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Afshari AR, Sanati M, Ahmadi SS, Kesharwani P, Sahebkar A. Harnessing the capacity of phytochemicals to enhance immune checkpoint inhibitor therapy of cancers: A focus on brain malignancies. Cancer Lett 2024; 593:216955. [PMID: 38750720 DOI: 10.1016/j.canlet.2024.216955] [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: 04/05/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
Brain cancers, particularly glioblastoma multiforme (GBM), are challenging health issues with frequent unmet aspects. Today, discovering safe and effective therapeutic modalities for brain tumors is among the top research interests. Immunotherapy is an emerging area of investigation in cancer treatment. Since immune checkpoints play fundamental roles in repressing anti-cancer immunity, diverse immune checkpoint inhibitors (ICIs) have been developed, and some monoclonal antibodies have been approved clinically for particular cancers; nevertheless, there are significant concerns regarding their efficacy and safety in brain tumors. Among the various tools to modify the immune checkpoints, phytochemicals show good effectiveness and excellent safety, making them suitable candidates for developing better ICIs. Phytochemicals regulate multiple immunological checkpoint-related signaling pathways in cancer biology; however, their efficacy for clinical cancer immunotherapy remains to be established. Here, we discussed the involvement of immune checkpoints in cancer pathology and summarized recent advancements in applying phytochemicals in modulating immune checkpoints in brain tumors to highlight the state-of-the-art and give constructive prospects for future research.
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Affiliation(s)
- Amir R Afshari
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran; Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mehdi Sanati
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran; Experimental and Animal Study Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Seyed Sajad Ahmadi
- Department of Ophthalmology, Khatam-Ol-Anbia Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
| | - Amirhossein Sahebkar
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Gu Y, Ma E, Jiang S, Shan Z, Xia G, Ma R, Fu J, Wang Z. Immune- and metabolism-related gene signature analysis uncovers the prognostic and immune microenvironments of hepatocellular carcinoma. J Cancer Res Clin Oncol 2024; 150:311. [PMID: 38896142 PMCID: PMC11186947 DOI: 10.1007/s00432-024-05849-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Metabolic reprogramming is an emerging hallmark that influences the tumour microenvironment (TME) by regulating the behavior of cancer cells and immune cells. The relationship between metabolism and immunity remains elusive. The purpose of this study was to explore the predictive value of immune- and metabolism-related genes in hepatocellular carcinoma (HCC) and their intricate interplay with TME. METHODS We established the immune- and metabolism-related signature (IMRPS) based on the LIHC cohort from The Cancer Genome Atlas (TCGA) dataset. Kaplan-Meier analysis, receiver operating characteristic (ROC) curve analysis and Cox regression analysis confirmed the prognostic value of IMRPS. We investigated differences in immune cell infiltration, clinical features, and therapeutic response between risk groups. The quantitative real-time PCR (qPCR) was used to confirm the expression of signature genes. Immunohistochemical staining was performed to evaluate immune infiltration features in HCC tissue samples. We conducted cell experiments including gene knockout, cell counting kit-8 (CCK-8), and flow cytometry to explore the role of the IMRPS key gene UCK2 in HCC. RNA-seq was used to further investigate the potential underlying mechanism involved. RESULTS The IMRPS, composed of four genes, SMS, UCK2, PFKFB4 and MAPT, exhibited significant correlations with survival, immune cell infiltration, clinical features, immune checkpoints and therapeutic response. The IMRPS was shown to be an excellent predictor of HCC prognosis. It could stratify patients appropriately and characterize the TME accurately. The high-risk HCC group exhibited an immunosuppressive microenvironment with abundant M2-like macrophage infiltration, which was confirmed by the immunohistochemistry results. The results of qPCR revealed that the expression of signature genes in 20 HCC tissues was significantly greater than that in adjacent normal tissues. After the key gene UCK2 was knocked out, the proliferation of the Huh7 cell line was significantly inhibited, and monocyte-derived macrophages polarized towards an M1-like phenotype in the coculture system. RNA-seq and GSEA suggested that the phenotypes were closely related to the negative regulation of growth and regulation of macrophage chemotaxis. CONCLUSIONS This study established a new IMRS for the accurate prediction of patient prognosis and the TME, which is also helpful for identifying new targets for the treatment of HCC.
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Affiliation(s)
- Yange Gu
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Ensi Ma
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Shengran Jiang
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | | | - Guixi Xia
- Bengbu Medical University, Bengbu, China
| | - Rui Ma
- Bengbu Medical University, Bengbu, China
| | - Jiaqi Fu
- Bengbu Medical University, Bengbu, China
| | - Zhengxin Wang
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Organ Transplantation, Fudan University, Shanghai, China.
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Baek MH, Chen L, Tekin C, Cristescu R, Jin XY, Shao C, Ihm SY, Jelinic P, Park JY. Prevalence and prognostic value of PD-L1 expression and tumor mutational burden in persistent, recurrent, or metastatic cervical cancer. J Gynecol Oncol 2024; 35:35.e105. [PMID: 38857910 DOI: 10.3802/jgo.2024.35.e105] [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: 10/13/2023] [Revised: 04/09/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
OBJECTIVE To evaluate the prevalence and prognostic role of programmed death ligand 1 (PD-L1) expression and tumor mutational burden (TMB) in patients with non-immunotherapy-treated advanced cervical cancer. METHODS Clinical data were retrospectively collected from medical records between January 1, 2008, and December 31, 2016, at Asan Medical Center (Korea); archived tumor samples were assessed for PD-L1 expression (combined positive score [CPS] ≥1) and TMB (≥175 mutations/exome). Overall survival (OS) was defined as time from advanced diagnosis or initiation of first-line or second-line systemic therapy until death/last follow-up. The association of OS with PD-L1 expression and TMB were analyzed using the log-rank test and Cox proportional hazards model adjusted for covariates. RESULTS Of 267 patients, 76.0% had squamous cell carcinoma (SCC), 24.0% had adenocarcinoma (AC)/adenosquamous carcinoma (ASC), 64.4% had PD-L1 CPS ≥1, and 32.6% had TMB ≥175 mutations/exome. PD-L1 CPS ≥1 and TMB ≥175 mutations/exome were more prevalent in SCC than in AC/ASC (73.9% and 37.2% vs. 34.4% and 17.7%). There was no association between OS and PD-L1 expression (CPS ≥1 vs. <1: adjusted hazard ratio [HR]=1.14; 95% confidence interval [CI]=0.84-1.53 from advanced diagnosis); OS trended shorter for the subgroup with TMB ≥175 versus <175 mutations/exome (adjusted HR=1.29; 95% CI=0.95-1.75). CONCLUSION Retrospective analysis of non-immunotherapy-treated patients with advanced cervical cancer demonstrated a higher prevalence of PD-L1 CPS ≥1 and TMB ≥175 mutations/exome in SCC versus AC/ASC. PD-L1 CPS ≥1 was not associated with OS; TMB ≥175 mutations/exome showed a trend toward shorter OS. Additional studies are needed to confirm these findings.
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Affiliation(s)
- Min-Hyun Baek
- Center for Gynecologic Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Lei Chen
- Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | | | | | | | - Jeong-Yeol Park
- Department of Obstetrics and Gynecology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Choi SY, Kim Y, Lim B, Wee CB, Chang IH, Kim CS. Prostate cancer therapy using immune checkpoint molecules to target recombinant dendritic cells. Investig Clin Urol 2024; 65:300-310. [PMID: 38714521 PMCID: PMC11076804 DOI: 10.4111/icu.20230348] [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: 10/19/2023] [Revised: 01/18/2024] [Accepted: 02/11/2024] [Indexed: 05/10/2024] Open
Abstract
PURPOSE We developed immune checkpoint molecules to target recombinant dendritic cells (DCs) and verified their anti-tumor efficacy and immune response against prostate cancer. MATERIALS AND METHODS DCs were generated from mononuclear cells in the tibia and femur bone marrow of mice. We knocked down the programmed death ligand 1 (PD-L1) on monocyte-derived DCs through siRNA PD-L1. Cell surface antigens were immune fluorescently stained through flow cytometry to analyze cultured cell phenotypes. Furthermore, we evaluated the efficacy of monocyte-derived DCs and recombinant DCs in a prostate cancer mouse model with subcutaneous TRAMP-C1 cells. Lastly, DC-induced mixed lymphocyte and lymphocyte-only proliferations were compared to determine cultured DCs' function. RESULTS Compared to the control group, siRNA PD-L1 therapeutic DC-treated mice exhibited significantly inhibited tumor volume and increased tumor cell apoptosis. Remarkably, this treatment substantially augmented interferon-gamma and interleukin-2 production by stimulating T-cells in an allogeneic mixed lymphocyte reaction. Moreover, we demonstrated that PD-L1 gene silencing improved cell proliferation and cytokine production. CONCLUSIONS We developed monocyte-derived DCs transfected with PD-L1 siRNA from mouse bone marrow. Our study highlights that PD-L1 inhibition in DCs increases antigen-specific immune responses, corroborating previous immunotherapy methodology findings regarding castration-resistant prostate cancer.
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Affiliation(s)
- Se Young Choi
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Yunlim Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Bumjin Lim
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chung Beum Wee
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - In Ho Chang
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Choung-Soo Kim
- Department of Urology, Ewha Womans University Mokdong Hospital, Ewha Womans University School of Medicine, Seoul, Korea.
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Xu M, Ren T, Deng J, Yang J, Lu T, Xi H, Yuan L, Zhang W, Zhou J. Correlation of CT parameters and PD-L1 expression status in gastric cancer. Abdom Radiol (NY) 2024; 49:1320-1329. [PMID: 38436699 DOI: 10.1007/s00261-024-04200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 03/05/2024]
Abstract
OBJECTIVE We aimed to explore the correlation between routine computed tomography (CT) imaging features and programmed cell death ligand-1(PD-L1) expression status in gastric cancer and evaluate the predictive value of imaging parameters for this immunotherapy biomarker. MATERIALS AND METHODS Patients with gastric adenocarcinoma who underwent abdominal CT three-stage enhanced scan and PD-L1 immunohistochemical testing before treatment were retrospectively examined. All diagnoses were confirmed through pathology. According to the expression status of PD-L1, they were divided into the positive (CPS ≥ 5) or negative group (CPS < 5). Baseline CT imaging features were collected. Diagnostic performances of the different variables were evaluated using receiver operating characteristic (ROC) curve. RESULTS In total, 67 patients (17 women and 50 men; mean age: 59.55 ± 10.22 years) with gastric adenocarcinoma were included in the study. The overall stages, probability of maximum lymph node short diameter > 1 cm and peak of lesion enhancement occurring in the arterial phase were statistically significant between the two groups (p < 0.05). Moreover, the arterial enhancement fraction (AEF) was significantly higher in the positive group than that in the negative group (p < 0.05), and ROC curve analysis showed that the AEF exhibited a high evaluation efficacy (area under the curve [AUC] = 0.724 [95% confidence interval (CI): 0.602-0.826]). The combined parameters had the best diagnostic efficacy (AUC = 0.825 [95%CI: 0.716-0.933]), sensitivity (75.00%), and specificity (81.40%). CONCLUSIONS These findings confirm a correlation between CT imaging features and PD-L1 expression status in gastric cancer, and AEF may help evaluate high PD-L1 expression and select patients suitable for immunotherapy.
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Affiliation(s)
- Min Xu
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Tiezhu Ren
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Juan Deng
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Jingjing Yang
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Ting Lu
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Huaze Xi
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Long Yuan
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China
- Second Clinical School, Lanzhou University, Lanzhou, China
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China
| | - Wenjuan Zhang
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China.
- Second Clinical School, Lanzhou University, Lanzhou, China.
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China.
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China.
| | - Junlin Zhou
- Department of Radiology, Lanzhou University Second Hospital, Cuiyingmen No.82, Chengguan District, Lanzhou, 730030, China.
- Second Clinical School, Lanzhou University, Lanzhou, China.
- Key Laboratory of Medical Imaging of Gansu Province, Lanzhou, China.
- Gansu International Scientific and Technological Cooperation Base of Medical Imaging Artificial Intelligence, Lanzhou, China.
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Ma C, Teng Q, Shang L, Du F, Li L. Tumor mutation load better predicts the prognosis of patients treated with immune checkpoint inhibitors in upper gastrointestinal cancers: A systematic review and meta-analysis. Cancer Rep (Hoboken) 2024; 7:e1959. [PMID: 38204354 PMCID: PMC10849990 DOI: 10.1002/cnr2.1959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Tumor mutational load (TML) has emerged as a potential biomarker for multiple solid tumors. However, data on its prognostic impact on upper gastrointestinal (UGI) cancer are limited. Therefore, the aim of this systematic review and meta-analysis was to assess the prognostic value of TML for the survival of patients with UGI cancer. METHOD A comprehensive search of the PubMed, Embase, Cochrane Library, and Web of Science databases was conducted up to February 13, 2023. Eleven studies met our inclusion criteria. Hazard ratios (HRs) for progression-free survival and overall survival and their 95% confidence intervals (CIs) were calculated. Subsequently, the combined HR and its 95% CI were calculated for UGI tract cancers in the high and low TML groups. I2 statistics and p-values were used to evaluate heterogeneity. Publication bias, sensitivity, and subgroup analyses were performed to determine sources of heterogeneity. RESULTS In total, 932 patients with UGI tract cancer from 11 publications were included. The high TML group treated with immunotherapy showed significantly improved overall survival (HR = 0.68; 95% CI: 0.53, 0.86; p = .001) and progression-free survival (HR = 0.74; 95% CI: 0.58, 0.95; p = .020) compared with the low TML group. CONCLUSION Our study demonstrated that patients with UGI tumors and higher TML have a better prognosis with immunotherapy, suggesting that TML is a promising predictive biomarker for immunotherapy. REGISTRATION The study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO Registration No: CRD42023405596).
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Affiliation(s)
- Chenghao Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Qiong Teng
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Fengying Du
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
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Gu Y, Li J, Guan H, Sun C. Prognostic and immunological values of SKA3 for overall survival in lung adenocarcinoma and its RNA binding protein involved mechanisms. J Chemother 2023:1-14. [PMID: 38146901 DOI: 10.1080/1120009x.2023.2298153] [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: 03/23/2023] [Accepted: 12/15/2023] [Indexed: 12/27/2023]
Abstract
This article aimed to investigate the correlations among SKA3 expression and prognosis, clinical relevance, tumor immunity, and RNA-binding protein (RBP)-involved mechanisms for overall survival (OS) in lung adenocarcinoma (LUAD). To explore the SKA3 expression level in LUAD by analyzing the genomic data as well as related clinical characteristics from the database of TCGA. Nomogram and gene set enrichment analysis (GSEA) were applied, respectively, to evaluate the performance of SKA3 in LUAD. Correlations between SKA3 and immunity and RBP-involved mechanisms were also performed. SKA3 had a higher expression level in LUAD samples than in adjacent normal lung samples, with shorter survival times in the high-SKA3-expressed LUAD subgroup (P < 0.05). qRT-PCR results remained consistent (P < 0.05). Uni-/multivariate Cox analyses revealed that SKA3 could have independent prognostic ability for LUAD (both P < 0.05). The nomogram model constructed with clinical pathological parameters and SKA3 expression levels predicted OS rates for LUAD and GSEA revealed SKA3-related pathways. In aspects of tumor immunity, SKA3 was significantly involved with tumor neoantigen burden, tumor mutational burden, immune cell pathways, and immune checkpoint inhibitor (ICI) molecules (all P < 0.05). The CellMiner database also found significant correlations between SKA3 and the antitumor drug sensitivity of chemotherapy, fenretinide, and PX-316. Besides, a total of nine LncRNA/RBP/SKA3 networks were revealed in LUAD for their RBP-involved mechanisms. SKA3 could serve as a potential biomarker for OS prognosis and immunotherapy in LUAD. LncRNA/RBP/SKA3 networks were identified in LUAD for their RBP-involved mechanisms, paving the way for further experimental verifications.
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Affiliation(s)
- Yinfeng Gu
- Department of Thoracic Surgery, Jianhu People's Hospital, Yancheng, Jiangsu, China
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jinjin Li
- Department of Thoracic Surgery, Jianhu People's Hospital, Yancheng, Jiangsu, China
| | - Hongjun Guan
- Department of Thoracic Surgery, Jianhu People's Hospital, Yancheng, Jiangsu, China
| | - Changpeng Sun
- Department of Thoracic Surgery, Jianhu People's Hospital, Yancheng, Jiangsu, China
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Zuo B, Wang L, Li X, Li X, Wang J, Xiong Y, Lei J, Zhang X, Chen Y, Liu Q, Jiao J, Sui M, Fan J, Wu N, Song Z, Li G. Abnormal low expression of SFTPC promotes the proliferation of lung adenocarcinoma by enhancing PI3K/AKT/mTOR signaling transduction. Aging (Albany NY) 2023; 15:12451-12475. [PMID: 37955668 PMCID: PMC10683597 DOI: 10.18632/aging.205191] [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: 06/23/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
The abnormality of surfactant protein C (SFTPC) has been linked to the development of a number of interstitial lung diseases, according to mounting evidence. Nonetheless, the function and mechanism of SFTPC in the biological progression of lung adenocarcinoma (LUAD) remain unclear. Analysis of public datasets and testing of clinical samples suggested that SFTPC expression was abnormally low in LUAD, which was associated with the onset and poor prognosis of LUAD. The SFTPC-related risk score was derived using least absolute shrinkage and selection operator Cox regression as well as multivariate Cox regression. The risk score was highly correlated with tumor purity and tumor mutation burden, and it could serve as an independent prognostic indicator for LUAD. Low-risk LUAD patients may benefit more from CTLA-4 or/and PD-1 inhibitors. Overall, the risk score is useful for LUAD patient prognostication and treatment guidance. Moreover, in vitro and in vivo experiments demonstrated that SFTPC inhibits the proliferation of LUAD by inhibiting PI3K/AKT/mTOR signaling transduction. These results reveal the molecular mechanism by which SFTPC inhibits the proliferation of LUAD and suggest that SFTPC could be a new therapeutic target for LUAD.
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Affiliation(s)
- Baile Zuo
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, The Air Force Military Medical University, Xi’an, Shaanxi, China
| | - Xiaoyan Li
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xin Li
- Department of Geriatric Medicine, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jinping Wang
- Department of Ultrasound, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xi Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yifan Chen
- College of Management, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Mengru Sui
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinhan Fan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ningxue Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- MOE Key Laboratory of Modern Teaching Technology, Center for Teacher Professional Ability Development, Shaanxi Normal University, Xi’an, Shaanxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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Ke L, Li S, Huang D. The predictive value of tumor mutation burden on survival of gastric cancer patients treated with immune checkpoint inhibitors: A systematic review and meta-analysis. Int Immunopharmacol 2023; 124:110986. [PMID: 37748223 DOI: 10.1016/j.intimp.2023.110986] [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: 03/15/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Tumor mutation burden (TMB) is a complement to traditional biomarkers related to the efficacy of immune checkpoint inhibitors (ICIs). The relationship between TMB and the efficacy of ICIs in gastric cancer was controversial. The systematic review and meta-analysis were conducted to investigate the predictive value of TMB on survival of gastric cancer patients treated with ICIs. METHODS We searched the databases PubMed, Embase, and Web of Science for articles, then screened eligible articles according to inclusion criteria. The effective data were extracted to calculate the pooled effects of hazard ratio (HR) for overall survival (OS) and progression-free survival (PFS), then perform publication bias, sensitivity analysis, and subgroup analysis by STATA 16.0. RESULTS The high TMB patients showed significantly longer survival than the low TMB patients (OS: HR 0.65,95% CI 0.55, 0.77, p < 0.001; PFS: HR 0.51, 95% CI 0.33, 0.77, p = 0.001). In the Asian subgroup, patients with high TMB exhibited better prognosis compared to low TMB (OS: HR 0.56, 95% CI 0.43, 0.72, p < 0.001; PFS: HR 0.45, 95% CI 0.28, 0.72, p = 0.001). In the non-Asian subgroup, the survival benefit was observed to be skewed toward patients with high TMB, but it was not statistically significant (OS:HR 0.61, 95% CI 0.32, 1.16, p = 0.133; PFS:HR 0.68, 95% CI 0.31, 1.48, p = 0.322). CONCLUSIONS This meta-analysis demonstrated that gastric cancer patients with high TMB showed significant benefits from ICIs compared to those with low TMB patients, particularly in Asian populations.
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Affiliation(s)
- Liyuan Ke
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China.
| | - Su Li
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Danxue Huang
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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Shen K, Wang Q, Wang L, Yang Y, Ren M, Li Y, Gao Z, Zheng S, Ding Y, Ji J, Wei C, Zhang T, Zhu Y, Feng J, Qin F, Yang Y, Wei C, Gu J. Prediction of survival and immunotherapy response by the combined classifier of G protein-coupled receptors and tumor microenvironment in melanoma. Eur J Med Res 2023; 28:352. [PMID: 37716991 PMCID: PMC10504724 DOI: 10.1186/s40001-023-01346-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Melanoma is the deadliest form of skin tumor, and G protein-coupled receptors (GPCRs) play crucial roles in its carcinogenesis. Furthermore, the tumor microenvironment (TME) affects the overall survival (OS) and the response to immunotherapy. The combination of GPCRs and TME from a multi-omics perspective may help to predict the survival of the melanoma patients and their response to immunotherapy. METHODS Bulk-seq, single-cell RNA sequencing (scRNA-seq), gene mutations, immunotherapy responses, and clinicopathologic feature data were downloaded from public databases, and prognostic GPCRs and immune cells were screened using multiple machine learning algorithms. The expression levels of GPCRs were detected using real-time quantitative polymerase chain reaction (qPCR) in A375 and HaCaT cell lines. The GPCR-TME classifier was constructed and verified using different cohorts and multi-omics. Gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and tracking tumor immunophenotype (TIP) were used to identify the key biological pathways among the GPCR-TME subgroups. Then, tumor mutational burden (TMB), vital mutant genes, antigen presentation genes, and immune checkpoints were compared among the subgroups. Finally, the differences in immunotherapy response rates among the GPCR-TME subgroups were investigated. RESULTS A total of 12 GPCRs and five immune cell types were screened to establish the GPCR-TME classifier. No significant differences in the expression levels of the 12 GPCRs were found in the two cell lines. Patients with high GPCR score or low TME score had a poor OS; thus, the GPCRlow/TMEhigh subgroup had the most favorable OS. The scRNA-seq result revealed that immune cells had a higher GPCR score than tumor and stromal cells. The GPCR-TME classifier acted as an independent prognostic factor for melanoma. GSEA, WGCNA, and TIP demonstrated that the GPCRlow/TMEhigh subgroup was related to the activation and recruitment of anti-tumor immune cells and the positive regulation of the immune response. From a genomic perspective, the GPCRlow/TMEhigh subgroup had higher TMB, and different mutant genes. Ultimately, higher expression levels of antigen presentation genes and immune checkpoints were observed in the GPCRlow/TMEhigh subgroup, and the melanoma immunotherapy cohorts confirmed that the response rate was highest in the GPCRlow/TMEhigh cohort. CONCLUSIONS We have developed a GPCR-TME classifier that could predict the OS and immunotherapy response of patients with melanoma highly effectively based on multi-omics analysis.
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Affiliation(s)
- Kangjie Shen
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Qiangcheng Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yang Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Min Ren
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yanlin Li
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Zixu Gao
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Shaoluan Zheng
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Xiamen, China
| | - Yiteng Ding
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Jiani Ji
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Chenlu Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Tianyi Zhang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yu Zhu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Jia Feng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Feng Qin
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yanwen Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China.
| | - Jianying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China.
- Xiamen Clinical Research Center for Cancer Therapy, Xiamen, China.
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Han X, Yan Z, Fan K, Guan X, Hu B, Li X, Ou Y, Cui B, An L, Zhang Y, Gong J. The combined signatures of telomere and immune cell landscape provide a prognostic and therapeutic biomarker in glioma. Front Immunol 2023; 14:1220100. [PMID: 37662954 PMCID: PMC10470026 DOI: 10.3389/fimmu.2023.1220100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/20/2023] [Indexed: 09/05/2023] Open
Abstract
Background Gliomas, the most prevalent primary malignant tumors of the central nervous system in adults, exhibit slow growth in lower-grade gliomas (LGG). However, the majority of LGG cases progress to high-grade gliomas, posing challenges for prognostication. The tumor microenvironment (TME), characterized by telomere-related genes and immune cell infiltration, strongly influences glioma growth and therapeutic response. Therefore, our objective was to develop a Telomere-TME (TM-TME) classifier that integrates telomere-related genes and immune cell landscape to assess prognosis and therapeutic response in glioma. Methods This study encompassed LGG patients from the TCGA and CCGA databases. TM score and TME score were derived from the expression signatures of telomere-related genes and the presence of immune cells in LGG, respectively. The TM-TME classifier was established by combining TM and TME scores to effectively predict prognosis. Subsequently, we conducted Kaplan-Meier survival estimation, univariate Cox regression analysis, and receiver operating characteristic curves to validate the prognostic prediction capacity of the TM-TME classifier across multiple cohorts. Gene Ontology (GO) analysis, biological processes, and proteomaps were performed to annotate the functional aspects of each subgroup and visualize the cellular signaling pathways. Results The TM_low+TME_high subgroup exhibited superior prognosis and therapeutic response compared to other subgroups (P<0.001). This finding could be attributed to distinct tumor somatic mutations and cancer cellular signaling pathways. GO analysis indicated that the TM_low+TME_high subgroup is associated with the neuronal system and modulation of chemical synaptic transmission. Conversely, the TM_high+TME_low subgroup showed a strong association with cell cycle and DNA metabolic processes. Furthermore, the classifier significantly differentiated overall survival in the TCGA LGG cohort and served as an independent prognostic factor for LGG patients in both the TCGA cohort (P<0.001) and the CGGA cohort (P<0.001). Conclusion Overall, our findings underscore the significance of the TM-TME classifier in predicting prognosis and immune therapeutic response in glioma, shedding light on the complex immune landscape within each subgroup. Additionally, our results suggest the potential of integrating risk stratification with precision therapy for LGG.
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Affiliation(s)
- Xu Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zihan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaiyu Fan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xueyi Guan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bohan Hu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yunwei Ou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bing Cui
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Lingxuan An
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Yaohua Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Jian Gong
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Gao Y, Liu H, Wan J, Chang F, Zhang L, Wang W, Zhang Q, Feng Q. Construction and Assessment of a Prognostic Risk Model for Cervical Cancer Based on Lactate Metabolism-Related lncRNAs. Int J Gen Med 2023; 16:2943-2960. [PMID: 37457750 PMCID: PMC10349608 DOI: 10.2147/ijgm.s411511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose Cervical cancer (CC) has the fourth highest incidence and mortality rate among female cancers. Lactate is a key regulator promoting tumor progression. Long non-coding RNAs (lncRNAs) are closely associated with cervical cancer (CC). The study was aimed to develop a prognostic risk model for cervical cancer based on lactate metabolism-associated lncRNAs and to determine their clinical prognostic value. Patients and Methods In this study, CESC transcriptome data were obtained from the TCGA database. 262 lactate metabolism-associated genes were extracted from MsigDB (Molecular Characterization Database). Then, correlation analysis was used to identify LRLs. Univariate Cox regression analysis was performed afterwards, followed by least absolute shrinkage and selection operator (LASSO) regression analysis and multiple Cox regression analysis. 10 lncRNAs were finally identified to construct a risk score model. They were divided into two groups of high risk and low risk according to the median of risk scores. The predictive performance of the models was assessed by Kaplan-Meier (K-M) analysis, subject work characteristics (ROC) analysis, and univariate and multivariate Cox analyses. To assess the clinical utility of the prognostic model, we performed functional enrichment analysis, immune microenvironment analysis, mutation analysis, and column line graph generation. Results We constructed a prognostic model consisting of 10 LRLs at CC. We observed that high-risk populations were strongly associated with poor survival outcomes. Risk score was an independent risk factor for CC prognosis and was strongly associated with immune microenvironment analysis and tumor mutational load. Conclusion We developed a risk model of lncRNAs associated with lactate metabolism and used it to predict prognosis of CC, which could guide and facilitate the progress of new treatment strategies and disease monitoring in CC patients.
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Affiliation(s)
- Ya Gao
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Junhu Wan
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Fenghua Chang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Lindong Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Wenjuan Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Qinshan Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Quanling Feng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
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Zhao G, Wu M, Yan Q. Comprehensive Analysis to Reveal Amino Acid Metabolism-Associated Genes as a Prognostic Index in Gastric Cancer. Mediators Inflamm 2023; 2023:3276319. [PMID: 37214189 PMCID: PMC10195167 DOI: 10.1155/2023/3276319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
Background Amino acid metabolism (AAM) is related to tumor growth, prognosis, and therapeutic response. Tumor cells use more amino acids with less synthetic energy than normal cells for rapid proliferation. However, the possible significance of AAM-related genes in the tumor microenvironment (TME) is poorly understood. Methods Gastric cancer (GC) patients were classified into molecular subtypes by consensus clustering analysis using AAMs genes. AAM pattern, transcriptional patterns, prognosis, and TME in distinct molecular subtypes were systematically investigated. AAM gene score was built by least absolute shrinkage and selection operator (Lasso) regression. Results The study revealed that copy number variation (CNV) changes were prevalent in selected AAM-related genes, and most of these genes exhibited a high frequency of CNV deletion. Three molecular subtypes (clusters A, B, and C) were developed based on 99 AAM genes, which cluster B had better prognosis outcome. We developed a scoring system (AAM score) based on 4 AAM gene expressions to measure the AAM patterns of each patient. Importantly, we constructed a survival probability prediction nomogram. The AAM score was substantially associated with the index of cancer stem cells and sensitivity to chemotherapy intervention. Conclusion Overall, we detected prognostic AAM features in GC patients, which may help define TME characteristics and explore more effective treatment approaches.
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Affiliation(s)
- Gangjun Zhao
- Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Mi Wu
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Qiuwen Yan
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Medical School of Ningbo University, Ningbo, China
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Zhong J, Xiang D, Ma X. Prediction and analysis of osteoarthritis hub genes with bioinformatics. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:66. [PMID: 36819525 PMCID: PMC9929772 DOI: 10.21037/atm-22-6450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Background Osteoarthritis (OA) is the most common type of arthritis. OA can cause joint pain, stiffness, and loss of function. The pathogenesis of OA is not completely clear. Moreover, there is no effective treatment, and clinical management is limited to symptomatic relief or joint surgery. This study utilized bioinformatics to analyze normal and OA articular cartilage samples to find biomarkers and therapeutic targets for OA. Methods The GSE169077 gene chip dataset was downloaded from the public gene chip data platform of the National Biotechnology Information Center. The dataset included 6 samples of OA tissues and 5 samples of healthy cartilage tissues. Differentially expressed genes (DEGs) were screened using the R language "limma" function package under the threshold of log2[fold change (FC)] ≥2 and a P value <0.05. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathways of the target genes were enriched and analyzed using the database for annotation, visualization, and integrated discovery (DAVID), and a protein-protein interaction (PPI) network was further constructed using the search tool for the retrieval of interacting genes/proteins (STRING) database. The coexpression relationship of the genes in the module was visualized and screened with Cytoscape. Results A total of 27 DEGs were identified, including 9 downregulated genes and 18 upregulated genes. GO signal pathway enrichment analysis showed involvement in hypoxic response, fibrous collagen trimer, and extracellular matrix structural components. KEGG analysis demonstrated associations with protein digestion and absorption, extracellular matrix receptor interaction, and the peroxisome proliferator-activated receptor signal pathway, among several other pathways. A PPI network was obtained through STRING analysis, and the results were imported into Cytoscape software. The 27 DEGs were sequenced by the cytoHubba plug-in by various calculation methods, and 5 hub genes (COL1A1, COL1A2, POSTN, BMP1, and MMP13) were finally selected. These genes were analyzed by PPI again and annotated with GO and KEGG in different colors. Conclusions Bioinformatics technology effectively identified differential genes in the knee cartilage tissue of healthy controls and patients with OA, providing opportunities to further explore the mechanism and treatment of OA on a transcriptional level.
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Affiliation(s)
- Junqing Zhong
- Integration of Traditional Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ding Xiang
- Department of Rehabilitation, Tianjin Hospital, Tianjin, China
| | - Xinlong Ma
- Department of Orthopedics, Tianjin Hospital, Tianjin, China
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Zhu D, Liu J, Wang J, Zhang L, Jiang M, Liu Y, Xiong Y, He X, Li G. Transcriptome and pan-cancer system analysis identify PM2.5-induced stanniocalcin 2 as a potential prognostic and immunological biomarker for cancers. Front Genet 2023; 13:1077615. [PMID: 36685853 PMCID: PMC9852732 DOI: 10.3389/fgene.2022.1077615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Epidemiological studies have shown that air pollution and particulate matter (PM) are closely related to the occurrence of cancer. However, the potential prognostic and immunological biomarkers for air pollution related cancers are lacking. In this study, we proved PM2.5 exposure was correlated with lung cancer through transcriptome analysis. Importantly, we identified STC2 as a key gene regulated by PM2.5, whose expression in epithelial cells was significantly increased after PM2.5 treatment and validated by using RT-qPCR and immunofluorescence. Kaplan-Meier OS curves suggested that high STC2 expression positively correlated with a poor prognosis in lung cancer. Furthermore, we discovered that STC2 was associated with multiple cancers and pathways in cancer. Next, Pan-Cancer Expression Landscape of STC2 showed that STC2 exhibited inconsistent expression across 26 types of human cancer, lower in KIRP in cancer versus adjacent normal tissues, and significantly higher in another cancers. Cox regression results suggested that STC2 expression was positively or negatively associated with prognosis in different cancers. Moreover, STC2 expression was associated with clinical phenotypes including age, gender, stage and grade. Mutation features of STC2 were also analyzed, in which the highest alteration frequency of STC2 was presented in KIRC with amplification. Meanwhile, the effects of copy number variation (CNV) on STC2 expression were investigated across various tumor types, suggesting that STC2 expression was significantly correlated with CNV in tumors. Additionally, STC2 was closely related to tumor heterogeneity, tumor stemness and tumor immune microenvironment like immune cell infiltration. In the meantime, we analyzed methylation modifications and immunological correlation of STC2. The results demonstrated that STC2 expression positively correlated with most RNA methylation genes and immunomodulators across tumors. Taken together, the findings revealed that PM2.5-induced STC2 might be a potential prognostic and immunological biomarker for cancers related to air pollution.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China,Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Jiliu Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Junyi Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China,Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Lei Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China,Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Manling Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China,Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Ying Xiong
- Department of Pulmonary and Critical Care Medicine, Sichuan Friendship Hospital, Chengdu, China,*Correspondence: Ying Xiong, ; Xiang He, ; Guoping Li,
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China,*Correspondence: Ying Xiong, ; Xiang He, ; Guoping Li,
| | - Guoping Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China,Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China,Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China,*Correspondence: Ying Xiong, ; Xiang He, ; Guoping Li,
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Zheng LP, Yang J, Chen XW, Li LC, Sun JG. Correlation of preclinical and clinical biomarkers with efficacy and toxicity of cancer immunotherapy. Ther Adv Med Oncol 2023; 15:17588359231163807. [PMID: 37113734 PMCID: PMC10126660 DOI: 10.1177/17588359231163807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revealed significant clinical values in different solid tumors and hematological malignancy, changing the landscape for the treatment of multiple types of cancer. However, only a subpopulation of patients has obvious tumor response and long-term survival after ICIs treatment, and many patients may experience other undesirable clinical features. Therefore, biomarkers are critical for patients to choose exact optimum therapy. Here, we reviewed existing preclinical and clinical biomarkers of immunotherapeutic efficacy and immune-related adverse events (irAEs). Based on efficacy prediction, pseudoprogression, hyperprogressive disease, or irAEs, these biomarkers were divided into cancer cell-derived biomarkers, tumor microenvironment-derived biomarkers, host-derived biomarkers, peripheral blood biomarkers, and multi-modal model and artificial intelligence assessment-based biomarkers. Furthermore, we describe the relation between ICIs efficacy and irAEs. This review provides the overall perspective of biomarkers of immunotherapeutic outcome and irAEs prediction during ICIs treatment.
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Affiliation(s)
| | | | - Xie-Wan Chen
- Department of Basic Medicine, Army Medical University, Chongqing, China
| | - Ling-Chen Li
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, China
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Miao TW, Chen FY, Du LY, Xiao W, Fu JJ. Signature based on RNA-binding protein-related genes for predicting prognosis and guiding therapy in non-small cell lung cancer. Front Genet 2022; 13:930826. [PMID: 36118863 PMCID: PMC9479344 DOI: 10.3389/fgene.2022.930826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Studies have reported that RNA-binding proteins (RBPs) are dysregulated in multiple cancers and are correlated with the progression and prognosis of disease. However, the functions of RBPs in non-small cell lung cancer (NSCLC) remain unclear. The present study aimed to explore the function of RBPs in NSCLC and their prognostic and therapeutic value.Methods: The mRNA expression profiles, DNA methylation data, gene mutation data, copy number variation data, and corresponding clinical information on NSCLC were downloaded from The Cancer Genome Atlas, Gene Expression Omnibus, and the University of California Santa Cruz Xena databases. The differentially expressed RBPs were identified between tumor and control tissues, and the expression and prognostic value of these RBPs were systemically investigated by bioinformatics analysis. A quantitative polymerase chain reaction (qPCR) was performed to validate the dysregulated genes in the prognostic signature.Results: A prognostic RBP-related signature was successfully constructed based on eight RBPs represented as a risk score using least absolute shrinkage and selection operator (LASSO) regression analysis. The high-risk group had a worse overall survival (OS) probability than the low-risk group (p < 0.001) with 1-, 3-, and 5-year area under the receiver operator characteristic curve values of 0.671, 0.638, and 0.637, respectively. The risk score was associated with the stage of disease (p < 0.05) and was an independent prognostic factor for NSCLC when adjusted for age and UICC stage (p < 0.001, hazard ratio (HR): 1.888). The constructed nomogram showed a good predictive value. The P53, focal adhesion, and NOD-like receptor signaling pathways were the primary pathways in the high-risk group (adjusted p value <0.05). The high-risk group was correlated with increased immune infiltration (p < 0.05), upregulated relative expression levels of programmed cell death 1 (PD1) (p = 0.015), cytotoxic T-lymphocyte-associated protein 4 (CTLA4) (p = 0.042), higher gene mutation frequency, higher tumor mutational burden (p = 0.034), and better chemotherapy response (p < 0.001). The signature was successfully validated using the GSE26939, GSE31210, GSE30219, and GSE157009 datasets. Dysregulation of these genes in patients with NSCLC was confirmed using the qPCR in an independent cohort (p < 0.05).Conclusion: An RBP-related signature was successfully constructed to predict prognosis in NSCLC, functioning as a reference for individualized therapy, including immunotherapy and chemotherapy.
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Affiliation(s)
- Ti-Wei Miao
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Fang-Ying Chen
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Xiao
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Juan-Juan Fu,
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