a higher Tumour Immune Dysfunction and Exclusion score, lower PD1 and CTLA4 immunophenoscore and lower level of immunoactivated cells, including CD8+ T cells and NK cells. The response rate was significantly higher in patients with low-risk scores in immunotherapy cohorts, including IMigor210 and GSE91061. The TRPS-based nomogram had a relatively good predictive value in evaluating the mortality risk at 1, 3 and 5 years in HCC. Overall, this study develops a TRPS by integrated bioinformatics analysis. This TRPS acted as an independent risk factor for the OS rate of HCC patients. It can screen for HCC patients who might benefit from immunotherapy, chemotherapy and targeted therapy.
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Affiliation(s)
- Dianqian Wang
- Health Science CenterNingbo UniversityNingboZhejiangChina
| | - Dongxiao Ding
- Department of Thoracic SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
| | - Junjie Ying
- Department of Thoracic SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
| | - Yunsheng Qin
- Department of Hepatobiliary and Pancreatic SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Department of Hepatobiliary SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
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Luo Y, Xie Y, Wu D, Wang B, Lu H, Wang Z, Quan Y, Han B. AL360181.1 promotes proliferation and invasion in colon cancer and is one of ten m6A-related lncRNAs that predict overall survival. PeerJ 2023; 11:e16123. [PMID: 37953780 PMCID: PMC10638913 DOI: 10.7717/peerj.16123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/27/2023] [Indexed: 11/14/2023] Open
Abstract
Background N6-methyladenosine (m6A) exerted a pivotal role in colon cancer. Nevertheless, the long non-coding RNAs (lncRNAs) associated with this process have yet to be elucidated. Methods The open-access data used for analysis was downloaded from The Cancer Genome Atlas (TCGA) database for analysis, employing the R software for computational evaluations. The RNA level of specific molecules was assessed using the quantitative real-time PCR. CCK8, colony formation and transwell assay were used to evaluate the proliferation, invasion and migration ability of colon cancer cells. Results Here, we identified the m6A regulators from TCGA data and subsequently pinpointed lncRNAs with a -Cor- > 0.3 and P < 0.05, categorizing them as m6A-associated lncRNAs. Moreover, we formulated a prognosis signature rooted in ten m6A-related lncRNAs, consisting of AL360181.1, PCAT6, SNHG26, AC016876.1, AC104667.2, AL114730.3, LINC02257, AC147067.1, AP006621.3 and AC009237.14. This signature exhibited notable predictive accuracy in gauging patient survival. Immune-related evaluations revealed varied immune cell infiltration patterns across different risk groups, with our findings suggesting superior immunotherapy response in low-risk patients. Biological enrichment analysis indicated that the high-risk patients had a higher activity of multiple carcinogenic pathways, including glycolysis. The previously unreported lncRNA, AL360181.1, displayed a connection to glycolytic activity and diminished survival rates, warranting further investigation. The result indicated that AL360181.1 was correlated with more aggressive clinical characteristics. Immune infiltration assessments found AL360181.1 to have a positive correlation with Tcm infiltration, but an inverse relationship with entities like Th2 cells, T cells, neutrophils and macrophages. Biological enrichment analysis indicated that the pathways of WNT/β-catenin, pancreas beta cells, hedgehog signaling and some metabolism pathways were upregulated in high AL360181.1 patients. In vitro experiments showed that AL360181.1 was upregulated in the colon cancer cells. Moreover, AL360181.1 significantly promotes the proliferation, invasion and migration of colon cancer cells. Conclusions Our results can provide direction for future studies on m6A-related lncRNA in colon cancer.
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Affiliation(s)
- Yi Luo
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yayun Xie
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dejun Wu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Bingyi Wang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Helei Lu
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiqiang Wang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjun Quan
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Han
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Wang Y, Yu T, Chen J, Zhao R, Diao M, Mei P, He S, Qiu W, Ye G, Jiang L, Xiao H, Liao Y. Immune characteristics analysis and construction of a four-gene prognostic signature for lung adenocarcinoma based on estrogen reactivity. BMC Cancer 2023; 23:1047. [PMID: 37907850 PMCID: PMC10619241 DOI: 10.1186/s12885-023-11415-y] [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: 03/03/2023] [Accepted: 09/17/2023] [Indexed: 11/02/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is a common type of malignant tumor with poor prognosis and high mortality. In our previous studies, we found that estrogen is an important risk factor for LUAD, and different estrogen statuses can predict different prognoses. Therefore, in this study, we constructed a prognostic signature related to estrogen reactivity to determine the relationship between different estrogen reactivities and prognosis. We downloaded the LUAD dataset from The Cancer Genome Atlas (TCGA) database, calculated the estrogen reactivity of each sample, and divided them into a high-estrogen reactivity group and a low-estrogen reactivity group. The difference in overall survival between the groups was significant. We also analyzed the status of immune cell infiltration and immune checkpoint expression between the groups. We analyzed the differential gene expression between the groups and screened four key prognostic factors by the least absolute shrinkage and selection operator (LASSO) regression and univariable and multivariable Cox regression. Based on the four genes, a risk signature was established. To a certain extent, the receiver operating characteristic (ROC) curve showed the predictive ability of the risk signature, which was further verified using the GSE31210 dataset. We also determined the role of estrogen in LUAD using an orthotopic mouse model. Additionally, we developed a predictive nomogram combining the risk signature with other clinical characteristics. In conclusion, our four-gene prognostic signature based on estrogen reactivity had prognostic value and can provide new insights into the development of treatment strategies for LUAD.
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Affiliation(s)
- Yangwei Wang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Yu
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaping Chen
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingxin Diao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Mei
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiwen He
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenlin Qiu
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guanchao Ye
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lijuan Jiang
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Xiao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yongde Liao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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10
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Shen C, Bi Y, Chai W, Zhang Z, Yang S, Liu Y, Wu Z, Peng F, Fan Z, Hu H. Construction and validation of a metabolism-associated gene signature for predicting the prognosis, immune landscape, and drug sensitivity in bladder cancer. BMC Med Genomics 2023; 16:264. [PMID: 37880682 PMCID: PMC10601123 DOI: 10.1186/s12920-023-01678-6] [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: 06/06/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023] Open
Abstract
Tumor Metabolism is strongly correlated with prognosis. Nevertheless, the prognostic and therapeutic value of metabolic-associated genes in BCa patients has not been fully elucidated. First, in this study, metabolism-related differential expressed genes DEGs with prognostic value in BCa were determined. Through the consensus clustering algorithm, we identified two molecular clusters with significantly different clinicopathological features and survival prognosis. Next, a novel metabolism-related prognostic model was established. Its reliable predictive performance in BCa was verified by multiple external datasets. Multivariate Cox analysis exhibited that risk score were independent prognostic factors. Interestingly, GSEA enrichment analysis of GO, KEGG, and Hallmark gene sets showed that the biological processes and pathways associated with ECM and collagen binding in the high-risk group were significantly enriched. Notely, the model was also significantly correlated with drug sensitivity, immune cell infiltration, and immunotherapy efficacy prediction by the wilcox rank test and chi-square test. Based on the 7 immune infiltration algorithm, we found that Neutrophils, Myeloid dendritic cells, M2 macrophages, Cancer-associated fibroblasts, etc., were more concentrated in the high-risk group. Additionally, in the IMvigor210, GSE111636, GSE176307, or our Truce01 (registration number NCT04730219) cohorts, the expression levels of multiple model genes were significantly correlated with objective responses to anti-PD-1/anti-PD-L1 immunotherapy. Finally, the expression of interested model genes were verified in 10 pairs of BCa tissues and para-carcinoma tissues by the HPA and real-time fluorescent quantitative PCR. Altogether, the signature established and validated by us has high predictive power for the prognosis, immunotherapy responsiveness, and chemotherapy sensitivity of BCa.
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Affiliation(s)
- Chong Shen
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Yuxin Bi
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Wang Chai
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Zhe Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Shaobo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Yuejiao Liu
- Department of Pharmacy, Zhu Xianyi Memorial Hospital of Tianjin Medical University, Tianjin, China
| | - Zhouliang Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China
| | - Fei Peng
- Department of Critical Care Medicine, the Peoples Hospital of Yuxi City, Yunnan, China
| | - Zhenqian Fan
- Department of Endocrinology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China.
| | - Hailong Hu
- Department of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Jianshan Street, Hexi, Tianjin, 300211, People's Republic of China.
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, Tianjin, 300211, China.
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11
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Cao F, Liu Y, Cheng Y, Wang Y, He Y, Xu Y. Multi-omics characteristics of tumor-associated macrophages in the tumor microenvironment of gastric cancer and their exploration of immunotherapy potential. Sci Rep 2023; 13:18265. [PMID: 37880233 PMCID: PMC10600170 DOI: 10.1038/s41598-023-38822-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/15/2023] [Indexed: 10/27/2023] Open
Abstract
The incidence and mortality rate of gastric cancer (GC) have remained high worldwide. Although some progress has been made in immunotargeted therapy, the treatment effect remains limited. With more attention has been paid to the immune potential of tumor-associated macrophages (TAMs), but the specific mechanisms of tumor immunity are still unclear. Thus, we screened marker genes in TAMs differentiation (MDMs) through single-cell RNA sequencing, and combined with GC transcriptome data from TCGA and GEO databases, the clinical and TME characteristics, prognostic differences, immune infiltration, and drug sensitivity among different subtypes of patients with GC in different data sets were analyzed. A prognostic model of GC was constructed to evaluate the prognosis and immunotherapy response of patients with GC. In this study, we extensively studied the mutations in MDMs such as CGN, S100A6, and C1QA, and found differences in the infiltration of immune cells and immune checkpoints including M2 TAMs, T cells, CD274, and CTLA4 in different GC subtypes. In the model, we constructed a predictive scoring system with high accuracy and screened out key MDMs-related genes associated with prognosis and M2 TAMs, among which VKORC1 may be involved in GC progression and iron death in tumor cells. Therefore, this study explores the therapeutic strategy of TAMs reprogramming in-depth, providing new ideas for the clinical diagnosis, treatment, and prognosis assessment of GC.
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Affiliation(s)
- Feng Cao
- Department of General Surgery, University Hospital RWTH Aachen, 52074, Aachen, Germany
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yanwei Liu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yunsheng Cheng
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yong Wang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
| | - Yan He
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
| | - Yanyan Xu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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12
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Wang Z, Ren H, Zhu G, Zhang L, Cao H, Chen B. High expression of CCDC69 is correlated with immunotherapy response and protective effects on breast cancer. BMC Cancer 2023; 23:974. [PMID: 37828454 PMCID: PMC10571395 DOI: 10.1186/s12885-023-11411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/16/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND As a molecule controlling the assembly of central spindles and recruitment of midzone component, coiled-coil domain-containing protein 69 (CCDC69) plays an important role in multiple cancers. Currently, the relationships between CCDC69 and immune infiltration or immunotherapy in breast cancer remain unclear. METHODS The expression and prognostic significance of CCDC69 in breast cancer were comprehensively analyzed by quantitative real-time PCR, immunohistochemical staining and various databases. The data source of differentially expressed genes, gene set enrichment analysis, and immune cell infiltration analysis came from The Cancer Genome Atlas (TCGA) database. Single-cell analysis based on IMMUcan database was used. The protein-protein interaction network was developed applying STRING, Cytoscape, CytoHubba, and GeneMANIA. TISIDB was employed in analyzing the CCDC69 co-expressed immune related genes. The correlations between CCDC69 and immunotherapy or immune-related scores were analyzed by CAMOIP and TISMO. Ctr-db was also used to conduct drug sensitivity analysis. RESULTS The mRNA of CCDC69 was downregulated in breast cancer tissues compared with normal tissues. Higher CCDC69 expression was associated with a better breast cancer prognosis. Enrichment analysis showed that the co-expression genes of CCDC69 were mainly related to immune-related pathways. The expression of CCDC69 was found to be positively correlated with multiple tumor-suppression immune infiltration cells, especially T cells and dendritic cells. Meanwhile, high CCDC69 expression can predict better immunotherapy responses when compared with low CCDC69 expression. After the interferon-gamma treatment, the CCDC69 expression was elevated in vitro. CCDC69 expression was a reliable predictor for the response status of two therapeutic strategies in breast cancer. CONCLUSIONS Our research revealed the clinical significance of CCDC69 in breast cancer and validated the critical roles of CCDC69 in the tumor immune infiltration and immunotherapy responses.
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Affiliation(s)
- Zhen Wang
- Department of Breast and Thyroid Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Huiyang Ren
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Guolian Zhu
- Department of Breast Surgery, The Fifth People's Hospital of Shenyang, Shenyang, China
| | - Lei Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China.
| | - Hongyi Cao
- Department of Pathology, The First Hospital of China Medical University and College of Basic Medical Sciences, Shenyang, China.
| | - Bo Chen
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China.
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13
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Gao T, Chen Y, Li M, Zhu K, Guo R, Tang Y, Huang S, Chen D. Nomogram for predicting survival in patients with mucinous breast cancer undergoing chemotherapy and surgery: a population-based study. Eur J Med Res 2023; 28:415. [PMID: 37817207 PMCID: PMC10563359 DOI: 10.1186/s40001-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The prognosis of patients with mucinous breast cancer (MuBC) is affected by several factors, but the low incidence of MuBC makes it difficult to conduct extensive and in-depth studies. This study was designed to establish a prognostic model and verify its accuracy in patients with MuBC after chemotherapy and surgery to help develop personalized treatment strategies. MATERIALS AND METHODS Patients with MuBC who underwent chemotherapy and surgery from 2004 to 2015 were identified in the Surveillance, Epidemiology, and End Results (SEER) database. The prognostic factors of patients with MuBC were investigated using a Cox proportional hazards regression analysis. Based on the identified factors, a nomogram was constructed to forecast the overall survival (OS) of patients at 3, 5, and 10 years. Internal (from SEER) and external (from Yunnan Cancer Center, YNCC) verification queues were used to verify the nomogram and demonstrate the predictive capacity of this model. RESULTS The study comprised 1668 MuBC patients from the SEER database and 107 from the YNCC. The nomogram included four characteristics: age, anatomical stage, surgical method, and radiotherapy. The concordance indices in the training, internal verification, and external verification queues were 0.680, 0.768, and 0.864, respectively. The calibration curves for the nomogram showed excellent agreement between the predictions and observations. This nomogram has good clinical application value according to the decision curve analysis. CONCLUSIONS The prognosis of patients with MuBC who have undergone chemotherapy and surgery can be forecasted using this nomogram, which would be beneficial to help create individualized treatment plans for the affected patients.
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Affiliation(s)
- Ting Gao
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
- The Department of Thyroid and Breast Surgery, Dali Bai Autonomous Prefecture People's Hospital, Dali, 671000, China
| | - Yuyuan Chen
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
- The Department of Thyroid and Breast Surgery, The Affiliated Hospital of Ningbo University Medical College, Ningbo, 315000, China
| | - Ming Li
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
| | - Keying Zhu
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
- The Department of General Surgery, Qujing Maternal and Child Health-Care Hospital, Qujing, 655000, China
| | - Rong Guo
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
| | - Yiyin Tang
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China
| | - Sheng Huang
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China.
| | - Dedian Chen
- The 2Nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Building 3, No. 519 Kunzhou Road, Kunming, 650118, China.
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14
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Wu R, Liu W, Yang Q, Zhang J, Hou P, Xiong J, Wu L, Li E. LncTUG1 promotes hepatocellular carcinoma immune evasion via upregulating PD-L1 expression. Sci Rep 2023; 13:16998. [PMID: 37813900 PMCID: PMC10562488 DOI: 10.1038/s41598-023-42948-8] [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: 02/02/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023] Open
Abstract
HCC is one of the most common malignant tumors worldwide. Although traditional treatment methods have been improved in recent years, the survival rate of HCC patients has not been significantly improved. Immunotherapy has shown extremely high clinical value in a variety of tumors. In this study, we found that TUG1 could regulate the expression of PD-L1 through JAK2/STAT3 to mediate immunosuppression. Here, The expression of TUG1 and PD-L1 in HCC tissues was evaluated through analysis of databases and verified in HCC tissue and HCC cancer cells by qRT-PCR. The effect of TUG1 on tumor immune escape was detected by coculture, and cell viability was detected with a CCK8 assay. The results demonstrated that TUG1 was closely associated with anticancer immunity. TUG1 and PD-L1 were highly expressed in HCC tissues and HCC cancer cells, and high expression of TUG1 and PD-L1 was related to the poor prognosis of HCC patients. In addition, knocking down TUG1 expression could reduce PD-L1 expression and enhance the cancer cell-killing capability of T cells. Downregulating TUG1 expression could also decrease the mRNA and protein expression of JAK2 and STAT3. To sum up, TUG1 and PD-L1 are overexpressed in patients with liver cancer and are related to the poor prognosis of these patients. Silencing TUG1 expression reduced the mRNA and protein expression of PD-L1 by affecting the JAK2/STAT3 pathway.
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Affiliation(s)
- Rongshou Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Weiwei Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Department of Hepatobiliary Surgery, Xinqiao Hospital, Third Military Medical University, 83 Xinqiao Main Street, Chongqing, 400000, People's Republic of China
| | - Qingping Yang
- Department of Assisted Reproductive, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jingling Zhang
- Department of Anesthesiology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Ping Hou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jianghui Xiong
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Linquan Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Enliang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
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15
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Chen J, Gao G, Zhang Y, Dai P, Huang Y. Comprehensive analysis and validation of SNX7 as a novel biomarker for the diagnosis, prognosis, and prediction of chemotherapy and immunotherapy response in hepatocellular carcinoma. BMC Cancer 2023; 23:899. [PMID: 37743471 PMCID: PMC10519071 DOI: 10.1186/s12885-023-11405-0] [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: 03/17/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Studies have demonstrated that Sorting nexin 7 (SNX7) functions as an anti-apoptotic protein in liver tissue and plays a crucial role in the survival of hepatocytes during early embryonic development. However, its diagnostic and prognostic value as well as the predictive value of chemotherapy and immunotherapy have not been reported in hepatocellular carcinoma (HCC). METHODS SNX7 mRNA expression and its diagnostic efficacy were examined in GEO datasets, and the findings were further confirmed in TCGA, ICGC cohorts, and cell lines. The protein level of SNX7 was determined using CPTAC and HPA databases, and the results were validated through immunohistochemistry (IHC). Survival analyses were performed in TCGA and ICGC cohorts, and the results were subsequently validated via Kaplan-Meier Plotter. The response to chemotherapy and immunotherapy was predicted via GDSC dataset and TIDE algorithm, respectively. R packages were employed to explore the relationship between SNX7 expression and immune infiltration, m6A modification, as well as the functional enrichment of differentially expressed genes (DEGs). RESULTS The expression of SNX7 at both mRNA and protein levels was significantly upregulated in HCC tissues. SNX7 exhibited superior diagnostic efficacy compared to AFP alone for HCC detection, and combining it with AFP improved the diagnostic accuracy for HCC. High SNX7 was associated with unfavorable outcomes, including poor overall survival, disease-specific survival, progression-free survival, and advanced pathological stage, in patients with HCC, and SNX7 was identified as an independent risk factor for HCC. Moreover, elevated SNX7 expression was positively correlated with increased sensitivity to various chemotherapy drugs, including sorafenib, while it was associated with resistance to immunotherapy in HCC patients. Correlation analysis revealed a relationship between SNX7 and multiple m6A-related genes and various immune cells. Finally, enrichment analysis demonstrated strong associations of SNX7 with critical biological processes, such as cell cycle regulation, cellular senescence, cell adhesion, DNA replication, and mismatch repair pathway in HCC. CONCLUSIONS Our study highlights the association of SNX7 with the immune microenvironment and its potential influence on HCC progression. SNX7 emerges as a promising novel biomarker for the diagnosis, prognosis, and prediction of response to chemotherapy and immunotherapy in patients with HCC.
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Affiliation(s)
- Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Gan Gao
- Departments of Clinical Laboratory of Liuzhou Hospital of Guangzhou Women and Children's Medical Center, Liuzhou, 545616, Guangxi, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Peng Dai
- Departments of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
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16
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Li J, Lv M, Huang Q, Hu R, Zhong X, Sun X, Feng W, Han Z, Ma M, Zhang W, Zhou X. FAT4 expression in peripheral blood mononuclear cells is associated with prognosis and immune cell infiltration in hepatocellular carcinoma. Sci Rep 2023; 13:15735. [PMID: 37735184 PMCID: PMC10514079 DOI: 10.1038/s41598-023-42560-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: 07/12/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Peripheral blood mononuclear cell (PBMC) genes reflect the host immune status and could be suitable for evaluating the prognosis of patients with hepatocellular carcinoma (HCC), for which a reliable biomarker is unavailable and the host immune responses to cancer cells. This study aimed to investigate prognostically relevant genes in HCC PBMCs and assessed whether their expression represents tumor immune infiltration. Gene expression in PBMCs from patients with advanced or terminal HCC who had survived or died was examined. Correlations among FAT atypical cadherin 4 (FAT4) expression, cancer immune characteristics, and infiltrated immune cell gene marker sets were analyzed. FAT4 expression was lower in the PBMCs of patients with advanced or terminal HCC who had died than that in patients who survived. Kaplan-Meier analysis indicated that FAT4 downregulation was associated with a relatively poor prognosis while overexpression was positively correlated with immune cell infiltration, several immune cell markers, and immune checkpoint expression. Hsa-miR-93-5p represented the most probable upstream microRNA of FAT4. Thus, upregulated FAT4 in PBMCs and HCC tissues might indicate a favorable prognosis and increased immune cell infiltration, while miRNA-93-5p could be a modulator of FAT4 expression. Collectively, these findings suggest novel immunotherapy targets for HCC.
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Affiliation(s)
- Jing Li
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
- Faculty of Chinese Medicine, Taipa, Macau University of Science and Technology, Macao, People's Republic of China
| | - Minling Lv
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Qi Huang
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Rui Hu
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
- Faculty of Chinese Medicine, Taipa, Macau University of Science and Technology, Macao, People's Republic of China
| | - Xin Zhong
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Xinfeng Sun
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Wenxing Feng
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Zhiyi Han
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - MengQing Ma
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Wei Zhang
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China
| | - Xiaozhou Zhou
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, People's Republic of China.
- Department of Liver Disease, The Fourth Clinical Medical School, Guangzhou University of Chinese Medicine, Shenzhen, 518033, People's Republic of China.
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Li N, Chen J, Yu W, Huang X. Construction of a novel signature based on immune-related lncRNA to identify high and low risk pancreatic adenocarcinoma patients. BMC Gastroenterol 2023; 23:312. [PMID: 37710166 PMCID: PMC10503173 DOI: 10.1186/s12876-023-02916-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/06/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma is one of the most lethal tumors in the world with a poor prognosis. Thus, an accurate prediction model, which identify patients within high risk of pancreatic adenocarcinoma is needed to adjust the treatment and elevate the prognosis of these patients. METHODS We obtained RNAseq data of The Cancer Genome Atlas (TCGA) pancreatic adenocarcinoma (PAAD) from UCSC Xena database, identified immune-related lncRNAs (irlncRNAs) by correlation analysis, and identified differential expressed irlncRNAs (DEirlncRNAs) between pancreatic adenocarcinoma tissues from TCGA and normal pancreatic tissues from TCGA and Genotype-Tissue Expression (GTEx). Further univariate and lasso regression analysis were performed to construct prognostic signature model. Then, we calculated the areas under curve and identified the best cut-off value to identify high- and low-risk patients with pancreatic adenocarcinoma. The clinical characteristics, immune cell infiltration, immunosuppressive microenvironment, and chemoresistance were compared between high- and low-risk patients with pancreatic adenocarcinoma. RESULTS We identified 20 DEirlncRNA pairs and grouped the patients by the best cut-off value. We proved that our prognostic signature model possesses a remarkable efficiency to predict prognosis of PAAD patients. The AUC for ROC curve was 0.905 for 1-year prediction, 0.942 for 2-year prediction, and 0.966 for 3-year prediction. Patients in high-risk group have poor survival rate and worse clinical characteristics. We also proved that patients in high-risk groups were in immunosuppressive status and may be resistant to immunotherapy. Anti-cancer drug evaluation was performed based on in-silico predated tool, such as paclitaxel, sorafenib, and erlotinib, may be suitable for PAAD patients in high-risk group. CONCLUSIONS Overall, our study constructed a novel prognostic risk model based on pairing irlncRNAs, exhibited a promising prediction value in patients with pancreatic adenocarcinoma. Our prognostic risk model may help distinguish PAAD patients suitable for medical treatments.
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Affiliation(s)
- Na Li
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jionghuang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weihua Yu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaoling Huang
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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18
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Xu C, Xie XL, Kang N, Jiang HQ. Evaluation of ITGB1 expression as a predictor of the therapeutic effects of immune checkpoint inhibitors in gastric cancer. BMC Gastroenterol 2023; 23:298. [PMID: 37667169 PMCID: PMC10478479 DOI: 10.1186/s12876-023-02930-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Gastric cancer (CC) is a disease with high incidence and mortality rate. Immunotherapy is an important method for gastric cancer while lack of effective predictor. Integrins play an important role in the development. We aimed to explore the predictive value of β1 integrin (ITGB1) as a predictor of immunnotherapy in gastric cancer. METHODS Differential expression analysis was conducted using the Gene Expression Profiling Interactive Analysis (GEPIA) 2.0 and GEO databases. GEPIA data were used to evaluate the prognostic value of ITGB1 in gastric cancer (GC). Transcriptomic and clinical data of GC and normal tissues were downloaded from The Cancer Genome Atlas database, and the TIMER database was used to evaluate the association between ITGB1 and immune infiltration. Time-dependent receiver operating characteristic (ROC) curve analysis was used to determine the prognostic value of ITGB1. To verify ITGB1 expression at the protein level, immunohistochemical staining was conducted. In addition, to analyze the correlation of ITGB1 with PD-1 and PD-L1, we examined levels of PD-1 and PD-L1 by IHC and determined the predictive value of ITGB1 for anti-PD-1 therapy in GC by ROC curve analysis. RESULTS Compared with normal tissues, analysis of GEPIA and data at protein levels showed significantly higher expression of ITGB1 in GC. In addition, higher expression of ITGB1 was associated with worse pathological G-staging and tumor T-staging, which suggested that ITGB1 is a risk factor for poor prognosis in GC. The level of ITGB1 expression was positively correlated with CD8 + T cells, neutrophils, macrophages, and dendritic cells. ITGB1 expression was also correlated with PD-L1 expression, and this was further verified at the protein level by immunohistochemical analysis. The area under the ROC curve was 0.808. CONCLUSION ITGB1 may be a promising prognostic biomarker and effective predictor for anti-PD-1 therapy in GC. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
- Chao Xu
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
- Handan Central Hospital, No.15, Zhonghua Road, Handan, 056001, Hebei Province, China
| | - Xiao-Li Xie
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Ning Kang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Hui-Qing Jiang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
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Zhang Y, Zhang T, Zhao Y, Wu H, Zhen Q, Zhu S, Hou S. Lactate dehydrogenase D serves as a novel biomarker for prognosis and immune infiltration in lung adenocarcinoma. BMC Cancer 2023; 23:759. [PMID: 37587457 PMCID: PMC10428593 DOI: 10.1186/s12885-023-11221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Lung cancer is reported to be the leading cause of death in males and females, globally. Increasing evidence highlights the paramount importance of Lactate dehydrogenase D (LDHD) in different types of cancers, though it's role in lung adenocarcinoma (LUAD) is still inadequately explored. In this study, we aimed to investigate and determine the relationship between LDHD and LUAD. METHODS The collection of the samples was guided by The Cancer Genome Atlas (TCGA) datasets and Gene Expression Omnibus (GEO). To ascertain various aspects around LDHD function, we analyzed different expression genes (DEGs), functional enrichment, and protein-protein interaction (PPI) networks. The predictive values for LDHD were collectively determined using the Kaplan-Meier method, Cox regression analysis, and a nomogram. Evaluation of the immune infiltration analysis was completed using Estimate and ssGSEA. The prediction of the immunotherapy response was based on TIDE and IPS. The LDHD expression levels in LUAD were validated through Western blot, qPCR, and immunohistochemistry methods. Wound healing and transwell assays were also performed to illustrate the aggressive features in LUAD cell lines. RESULTS The results showed that LDHD was generally downregulated in LUAD patients, with the low LDHD group presenting a decline in OS, DSS, and PFI. Enriched pathways, which include pyruvate metabolism, central carbon metabolism, and oxidative phosphorylation were observed through KEGG analysis. It was also noted that the expression of LDHD expression was inversely related to immune cell infiltration and typical checkpoints. The high LDHD group's response to immunotherapy was remarkable, particularly in CTAL4 + /PD1- therapy. In vitro studies revealed that the overexpression of LDHD caused tumor migration and invasion to be suppressed. CONCLUSION In conclusion, our study revealed that LDHD might be an effective predictor of prognosis and immune filtration, possibly leading to better choices for immunotherapy.
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Affiliation(s)
- Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Tianyi Zhang
- Research Center of Translational Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Yingdong Zhao
- Liaocheng Third People's Hospital, Liaocheng, Shandong, 252000, China
| | - Hongdi Wu
- Department of Fundamental, Air Force Communications NCO Academy, Dalian, Liaoning, 116000, China
| | - Qiang Zhen
- College of Pharmacy, Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Suwei Zhu
- Department of Critical-Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
| | - Shaoshuai Hou
- Department of Pharmacy, Tengzhou Central People's Hospital, Tengzhou, Shandong, 277500, China.
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20
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Wang X, Peng H, Zhang G, Li Z, Du Z, Peng B, Cao P. ADNP is associated with immune infiltration and radiosensitivity in hepatocellular carcinoma for predicting the prognosis. BMC Med Genomics 2023; 16:178. [PMID: 37525242 PMCID: PMC10391866 DOI: 10.1186/s12920-023-01592-x] [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: 03/04/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most lethal diseases due to its high faculty of invasiveness and metastasis. Activity-dependent neuroprotective protein (ADNP) has been regarded as an oncogene in bladder cancer and ovarian cancer. However, the role of ADNP in the regulation of tumor immune response, development, and treatment resistance in HCC remains unknown and is worth exploring. METHODS The correlation between ADNP and prognosis, immune cell infiltration, immune checkpoints, chemokines, tumor mutation burden, microsatellite instability, and genomic mutation of pan-cancer cohorts in The Cancer Genome Atlas was analyzed. ADNP expression in HCC cell lines, HCC and the adjacent normal tissues was measured by western blotting and immunochemistry. Nomogram was constructed to predict the survival of patients with HCC based on the ADNP expression and significant clinical characteristics. The potential biological functions and impacts on radiotherapy of ADNP in HCC cell lines were verified by vitro experiments. RESULTS ADNP was upregulated in most cancers and patients with elevated ADNP expression were related to poor survival in several types of cancers including HCC. Functional enrichment analysis showed ADNP participated in the pathways correlated with coagulation cascades and DNA double strand break repair. Further, ADNP exhibited a negative correlation with the immune score, stromal score, estimated score, and chemokines, and a positive correlation with cancer-associated fibroblasts, myeloid-derived suppressor cells, neutrophils, regulatory T cells, and endothelial cells. Immunochemistry and western blotting results demonstrated ADNP was up-regulated in HCC. Vitro experiments verified that suppressing the ADNP expression significantly inhibited the proliferation, invasion and migration and elevated the radiosensitivity via decreasing DNA damage repair in HCC. CONCLUSION ADNP might play an oncogene and immunosuppression role in tumor immune infiltration and response, thus influencing the prognosis. Its downregulation could attenuate the proliferation, invasion, migration, radioresistance of HCC. Our results indicated the potential of ADNP as a promising biomarker to predict the survival of HCC patients, providing a theoretical basis for novel integrative strategies.
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Affiliation(s)
- Xuan Wang
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Honghua Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Ganghua Zhang
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Zeyuan Li
- Department of General Practice, Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Zhangyan Du
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Bin Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Peiguo Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China.
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21
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Lun W, Luo C. Second primary colorectal cancer in adults: a SEER analysis of incidence and outcomes. BMC Gastroenterol 2023; 23:253. [PMID: 37495987 PMCID: PMC10373234 DOI: 10.1186/s12876-023-02893-2] [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: 04/11/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND At present, there was no large epidemiological study exploring the actual incidence and survival of second primary colorectal cancer (spCRC). The different characteristics and survival of patients with spCRC and initial primary colorectal cancer (ipCRC) still need to be elucidated. In addition, the factors leading to different survival status of spCRC and ipCRC were still unclear. Our study plan to explore the annual incidence trend of spCRC as well as the factors influencing the occurrence and survival outcome of spCRC. METHODS This cohort study analyzed the data of 4680 spCRC patients and 330,937 initial primary colorectal cancer (ipCRC) patients. Whether patients had spCRC and whether spCRC patients survived or died were regarded as outcomes. The annual incidence of spCRC from 2004 to 2016 was analyzed by Jointpoint regression analysis. The truncation points were found, and the annual percentage change (APC) of each segment was calculated to explore the trend of spCRC change in the United States. Univariate and multivariable cox regression analyses were conducted to identify factors associated with the occurrence and prognosis of spCRC patients. RESULTS The total incidence of spCRC was decreased during 2000-2016 on the whole. The overall incidence of spCRC was lowered in both males and females despite 2013-2014, in the left colon, right colon, rectum and others. The incidence of spCRC was decreased in both 18-49 years' people and ≥ 50 years' people during 2000-2016, and the incidence of spCRC in the ≥ 50 years' people group was higher than those of 18-49 years. Insured (OR = 0.867 (0.778-0.966), initial primary site of other digestive (OR = 0.46, 95%CI: 0.42-0.50), rectum (OR = 0.74, 95%CI: 0.66-0.82), or right colon (OR = 0.73, 95%CI: 0.68-0.79), N 1 stage (OR = 0.87, 95%CI: 0.76-0.99), M 1 stage (OR = 0.49, 95%CI: 0.30-0.80), AJCC II stage (OR = 0.70, 95%CI: 0.60-0.82), AJCC III stage (OR = 0.69, 95%CI: 0.56-0.84), and radiation (OR = 0.69, 95%CI: 0.57-0.83) were associated with the risk of spCRC. At the end of follow-up, 2,246 spCRC patients were survived and 2,434 spCRC patients were dead. Patients with spCRC had poor survival probability than patients with ipCRC. Older age (HR = 1.02, 95%CI: 1.02-1.03), male (HR = 1.13, 95%CI: 1.04-1.23), Black (HR = 1.20, 95%CI: 1.06-1.35), uninsured (HR = 1.36, 95%CI: 1.16-1.59), Signet ring cell carcinoma (HR = 1.64, 95%CI: 1.19-2.25), T4 stage (HR = 1.63, 95%CI: 1.32-2.01), N2 stage (HR = 1.36, 95%CI: 1.08-1.72), M1 stage (HR = 4.51, 95%CI: 2.00-10.18), AJCC III (HR = 1.47, 95%CI: 1.08-1.98), and radiation (HR = 1.82, 95%CI: 1.43-2.33) were associated with increased risk of mortality in spCRC patients. CONCLUSION The incidence of spCRC was decreased except in people with initial primary tumor grade IV and those aged 15-39 years. The overall survival of spCRC patients was lower than ipCRC patients. Cancer patients with older age, high tumor grade, TNM stage, and AJCC stage should be caution to the occurrence of spCRC and timely interventions should be provided for spCRC patients to improve their outcomes.
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Affiliation(s)
- Weijian Lun
- Gastroenterology department of The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, 120# Guidan Road, Nanhai District, Foshan, 528200, Guangdong Province, China.
| | - Canhua Luo
- Gastroenterology department of The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, 120# Guidan Road, Nanhai District, Foshan, 528200, Guangdong Province, China
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Zhang C, Gu L, Xiao J, Jin F. Knockdown of RBM15 inhibits tumor progression and the JAK-STAT signaling pathway in cervical cancer. BMC Cancer 2023; 23:684. [PMID: 37474926 PMCID: PMC10360283 DOI: 10.1186/s12885-023-11163-z] [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: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND RNA binding motif protein 15 (RBM15), a writer of N6-methyladenosine (m6A) methylation, contributes significantly to the development of various tumors. However, the function of RBM15 in cervical cancer (CC) has not been determined. METHODS Based on the GSE9750, GSE63514, and m6A datasets, m6A-related differentially expressed genes (DEGs) were screened out. The hub genes were identified by generating a Protein-Protein Interaction (PPI) network. RT-qPCR was conducted to assess the mRNA expression of hub genes. CCK8, scratch wound healing, and transwell assays were utilized to examine the influence of RBM15 on HeLa and SiHa cells. Tumor xenograft models were used to assess the effects of RBM15 on tumorigenesis. A mechanistic analysis of RBM15 in CC tumors was conducted using the GeneCards and Coxpresdb databases, followed by a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the pathway-related genes were subsequently validated using Western blotting. RESULTS Five DEGs were screened, including WTAP, RBM15, CBLL1, and YTHDC2. Among them, WTAP, RBM15, CBLL1, and YTHDC2 were hub genes and can be used as biomarkers for CC. RBM15 expression was considerably increased, while WTAP, CBLL1, and YTHDC2 were significantly downregulated. Knockdown of RBM15 significantly suppressed the proliferation, invasion, and migration of CC cells and tumorigenesis. Moreover, knockdown of RBM15 significantly reduced the expression levels of proteins related to the JAK-STAT pathway. CONCLUSIONS Knockdown of RBM15 inhibited the progression of CC cells, which probably by inhibiting the JAK-STAT pathway pathway.
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Affiliation(s)
- Chunnian Zhang
- Department of Gynecology, Ganzhou People's Hospital, No. 16, Meiguan Avenue, Ganzhou City, 341000, Jiangxi Province, China.
| | - Liqin Gu
- Department of Gynecology, Ganzhou People's Hospital, No. 16, Meiguan Avenue, Ganzhou City, 341000, Jiangxi Province, China
| | - Juan Xiao
- Department of Gynecology, Ganzhou People's Hospital, No. 16, Meiguan Avenue, Ganzhou City, 341000, Jiangxi Province, China
| | - Feng Jin
- Department of Gynecology, Ganzhou People's Hospital, No. 16, Meiguan Avenue, Ganzhou City, 341000, Jiangxi Province, China
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Huang H, Qiu D, Zhou Z, Wu B, Shao L, Pu Y, He T, Wu Y, Cui D, Zhong F. A pan-cancer analysis for the oncogenic role of cyclin-dependent kinase inhibitor 1B in human cancers. Discov Oncol 2023; 14:126. [PMID: 37432583 DOI: 10.1007/s12672-023-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Human health and life are threatened by cancer with high morbidity and mortality worldwide. In many experiments, CDKN1B level is associated with cancer risk, Nevertheless, no pan-cancer analysis has been conducted on CDKN1B in human cancers. METHODS With the help of bioinformatics, a pan-cancer analysis was conducted on the expression levels of CDKN1B in cancer tissues and adjacent tissues from the TCGA, CPTAC and GEO databases. The CDKN1B expression levels in tumor patients was further validated using immunohistochemistry (IHC) and quantitative real-time PCR. RESULTS In the study, we first investigated the cancer-related roles of CDKN1B's in 40 tumors with malignancy. The CDKN1B gene encodes the p27Kip1 protein, which can block the production cyclin-dependent kinase (CDK), which is obviously related to the function and survival of cancer cells and alters the prognosis of cancer patients. Furthermore, CDKN1B function requires both protein processing and RNA metabolism. Additionally, the elevated expression of the CDKN1B gene and protein was validated in several cancer tissues from the patients. CONCLUSIONS These results showed that the levels of CDKN1B were considerably different in a number of cancer tissues, offering a potential future target for cancer therapy.
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Affiliation(s)
- Hao Huang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Duoliang Qiu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhengyang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Biaobiao Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lening Shao
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuwei Pu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Tengfei He
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yongyou Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Fengyun Zhong
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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Zhou F, Chen L, Lu P, Cao Y, Deng C, Liu G. An integrative bioinformatics investigation and experimental validation of chromobox family in diffuse large B-cell lymphoma. BMC Cancer 2023; 23:641. [PMID: 37430195 DOI: 10.1186/s12885-023-11108-6] [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: 11/10/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is one of the most aggressive malignant tumors. Chromobox (CBX) family plays the role of oncogenes in various malignancies. METHODS The transcriptional and protein levels of CBX family were confirmed by GEPIA, Oncomine, CCLE, and HPA database. Screening of co-expressed genes and gene function enrichment analysis were performed by GeneMANIA and DAVID 6.8. The prognostic value, immune cell infiltration and drug sensitivity analysis of CBX family in DLBCL were performed by Genomicscape, TIMER2.0, and GSCALite database. Confirmatory Tests of CBX family protein expression in DLBCL were performed by immunohistochemistry. RESULTS The mRNA and protein expressions of CBX1/2/3/5/6 were higher in DLBCL tissues than control groups. Enrichment analysis showed that the functions of CBX family were mainly related to chromatin remodeling, methylation-dependent protein binding, and VEGF signaling pathway. The high mRNA expressions of CBX2/3/5/6 were identified to be associated with short overall survival (OS) in DLBCL patients. Multivariate COX regression indicated that CBX3 was independent prognostic marker. Immune infiltration analysis revealed that the mRNA expressions of CBX family (especially CBX1, CBX5, and CBX6) in DLBCL were significantly correlated with the infiltration of most immune cells (including B cells, CD8 + T cells, CD4 + T cells, neutrophils, monocytes, macrophages, and Treg cells). Meanwhile, there was a strong correlation between the expression levels of CBX1/5/6 and surface markers of immune cells, such as the widely studied PVR-like protein receptor/ligand and PDL-1 immune checkpoint. Notably, our study found that DLBCL cells with CBX1 over-expression were resistant to the common anti-tumor drugs, but CBX2/5 had two polarities. Finally, we confirmed the higher expressions of CBX1/2/3/5/6 in DLBCL tissues compared with control groups by immunohistochemistry. CONCLUSION We provided a detailed analysis of the relationship between the CBX family and the prognosis of DLBCL. Distinguished from other studies, We found that high mRNA expressions of CBX2/3/5/6 were associated with poor prognosis in DLBCL patients, and Multivariate COX regression indicated that CBX3 was independent prognostic marker. Besides, our study also found an association between the CBX family and anti-tumour drug resistance, and provided a relationship between CBX family expression and immune cell infiltration.
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Affiliation(s)
- Fenling Zhou
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Lu Chen
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Peng Lu
- Departpent of Vascular Surgery, The Second Xiangya Hospital, Central South University, Hunan Province, No. 139, Renmin Road, Changsha, China
| | - Yuli Cao
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Cuilan Deng
- Department of Hematology, First Affiliated Hospital, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Gexiu Liu
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China.
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Fu J, Du F, Tian T, Huang H, Zhang L, Li D, Liu Y, Zhang D, Gao L, Zheng T, Liu Y, Zhao Y. Development and validation of prognostic nomograms based on De Ritis ratio and clinicopathological features for patients with stage II/III colorectal cancer. BMC Cancer 2023; 23:620. [PMID: 37400788 DOI: 10.1186/s12885-023-11125-5] [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: 04/25/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Metabolic derangements and systemic inflammation are related to the progression of colorectal cancer (CRC) and the prognoses of these patients. The survival of stage II and III CRC patients existed considerable heterogeneity highlighting the urgent need for new prediction models. This study aimed to develop and validate prognostic nomograms based on preoperative serum liver enzyme as well as evaluate the clinical utility. METHODS A total of 4014 stage II/III primary CRC patients pathologically diagnosed from January 2007 to December 2013 were included in this study. These patients were randomly divided into a training set (n = 2409) and a testing set (n = 1605). Univariate and multivariate Cox analyses were used to select the independent factors for predicting overall survival (OS) and disease-free survival (DFS) of stage II/III CRC patients. Next, nomograms were constructed and validated to predict the OS and DFS of individual CRC patients. The clinical utility of nomograms, tumor-node-metastasis (TNM), and the American Joint Committee on Cancer (AJCC) system was evaluated using time-dependent ROC and decision curve analyses. RESULTS Among seven preoperative serum liver enzyme markers, aspartate aminotransferase-to-alanine aminotransferase ratio (De Ritis ratio) was identified as an independent factor for predicting both OS and DFS of stage II/III CRC patients. The nomograms incorporated De Ritis ratio and significant clinicopathological features achieved good accuracy in terms of OS and DFS prediction, with C-index of 0.715 and 0.692, respectively. The calibration curve showed good agreement between prediction by nomogram and actual observation. The results of time-dependent ROC and decision curve analyses suggested that the nomograms had improved discrimination and greater clinical benefits compared with TNM and AJCC staging. CONCLUSIONS De Ritis ratio was an independent predictor in predicting both the OS and DFS of patients with stage II/III CRC. Nomograms based on De Ritis ratio and clinicopathological features showed better clinical utility, which is expected to help clinicians develop appropriate individual treatment strategies for patients with stage II /III CRC.
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Affiliation(s)
- Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, China
| | - Fenqi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, 150 Haping Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Tian Tian
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Lijing Gao
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, 150 Haping Road, Harbin, 150081, Heilongjiang Province, People's Republic of China.
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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Zhao Z, Sun C, Hou J, Yu P, Wei Y, Bai R, Yang P. Identification of STEAP3-based molecular subtype and risk model in ovarian cancer. J Ovarian Res 2023; 16:126. [PMID: 37386521 DOI: 10.1186/s13048-023-01218-x] [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: 03/29/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most common malignancies in women. It has a poor prognosis owing to its recurrence and metastasis. Unfortunately, reliable markers for early diagnosis and prognosis of OC are lacking. Our research aimed to investigate the value of the six-transmembrane epithelial antigen of prostate family member 3 (STEAP3) as a prognostic predictor and therapeutic target in OC using bioinformatics analysis. METHODS STEAP3 expression and clinical data were acquired from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO). Unsupervised clustering was used to identify molecular subtypes. Prognosis, tumor immune microenvironment (TIME), stemness indexes, and functional enrichment analysis were compared between two definite clusters. Through the least absolute shrinkage and selection operator (LASSO) regression analysis, a STEAP3-based risk model was developed, and the predictive effectiveness of this signature was confirmed using GEO datasets. A nomogram was used to predict the survival possibility of patients. Additionally, TIME, tumor immune dysfunction and exclusion (TIDE), stemness indexes, somatic mutations, and drug sensitivity were evaluated in different risk groups with OC. STEAP3 protein expression was detected using immunohistochemistry (IHC). RESULTS STEAP3 displayed marked overexpression in OC. STEAP3 is an independent risk factor for OC. Based on the mRNA levels of STEAP3-related genes (SRGs), two distinct clusters were identified. Patients in the cluster 2 (C2) subgroup had a considerably worse prognosis, higher immune cell infiltration, and lower stemness scores. Pathways involved in tumorigenesis and immunity were highly enriched in the C2 subgroup. A prognostic model based on 13 SRGs was further developed. Kaplan-Meier analysis indicated that the overall survival (OS) of high-risk patients was poor. The risk score was significantly associated with TIME, TIDE, stemness indexes, tumor mutation burden (TMB), immunotherapy response, and drug sensitivity. Finally, IHC revealed that STEAP3 protein expression was noticeably elevated in OC, and overexpression of STEAP3 predicted poor OS and relapse-free survival (RFS) of patients. CONCLUSION In summary, this study revealed that STEAP3 reliably predicts patient prognosis and provides novel ideas for OC immunotherapy.
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Affiliation(s)
- Zouyu Zhao
- First Affiliated Hospital, Shihezi University, Shihezi, China
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Chongfeng Sun
- First Affiliated Hospital, Shihezi University, Shihezi, China
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Jishuai Hou
- First Affiliated Hospital, Shihezi University, Shihezi, China
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Panpan Yu
- First Affiliated Hospital, Shihezi University, Shihezi, China
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Yan Wei
- First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Rui Bai
- First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Ping Yang
- First Affiliated Hospital, Shihezi University, Shihezi, China.
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China.
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Lin CF, Chen ZW, Kang FP, Hu JF, Huang L, Liao CY, Lai JL, Huang Y, Wang ZW, Tian YF, Chen S. Analyzing molecular typing and clinical application of immunogenic cell death-related genes in hepatocellular carcinoma. BMC Cancer 2023; 23:522. [PMID: 37291495 DOI: 10.1186/s12885-023-10992-2] [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: 02/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is considered one of the most common cancers, characterized by low early detection and high mortality rates, and is a global health challenge. Immunogenic cell death (ICD) is defined as a specific type of regulated cell death (RCD) capable of reshaping the tumor immune microenvironment by releasing danger signals that trigger immune responses, which would contribute to immunotherapy. METHODS The ICD gene sets were collected from the literature. We collected expression data and clinical information from public databases for the HCC samples in our study. Data processing and mapping were performed using R software to analyze the differences in biological characteristics between different subgroups. The expression of the ICD representative gene in clinical specimens was assessed by immunohistochemistry, and the role of the representative gene in HCC was evaluated by various in vitro assays, including qRT-PCR, colony formation, and CCK8 assay. Lasso-Cox regression was used to screen prognosis-related genes, and an ICD-related risk model (ICDRM) was constructed. To improve the clinical value of ICDRM, Nomograms and calibration curves were created to predict survival probabilities. Finally, the critical gene of ICDRM was further investigated through pan-cancer analysis and single-cell analysis. RESULTS We identified two ICD clusters that differed significantly in terms of survival, biological function, and immune infiltration. As well as assessing the immune microenvironment of tumors in HCC patients, we demonstrate that ICDRM can differentiate ICD clusters and predict the prognosis and effectiveness of therapy. High-risk subpopulations are characterized by high TMB, suppressed immunity, and poor survival and response to immunotherapy, whereas the opposite is true for low-risk subpopulations. CONCLUSIONS This study reveals the potential impact of ICDRM on the tumor microenvironment (TME), immune infiltration, and prognosis of HCC patients, but also a potential tool for predicting prognosis.
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Affiliation(s)
- Cai-Feng Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Zhi-Wen Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Feng-Ping Kang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Jian-Fei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Long Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Cheng-Yu Liao
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Jian-Lin Lai
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Yi Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Zu-Wei Wang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China.
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China.
| | - Yi-Feng Tian
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China.
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China.
- Department of Hepatobiliary Surgery, Shengli Clinical Medical College of Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, PR China.
| | - Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian Province, People's Republic of China.
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China.
- Department of Hepatobiliary Surgery, Shengli Clinical Medical College of Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, PR China.
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Zhao Y, Liang X, Duan X, Zhang C. Exploring the prognostic function of TMB-related prognostic signature in patients with colon cancer. BMC Med Genomics 2023; 16:116. [PMID: 37237274 DOI: 10.1186/s12920-023-01555-2] [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: 02/27/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tumor mutation burden (TMB) level is identified as a useful predictor in multiple tumors including colon adenocarcinoma (COAD). However, the function of TMB related genes has not been explored previously. In this study, we obtained patients' expression and clinical data from The Cancer Genome Atlas (TCGA) and the National Center for Biotechnology Information (NCBI). TMB genes were screened and subjected to differential expression analysis. Univariate Cox and LASSO analyses were utilized to construct the prognostic signature. The efficiency of the signature was tested by using a receiver operating characteristic (ROC) curve. A nomogram was further plotted to assess the overall survival (OS) time of patients with COAD. In addition, we compared the predictive performance of our signature with other four published signatures. Functional analyses indicated that patients in the low-risk group have obviously different enrichment of tumor related pathways and tumor infiltrating immune cells from that of high-risk patients. Our findings suggested that the ten genes' prognostic signature could exert undeniable prognostic functions in patients with COAD, which might provide significant clues for the development of personalized management of these patients.
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Affiliation(s)
- Yan Zhao
- Department of Nuclear Medicine, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China
| | - Xiaolong Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Xudong Duan
- Oncology Department, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China.
| | - Chengli Zhang
- Department of Nuclear Medicine, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China.
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29
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Man Y, Dai C, Guo Q, Jiang L, Shi Y. A novel PD-1/PD-L1 pathway molecular typing-related signature for predicting prognosis and the tumor microenvironment in breast cancer. Discov Oncol 2023; 14:59. [PMID: 37154982 PMCID: PMC10167089 DOI: 10.1007/s12672-023-00669-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Currently, the development of breast cancer immunotherapy based on the PD-1/PD-L1 pathway is relatively slow, and the specific mechanism affecting the immunotherapy efficacy in breast cancer is still unclear. METHODS Weighted correlation network analysis (WGCNA) and the negative matrix factorization (NMF) were used to distinguish subtypes related to the PD-1/PD-L1 pathway in breast cancer. Then univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression were used to construct the prognostic signature. A nomogram was established based on the signature. The relationship between the signature gene IFNG and breast cancer tumor microenvironment was analyzed. RESULTS Four PD-1/PD-L1 pathway-related subtypes were distinguished. A prognostic signature related to PD-1/PD-L1 pathway typing was constructed to evaluate breast cancer's clinical characteristics and tumor microenvironment. The nomogram based on the RiskScore could be used to accurately predict breast cancer patients' 1-year, 3-year, and 5-year survival probability. The expression of IFNG was positively correlated with CD8+ T cell infiltration in the breast cancer tumor microenvironment. CONCLUSION A prognostic signature is constructed based on the PD-1/PD-L1 pathway typing in breast cancer, which can guide the precise treatment of breast cancer. The signature gene IFNG is positively related to CD8+ T cell infiltration in breast cancer.
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Affiliation(s)
- Yuxin Man
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Chao Dai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Qian Guo
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, 610072, Sichuan, China.
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30
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Zhang SM, Shen C, Gu J, Li J, Jiang X, Wu Z, Shen A. Succinylation-associated lncRNA signature to predict the prognosis of colon cancer based on integrative bioinformatics analysis. Sci Rep 2023; 13:7366. [PMID: 37147453 PMCID: PMC10163232 DOI: 10.1038/s41598-023-34503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
Colon cancer (CC) has a poor 5-year survival rate though the treatment techniques and strategies have been improved. Succinylation and long noncoding RNAs (lncRNAs) have prognostic value for CC patients. We analyzed and obtained succinylation-related lncRNA by co-expression in CC. A novel succinylation-related lncRNA model was developed by univariate and Least absolute shrinkage and selection operator (Lasso) regression analysis and we used principal component analysis (PCA), functional enrichment annotation, tumor immune environment, drug sensitivity and nomogram to verify the model, respectively. Six succinylation-related lncRNAs in our model were finally confirmed to distinguish the survival status of CC and showed statistically significant differences in training set, testing set, and entire set. The prognosis of with this model was associated with age, gender, M0 stage, N2 stage, T3 + T4 stage and Stage III + IV. The high-risk group showed a higher mutation rate than the low-risk group. We constructed a model to predict overall survival for 1-, 3-, and 5-year with AUCs of 0.694, 0.729, and 0.802, respectively. The high-risk group was sensitive to Cisplatin and Temozolomide compounds. Our study provided novel insights into the value of the succinylation-related lncRNA signature as a predictor of prognosis, which had high clinical application value in the future.
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Affiliation(s)
- Si-Ming Zhang
- Cancer Research Center, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Cheng Shen
- Department of Computer Science and Engineering, Tandon School of Engineering, New York University, Brooklyn, USA
| | - Jue Gu
- Affiliated Hospital of Nantong University, Nantong, China
| | - Jing Li
- Cancer Research Center, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xiaohui Jiang
- Department of General Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Zhijun Wu
- Department of Oncology, Nantong Second People's Hospital, Nantong, China
| | - Aiguo Shen
- Cancer Research Center, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province, China.
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Establishment and Validation of a Machine Learning Prediction Model Based on Big Data for Predicting the Risk of Bone Metastasis in Renal Cell Carcinoma Patients. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5676570. [PMID: 36226243 PMCID: PMC9550489 DOI: 10.1155/2022/5676570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022]
Abstract
Purpose Since the prognosis of renal cell carcinoma (RCC) patients with bone metastasis (BM) is poor, this study is aimed at using big data to build a machine learning (ML) model to predict the risk of BM in RCC patients. Methods A retrospective study was conducted on 40,355 RCC patients in the SEER database from 2010 to 2017. LASSO regression and multivariate logistic regression analysis was performed to determine independent risk factors of RCC-BM. Six ML algorithm models, including LR, GBM, XGB, RF, DT, and NBC, were used to establish risk models for predicting RCC-BM. The prediction performance of ML models was weighed by 10-fold cross-validation. Results The study investigated 40,355 patients diagnosed with RCC in the SEER database, where 1,811 (4.5%) were BM patients. Independent risk factors for BM were tumor grade, T stage, N stage, liver metastasis, lung metastasis, and brain metastasis. Among the RCC-BM risk prediction models established by six ML algorithms, the XGB model showed the best prediction performance (AUC = 0.891). Therefore, a network calculator based on the XGB model was established to individually assess the risk of BM in patients with RCC. Conclusion The XGB risk prediction model based on the ML algorithm performed a good prediction effect on BM in RCC patients.
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