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Zhang D, Liang P, Xia B, Wu J, Hu X. Comprehensive pan-cancer analysis of ZNF337 as a potential diagnostic, immunological, and prognostic biomarker. BMC Cancer 2024; 24:987. [PMID: 39123194 DOI: 10.1186/s12885-024-12703-x] [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: 10/10/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Zinc Finger Protein 337 (ZNF337) is a novel Zinc Finger (ZNF) protein family member. However, the roles of ZNF337 in human cancers have not yet been investigated. METHODS In this study, with the aid of TCGA databases, GTEx databases, and online websites, we determined the expression levels of ZNF337 in pan-cancer and its potential value as a diagnostic and prognostic marker for pan-cancer and analyzed the relationship between ZNF337 expression and immune cell infiltration and immune checkpoint genes. We then focused our research on the potential of ZNF337 as a biomarker for diagnostic and prognostic in KIRC (kidney renal clear cell carcinoma) and validated in the E-MTAB-1980 database. Moreover, the expression of ZNF337 was detected through qRT-PCR and Western blotting (WB). CCK-8 experiment, colony formation experiment, and EDU experiment were performed to evaluate cell proliferation ability. Wound healing assay and transwell assay were used to analyze its migration ability. The qRT-PCR and WB were used to detect the expression of ZNF337 in tumor tissues and paracancerous tissues of KIRC patients. RESULTS The pan-cancer analysis revealed that abnormal ZNF337 expression was found in multiple human cancer types. ZNF337 had a high diagnostic value in pan-cancer and a significant association with the prognosis of certain cancers, indicating that ZNF337 may be a valuable prognostic biomarker for multiple cancers. Further analysis demonstrated that the expression level of ZNF337 displayed significant correlations with cancer-associated fibroblasts, immune cell infiltration, and immune checkpoint genes in many tumors. Additionally, ZNF337 was observed to have a high expression in KIRC. Its expression was significantly associated with poor prognosis [overall survival (OS), disease-specific survival (DSS)], age, TNM stage, histologic grade, and pathologic stage. The high ZNF337 expression was associated with poor prognosis in the E-MTAB-1980 validation cohort. The in vitro experiments suggested that the expression of ZNF337 in KIRC tumor tissues was higher than in adjacent tissues, and ZNF337 knockdown inhibited the proliferation and migration of KIRC cells, whereas overexpression of ZNF337 had the opposite effects. CONCLUSIONS ZNF337 might be an important prognostic and immunotherapeutic biomarker for pan-cancer, especially in KIRC.
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Affiliation(s)
- Dongxu Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Pu Liang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, 100015, China
| | - Bowen Xia
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jitao Wu
- Department of Urology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China.
- Institute of Urology, Capital Medical University, Beijing, China.
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Quan S, Li N, Lian S, Wang Y, Liu Y, Liu J, Zhang Z, Gao D, Li Y. SLC4A4 as a novel biomarker involved in immune system response and lung adenocarcinoma progression. Int Immunopharmacol 2024; 140:112756. [PMID: 39083932 DOI: 10.1016/j.intimp.2024.112756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Altered expression and activity of solute carrier family 4 member 4 (SLC4A4) could affect the growth, survival and metastasis of tumor cells. Currently, the role of SLC4A4 in lung adenocarcinoma (LUAD) immunotherapy and prognosis was not entirely clear. METHODS We analyzed SLC4A4 expression in LUAD tissues and cell lines using quantitative reverse transcription-polymerase chain reaction, Western blotting, and immunohistochemistry. The effects of SLC4A4 overexpression on angiogenesis, cell migration, invasion, and epithelial-mesenchymal transition were examined. Public databases helped construct a risk model evaluating SLC4A4's expression on LUAD prognosis and immunotherapy response. Additionally, a xenograft model, flow cytometry, and enzyme-linked immunosorbent assay further explored SLC4A4's role in tumor immune microenvironment infiltration. RESULTS Upregulation of SLC4A4 promoted apoptosis in the LUAD cell line and significantly inhibited the migration and invasive ability of cancer cells (P<0.01). A total of 10 key genes (including SIGLEC6, RHOV, PIR, MOB3B, MIR3135B, LPAR6, KRT8, ITGA2, CPS1, and C6) were screened according to SLC4A4 expression, immune score and stromal score, and a prognostic model with good outcome was constructed (AUC values of which in the training cohort at 1,3, and 5 years reached 0.73, 0.73, and 0.72, respectively). Importantly, we demonstrated that high expression of SLC4A4 was able to increase the proliferation level and cytokine secretion of CD8+ T cells for the purpose of promoting the immune system response to LUAD. CONCLUSION Our study revealed that SLC4A4 can serve as a prognostic indicator for LUAD, providing new insights into the treatment and diagnosis of LUAD.
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Affiliation(s)
- Siyu Quan
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Na Li
- Nephrology Department, Jinan Zhangqiu District People's Hospital, Jinan 250200, China
| | - Shihai Lian
- Out-patient Department, Zaozhuang Municipal Hospital, Zaozhuang 277102, China
| | - Yuanyuan Wang
- The Department of Hospital Infection, Jinan Fifth People's Hospital, Jinan 250022, China
| | - Yang Liu
- Thoracic Surgery, PLA 80th Group Army Hospital, Weifang 261011, China
| | - Jianbo Liu
- Department of Thoracic Surgery, The Fourth People's Hospital of Heze, Heze 274100, China
| | - Zewei Zhang
- Department of Thoracic Surgery, Gaoqing County People's Hospital, Gaoqing 256399, China
| | - Dejun Gao
- Department of Thoracic Surgery, The Second People's Hospital of Liaocheng, Liaocheng 252600, China
| | - Yun Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.
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Sha H, Tong F, Ni J, Sun Y, Zhu Y, Qi L, Li X, Li W, Yang Y, Gu Q, Zhang X, Wang X, Zhu C, Chen D, Liu B, Du J. First-line penpulimab (an anti-PD1 antibody) and anlotinib (an angiogenesis inhibitor) with nab-paclitaxel/gemcitabine (PAAG) in metastatic pancreatic cancer: a prospective, multicentre, biomolecular exploratory, phase II trial. Signal Transduct Target Ther 2024; 9:143. [PMID: 38844468 PMCID: PMC11156675 DOI: 10.1038/s41392-024-01857-6] [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: 12/20/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 06/09/2024] Open
Abstract
Metastatic pancreatic cancer (mPC) has a dismal prognosis. Herein, we conducted a prospective, multicentre, single-arm, phase II trial evaluating the efficacy and safety of penpulimab and anlotinib in combination with nab-paclitaxel/gemcitabine (PAAG) in patients with first-line mPC (NCT05493995). The primary endpoints included the objective response rate (ORR) and disease control rate (DCR), while secondary endpoints encompassed progression-free survival (PFS), overall survival (OS), and safety. In 66 patients analysed for efficacy, the best response, indicated by the ORR, was recorded at 50.0% (33/66) (95% CI, 37.4-62.6%), with 33 patients achieving partial response (PR). Notably, the DCR was 95.5% (63/66, 95% CI, 87.3-99.1%). The median PFS (mPFS) and OS (mOS) were 8.8 (95% CI, 8.1-11.6), and 13.7 (95% CI, 12.4 to not reached) months, respectively. Grade 3/4 treatment-related adverse events (TRAEs) were reported in 39.4% of patients (26/66). In prespecified exploratory analysis, patients with altered SWI/SNF complex had a poorer PFS. Additionally, low serum CA724 level, high T-cell recruitment, low Th17 cell recruitment, and high NK CD56dim cell scores at baseline were potential predicative biomarkers for more favourable efficacy. In conclusion, PAAG as a first-line therapy demonstrated tolerability with promising clinical efficacy for mPC. The biomolecular findings identified in this study possess the potential to guide the precise clinical application of the triple-combo regimen.
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Affiliation(s)
- Huizi Sha
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Fan Tong
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiayao Ni
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Sun
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Yahui Zhu
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Liang Qi
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Xiaoqin Li
- Department of Oncology, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yan Yang
- Department of Oncology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Qing Gu
- National Institute of Healthcare Data Science at Nanjing University, Nanjing, China
| | - Xing Zhang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Xiaoxuan Wang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Chan Zhu
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Dongsheng Chen
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Baorui Liu
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China.
| | - Juan Du
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China.
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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Xu ZJ, Li JA, Cao ZY, Xu HX, Ying Y, Xu ZH, Liu RJ, Guo Y, Zhang ZX, Wang WQ, Liu L. Construction of S100 family members prognosis prediction model and analysis of immune microenvironment landscape at single-cell level in pancreatic adenocarcinoma: a tumor marker prognostic study. Int J Surg 2024; 110:3591-3605. [PMID: 38498399 PMCID: PMC11175822 DOI: 10.1097/js9.0000000000001293] [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: 10/16/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
Pancreatic adenocarcinoma characterized by a mere 10% 5-year survival rate, poses a formidable challenge due to its specific anatomical location, making tumor tissue acquisition difficult. This limitation underscores the critical need for novel biomarkers to stratify this patient population. Accordingly, this study aimed to construct a prognosis prediction model centered on S100 family members. Leveraging six S100 genes and their corresponding coefficients, an S100 score was calculated to predict survival outcomes. The present study provided comprehensive internal and external validation along with power evaluation results, substantiating the efficacy of the proposed model. Additionally, the study explored the S100-driven potential mechanisms underlying malignant progression. By comparing immune cell infiltration proportions in distinct patient groups with varying prognoses, the research identified differences driven by S100 expression. Furthermore, the analysis explored significant ligand-receptor pairs between malignant cells and immune cells influenced by S100 genes, uncovering crucial insights. Notably, the study identified a novel biomarker capable of predicting the sensitivity of neoadjuvant chemotherapy, offering promising avenues for further research and clinical application.
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Affiliation(s)
- Zi-jin Xu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
- Department of General Surgery, QingPu Branch of Zhongshan Hospital, Fudan University
| | - Jian-ang Li
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Ze-yuan Cao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, People’s Republic of China
| | - Hua-xiang Xu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Ying Ying
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Zhi-hang Xu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Run-jie Liu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Yuquan Guo
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Zi-xin Zhang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Wen-quan Wang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
| | - Liang Liu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University
- Cancer Center, Zhongshan Hospital, Fudan University
- Department of Oncology, Shanghai Medical College, Fudan University
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Gu Y, Bian C, Wang H, Fu C, Xue W, Zhang W, Mu G, Xia Y, Wei K, Wang J. Inflammation-based lung adenocarcinoma molecular subtype identification and construction of an inflammation-related signature with bulk and single-cell RNA-seq data. Aging (Albany NY) 2024; 16:8822-8842. [PMID: 38771142 PMCID: PMC11164500 DOI: 10.18632/aging.205840] [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: 12/11/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
The role of inflammation is increasingly understood to have a central influence on therapeutic outcomes and prognosis in lung adenocarcinoma (LUAD). However, the detailed molecular divisions involved in inflammatory responses are yet to be fully elucidated. Our study identified two main inflammation-oriented LUAD grades: the inflammation-low (INF-low) and the inflammation-high (INF-high) subtypes. Both presented with unique clinicopathological features, implications for prognosis, and distinctive tumor microenvironment profiles. Broadly, the INF-low grade, marked by its dominant immunosuppressive tumor microenvironment, was accompanied by less favorable prognostic outcomes and a heightened prevalence of oncogenic mutations. In contrast, the INF-high grade exhibited more optimistic clinical trajectories, underscored by its immune-active environment. In addition, our efforts led to the conceptualization and empirical validation of an inflammation-centric predictive model with considerable predictive potency. Our study paves the way for a refined inflammation-centric LUAD classification and fosters a deeper understanding of tumor microenvironment intricacies.
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Affiliation(s)
- Yan Gu
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Chengyu Bian
- Department of Thoracic Surgery, The First People’s Hospital of Changzhou and The Third Affiliated Hospital of Soochow University, Changzhou 213004, Jiangsu, China
| | - Hongchang Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Chenghao Fu
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Wentao Xue
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Wenhao Zhang
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Guang Mu
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Yang Xia
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Ke Wei
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Jun Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
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Voisin A, Terret C, Schiffler C, Bidaux AS, Vanacker H, Perrin-Niquet M, Barbery M, Vinceneux A, Eberst L, Stéphan P, Garin G, Spaggiari D, Pérol D, Grinberg-Bleyer Y, Cassier PA. Xevinapant Combined with Pembrolizumab in Patients with Advanced, Pretreated, Colorectal and Pancreatic Cancer: Results of the Phase Ib/II CATRIPCA Trial. Clin Cancer Res 2024; 30:2111-2120. [PMID: 38502104 DOI: 10.1158/1078-0432.ccr-23-2893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
PURPOSE Xevinapant is an orally available inhibitor of apoptosis proteins (IAP) inhibitor. Preclinical data suggest that IAP antagonism may synergize with immune checkpoint blockers by modulating the NFκB pathway in immune cells. PATIENTS AND METHODS Adult patients with non-high microsatellite instability advanced/metastatic pancreatic ductal adenocarcinoma (PDAC) or colorectal cancer were enrolled in this phase Ib/II study and received pembrolizumab 200 mg every 3 weeks intravenously, and ascending doses of oral xevinapant (100, 150, and 200 mg daily for 14 days on/7 days off). Dose escalation followed a 3+3 design with a 21-day dose-limiting toxicity (DLT) evaluation period. Following the determination of the recommended phase II dose (RP2D), 14 patients with PDAC and 14 patients with colorectal cancer were enrolled in expansion cohorts to assess preliminary efficacy. RESULTS Forty-one patients (26 males) with a median age of 64 years were enrolled: 13 in the dose escalation and 28 in the two expansion cohorts. No DLT was observed during dose escalation. The RP2D was identified as xevinapant 200 mg/day + pembrolizumab 200 mg every 3 weeks. The most common adverse events (AE) were fatigue (37%), gastrointestinal AE (decreased appetite in 37%, nausea in 24%, stomatitis in 12%, and diarrhea and vomiting in 10% each), and cutaneous AE (pruritus, dry skin, and rash seen in 20%, 15%, and 15% of patients, respectively). The best overall response according to RECIST1.1 was partial response (confirmed) in 1 (3%), stable disease in 4 (10%), and progressive disease in 35 (88%). CONCLUSIONS Xevinapant combined with pembrolizumab was well tolerated with no unexpected AEs. However, antitumor activity was low.
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Affiliation(s)
- Allison Voisin
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine Terret
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Camille Schiffler
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Anne-Sophie Bidaux
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Hélène Vanacker
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Marlène Perrin-Niquet
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Maud Barbery
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Lauriane Eberst
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Pierre Stéphan
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Gwenaële Garin
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | | | - David Pérol
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Yenkel Grinberg-Bleyer
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe A Cassier
- Molecular Regulation of Cancer Immunity, Cancer Research Center of Lyon, Labex DEV2CAN, Centre Léon Bérard, INSERM U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
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7
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Ren K, Ling X, Chen L, Li Z, Huang T. Prognostic and immunotherapeutic implications of bilirubin metabolism-associated genes in lung adenocarcinoma. J Cell Mol Med 2024; 28:e18346. [PMID: 38693853 PMCID: PMC11063731 DOI: 10.1111/jcmm.18346] [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: 01/07/2024] [Revised: 03/25/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is a major subtype of non-small-cell lung cancer and accompanies high mortality rates. While the role of bilirubin metabolism in cancer is recognized, its specific impact on LUAD and patient response to immunotherapy needs to be elucidated. This study aimed to develop a prognostic signature of bilirubin metabolism-associated genes (BMAGs) to predict outcomes and efficacy of immunotherapy in LUAD. We analysed gene expression data from The Cancer Genome Atlas (TCGA) to identify survival-related BMAGs and construct a prognostic model in LUAD. The prognostic efficacy of our model was corroborated by employing TCGA-LUAD and five Gene Expression Omnibus datasets, effectively stratifying patients into risk-defined cohorts with marked disparities in survival. The BMAG signature was indeed an independent prognostic determinant, outperforming established clinical parameters. The low-risk group exhibited a more favourable response to immunotherapy, highlighted by increased immune checkpoint expression and immune cell infiltration. Further, somatic mutation profiling differentiated the molecular landscapes of the risk categories. Our screening further identified potential drug candidates preferentially targeting the high-risk group. Our analysis of critical BMAGs showed the tumour-suppressive role of FBP1, highlighting its suppression in LUAD and its inhibitory effects on tumour proliferation, migration and invasion, in addition to its involvement in cell cycle and apoptosis regulation. These findings introduce a potent BMAG-based prognostic indicator and offer valuable insights for prognostication and tailored immunotherapy in LUAD.
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Affiliation(s)
- Kangqi Ren
- Department of Thoracic SurgeryShenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
| | - Xiean Ling
- Department of Thoracic SurgeryShenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
| | - Lin Chen
- Department of Thoracic SurgeryShenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
| | - Zeyao Li
- Department of Thoracic SurgeryShenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
| | - Tonghai Huang
- Department of Thoracic SurgeryShenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
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Lin Y, Li R, Li T, Zhao W, Ye Q, Dong C, Gao Y. A prognostic model for hepatocellular carcinoma patients based on polyunsaturated fatty acid-related genes. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38682322 DOI: 10.1002/tox.24273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVE Polyunsaturated fatty acids (PUFAs) have attracted increasing attention for their role in liver cancer development. The objective of this study is to develop a prognosis prediction model for patients with liver cancer based on PUFA-related metabolic gene characteristics. METHOD Transcriptome data and clinical data were obtained from public databases, while gene sets related to PUFAs were acquired from the gene set enrichment analysis (GSEA) database. Univariate Cox analysis was conducted on the training set, followed by LASSO logistic regression and multivariate Cox analysis on genes with p < .05. Subsequently, the stepwise Akaike information criterion method was employed to construct the model. The high- and low-risk groups were divided based on the median score, and the model's survival prediction ability, diagnostic efficiency, and risk score distribution of clinical features were validated. The above procedures were also validated in the validation set. Immune infiltration levels were evaluated using four algorithms, and the immunotherapeutic potential of different groups was explored. Significant enrichment pathways among different groups were selected based on the GSEA algorithm, and mutation analyses were conducted. Nomogram prognostic models were constructed by incorporating clinical factors and risk scores using univariate and multivariate Cox regression analysis, validated through calibration curves and clinical decision curves. Additionally, sensitivity analysis of drugs was performed to screen potential targeted drugs. RESULTS We constructed a prognostic model comprising eight genes (PLA2G12A, CYP2C8, ABCCI, CD74, CCR7, P2RY4, P2RY6, and YY1). Validation across multiple datasets indicated the model's favorable prognostic prediction ability and diagnostic efficiency, with poorer grading and staging observed in the high-risk group. Variations in mutation status and pathway enrichment were noted among different groups. Incorporating Stage, Grade, T.Stage, and RiskScore into the nomogram prognostic model demonstrated good accuracy and clinical decision benefits. Multiple immune analyses suggested greater benefits from immunotherapy in the low-risk group. We predicted multiple targeted drugs, providing a basis for drug development. CONCLUSION Our study's multifactorial prognostic model across multiple datasets demonstrates good applicability, offering a reliable tool for personalized therapy. Immunological and mutation-related analyses provide theoretical foundations for further research. Drug predictions offer important insights for future drug development and treatment strategies. Overall, this study provides comprehensive insights into tumor prognosis assessment and personalized treatment planning.
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Affiliation(s)
- Yun Lin
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Ruihao Li
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Tong Li
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Wenrong Zhao
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Qianling Ye
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Chunyan Dong
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
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Yang S, Wang X, Huan R, Deng M, Kong Z, Xiong Y, Luo T, Jin Z, Liu J, Chu L, Han G, Zhang J, Tan Y. Machine learning unveils immune-related signature in multicenter glioma studies. iScience 2024; 27:109317. [PMID: 38500821 PMCID: PMC10946333 DOI: 10.1016/j.isci.2024.109317] [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: 09/16/2023] [Revised: 01/11/2024] [Accepted: 02/17/2024] [Indexed: 03/20/2024] Open
Abstract
In glioma molecular subtyping, existing biomarkers are limited, prompting the development of new ones. We present a multicenter study-derived consensus immune-related and prognostic gene signature (CIPS) using an optimal risk score model and 101 algorithms. CIPS, an independent risk factor, showed stable and powerful predictive performance for overall and progression-free survival, surpassing traditional clinical variables. The risk score correlated significantly with the immune microenvironment, indicating potential sensitivity to immunotherapy. High-risk groups exhibited distinct chemotherapy drug sensitivity. Seven signature genes, including IGFBP2 and TNFRSF12A, were validated by qRT-PCR, with higher expression in tumors and prognostic relevance. TNFRSF12A, upregulated in GBM, demonstrated inhibitory effects on glioma cell proliferation, migration, and invasion. CIPS emerges as a robust tool for enhancing individual glioma patient outcomes, while IGFBP2 and TNFRSF12A pose as promising tumor markers and therapeutic targets.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
| | - Xiang Wang
- Department of Neurosurgery, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Renzheng Huan
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Mei Deng
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhuo Kong
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yunbiao Xiong
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Tao Luo
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zheng Jin
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Jian Liu
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Liangzhao Chu
- Department of Neurosurgery, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Guoqiang Han
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
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10
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Xiong H, Chen Z, Li Y, Wu Z, Qian D, Chen L, Li Q, Liu H, Chen W, Lin B, Jia Y, Wang C. Pan-cancer analysis of the prognostic and immunological role of FKBP4. Heliyon 2024; 10:e29098. [PMID: 38601662 PMCID: PMC11004885 DOI: 10.1016/j.heliyon.2024.e29098] [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: 10/19/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/12/2024] Open
Abstract
Objectives Our previous studies revealed the significant roles of FK506-binding protein 4 (FKBP4) in tumorigenesis, however, there has been no pan-cancer analysis of FKBP4. Using bioinformatics, the current study reported the expression and prognostic role of FKBP4, and the correlation between FKBP4 and clinicopathological parameters, methylation, molecular network, immunological traits and drug sensitivity. Methods RNA sequencing data, somatic mutation, and related clinical information were obtained from TCGA using UCSC Xena. The association between FKBP4 expression and clinical features was assessed using TISIDB. The relationships between FKBP4 expression and tumour stage, OS, DSS, DFS, and PFS were analysed using univariate cox regression analysis. The radar plots for TMB and MSI were obtained using "Fmsb" R package. UALCAN was used to explore the effect of FKBP4 methylation on tumour and normal samples. CBioportal was used to analyse copy number mutations in FKBP4 Gene expression and drug sensitivity data were downloaded from the CellMiner database. GO analysis was performed for the high and the low expression of FKBP4 compared with the median level of FKBP4 using clusterProfiler4.0. Results FKBP4 expression is significantly upregulated in various types of cancers. Cox regression analysis showed that high FKBP4 levels were correlated with poor OS, DSS, DFS, and PFS in most patients with cancer. Methylation of FKBP4 DNA was upregulated in most cancers, and FKBP4 expression is positively associated with transmethylase expression. FKBP4 and its copy were significantly associated with the expression of immune-infiltrating cells, immune checkpoint genes, immune modulators, TMB, MMR, and MSI. FKBP4 expression levels significantly correlated with 16 different drug sensitivities (all p < 0.05). Conclusions Our pan-cancer bioinformatic analysis revealed a potential mechanism underlying the effects of FKBP4 on the prognosis and progression of various cancers.
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Affiliation(s)
- Hanchu Xiong
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zihan Chen
- Surgical Intensive Care Unit, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yucheng Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zhuazhua Wu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, The Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215000, China
| | - Long Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Qiang Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Huaxin Liu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Weijun Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Baihua Lin
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Yongshi Jia
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Cheng Wang
- Heart Center, Department of Cardiovascular Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
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11
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Duan W, Yang L, Liu J, Dai Z, Wang Z, Zhang H, Zhang X, Liang X, Luo P, Zhang J, Liu Z, Zhang N, Mo H, Qu C, Xia Z, Cheng Q. A TGF-β signaling-related lncRNA signature for prediction of glioma prognosis, immune microenvironment, and immunotherapy response. CNS Neurosci Ther 2024; 30:e14489. [PMID: 37850692 PMCID: PMC11017415 DOI: 10.1111/cns.14489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 07/27/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
AIMS The dysregulation of TGF-β signaling is a crucial pathophysiological process in tumorigenesis and progression. LncRNAs have diverse biological functions and are significant participants in the regulation of tumor signaling pathways. However, the clinical value of lncRNAs related to TGF-β signaling in glioma is currently unclear. METHODS Data on glioma's RNA-seq transcriptome, somatic mutation, DNA methylation data, and clinicopathological information were derived from the CGGA and TCGA databases. A prognostic lncRNA signature was constructed by Cox and LASSO regression analyses. TIMER2.0 database was utilized to deduce immune infiltration characteristics. "ELMER v.2" was used to reconstruct TF-methylation-gene regulatory network. Immunotherapy and chemotherapy response predictions were implemented by the TIDE algorithm and GDSC database, respectively. In vitro and in vivo experiments were conducted to verify the results and clarify the regulatory mechanism of lncRNA. RESULTS In glioma, a TGF-β signaling-related 15-lncRNA signature was constructed, including AC010173.1, HOXA-AS2, AC074286.1, AL592424.1, DRAIC, HOXC13-AS, AC007938.1, AC010729.1, AC013472.3, AC093895.1, AC131097.4, AL606970.4, HOXC-AS1, AGAP2-AS1, and AC002456.1. This signature proved to be a reliable prognostic tool, with high risk indicating an unfavorable prognosis and being linked to malignant clinicopathological and genomic mutation traits. Risk levels were associated with different immune infiltration landscapes, where high risk was indicative of high levels of macrophage infiltration. In addition, high risk also suggested better immunotherapy and chemotherapy response. cg05987823 was an important methylation site in glioma progression, and AP-1 transcription factor family participated in the regulation of signature lncRNA expression. AGAP2-AS1 knockdown in in vitro and in vivo experiments inhibited the proliferation, migration, and invasion of glioma cells, as well as the growth of glioma, by downregulating the expression levels of NF-κB and ERK 1/2 in the TGF-β signaling pathway. CONCLUSIONS A prognostic lncRNA signature of TGF-β signaling was established in glioma, which can be used for prognostic judgment, immune infiltration status inference, and immunotherapy response prediction. AGAP2-AS1 plays an important role in glioma progression.
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Affiliation(s)
- Wei‐Wei Duan
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Li‐Ting Yang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jian Liu
- Experiment Center of Medical InnovationThe First Hospital of Hunan University of Chinese MedicineChangshaHunanChina
| | - Zi‐Yu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ze‐Yu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xi‐Song Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zao‐Qu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Nan Zhang
- One‐third Lab, College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHei LongjiangChina
| | - Hao‐Yang Mo
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chun‐Run Qu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhi‐Wei Xia
- Department of NeurologyHunan Aerospace HospitalChangshaHunanChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
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12
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Ma Y, Fang F, Liao K, Zhang J, Wei C, Liao Y, Zhao B, Fang Y, Chen Y, Zhang X, Tang D. Identification and validation of the clinical prediction model and biomarkers based on chromatin regulators in colon cancer by integrated analysis of bulk- and single-cell RNA sequencing data. Transl Cancer Res 2024; 13:1290-1313. [PMID: 38617504 PMCID: PMC11009811 DOI: 10.21037/tcr-23-1886] [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: 10/12/2023] [Accepted: 02/08/2024] [Indexed: 04/16/2024]
Abstract
Background Chromatin regulators (CRs) are implicated in the development of cancer, but a comprehensive investigation of their role in colon adenocarcinoma (COAD) is inadequate. The purpose of this study is to find CRs that can provide recommendations for clinical diagnosis and treatment, and to explore the reasons why they serve as critical CRs. Methods We obtained data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Weighted Gene Co-Expression Network Analysis (WGCNA) screened tumor-associated CRs. LASSO-Cox regression was used to construct the model and to screen key CRs together with support vector machine (SVM), the univariate Cox regression. We used single-cell data to explore the expression of CRs in cells and their communication. Immune infiltration, immune checkpoints, mutation, methylation, and drug sensitivity analyses were performed. Gene expression was verified by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Pan-cancer analysis was used to explore the importance of hub CRs. Results We finally obtained 32 tumor-associated CRs. The prognostic model was constructed based on RCOR2, PPARGC1A, PKM, RAC3, PHF19, MYBBP1A, ORC1, and EYA2 by the LASSO-Cox regression. Single-cell data revealed that the model was immune-related. Combined with immune infiltration analysis, immune checkpoint analysis, and tumor immune dysfunction and exclusion (TIDE) analysis, the low-score risk group had more immune cell infiltration and better immune response. Mutation and methylation analysis showed that multiple CRs may be mutated and methylated in colon cancer. Drug sensitivity analysis revealed that the low-risk group may be more sensitive to several drugs and PKM was associated with multiple drugs. Combined with machine learning, PKM is perhaps the most critical gene in CRs. Pan-cancer analysis showed that PKM plays a role in the prognosis of cancers. Conclusions We developed a prognostic model for COAD based on CRs. Increased expression of the core gene PKM is linked with a poor prognosis in several malignancies.
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Affiliation(s)
- Yichao Ma
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Fang Fang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Kai Liao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Jingqiu Zhang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Chen Wei
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Yiqun Liao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Bin Zhao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yongkun Fang
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yuji Chen
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Xinyue Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Dong Tang
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
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13
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Zhang H, Lin J, Yahaya BH. Comprehensive analysis of co-expressed genes with TDP-43: prognostic and therapeutic potential in lung adenocarcinoma. J Cancer Res Clin Oncol 2024; 150:44. [PMID: 38281298 PMCID: PMC10822823 DOI: 10.1007/s00432-023-05554-9] [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: 07/24/2023] [Accepted: 11/09/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Transactivating DNA-binding protein 43 (TDP-43) is intimately associated with tumorigenesis and progression by regulating mRNA splicing, transport, stability, and non-coding RNA molecules. The exact role of TDP-43 in lung adenocarcinoma (LUAD) has not yet been fully elucidated, despite extensive research on its function in various cancer types. An imperative aspect of comprehending the underlying biological characteristics associated with TDP-43 involves investigating the genes that are co-expressed with this protein. This study assesses the prognostic significance of these co-expressed genes in LUAD and subsequently explores potential therapeutic strategies based on these findings. METHODS Transcriptomic and clinical data pertaining to LUAD were retrieved from open-access databases to establish an association between mRNA expression profiles and the presence of TDP-43. A risk-prognosis model was developed to compare patient survival rates across various groups, and its accuracy was also assessed. Additionally, differences in tumor stemness, mutational profiles, tumor microenvironment (TME) characteristics, immune checkpoints, and immune cell infiltration were analyzed in the different groups. Moreover, the study entailed predicting the potential response to immunotherapy as well as the sensitivity to commonly employed chemotherapeutic agents and targeted drugs for each distinct group. RESULTS The TDP-43 Co-expressed Gene Risk Score (TCGRS) model was constructed utilizing four genes: Kinesin Family Member 20A (KIF20A), WD Repeat Domain 4 (WDR4), Proline Rich 11 (PRR11), and Glia Maturation Factor Gamma (GMFG). The value of this model in predicting LUAD patient survival is effectively illustrated by both the Kaplan-Meier (K-M) survival curve and the area under the receiver operating characteristic curve (AUC-ROC). The Gene Set Enrichment Analysis (GSEA) revealed that the high TCGRS group was primarily enriched in biological pathways and functions linked to DNA replication and cell cycle; the low TCGRS group showed primary enrichment in immune-related pathways and functions. The high and low TCGRS groups showed differences in tumor stemness, mutational burden, TME, immune infiltration level, and immune checkpoints. The predictions analysis of immunotherapy indicates that the Tumor Immune Dysfunction and Exclusion (TIDE) score (p < 0.001) and non-response rate (74% vs. 51%, p < 0.001) in the high TCGRS group are higher than those in the low TCGRS group. The Immune Phenotype Score (IPS) in the high TCGRS group is lower than in the low TCGRS group (p < 0.001). The drug sensitivity analysis revealed that the half-maximal inhibitory concentration (IC50) values for cisplatin, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, vincristine, erlotinib, and gefitinib (all p < 0.01) in the high TCGRS group are lower than those in the low TCGRS group. CONCLUSIONS The TCGRS derived from the model exhibits a reliable biomarker for evaluating both prognosis and treatment effectiveness among patients with LUAD. This study is anticipated to offer valuable insights into developing effective treatment strategies for this patient population. It is believed that this study is anticipated to contribute significantly to clinical diagnostics, the development of therapeutic drugs, and the enhancement of patient care.
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Affiliation(s)
- Hao Zhang
- Lung Stem Cell and Gene Therapy Group (LSCGT), Department of Biomedical Sciences, Advanced Medical and Dental Institute (IPPT), Universiti Sains Malaysia, SAINS@Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Juntang Lin
- Henan Joint International Research Laboratory of Stem Cell Medicine, School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, China
| | - Badrul Hisham Yahaya
- Lung Stem Cell and Gene Therapy Group (LSCGT), Department of Biomedical Sciences, Advanced Medical and Dental Institute (IPPT), Universiti Sains Malaysia, SAINS@Bertam, 13200, Kepala Batas, Penang, Malaysia.
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14
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Voissière A, Gomez-Roca C, Chabaud S, Rodriguez C, Nkodia A, Berthet J, Montane L, Bidaux AS, Treilleux I, Eberst L, Terret C, Korakis I, Garin G, Pérol D, Delord JP, Caux C, Dubois B, Ménétrier-Caux C, Bendriss-Vermare N, Cassier PA. The CSF-1R inhibitor pexidartinib affects FLT3-dependent DC differentiation and may antagonize durvalumab effect in patients with advanced cancers. Sci Transl Med 2024; 16:eadd1834. [PMID: 38266104 DOI: 10.1126/scitranslmed.add1834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Tumor-associated macrophages (TAMs) are a critical determinant of resistance to PD-1/PD-L1 blockade. This phase 1 study (MEDIPLEX, NCT02777710) investigated the safety and efficacy of pexidartinib, a CSF-1R-directed tyrosine kinase inhibitor (TKI), and durvalumab (anti-PD-L1) in patients with advanced colorectal and pancreatic carcinoma with the aim to enhance responses to PD-L1 blockade by eliminating CSF-1-dependent suppressive TAM. Forty-seven patients were enrolled. No unexpected toxicities were observed, one (2%) high microsatellite instability CRC patient had a partial response, and seven (15%) patients experienced stable disease as their best response. Increase of CSF-1 concentrations and decrease of CD14lowCD16high monocytes in peripheral blood mononuclear cells (PBMCs) confirmed CSF-1R engagement. Treatment decreased blood dendritic cell (DC) subsets and impaired IFN-λ/IL-29 production by type 1 conventional DCs in ex vivo TLR3-stimulated PBMCs. Pexidartinib also targets c-KIT and FLT3, both key growth factor receptors of DC development and maturation. In patients, FLT3-L concentrations increased with pexidartinib treatment, and AKT phosphorylation induced by FLT3-L ex vivo stimulation was abrogated by pexidartinib in human blood DC subsets. In addition, pexidartinib impaired the FLT3-L- but not GM-CSF-dependent generation of DC subsets from murine bone marrow (BM) progenitors in vitro and decreased DC frequency in BM and tumor-draining lymph node in vivo. Our results demonstrate that pexidartinib, through the inhibition of FLT3 signaling, has a deleterious effect on DC differentiation, which may explain the limited antitumor clinical activity observed in this study. This work suggests that inhibition of FLT3 should be considered when combining TKIs with immune checkpoint inhibitors.
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Affiliation(s)
- Aurélien Voissière
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
| | - Carlos Gomez-Roca
- Department of Medical Oncology, Institut Claudius Regaud/Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Sylvie Chabaud
- Clinical Research Platform (DRCI), Centre Léon Bérard, Lyon, France
| | - Céline Rodriguez
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Axelle Nkodia
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Justine Berthet
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Laure Montane
- Clinical Research Platform (DRCI), Centre Léon Bérard, Lyon, France
| | | | | | - Lauriane Eberst
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, Lyon, France
| | - Catherine Terret
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, Lyon, France
| | - Iphigénie Korakis
- Department of Medical Oncology, Institut Claudius Regaud/Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Gwenaelle Garin
- Clinical Research Platform (DRCI), Centre Léon Bérard, Lyon, France
| | - David Pérol
- Clinical Research Platform (DRCI), Centre Léon Bérard, Lyon, France
| | - Jean-Pierre Delord
- Department of Medical Oncology, Institut Claudius Regaud/Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Christophe Caux
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Bertrand Dubois
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Christine Ménétrier-Caux
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Nathalie Bendriss-Vermare
- Université Claude Bernard Lyon 1, INSERM U-1052, CNRS 5286, Cancer Research Center of Lyon, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory (LICL), Centre Léon Bérard, Lyon, France
| | - Philippe A Cassier
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, Lyon, France
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Wu J, Wu C, Cai X, Li P, Lin J, Wang F. Malignant cell receptor-ligand subtypes guide the prediction of prognosis and personalized immunotherapy of liver cancer. Aging (Albany NY) 2024; 16:1712-1732. [PMID: 38244584 PMCID: PMC10866410 DOI: 10.18632/aging.205453] [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: 06/26/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
OBJECTIVE Liver cancer is a prevalent disease with a dismal prognosis. The aim of the research is to identify subgroups based on malignant cell receptor ligand gene from single-cell RNA, which might lead to customized immunotherapy for patients with liver cancer. METHODS Based on scRNA-seq data, we identified the receptor-ligand genes associated with prognosis and classify patients into molecular subtypes by univariate Cox regression and consensus clustering. LASSO regression was performed to construct a prognostic model, which was validated in TCGA and ICGC datasets. Immune infiltration and prediction of immunotherapy response were analyzed using ssGSEA, ESTIMATE, TIDE, and TRS score calculation. Finally, qPCR and Western blot validation of key genes and protein levels in cell lines. RESULTS A risk model using 16-gene expression levels predicted liver cancer patients' prognosis. The RiskScore associated significantly with tumor clinical characteristics and immunity, integrated with clinicopathological features for survival prediction. Differential expression of SRXN1 was verified in hepatocellular carcinoma and normal liver cells. CONCLUSION Our study utilizes single-cell analysis to investigate the communication between malignant cells and other cell types, identifying molecular subtypes based on malignant cell receptor ligand genes, offering new insights for the development of personalized immunotherapy and prognostic prediction models.
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Affiliation(s)
- Junzheng Wu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Chuncheng Wu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Xianhui Cai
- Xiamen Xianyue Hospital, Xiamen, Fujian, China
| | - Peipei Li
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Jianjun Lin
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Fuqiang Wang
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
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Dai Z, Wang Y, Sun N, Zhang C. Characterizing ligand-receptor interactions and unveiling the pro-tumorigenic role of CCL16-CCR1 axis in the microenvironment of hepatocellular carcinoma. Front Immunol 2024; 14:1299953. [PMID: 38274805 PMCID: PMC10808667 DOI: 10.3389/fimmu.2023.1299953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background The heterogeneity of the tumor microenvironment significantly influences the prognosis of hepatocellular carcinoma (HCC) patients, with cell communication through ligand-receptor complexes playing a central role. Methods We conducted single-cell transcriptomic analysis on ten HCC tissues to identify ligand-receptor genes involved in malignant HCC cell communication using CellChat. Leveraging RNA-Seq data from the TCGA Liver Cancer (TCGA-LIHC) and Liver Cancer - RIKEN, JP (LIRI-JP) cohorts, we employed Cox regression analysis to screen for prognosis-related genes. Prognostic risk models were constructed through unsupervised clustering and differential gene expression analysis. Subsequently, a co-culture system involving tumor cells and macrophages was established. A series of experiments, including Transwell assays, immunofluorescence staining, immunoprecipitation, flow cytometry, and immunohistochemistry, were conducted to elucidate the mechanism through which HCC cells recruit macrophages via the CCL16-CCR1 axis. Results Single-cell analysis unveiled significant interactions between malignant HCC cells and macrophages, identifying 76 related ligand-receptor genes. Patients were classified into three subtypes based on the expression patterns of eight prognosis-related ligand-receptor genes. The subtype with the worst prognosis exhibited reduced infiltration of T cell-related immune cells, downregulation of immune checkpoint genes, and increased M2-like tumor-associated macrophage scores. In vitro experiments confirmed the pivotal role of the CCL16-CCR1 axis in the recruitment and M2 polarization of tumor-associated macrophages. Clinical samples demonstrated a significant association between CCL16 protein expression levels and advanced stage, lymph node metastasis, and distant metastasis. Immunohistochemistry and immunofluorescence staining further confirmed the correlation between CCL16 and CCR1, CD68, and CD206, as well as CD68+CCR1+ macrophage infiltration. Conclusions Our study identified molecular subtypes, a prognostic model, and immune microenvironment features based on ligand-receptor interactions in malignant HCC cell communication. Moreover, we revealed the pro-tumorigenic role of HCC cells in recruiting M2-like tumor-associated macrophages through the CCL16-CCR1 axis.
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Affiliation(s)
- Zongbo Dai
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
| | - Yu Wang
- Department of General Surgery, Anshan Central Hospital, Anshan, China
| | - Ning Sun
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
| | - Chengshuo Zhang
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
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Luo W, Wen T, Qu X. Tumor immune microenvironment-based therapies in pancreatic ductal adenocarcinoma: time to update the concept. J Exp Clin Cancer Res 2024; 43:8. [PMID: 38167055 PMCID: PMC10759657 DOI: 10.1186/s13046-023-02935-3] [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: 10/06/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. The tumor immune microenvironment (TIME) formed by interactions among cancer cells, immune cells, cancer-associated fibroblasts (CAF), and extracellular matrix (ECM) components drives PDAC in a more immunosuppressive direction: this is a major cause of therapy resistance and poor prognosis. In recent years, research has advanced our understanding of the signaling mechanism by which TIME components interact with the tumor and the evolution of immunophenotyping. Through revolutionary technologies such as single-cell sequencing, we have gone from simply classifying PDACs as "cold" and "hot" to a more comprehensive approach of immunophenotyping that considers all the cells and matrix components. This is key to improving the clinical efficacy of PDAC treatments. In this review, we elaborate on various TIME components in PDAC, the signaling mechanisms underlying their interactions, and the latest research into PDAC immunophenotyping. A deep understanding of these network interactions will contribute to the effective combination of TIME-based therapeutic approaches, such as immune checkpoint inhibitors (ICI), adoptive cell therapy, therapies targeting myeloid cells, CAF reprogramming, and stromal normalization. By selecting the appropriate integrated therapies based on precise immunophenotyping, significant advances in the future treatment of PDAC are possible.
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Affiliation(s)
- Wenyu Luo
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China
| | - Ti Wen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China.
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China.
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Wang C, Chen Y, Zhou R, Yang Y, Fang Y. Systematic Analysis of Tumor Stem Cell-related Gene Characteristics to Predict the PD-L1 Immunotherapy and Prognosis of Gastric Cancer. Curr Med Chem 2024; 31:2467-2482. [PMID: 37936456 DOI: 10.2174/0109298673278775231101064235] [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: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
AIMS We aimed to develop a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in gastric cancer (GC). BACKGROUND Tumor stemness is related to intratumoral heterogeneity, immunosuppression, and anti-tumor resistance. We developed a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in GC. OBJECTIVE We aimed to develop a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in GC. METHODS We downloaded single-cell RNA sequencing (scRNA-seq) data of GC patients from the Gene-Expression Omnibus (GEO) database and screened GC stemness- related genes using CytoTRACE. We characterized the association of tumor stemness with immune checkpoint blockade (ICB) and immunity. Thereafter, a 9-stemness signature-based prognostic model was developed using weighted gene co-expression network analysis (WGCNA), univariate Cox regression analysis, and the least absolute shrinkage and selection operator (LASSO) regression analysis. The model predictive value was evaluated with a nomogram. RESULTS Early GC patients had significantly higher levels of stemness. The stemness score showed a negative relationship to tumor immune dysfunction and exclusion (TIDE) score and immune infiltration, especially T cells and B cells. A stemness-based signature based on 9 genes (ERCC6L, IQCC, NKAPD1, BLMH, SLC25A15, MRPL4, VPS35, SUMO3, and CINP) was constructed with good performance in prognosis prediction, and its robustness was validated in GSE26942 cohort. Additionally, nomogram and risk score exhibited the most powerful ability for prognosis prediction. High-risk patients exhibited a tendency to develop immune escape and low response to PD-L1 immunotherapy. CONCLUSION We developed a stemness-based gene signature for prognosis prediction with accuracy and reliability. This signature also helps clinical decision-making of immunotherapy for GC patients.
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Affiliation(s)
- Chenchen Wang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200000, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| | - Ying Chen
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Ru Zhou
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiaotong University School of Medicine, Shanghai, 200000, China
| | - Ya'nan Yang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200000, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| | - Yantian Fang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
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Wang J, Shu J. Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma. Curr Med Chem 2024; 31:1539-1560. [PMID: 37680151 DOI: 10.2174/0929867331666230901110629] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis. METHODS RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package. RESULTS Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy. CONCLUSION The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.
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Affiliation(s)
- Jiajing Wang
- Department of Clinical Laboratory, Beilun People's Hospital, Ningbo, 315000, China
| | - Jianfeng Shu
- Huamei Hospital, University of Chinese Academy of Sciences, Ningbo, 315000, China
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Li X, Lei J, Shi Y, Peng Z, Gong M, Shu X. Developing a RiskScore Model based on Angiogenesis-related lncRNAs for Colon Adenocarcinoma Prognostic Prediction. Curr Med Chem 2024; 31:2449-2466. [PMID: 37961859 DOI: 10.2174/0109298673277243231108071620] [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: 08/29/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
AIM We screened key angiogenesis-related lncRNAs based on colon adenocarcinoma (COAD) to construct a RiskScore model for predicting COAD prognosis and help reveal the pathogenesis of the COAD as well as optimize clinical treatment. BACKGROUND Regulatory roles of lncRNAs in tumor progression and prognosis have been confirmed, but few studies have probed into the role of angiogenesis-related lncRNAs in COAD. OBJECTIVE To identify key angiogenesis-related lncRNAs and build a RiskScore model to predict the survival probability of COAD patients and help optimize clinical treatment. METHODS Sample data were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The HALLMARK pathway score in the samples was calculated using the single sample gene set enrichment analysis (ssGSEA) method. LncRNAs associated with angiogenesis were filtered by an integrated pipeline algorithm. LncRNA-based subtypes were classified by ConsensusClusterPlus and then compared with other established subtypes. A RiskScore model was created based on univariate Cox, least absolute shrinkage and selection operator (LASSO) regression and stepwise regression analysis. The Kaplan-Meier curve was drawn by applying R package survival. The time-dependent ROC curves were drawn by the timeROC package. Finally, immunotherapy benefits and drug sensitivity were analyzed using tumor immune dysfunction and exclusion (TIDE) software and pRRophetic package. RESULTS Pathway analysis showed that the angiogenesis pathway was a risk factor affecting the prognosis of COAD patients. A total of 66 lncRNAs associated with angiogenesis were screened, and three molecular subtypes (S1, S2, S3) were obtained. The prognosis of S1 and S2 was better than that of S3. Compared with the existing subtypes, the S3 subtype was significantly different from the other two subtypes. Immunoassay showed that immune cell scores of the S2 subtype were lower than those of the S1 and S3 subtypes, which also had the highest TIDE scores. We recruited 8 key lncRNAs to develop a RiskScore model. The high RiskScore group with inferior survival and higher TIDE scores was predicted to benefit limitedly from immunotherapy, but it may be more sensitive to chemotherapeutics. A nomogram designed by RiskScore signature and other clinicopathological characteristics shed light on rational predictive power for COAD treatment. CONCLUSION We constructed a RiskScore model based on angiogenesis-related lncRNAs, which could serve as potential prognostic predictors for COAD patients and may offer clues for the intervention of anti-angiogenic application. Our results may help evaluate the prognosis of COAD and provide better treatment strategies.
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Affiliation(s)
- Xianguo Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Junping Lei
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441021, China
| | - Yongping Shi
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Zuojie Peng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Minmin Gong
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441021, China
| | - Xiaogang Shu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
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Xie Y, Pan X, Wang Z, Ma H, Xu W, Huang H, Zhang J, Wang X, Lian C. Multi-omics identification of GPCR gene features in lung adenocarcinoma based on multiple machine learning combinations. J Cancer 2024; 15:776-795. [PMID: 38213730 PMCID: PMC10777041 DOI: 10.7150/jca.90990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Background: Lung adenocarcinoma is a common malignant tumor that ranks second in the world and has a high mortality rate. G protein-coupled receptors (GPCRs) have been reported to play an important role in cancer; however, G protein-coupled receptor-associated features have not been adequately investigated. Methods: In this study, GPCR-related genes were screened at single-cell and bulk transcriptome levels based on AUcell, single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network (WGCNA) analysis. And a new machine learning framework containing 10 machine learning algorithms and their multiple combinations was used to construct a consensus G protein-coupled receptor-related signature (GPCRRS). GPCRRS was validated in the training set and external validation set. We constructed GPCRRS-integrated nomogram clinical prognosis prediction tools. Multi-omics analyses included genomics, single-cell transcriptomics, and bulk transcriptomics to gain a more comprehensive understanding of prognostic features. We assessed the response of risk subgroups to immunotherapy and screened for personalized drugs targeting specific risk subgroups. Finally, the expression of key GPCRRS genes was verified by RT-qPCR. Results: In this study, we identified 10 GPCR-associated genes that were significantly associated with the prognosis of lung adenocarcinoma by single-cell transcriptome and bulk transcriptome. Univariate and multivariate showed that the survival rate was higher in low risk than in high risk, which also suggested that the model was an independent prognostic factor for LUAD. In addition, we observed significant differences in biological function, mutational landscape, and immune cell infiltration in the tumor microenvironment between high and low risk groups. Notably, immunotherapy was also relevant in the high and low risk groups. In addition, potential drugs targeting specific risk subgroups were identified. Conclusion: In this study, we constructed and validated a lung adenocarcinoma G protein-coupled receptor-related signature, which has an important role in predicting the prognosis of lung adenocarcinoma and the effect of immunotherapy. It is hypothesized that LDHA, GPX3 and DOCK4 are new potential targets for lung adenocarcinoma, which can achieve breakthroughs in prognosis prediction, targeted prevention and treatment of lung adenocarcinoma and provide important guidance for anti-tumor.
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Affiliation(s)
- Yiluo Xie
- Department of Clinical Medicine, Bengbu Medical College, Bengbu 233030, China
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center pulmonary critical care medicine, First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China
| | - Xinyu Pan
- Department of Medical Imaging, Bengbu Medical College, Bengbu 233030, China
| | - Ziqiang Wang
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu 233030, China
| | - Hongyu Ma
- Department of Clinical Medicine, Bengbu Medical College, Bengbu 233030, China
| | - Wanjie Xu
- Department of Clinical Medicine, Bengbu Medical College, Bengbu 233030, China
| | - Hua Huang
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu 233030, China
| | - Jing Zhang
- Department of Genetics, School of Life Sciences, Bengbu Medical College, Bengbu 233000, China
| | - Xiaojing Wang
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center pulmonary critical care medicine, First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China
| | - Chaoqun Lian
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu 233030, China
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Sun X, Meng F, Nong M, Fang H, Lu C, Wang Y, Zhang P. Single-cell dissection reveals the role of aggrephagy patterns in tumor microenvironment components aiding predicting prognosis and immunotherapy on lung adenocarcinoma. Aging (Albany NY) 2023; 15:14333-14371. [PMID: 38095634 PMCID: PMC10756128 DOI: 10.18632/aging.205306] [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: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is one of the leading malignant cancers. Aggrephagy plays a critical role in key genetic events for various cancers; yet, how aggrephagy functions within the tumor microenvironment (TME) in LUAD remains to be elucidated. METHODS In this study, by sequential non-negative matrix factorization (NMF) algorithm, pseudotime analysis, cell-cell interaction analysis, and SCENIC analysis, we have shown that aggrephagy genes demonstrated various patterns among different cell types in LUAD TME. LUAD and Immunotherapy cohorts from public repository were used to determine the prognosis and immune response of aggrephagy TME subtypes. The aggrephagy-deprived prognostic score (ADPS) was quantified based on machine learning algorithms. RESULTS The cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), and CD8+ T cells have various aggrephagy patterns, which enhance the intensity of intercellular communication and transcription factor activation. Furthermore, based on the signatures of the newly defined aggrephagy cell subtypes and expression profiles of large cohorts in LUAD patients, we determine that DYNC1I2+CAF-C1, DYNLL1+CAF-C2, PARK7+CAF-C3, VIM+Mac-C1, PARK7+Mac-C2, VIM+CD8+T_cells-C1, UBA52+CD8+T_cells-C2, TUBA4A+CD8+T_ cells-C3, and TUBA1A+CD8+T_cells-C4 are crucial prognostic factors for LUAD patients. The developed ADPS could predict survival outcomes and immunotherapeutic response across ten cohorts (n = 1838), and patients with low ADPS owned a better prognosis, lower genomic alterations, and are more sensitive to immunotherapy. Meanwhile, based on PRISM, CTRP, and CMAP databases, PLK inhibitor BI-2536, may be a potential agent for patients with high ADPS. CONCLUSIONS Taken together, our novel and systematic single-cell analysis has revealed the unique role of aggrephagy in remodeling the TME of LUAD. As a newly demonstrated biomarker, the ADPS facilitates the clinical management and individualized treatment of LUAD.
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Affiliation(s)
- Xinti Sun
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Fei Meng
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Minyu Nong
- School of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Hao Fang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chenglu Lu
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Wang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
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Hong X, Fu R. Construction of a 5-gene prognostic signature based on oxidative stress related genes for predicting prognosis in osteosarcoma. PLoS One 2023; 18:e0295364. [PMID: 38039294 PMCID: PMC10691720 DOI: 10.1371/journal.pone.0295364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The understanding of the complex biological scenario of osteosarcoma will open the way to identifying new strategies for its treatment. Oxidative stress is a cancer-related biological scenario. At present, it is not clear the oxidative stress genes in affecting the prognosis and progression of osteosarcoma, the underlying mechanism as well as their impact on the classification of osteosarcoma subtypes. METHODS We selected samples and sequencing data from TARGET data set and GSE21257 data set, and downloaded oxidative stress related-genes (OSRGs) from MsigDB. Univariate Cox analysis of OSRG was conducted using TARGET data, and the prognostic OSRG was screened to conduct unsupervised clustering analysis to identify the molecular subtypes of osteosarcoma. Through least absolute shrinkage and selection operator (LASSO) regression analysis and COX regression analysis of differentially expressed genes (DEGs) between subgroups, a risk assessment system for osteosarcoma was developed. RESULTS 45 prognosis-related OSRGs genes were acquired, and two molecular subtypes of osteosarcoma were clustered. C2 cluster displayed prolonged overall survival (OS) accompanied with high degree of immune infiltration and enriched immune pathways. While cell cycle related pathways were enriched in C2 cluster. Based on DEGs between subgroups and Lasso analysis, 5 hub genes (ZYX, GJA5, GAL, GRAMD1B, and CKMT2) were screened to establish a robust prognostic risk model independent of clinicopathological features. High-risk group had more patients with cancer metastasis and death as well as C1 subtype with poor prognosis. Low-risk group exhibited favorable OS and high immune infiltration status. Additionally, the risk assessment system was optimized by building decision tree and nomogram. CONCLUSIONS This study defined two molecular subtypes of osteosarcoma with different prognosis and tumor immune microenvironment status based on the expression of OSRGs, and provided a new risk assessment system for the prognosis of osteosarcoma.
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Affiliation(s)
- Xiaofang Hong
- Department of Stomatology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Ribin Fu
- Department of Joint Surgery and Sports Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
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Chen Q, Zhao H, Hu J. A robust six-gene prognostic signature based on two prognostic subtypes constructed by chromatin regulators is correlated with immunological features and therapeutic response in lung adenocarcinoma. Aging (Albany NY) 2023; 15:12330-12368. [PMID: 37938151 PMCID: PMC10683604 DOI: 10.18632/aging.205183] [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: 02/20/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023]
Abstract
Accumulating evidence has demonstrated that chromatin regulators (CRs) regulate immune cell infiltration and are correlated with prognoses of patients in some cancers. However, the immunological and prognostic roles of CRs in lung adenocarcinoma (LUAD) are still unclear. Here, we systematically revealed the correlations of CRs with immunological features and the survival in LUAD patients based on a cohort of gene expression datasets from the public TCGA and GEO databases and real RNA-seq data by an integrative analysis using a comprehensive bioinformatics method. Totals of 160 differentially expressed CRs (DECRs) were identified between LUAD and normal lung tissues, and two molecular prognostic subtypes (MPSs) were constructed and evaluated based on 27 prognostic DECRs using five independent datasets (p =0.016, <0.0001, =0.008, =0.00038 and =0.00055, respectively). Six differentially expressed genes (DEGs) (CENPK, ANGPTL4, CCL20, CPS1, GJB3, TPSB2) between two MPSs had the most important prognostic feature and a six-gene prognostic model was established. LUAD patients in the low-risk subgroup showed a higher overall survival (OS) rate than those in the high-risk subgroup in nine independent datasets (p <0.0001, =0.021, =0.016, =0.0099, <0.0001, =0.0045, <0.0001, =0.0038 and =0.00013, respectively). Six-gene prognostic signature had the highest concordance index of 0.673 compared with 19 reported prognostic signatures. The risk score was significantly correlated with immunological features and activities of oncogenic signaling pathways. LUAD patients in the low-risk subgroup benefited more from immunotherapy and were less sensitive to conventional chemotherapy agents. This study provides novel insights into the prognostic and immunological roles of CRs in LUAD.
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Affiliation(s)
- Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hongbo Zhao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, China
| | - Jing Hu
- Department of Medical Oncology, First People’s Hospital of Yunnan Province, Kunming, China
- Department of Medical Oncology, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
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Luo Y, Wang H, Zhong J, Shi J, Zhang X, Yang Y, Wu R. Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma. Heliyon 2023; 9:e21336. [PMID: 37954334 PMCID: PMC10637964 DOI: 10.1016/j.heliyon.2023.e21336] [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: 07/19/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
Background APOBEC family play an important role in cancer mutagenesis and tumor development. The role of APOBEC family in lung adenocarcinoma (LUAD) has not been studied comprehensively. Materials and methods The expression data of pan-cancer as well as LUAD was obtained from public databases. The expression level of APOBEC family genes was analyzed in different normal and cancer tissues. APOBEC mutagenesis enrichment score (AMES) was utilized to evaluate the APOBEC-induced mutations and the relation of APOBEC with genomic instability. Gene set enrichment analysis was used to identify differentially enriched pathways. Univariate Cox regression and Lasso regression were applied to screen key prognostic genes. The immune cell infiltration was estimated by CIBERSORT. RT-qPCR assay, CCK-8 and Transwell assay were conducted to explore gene expression and lung cancer cell invasion. Results Cancer tissues had significantly altered expression of APOBEC family genes and the expression patterns of APOBEC family were different in different cancer types. APOBEC3B was the most aberrantly expressed in most cancer types. In LUAD, we observed a significantly positive correlation of AMES with intratumor heterogeneity (ITH), tumor neoantigen burden (TNB), and tumor mutation burden (TMB). High AMES group had high mutation counts of DNA damage repair pathways, and high enrichment of cell cycle and DNA repair pathways. We identified four prognostic genes (LYPD3, ANLN, MUC5B, and FOSL1) based on AMES, and constructed an AMES-related gene signature. The expressions of four genes were enhanced and accelerated the invasion ability and viability of lung cancer cells. Furthermore, we found that high group increased oxidative stress level. Conclusions APOBEC family was associated with genomic instability, DNA damage-related pathways, and cell cycle in LUAD. The AMES-related gene signature had a great potential to indicate the prognosis and guide immunotherapy/chemotherapy for patients suffering from LUAD.
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Affiliation(s)
- Yu Luo
- Gynecology Department of Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
- Beijing University of Traditional Chinese Medicine Guoyitang Expert Clinic, National Medical Hall of Beijing University of Traditional Chinese Medicine, Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
| | - Huiru Wang
- Clinical College of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Wuhan, 430014, China
| | - Jian Zhong
- Department of Nephrology, Dongzhimen Hospital, Beijing University of Traditional Chinese Medicine, Beijing, 100105, China
| | - Jianrong Shi
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xianlin Zhang
- Department of Endocrinology, Wuhan Hospital of Traditional Chinese Medicine, Wuhan Traditional Chinese Medicine Hospital, Wuhan, 430014, China
| | - Yanni Yang
- Health Management Center of Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
| | - Ruixin Wu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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Cong D, Zhao Y, Zhang W, Li J, Bai Y. Applying machine learning algorithms to develop a survival prediction model for lung adenocarcinoma based on genes related to fatty acid metabolism. Front Pharmacol 2023; 14:1260742. [PMID: 37920207 PMCID: PMC10619909 DOI: 10.3389/fphar.2023.1260742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Background: The progression of lung adenocarcinoma (LUAD) may be related to abnormal fatty acid metabolism (FAM). The present study investigated the relationship between FAM-related genes and LUAD prognosis. Methods: LUAD samples from The Cancer Genome Atlas were collected. The scores of FAM-associated pathways from the Kyoto Encyclopedia of Genes and Genomes website were calculated using the single sample gene set enrichment analysis. ConsensusClusterPlus and cumulative distribution function were used to classify molecular subtypes for LUAD. Key genes were obtained using limma package, Cox regression analysis, and six machine learning algorithms (GBM, LASSO, XGBoost, SVM, random forest, and decision trees), and a RiskScore model was established. According to the RiskScore model and clinical features, a nomogram was developed and evaluated for its prediction performance using a calibration curve. Differences in immune abnormalities among patients with different subtypes and RiskScores were analyzed by the Estimation of STromal and Immune cells in MAlignant Tumours using Expression data, CIBERSORT, and single sample gene set enrichment analysis. Patients' drug sensitivity was predicted by the pRRophetic package in R language. Results: LUAD samples had lower scores of FAM-related pathways. Three molecular subtypes (C1, C2, and C3) were defined. Analysis on differential prognosis showed that the C1 subtype had the most favorable prognosis, followed by the C2 subtype, and the C3 subtype had the worst prognosis. The C3 subtype had lower immune infiltration. A total of 12 key genes (SLC2A1, PKP2, FAM83A, TCN1, MS4A1, CLIC6, UBE2S, RRM2, CDC45, IGF2BP1, ANGPTL4, and CD109) were screened and used to develop a RiskScore model. Survival chance of patients in the high-RiskScore group was significantly lower. The low-RiskScore group showed higher immune score and higher expression of most immune checkpoint genes. Patients with a high RiskScore were more likely to benefit from the six anticancer drugs we screened in this study. Conclusion: We developed a RiskScore model using FAM-related genes to help predict LUAD prognosis and develop new targeted drugs.
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Affiliation(s)
- Dan Cong
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yanan Zhao
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wenlong Zhang
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jun Li
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yuansong Bai
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
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Cheng X, Yin X, Song J. Integrated analysis of NET-DNA receptor CCDC25 in malignant tumors: Pan-cancer analysis. Health Sci Rep 2023; 6:e1621. [PMID: 37841944 PMCID: PMC10568976 DOI: 10.1002/hsr2.1621] [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: 07/07/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Background Previously, it was reported that the coiled-coil domain containing 25 (CCDC25) plays a role in the formation of neutrophil extracellular traps (NETs). This study systematically analyzed the expression profiles of CCDC25 in 30 different types of cancer and one type of blood cancer, acute myeloid leukemia. Methods The GTEx and CCLE databases were used to evaluate the distribution of CCDC25 expression in both normal tissue and cancer cell lines. A comparison was performed between normal tissue and tumor tissue to analyze the differential expression of CCDC25. We assessed the impact of CCDC25 on the clinical outlook in the TCGA pan-cancer data set by analyzing the Kaplan-Meier survival plot and conducting COX regression analysis. Moreover, the association between the expression levels of CCDC25 and the tumor microenvironment in multiple cancers was conducted. Additionally, the investigation also examined the link between CCDC25 and immune neoantigen, tumor mutational burden, microsatellite instability, mismatch repair genes (MMRs), HLA-related genes, and DNA methyltransferase (DNMT). Results CCDC25 was expressed in nearly all of the 31 normal tissues while exhibiting a moderate to low level of expression in cancer cell lines. While abnormal expression was detected in the majority of malignancies, there was no link found between elevated CCDC25 levels and overall survival, disease-free survival, recurrence-free survival, and disease-free interval in the TCGA comprehensive cancer data set. Nevertheless, the expression of CCDC25 exhibited a notable link with the infiltration levels of activated CD4 memory T cells, quiescent mast cells, dendritic cells in an activated state, T cells that assist in follicle development, M2 macrophages, and neutrophils in various tumors. Conclusions In most cancers, the results indicate that there is no link between CCDC25 and prognosis. However, CCDC25 can be targeted for therapeutic purposes concerning metastasis and immune infiltration.
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Affiliation(s)
- Xianlin Cheng
- Department of Oral and Maxillofacial SurgeryGuizhou Provincial People's HospitalGuizhouChina
| | - Xinhai Yin
- Department of Oral and Maxillofacial SurgeryGuizhou Provincial People's HospitalGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial SurgeryThe Affiliated Stomatological Hospital of Guizhou Medical UniversityGuiyangChina
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Gui Z, Tian Y, Yu T, Liu S, Liu C, Zhang L. Clinical implications and immune features of CENPN in breast cancer. BMC Cancer 2023; 23:851. [PMID: 37697245 PMCID: PMC10496242 DOI: 10.1186/s12885-023-11376-2] [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: 06/08/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND A number of human diseases have been associated with Centromere protein N (CENPN), but its role in breast cancer is unclear. METHODS A pan-cancer database of Genotype Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) were used to examine the expression of CENPN. Using TCGA clinical survival data and breast cancer specimens from our center for validation, the relationship between CENPN expression, breast cancer prognosis, and clinicopathological characteristics of patients was examined. Bioinformatics was utilized to conduct an enrichment study of CENPN. Additionally, the potential of CENPN as a predictive biomarker for immunotherapy success was confirmed by analyzing the co-expression of CENPN with immune-checkpoint related genes, reviewing the TCGA database, and evaluating the correlation between CENPN expression and immune cell infiltration. Using the CCK8 test and colony formation assay, CENPN was evaluated for its ability to inhibit breast cancer cell proliferation. Transwell assays and scratch tests were used to assess the impact of CENPN on breast cancer cell migration. RESULTS CENPN is found in a wide range of tumors, including breast cancer. Additional investigation revealed that CENPN was co-expressed with the majority of immune checkpoint-related genes, had the potential to serve as a predictive biomarker for immunotherapy effectiveness, and that high CENPN expression was linked to high Tregs and low CD8 + T cells and NK cells. Breast cancer cells' malignant characteristics, such as migration and cell proliferation, were inhibited by CENPN knockdown. CONCLUSIONS According to our findings, CENPN may be an oncogene in breast cancer, as well as a new therapeutic target for immune checkpoint inhibitors.
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Affiliation(s)
- Zhengwei Gui
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China
| | - Yao Tian
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China
| | - Tianyao Yu
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China
| | - Shiyang Liu
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China
| | - Chenguang Liu
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China
| | - Lin Zhang
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong, University of Science and Technology, 1095 Jiefang Avenue, Wuhan City, 430030, Hubei Province, China.
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Zhang C, Xu T, Ji K, Cao S, Cao Y, Ai J, Jing L, Sun JH. An integrative analysis reveals the prognostic value and potential functions of PSMD11 in hepatocellular carcinoma. Mol Carcinog 2023; 62:1355-1368. [PMID: 37212487 DOI: 10.1002/mc.23568] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
The global burden of hepatocellular carcinoma (HCC) as a preeminent etiology of cancer-related mortalities sheds light on the imperative necessity for a more profound comprehension of its fundamental biological mechanisms. In this context, the precise function of the 26S proteasome non-ATPase regulatory subunit 11 (PSMD11) in HCC remains equivocal. To address this vital knowledge gap, we interrogated the cancer genome atlas, genotype-tissue expression, International cancer genome consortium, gene expression omnibus, the cancer cell line encyclopedia, and tumor immune single-cell hub databases to evaluate the expression pattern of PSMD11, further confirmed by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in LO2, MHCC-97H, HepG2, and SMMC7721 cell lines. Additionally, we meticulously assessed the clinical significance and prognostic value of PSMD11, while also exploring its potential molecular mechanisms in HCC. Our findings demonstrated that PSMD11 was highly expressed in HCC tissues, correlating with pathologic stage and histologic grade, thereby conferring a poor prognosis. Mechanistically, PSMD11 appears to exert its tumorigenic effects through the modulation of tumor metabolism-related pathways. Impressively, low PSMD11 expression was associated with increased immune effector cell infiltration, heightened responsiveness to molecular targeted drugs such as dasatinib, erlotinib, gefitinib, and imatinib, as well as reduced somatic mutation rate. Additionally, we demonstrated that PSMD11 might modulate HCC development through intricate interactions with cuproptosis-related genes ATP7A, DLAT, and PDHA1. Our comprehensive analyses collectively suggest that PSMD11 represents a promising therapeutic target in HCC.
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Affiliation(s)
- Cong Zhang
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Tiantian Xu
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Kun Ji
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Shoujin Cao
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Yunbo Cao
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Jing Ai
- Department of Ophthalmology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Li Jing
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
| | - Jun-Hui Sun
- Hepatobiliary and Pancreatic Interventional Treatment Center, Division of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang Provincial Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
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Mo S, Zou L, Hu Y, Chang X, Chen J. Expression of PD-L1 and VISTA in Intraductal Papillary Mucinous Neoplasm With Associated Invasive Carcinoma of the Pancreas. Mod Pathol 2023; 36:100223. [PMID: 37244388 DOI: 10.1016/j.modpat.2023.100223] [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: 11/04/2022] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Early detection and treatment of invasive carcinoma arising in association with intraductal papillary mucinous neoplasm (IPMN), which is biologically and (epi)genetically distinct from conventional pancreatic ductal adenocarcinoma, provide an opportunity to improve the prognosis of this lethal disease. Despite the successful application of programmed death (ligand) 1 (PD-[L]1)-blocking strategies in numerous cancers, the immune microenvironment of IPMN with associated invasive carcinoma remains elusive. Here, we investigated CD8+ T cells, CD68+ macrophages, PD-L1, and V-domain immunoglobulin suppressor of T-cell activation (VISTA) in 60 patients with IPMN with associated invasive carcinoma using immunohistochemistry, explored their correlations with clinicopathologic variables and prognosis, and compared them with those in 76 patients with IPMN without invasive carcinoma (60 low-grade and 16 high-grade lesions). Using antibodies against CD8, CD68, and VISTA, we evaluated tumor-infiltrating immune cells in 5 high-power fields (×400) and calculated the corresponding mean counts. PD-L1 with a combined positive score of ≥1 was regarded as positive, and VISTA expression on tumor cells (TCs) was deemed positive when ≥1% of TCs showed membranous/cytoplasmic staining. A reduction of CD8+ T cells and an increase of macrophages were observed during carcinogenesis. Positive PD-L1 combined positive score and VISTA expression on TCs were 13% and 11% in the intraductal component of IPMN with associated invasive carcinoma, 15% and 12% in the associated invasive carcinoma, and 6% and 4% in IPMN without an invasive carcinoma, respectively. Interestingly, the PD-L1 positivity rate was the highest in a subset of associated invasive carcinomas (predominantly gastric-type-derived) and was associated with higher counts of CD8+ T cells, macrophages, and VISTA+ immune cells. Accumulation of VISTA+ immune cells was observed in the intraductal component of IPMN with associated invasive carcinoma compared with that of low-grade IPMN, whereas in intestinal-type IPMN with associated invasive carcinoma, the number of these cells decreased during the transition from the intraductal component to the associated invasive carcinoma. Survival analysis revealed that a higher number of macrophages predicted poorer prognosis. In conclusion, our results might help in individualized immunotherapeutic strategies for these patients.
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Affiliation(s)
- Shengwei Mo
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Long Zou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ya Hu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyan Chang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie Chen
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Zhu Y, Liang L, Li J, Zeng J, Yao H, Wu L. Establishing Molecular Subgroups of CD8+ T Cell-Associated Genes in the Ovarian Cancer Tumour Microenvironment and Predicting the Immunotherapy Response. Biomedicines 2023; 11:2399. [PMID: 37760841 PMCID: PMC10525231 DOI: 10.3390/biomedicines11092399] [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: 06/02/2023] [Revised: 08/04/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The mechanism by which infiltrating CD8+ T lymphocytes in the tumour microenvironment influence the survival of patients with ovarian cancer (OC) remains unclear. METHODS To identify biomarkers to optimise OC treatment, 13 immune-cell-line-associated datasets, RNA sequencing data, and clinical data from the GEO, TCGA, and the ICGC were collected. Gene expression in OC was assessed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) staining. RESULTS We identified 520 genes and three immunological clusters (IC1, IC2, and IC3) associated with CD8+ T cells. Higher IFN scores, immune T cell lytic activity, and immune cell infiltration and upregulated expression of immune-checkpoint-related genes indicated that IC3 is more responsive to immunotherapy, whereas IC1 and IC2 have a poorer prognosis. A 10-gene signature, including SEMA4F, CX3CR1, STX7, PASK, AKIRIN2, HEMGN, GBP5, NSG1, and CXorf65, was constructed, and a multivariate Cox regression analysis revealed a significant association between the 10-gene signature-based risk model and overall survival (p < 0.001). A nomogram was constructed with age and the 10-gene signature. Consistent with the bioinformatics analysis, IHC and qRT-PCR confirmed the accuracy of the signatures in OC tissue samples. The predictive ability of the risk model was demonstrated using the Imvigor210 immunotherapy dataset. CONCLUSIONS The development of a novel gene signature associated with CD8+ T cells could facilitate more accurate prognostics and prediction of the immunotherapeutic response of patients with OC.
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Affiliation(s)
| | | | | | | | - Hongwen Yao
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Sun X, Yuan Z, Zhang L, Ren M, Yang J, Xu Y, Hao J. Comprehensive Analysis of SLC35A2 in Pan-Cancer and Validation of Its Role in Breast Cancer. J Inflamm Res 2023; 16:3381-3398. [PMID: 37593196 PMCID: PMC10427759 DOI: 10.2147/jir.s419994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023] Open
Abstract
Purpose Elucidation of the oncogenic role of SLC35A2 in human tumors and the potential function and clinical significance in breast cancer. Methods Pan-cancer analysis was performed via various bioinformatics tools to explain the pathogenic role of SLC35A2. A prognostic nomogram was also developed based on the SLC35A2 expression and clinicopathological characteristics in breast cancer patients. In addition, the role of SLC35A2 was validated in breast cancer by in vivo and in vitro experiments. Results SLC35A2 expression is increased in 27 tumor types, and its high expression is substantially correlated with poor prognosis in patients with a variety of cancers. Receiver operating characteristic (ROC) curves showed that SLC35A2 expression levels could accurately distinguish most tumor tissues from normal tissues. High SLC35A2 expression was linked to increased immune infiltration in myeloid-derived suppressor cells (MDSC), as well as immune checkpoints, ferroptosis-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI). SLC35A2 may be involved in tumorigenesis by regulating the glycosylation process. Furthermore, multivariate Cox analysis showed that SLC35A2 was an independent prognostic factor for breast cancer. And the nomogram model had good predictive accuracy for the prognosis of breast cancer patients. Meanwhile, cellular experiments demonstrated that knockdown of SLC35A2 could significantly inhibit the proliferation, migration and invasion of breast cancer cells, while increasing the protein level of E-cadherin and decreasing N-cadherin. A nude mouse xenograft model showed that inhibition of SLA35A2 expression could significantly inhibit tumor growth. Conclusion SLC35A2 has good diagnostic and prognostic values in multiple cancers and is closely related to tumor immune infiltration. In addition, SLA35A2 as an oncogene in breast cancer may be involved in the progression of epithelial mesenchymal transition (EMT).
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Affiliation(s)
- Xiaonan Sun
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Zhichao Yuan
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Lu Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Min Ren
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Jing Yang
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Yidan Xu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Jiqing Hao
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
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Hui H, Li D, Lin Y, Miao H, Zhang Y, Li H, Qiu F, Jiang B. Construction of subtype classifiers and validation of a prognostic risk model based on hypoxia-associated lncRNAs for lung adenocarcinoma. J Thorac Dis 2023; 15:3919-3933. [PMID: 37559652 PMCID: PMC10407533 DOI: 10.21037/jtd-23-952] [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: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Studies have shown that long non-coding RNAs (lncRNAs) are found to be hypoxia-regulated lncRNAs in cancer. Lung adenocarcinoma (LUAD) is the leading cause of cancer death worldwide, and despite early surgical removal, has a poor prognosis and a high recurrence rate. Thus, we aimed to identify subtype classifiers and construct a prognostic risk model using hypoxia-associated long noncoding RNAs (hypolncRNAs) for LUAD. METHODS Clinical data of LUAD samples with prognosis information obtained from the Gene Expression Omnibus (GEO), acted as validation dataset, and The Cancer Genome Atlas (TCGA) databases, served as training dataset, were used to screen hypolncRNAs in each dataset by univariate Cox regression analysis; the intersection set was used for subsequent analyses. Unsupervised clustering analysis was performed based on the expression of hypolncRNAs using the 'ConsensuClusterPlus' package. The tumor microenvironment (TME) was compared between LUAD subgroups by analyzing the expression of immune cell infiltration, immune components, stromal components, immune checkpoints, and chemokine secretion. To identify robust prognostically associated hypolncRNAs and construct a risk score model, multivariate Cox regression analysis was performed. RESULTS A total of 14 hypolncRNAs were identified. Based on the expression of these hypolncRNAs, patients with LUAD were classified into three hypolncRNA-regulated subtypes. The three subtypes differed significantly in immune cell infiltration, stromal score, specific immune checkpoints, and secretion of chemokines and their receptors. The Tumor Immune Dysfunction and Exclusion (TIDE) scores and myeloid-derived suppressor cell (MDSC) scores were also found to differ significantly among the three hypolncRNA-regulated subtypes. Four of the 14 hypolncRNAs were used to construct a signature to distinguish the overall survival (OS) in TCGA dataset (P<0.0001) and GEO dataset (P=0.0032) and sensitivity to targeted drugs in patients at different risks of LUAD. CONCLUSIONS We characterized three regulatory subtypes of hypolncRNAs with different TMEs. We developed a signature based on hypolncRNAs, contributing to the development of personalized therapy and representing a new potential therapeutic target for LUAD.
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Affiliation(s)
- Hongliang Hui
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Dan Li
- Community Health Center, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yangui Lin
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Haoran Miao
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yiqian Zhang
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Huaming Li
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Fan Qiu
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Bo Jiang
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Feng X, Shan R, Hu X. The linkage of NF-κB signaling pathway-associated long non-coding RNAs with tumor microenvironment and prognosis in cervical cancer. BMC Med Genomics 2023; 16:169. [PMID: 37461017 PMCID: PMC10351132 DOI: 10.1186/s12920-023-01605-9] [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: 03/28/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND NF-κB signaling pathway participate closely in regulating inflammation and immune response in many cancers. Long non-coding RNAs (lncRNAs) associated with NF-κB signaling have not been characterized in cervical cancer. This study revealed the linkage between tumor microenvironment and NF-κB signaling-associated lncRNAs in cervical cancer. MATERIALS AND METHODS The expression profiles of cervical cancer samples from The Cancer Genome Atlas (TCGA) database were downloaded. NF-κB signaling-associated lncRNAs were screened as a basis to perform molecular subtyping. Immune cell infiltration was assessed by ESTIMATE, Microenvironment Cell Populations (MCP)-counter and single sample gene set enrichment analysis (ssGSEA). The key NF-κB signaling-associated lncRNAs were identified by univariate analysis, least absolute shrinkage and selection operator, and stepAIC. RESULTS Three molecular subtypes or clusters (cluster 3, cluster 2, and cluster 1) were categorized based on 27 prognostic NF-κB signaling-associated lncRNAs. Cluster 2 had the worst prognosis, highest immune infiltration, as well as the highest expression of most of immune checkpoints. Three clusters showed different sensitivities to immunotherapy and chemotherapy. Six key NF-κB signaling-associated lncRNAs were screened to establish a six-lncRNA risk model for predicting cervical cancer prognosis. CONCLUSIONS NF-κB signaling-associated lncRNAs played an important role in regulating immune microenvironment. The subtyping based on NF-κB signaling-associated lncRNAs may assist in the selection of optimal treatments. The six key NF-κB signaling-associated lncRNAs could act as prognostic biomarkers in prognostic prediction for cervical cancer.
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Affiliation(s)
- Xue Feng
- Department of Reproductive Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150010, China
| | - Ru Shan
- Department of Reproductive Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150010, China
| | - Xiaomeng Hu
- Department of Medical Psychology, Harbin Medical University, Harbin, 150010, China.
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Lian QX, Song Y, Han L, Wang Z, Song Y. Development of a circHIPK3-based ceRNA network and identification of mRNA signature in breast cancer patients harboring BRCA mutation. PeerJ 2023; 11:e15572. [PMID: 37426414 PMCID: PMC10329424 DOI: 10.7717/peerj.15572] [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: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
Background Exploring the regulatory network of competing endogenous RNAs (ceRNAs) as hallmarks for breast cancer development has great significance and could provide therapeutic targets. An mRNA signature predictive of prognosis and therapy response in BRCA carriers was developed according to circular RNA homeodomain-interacting protein kinase 3 (circHIPK3)-based ceRNA network. Method We constructed a circHIPK3-based ceRNA network based on GSE173766 dataset and identified potential mRNAs that were associated with BRCA mutation patients within this ceRNA network. A total of 11 prognostic mRNAs and a risk model were identified and developed by univariate Cox regression analysis and the LASSO regression analysis as well as stepAIC method. Genomic landscape was treated by mutect2 and fisher. Immune characteristics was analyzed by ESTIMATE, MCP-counter. TIDE analysis was conducted to predict immunotherapy. The clinical treatment outcomes of BRCA mutation patients were assessed using a nomogram. The proliferation, migration and invasion in breast cancer cell lines were examined using CCK8 assay and transwell assay. Result We found 241 mRNAs within the circHIPK3-based ceRNA network. An 11 mRNA-based signature was identified for prognostic model construction. High risk patients exhibited dismal prognosis, low response to immunotherapy, less immune cell infiltration and tumor mutation burden (TMB). High-risk patients were sensitive to six anti-tumor drugs, while low-risk patient were sensitive to 47 drugs. The risk score was the most effective on evaluating patients' survival. The robustness and good prediction performance were validated in The Cancer Genome Atlas (TCGA) dataset and immunotherapy datasets, respectively. In addition, circHIPK3 mRNA level was upregulated, and promoted cell viability, migration and invasion in breast cancer cell lines. Conclusion The current study could improve the understanding of mRNAs in relation to BRCA mutation and pave the way to develop mRNA-based therapeutic targets for breast cancer patients with BRCA mutation.
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Affiliation(s)
- Qi-xin Lian
- Oncology Department, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yang Song
- Pathology Department, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Lili Han
- General Surgery, The Seventh Medical Center of the General Hospital of the Chinese People’s Liberation, Jiamusi, China
| | - Zunxian Wang
- Chemoradiotherapy, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yinhui Song
- Department of Breast Surgery, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Qiqihar, China
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Yang W, Zhao X, Duan L, Niu L, Zhang Y, Zhou W, Li Y, Chen J, Fan A, Xie Q, Liu J, Han Y, Fan D, Hong L. Development and validation of a ligand-receptor pairs signature to predict outcome and provide a therapeutic strategy in gastric cancer. Expert Rev Mol Diagn 2023; 23:619-634. [PMID: 37248704 DOI: 10.1080/14737159.2023.2219843] [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: 12/29/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND An important factor in tumor development and progression is the tumor microenvironment (TME), which is heterogeneous. Previous studies have mainly investigated the expression profile and prognostic values of genes in gastric cancer (GC) at the cell population level but neglected the interactions and heterogeneity between cells. METHODS The pattern of ligand-receptor (LR) interactions was delineated on a scRNA-seq dataset containing 44,953 cells from nine GC patients and a fourth bulk RNA-seq dataset including data from 1159 GC patients. We then constructed an LR.Score scoring model to comprehensively evaluate the influence of LR-pairs on the TME, overall survival, and immunotherapy response in GC patients from several cohorts. RESULTS Cell communication network among 13 cell types was constructed based on the LR-pairs. We proposed a new molecular subtyping model for GC based on the LR-pairs and revealed the differences in prognosis, pathophysiologic features, mutation characteristics, function enrichment, and immunological characteristics among the three subtypes. Finally, an LR.Score model based on LR-pairs was developed and validated on several datasets. CONCLUSIONS Based on the selected LR-pairs, we successfully constructed a novel prediction model and observed its well performance on molecular subtyping, target and pathway screening, prognosis judging, and immunotherapy response predicting.
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Affiliation(s)
- Wanli Yang
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Xinhui Zhao
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Northwest University & Xi'an No.3 Hospital, Northwest University, Xi'an, Shaanxi Province, China
| | - Lili Duan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liaoran Niu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yujie Zhang
- Department of Histology and Embryology, School of Basic Medicine, Xi'an Medical University, Xi'an, Shaanxi Province, China
| | - Wei Zhou
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yiding Li
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Junfeng Chen
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Aqiang Fan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Qibin Xie
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Jinqiang Liu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yu Han
- Department of Otolaryngology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liu Hong
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
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Tang L, Zhang Z, Fan J, Xu J, Xiong J, Tang L, Jiang Y, Zhang S, Zhang G, Luo W, Xu Y. Comprehensively analysis of immunophenotyping signature in triple-negative breast cancer patients based on machine learning. Front Pharmacol 2023; 14:1195864. [PMID: 37426809 PMCID: PMC10328722 DOI: 10.3389/fphar.2023.1195864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Immunotherapy is a promising strategy for triple-negative breast cancer (TNBC) patients, however, the overall survival (OS) of 5-years is still not satisfactory. Hence, developing more valuable prognostic signature is urgently needed for clinical practice. This study established and verified an effective risk model based on machine learning methods through a series of publicly available datasets. Furthermore, the correlation between risk signature and chemotherapy drug sensitivity were also performed. The findings showed that comprehensive immune typing is highly effective and accurate in assessing prognosis of TNBC patients. Analysis showed that IL18R1, BTN3A1, CD160, CD226, IL12B, GNLY and PDCD1LG2 are key genes that may affect immune typing of TNBC patients. The risk signature plays a robust ability in prognosis prediction compared with other clinicopathological features in TNBC patients. In addition, the effect of our constructed risk model on immunotherapy response was superior to TIDE results. Finally, high-risk groups were more sensitive to MR-1220, GSK2110183 and temsirolimus, indicating that risk characteristics could predict drug sensitivity in TNBC patients to a certain extent. This study proposes an immunophenotype-based risk assessment model that provides a more accurate prognostic assessment tool for patients with TNBC and also predicts new potential compounds by performing machine learning algorithms.
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Shi Q, Xue C, Zeng Y, Gu X, Wang J, Li L. A novel prognostic model for hepatocellular carcinoma based on pyruvate metabolism-related genes. Sci Rep 2023; 13:9780. [PMID: 37328616 PMCID: PMC10275940 DOI: 10.1038/s41598-023-37000-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent form of primary liver cancer, accounting for over 90% of cases. As pyruvate metabolic pathways are often dysregulated in cancer cells, investigating pyruvate metabolism-related genes may help identify prognostic gene signature and develop potential strategies for the management of patients with HCC. The mRNA expression profile, gene mutation data, and clinical information of HCC were obtained from open-source databases. A list of pyruvate metabolism-related genes was downloaded from the MSigDB dataset. Our findings revealed that certain pyruvate metabolism-related genes had copy number variations and single nucleotide variations in patients with liver cancer. Based on pyruvate metabolism-related genes, we stratified patients with HCC into three subtypes with different prognoses, clinical features, mutation profiles, functional annotation, and immune infiltration status. Next, we identified 13 key pyruvate metabolism-related genes significantly correlated with the prognosis of HCC using six machine learning algorithms and constructed a risk model. We also observed that the risk score was positively associated with a worse prognosis and increased immune infiltration. In summary, our study established a prognostic risk model for HCC based on pyruvate metabolism-related genes, which may contribute to the identification of potential prognostic targets and the development of new clinical management strategies for HCC.
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Affiliation(s)
- Qingmiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Yifan Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Jinzhi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China.
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Chen J, Wu S, Peng Y, Zhao Y, Dong Y, Ran F, Geng H, Zhang K, Li J, Huang S, Wang Z. Constructing a cancer stem cell related prognostic model for predicting immune landscape and drug sensitivity in colorectal cancer. Front Pharmacol 2023; 14:1200017. [PMID: 37377935 PMCID: PMC10292801 DOI: 10.3389/fphar.2023.1200017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Background: Colorectal cancer (CRC) ranks the second malignancy with high incidence and mortality worldwide. Cancer stem cells (CSCs) function critically in cancer progression and metastasis via the interplay with immune cells in tumor microenvironment. This study aimed to identify important CSC marker genes and parsed the role of these marker genes in CRC. Materials and methods: CRC samples' single-cell RNA sequencing data and bulk transcriptome data were utilized. Seurat R package annotated CSCs and identified CSC marker genes. Consensus clustering subtyped CRC samples based on CSC marker genes. Immune microenvironment, pathway and oxidative stress analysis was performed using ESTIMATE, MCP-counter analysis and ssGSEA analysis. A prognostic model was established by Lasso and stepAIC. Sensitivity to chemotherapeutic drugs was determined by the biochemical half maximal inhibitory concentration with pRRophetic R package. Results: We identified a total of 29 CSC marker genes related to disease-specific survival (DSS). Two clusters (CSC1 and CSC2) were determined, and CSC2 showed shorter DSS, a larger proportion of late-stage samples, and higher oxidative stress response. Two clusters exhibited differential activation of biological pathways associated with immune response and oncogenic signaling. Drug sensitivity analysis showed that 44 chemotherapy drugs were more sensitive to CSC2 that those in CSC1. We constructed a seven-gene prognostic model (DRD4, DPP7, UCN, INHBA, SFTA2, SYNPO2, and NXPH4) that was effectively to distinguish high-risk and low-risk patients. 14 chemotherapy drugs were more sensitive to high-risk group and 13 chemotherapy drugs were more sensitive to low-risk group. Combination of higher oxidative stress and risk score indicated dismal prognosis. Conclusion: The CSC marker genes we identified may help to further decipher the role of CSCs in CRC development and progression. The seven-gene prognostic model could serve as an indicator for predicting the response to immunotherapy and chemotherapy as well as prognosis of CRC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianjun Li
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
| | - Shuo Huang
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
| | - Zhe Wang
- *Correspondence: Jianjun Li, ; Shuo Huang, ; Zhe Wang,
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Li C, Zhang K, Gong Y, Wu Q, Zhang Y, Dong Y, Li D, Wang Z. Based on cuproptosis-related lncRNAs, a novel prognostic signature for colon adenocarcinoma prognosis, immunotherapy, and chemotherapy response. Front Pharmacol 2023; 14:1200054. [PMID: 37377924 PMCID: PMC10291194 DOI: 10.3389/fphar.2023.1200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction: Colon adenocarcinoma (COAD) is a special pathological subtype of colorectal cancer (CRC) with highly heterogeneous solid tumors with poor prognosis, and novel biomarkers are urgently required to guide its prognosis. Material and methods: RNA-Seq data of COAD were downloaded through The Cancer Genome Atlas (TCGA) database to determine cuproptosis-related lncRNAs (CRLs) using weighted gene co-expression network analysis (WGCNA). The scores of the pathways were calculated by single-sample gene set enrichment analysis (ssGSEA). CRLs that affected prognoses were determined via the univariate COX regression analysis to develop a prognostic model using multivariate COX regression analysis and LASSO regression analysis. The model was assessed by applying Kaplan-Meier (K-M) survival analysis and receiver operating characteristic curves and validated in GSE39582 and GSE17538. The tumor microenvironment (TME), single nucleotide variants (SNV), and immunotherapy response/chemotherapy sensitivity were assessed in high- and low-score subgroups. Finally, the construction of a nomogram was adopted to predict survival rates of COAD patients during years 1, 3, and 5. Results: We found that a high cuproptosis score reduced the survival rates of COAD significantly. A total of five CRLs affecting prognosis were identified, containing AC008494.3, EIF3J-DT, AC016027.1, AL731533.2, and ZEB1-AS1. The ROC curve showed that RiskScore could perform well in predicting the prognosis of COAD. Meanwhile, we found that RiskScore showed good ability in assessing immunotherapy and chemotherapy sensitivity. Finally, the nomogram and decision curves showed that RiskScore would be a powerful predictor for COAD. Conclusion: A novel prognostic model was constructed using CRLs in COAD, and the CRLs in the model were probably a potential therapeutic target. Based on this study, RiskScore was an independent predictor factor, immunotherapy response, and chemotherapy sensitivity for COAD, providing a new scientific basis for COAD prognosis management.
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Affiliation(s)
- Chong Li
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, China
- Department of Oncology, Dazu Hospital of Chongqing Medical University, Chongqing, China
| | - Keqian Zhang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuzhu Gong
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qinan Wu
- Endocrinology Department, Dazu Hospital of Chongqing Medical University, Chongqing, China
| | - Yanyan Zhang
- Department of Oncology, Dazu Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Dong
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dejia Li
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, China
| | - Zhe Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Sun G, Yang Z, Fang K, Xiong Y, Tu S, Yi S, Xiao W. Distribution characteristics and clinical significance of infiltrating T cells in the tumor microenvironment of pancreatic cancer. Oncol Lett 2023; 25:261. [PMID: 37205920 PMCID: PMC10189847 DOI: 10.3892/ol.2023.13847] [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: 07/28/2022] [Accepted: 03/24/2023] [Indexed: 05/21/2023] Open
Abstract
Tumor-infiltrating lymphocytes (TILs) are important components of the tumor microenvironment (TME). However, the distribution characteristics of TILs and their significance in pancreatic cancer (PC) remain largely unexplored. The levels of TILs, including the total number of T cells, cluster of differentiation (CD)4+ T cells, CD8+ cytotoxic T lymphocytes (CTLs), regulatory T-cells (Tregs), programmed cell death protein 1+ T cells and programmed cell death ligand 1 (PD-L1)+ T cells, in the TME of patients with PC were detected using multiple fluorescence immunohistochemistry. The associations between the number of TILs and the clinicopathological characteristics were investigated using χ2 tests. In addition, Kaplan-Meier survival and Cox regression analyses were used to assess the prognostic value of these TIL types. Compared with paracancerous tissues, in PC tissues, the proportions of total T cells, CD4+ T cells and CD8+ CTLs were markedly decreased, while those of Tregs and PD-L1+ T cells were significantly increased. The levels of CD4+ T cell and CD8+ CTL infiltrates were inversely associated with tumor differentiation. Higher infiltrates of Tregs and PD-L1+ T cells were closely associated with advanced N and TNM stages. It is important to note that the infiltrates of total T cells, CD4+ T cells, Tregs and PD-L1+ T cells in the TME were independent risk factors for the prognosis of PC. PC was characterized by an immunosuppressive TME with a decrease in the number of CD4+ T cells and CD8+ CTLs, and an increase in the number of Tregs and PD-L1+ T cells. Overall, the number of total T cells, CD4+ T cells, Tregs and PD-L1+ T cells in the TME was a potential predictive marker for the prognosis of PC.
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Affiliation(s)
- Gen Sun
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhengjiang Yang
- Department of General Surgery, The Affiliated Hospital of Jiujiang College, Jiujiang, Jiangxi 332001, P.R. China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Siqing Yi
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Correspondence to: Dr Weidong Xiao, Department of General Surgery, The First Affiliated Hospital of Nanchang University, 17 Yongwaizhengjie, Nanchang, Jiangxi 330006, P.R. China, E-mail:
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Lian W, Zheng X. Identification and validation of TME-related signatures to predict prognosis and response to anti-tumor therapies in skin cutaneous melanoma. Funct Integr Genomics 2023; 23:153. [PMID: 37160578 DOI: 10.1007/s10142-023-01051-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: 12/17/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023]
Abstract
The tumor microenvironment (TME) dynamically regulates cancer progression and affects clinical outcomes. This study aimed to identify molecular subtypes and construct a prognostic risk model based on TME-related signatures in skin cutaneous melanoma (SKCM) patients. We categorized SKCM patients based on transcriptome data of SKCM from The Cancer Genome Atlas (TCGA) database and 29 TME-related gene signatures. Differentially expressed genes were identified using univariate Cox regression and Lasso regression analysis, which were used for risk model construction. The robustness of this model was validated in independent external cohorts. Genetic landscape alterations, immune characteristics, and responsiveness to immunotherapy/chemotherapy were evaluated. Three TME-related subtypes were identified, and subtype C3 exhibited the most favorable prognosis, had enriched immune-related pathways, and possessed more infiltration of T_cells_CD8, T_cells_CD4_memory_activated, and Macrophages_M1 but a lower TumorPurity, whereas Macrophages_M2 were increased in subtype C1 and subtype C2. Subtype C1 was more sensitive to Cisplatin, subtype C2 was more sensitive to Temozolomide, and subtype C3 was more sensitive to Paclitaxel; 8 TME-related genes (NOTCH3, HEYL, ZNF703, ABCC2, PAEP, CCL8, HAPLN3, and HPDL) were screened for risk model construction. High-risk patients had dismal prognosis with good prediction performance. Moreover, low-risk patients were more sensitive to Paclitaxel and Temozolomide, whereas high-risk patients were more sensitive to Cisplatin. This risk model had robustness in predicting prognosis in SKCM patients. The results facilitate the understanding of TME-related genes in SKCM and provide a TME-related genes-based predictive model in prognosis and direction of personalized options for SKCM patients.
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Affiliation(s)
- Wenqin Lian
- Department of Burns and Plastic & Wound Repair Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361100, China
| | - Xiao Zheng
- Department of General Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
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Duan Y, Zhang X, Ying H, Xu J, Yang H, Sun K, He L, Li M, Ji Y, Liang T, Bai X. Targeting MFAP5 in cancer-associated fibroblasts sensitizes pancreatic cancer to PD-L1-based immunochemotherapy via remodeling the matrix. Oncogene 2023:10.1038/s41388-023-02711-9. [PMID: 37156839 DOI: 10.1038/s41388-023-02711-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Highly desmoplastic and immunosuppressive tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) contributes to tumor progression and resistance to current therapies. Clues targeting the notorious stromal environment have offered hope for improving therapeutic response whereas the underlying mechanism remains unclear. Here, we find that prognostic microfibril associated protein 5 (MFAP5) is involved in activation of cancer-associated fibroblasts (CAFs). Inhibition of MFAP5highCAFs shows synergistic effect with gemcitabine-based chemotherapy and PD-L1-based immunotherapy. Mechanistically, MFAP5 deficiency in CAFs downregulates HAS2 and CXCL10 via MFAP5/RCN2/ERK/STAT1 axis, leading to angiogenesis, hyaluronic acid (HA) and collagens deposition reduction, cytotoxic T cells infiltration, and tumor cells apoptosis. Additionally, in vivo blockade of CXCL10 with AMG487 could partially reverse the pro-tumor effect from MFAP5 overexpression in CAFs and synergize with anti-PD-L1 antibody to enhance the immunotherapeutic effect. Therefore, targeting MFAP5highCAFs might be a potential adjuvant therapy to enhance the immunochemotherapy effect in PDAC via remodeling the desmoplastic and immunosuppressive microenvironment.
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Affiliation(s)
- Yi Duan
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Xiaozhen Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Honggang Ying
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Jian Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Hanshen Yang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Kang Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Lihong He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Muchun Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Yongtao Ji
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China
- Cancer Center, Zhejiang University, Hangzhou, 310000, China
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China.
- Cancer Center, Zhejiang University, Hangzhou, 310000, China.
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China.
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Innovation Center for The Study of Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Clinical Research Center for The Study of Hepatobiliary & Pancreatic Diseases, Zhejiang University, Hangzhou, 310000, China.
- Cancer Center, Zhejiang University, Hangzhou, 310000, China.
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, 310000, Zhejiang, China.
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Zhang Y, Li T, Liu H, Wang L. Function and prognostic value of basement membrane -related genes in lung adenocarcinoma. Front Pharmacol 2023; 14:1185380. [PMID: 37214471 PMCID: PMC10196008 DOI: 10.3389/fphar.2023.1185380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD) has become a common cause of cancer-related death. Many studies have shown that the basement membrane (BM) is associated with the development of cancer. However, BM-related gene expression and its relationship to LUAD prognosis remains unclear. Methods: BM-related genes from previous studies were used. Clinical and mRNA expression information were obtained from TCGA database. Cox, minimum absolute contraction, and selection operator regression were applied to analyze the selected genes affecting LUAD prognosis. A prognostic-risk model was then established. Furthermore, this study applied Kaplan-Meier analysis to assess the outcomes of high- and low-risk groups, then explored their differences in drug sensitivity. The DSigDB database was used to screen for therapeutic small-molecule drugs. Results: Fourteen prognostic models based on BM-related genes were successfully constructed and validated in patients with LUAD. We also found that independence was a prognostic factor in all 14 BM-based models. Functional analysis showed that the enrichment of BM-related genes mainly originated from signaling pathways related to cancer. The BM-based model also suggested that immune cell infiltration is associated with checkpoints. The low-risk patients may benefit from cyclopamine and docetaxel treatments. Conclusion: This study identified a reliable biomarker to predict survival in patients with LUAD and offered new insights into the function of BM-related genes in LUAD.
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Affiliation(s)
- Yurong Zhang
- Department of Scientific Research, The First Affiliated Hospital, Xi’an Medical University, Xi’an, Shaanxi, China
| | - Tingting Li
- Department of Pharmacy, Xi’an Chest Hospital, Xi’an, Shaanxi, China
| | - Huanqing Liu
- Information Construction and Management Office, Northwest Polytechnical University, Xi’an, Shaanxi, China
| | - Li Wang
- Department of Scientific Research, The First Affiliated Hospital, Xi’an Medical University, Xi’an, Shaanxi, China
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Xi Y, Song L, Wang S, Zhou H, Ren J, Zhang R, Fu F, Yang Q, Duan G, Wang J. Identification of basement membrane-related prognostic signature for predicting prognosis, immune response and potential drug prediction in papillary renal cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10694-10724. [PMID: 37322956 DOI: 10.3934/mbe.2023474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Papillary renal cell carcinoma (PRCC) is a malignant neoplasm of the kidney and is highly interesting due to its increasing incidence. Many studies have shown that the basement membrane (BM) plays an important role in the development of cancer, and structural and functional changes in the BM can be observed in most renal lesions. However, the role of BM in the malignant progression of PRCC and its impact on prognosis has not been fully studied. Therefore, this study aimed to explore the functional and prognostic value of basement membrane-associated genes (BMs) in PRCC patients. We identified differentially expressed BMs between PRCC tumor samples and normal tissue and systematically explored the relevance of BMs to immune infiltration. Moreover, we constructed a risk signature based on these differentially expressed genes (DEGs) using Lasso regression analysis and demonstrated their independence using Cox regression analysis. Finally, we predicted 9 small molecule drugs with the potential to treat PRCC and compared the differences in sensitivity to commonly used chemotherapeutic agents between high and low-risk groups to better target patients for more precise treatment planning. Taken together, our study suggested that BMs might play a crucial role in the development of PRCC, and these results might provide new insights into the treatment of PRCC.
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Affiliation(s)
- Yujia Xi
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Liying Song
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Shuang Wang
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Haonan Zhou
- First School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jieying Ren
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Ran Zhang
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Feifan Fu
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Qian Yang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Guosheng Duan
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jingqi Wang
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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Pearce H, Croft W, Nicol SM, Margielewska-Davies S, Powell R, Cornall R, Davis SJ, Marcon F, Pugh MR, Fennell É, Powell-Brett S, Mahon BS, Brown RM, Middleton G, Roberts K, Moss P. Tissue-Resident Memory T Cells in Pancreatic Ductal Adenocarcinoma Coexpress PD-1 and TIGIT and Functional Inhibition Is Reversible by Dual Antibody Blockade. Cancer Immunol Res 2023; 11:435-449. [PMID: 36689623 PMCID: PMC10068448 DOI: 10.1158/2326-6066.cir-22-0121] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/02/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a poor clinical outlook. Responses to immune checkpoint blockade are suboptimal and a much more detailed understanding of the tumor immune microenvironment is needed if this situation is to be improved. Here, we characterized tumor-infiltrating T-cell populations in patients with PDAC using cytometry by time of flight (CyTOF) and single-cell RNA sequencing. T cells were the predominant immune cell subset observed within tumors. Over 30% of CD4+ T cells expressed a CCR6+CD161+ Th17 phenotype and 17% displayed an activated regulatory T-cell profile. Large populations of CD8+ tissue-resident memory (TRM) T cells were also present and expressed high levels of programmed cell death protein 1 (PD-1) and TIGIT. A population of putative tumor-reactive CD103+CD39+ T cells was also observed within the CD8+ tumor-infiltrating lymphocytes population. The expression of PD-1 ligands was limited largely to hemopoietic cells whilst TIGIT ligands were expressed widely within the tumor microenvironment. Programmed death-ligand 1 and CD155 were expressed within the T-cell area of ectopic lymphoid structures and colocalized with PD-1+TIGIT+ CD8+ T cells. Combinatorial anti-PD-1 and TIGIT blockade enhanced IFNγ secretion and proliferation of T cells in the presence of PD-1 and TIGIT ligands. As such, we showed that the PDAC microenvironment is characterized by the presence of substantial populations of TRM cells with an exhausted PD-1+TIGIT+ phenotype where dual checkpoint receptor blockade represents a promising avenue for future immunotherapy.
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Affiliation(s)
- Hayden Pearce
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Wayne Croft
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Samantha M. Nicol
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sandra Margielewska-Davies
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Richard Powell
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Richard Cornall
- Nuffield Department of Medicine and Medical Research Council Human Immunology Unit, University of Oxford, Oxford, United Kingdom
| | - Simon J. Davis
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, University of Oxford, Oxford, United Kingdom
| | - Francesca Marcon
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Matthew R. Pugh
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Éanna Fennell
- Health Research Institute, Bernal Institute and School of Medicine, University of Limerick, Limerick, Ireland
| | - Sarah Powell-Brett
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Brinder S. Mahon
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Rachel M. Brown
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Keith Roberts
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
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Chen H, Xu S, Zhang Y, Chen P. Systematic analysis of lncRNA gene characteristics based on PD-1 immune related pathway for the prediction of non-small cell lung cancer prognosis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9818-9838. [PMID: 37322912 DOI: 10.3934/mbe.2023430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is heterogeneous. Molecular subtyping based on the gene expression profiles is an effective technique for diagnosing and determining the prognosis of NSCLC patients. METHODS Here, we downloaded the NSCLC expression profiles from The Cancer Genome Atlas and the Gene Expression Omnibus databases. ConsensusClusterPlus was used to derive the molecular subtypes based on long-chain noncoding RNA (lncRNA) associated with the PD-1-related pathway. The LIMMA package and least absolute shrinkage and selection operator (LASSO)-Cox analysis were used to construct the prognostic risk model. The nomogram was constructed to predict the clinical outcomes, followed by decision curve analysis (DCA) to validate the reliability of this nomogram. RESULTS We discovered that PD-1 was strongly and positively linked to the T-cell receptor signaling pathway. Furthermore, we identified two NSCLC molecular subtypes yielding a significantly distinctive prognosis. Subsequently, we developed and validated the 13-lncRNA-based prognostic risk model in the four datasets with high AUC values. Patients with low-risk showed a better survival rate and were more sensitive to PD-1 treatment. Nomogram construction combined with DCA revealed that the risk score model could accurately predict the prognosis of NSCLC patients. CONCLUSIONS This study demonstrated that lncRNAs engaged in the T-cell receptor signaling pathway played a significant role in the onset and development of NSCLC, and that they could influence the sensitivity to PD-1 treatment. In addition, the 13 lncRNA model was effective in assisting clinical treatment decision-making and prognosis evaluation.
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Affiliation(s)
- Hejian Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
| | - Shuiyu Xu
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Yuhong Zhang
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Peifeng Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
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Dai Z, Zhang J, Xu W, Du P, Wang Z, Liu Y. Single-Cell Sequencing-Based Validation of T Cell-Associated Diagnostic Model Genes and Drug Response in Crohn's Disease. Int J Mol Sci 2023; 24:ijms24076054. [PMID: 37047025 PMCID: PMC10093907 DOI: 10.3390/ijms24076054] [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: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Crohn's disease is a highly heterogeneous autoimmune disease with a unique inflammatory phenotype of T cells at the lesion site. We aim to further explore the diagnosis of Crohn's disease and drug prediction of T cell marker gene expression. We obtained single-cell expression profile data from 22 CDs or normal samples and performed cell annotation and cellular communication analysis. Through the intersection of T cell marker genes, differential genes, and WGCNA results, we identified T cell-specific key genes and their immune landscapes and potential pathogenesis, and validated them across multiple datasets and patient tissue samples. We also explored the differentiation characteristics of genes by pseudo-temporal analysis and assessed their diagnostic performance and drug sensitivity by molecular docking. Finally, we extended this study to the prognosis of IBD-associated colon cancer. TNF-centered 5-gene diagnostic model not only has excellent diagnostic efficacy, but is also closely associated with KRAS, P53, and IL6/JAK/STAT3 pathways and physiological processes, such as EMT, coagulation, and apoptosis. In addition, this diagnostic model may have potential synergistic immunotherapeutic effects, with positive correlations with immune checkpoints such as CTLA4, CD86, PDCD1LG2, and CD40. Molecular docking demonstrated that BIRC3 and ANXA1 have strong binding properties to Azathioprine and Glucoocorticoid. Furthermore, the 5-gene model may suggest antagonism to IFX and prognosis for colon cancer associated with inflammatory bowel disease. Single-cell sequencing targeting T cell-related features in patients with Crohn's disease may aid in new diagnostic decisions, as well as the initial exploration of high-potential therapies.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Jie Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Weimin Xu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Zhongchuan Wang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Yun Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
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Liu P, Luo J, Tan N, Li C, Xu J, Yang X. Establishing a prognostic model of chromatin modulators and identifying potential drug candidates in renal clear cell patients. BMC Bioinformatics 2023; 24:104. [PMID: 36941564 PMCID: PMC10029171 DOI: 10.1186/s12859-023-05229-9] [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: 11/14/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Renal carcinoma is a common malignant tumor of the urinary system. Advanced renal carcinoma has a low 5-year survival rate and a poor prognosis. More and more studies have confirmed that chromatin regulators (CRs) can regulate the occurrence and development of cancer. This article investigates the functional and prognostic value of CRs in renal carcinoma patients. METHODS mRNA expression and clinical information were obtained from The Cancer Genome Atlas database. Univariate Cox regression analysis and LASSO regression analysis were used to select prognostic chromatin-regulated genes and use them to construct a risk model for predicting the prognosis of renal cancer. Differences in prognosis between high-risk and low-risk groups were compared using Kaplan-Meier analysis. In addition, we analyzed the relationship between chromatin regulators and tumor immune infiltration, and explored differences in drug sensitivity between risk groups. RESULTS We constructed a model consisting of 11 CRs to predict the prognosis of renal cancer patients. We not only successfully validated its feasibility, but also found that the 11 CR-based model was an independent prognostic factor. Functional analysis showed that CRs were mainly enriched in cancer development-related signalling pathways. We also found through the TIMER database that CR-based models were also associated with immune cell infiltration and immune checkpoints. At the same time, the genomics of drug sensitivity in cancer database was used to analyze the commonly used drugs of renal clear cell carcinoma patients. It was found that patients in the low-risk group were sensitive to medicines such as axitinib, pazopanib, sorafenib, and gemcitabine. In contrast, those in the high-risk group may be sensitive to sunitinib. CONCLUSION The chromatin regulator-related prognostic model we constructed can be used to assess the prognostic risk of patients with clear cell renal cell carcinoma. The results of this study can bring new ideas for targeted therapy of clear cell renal carcinoma, helping doctors to take corresponding measures in advance for patients with different risks.
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Affiliation(s)
- Puyu Liu
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Jihang Luo
- Department of Infectious Diseases, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Na Tan
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Chengfang Li
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Jieyu Xu
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Xiaorong Yang
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China.
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50
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Yu L, He R, Cui Y. Characterization of tumor microenvironment and programmed death-related genes to identify molecular subtypes and drug resistance in pancreatic cancer. Front Pharmacol 2023; 14:1146280. [PMID: 37007021 PMCID: PMC10063807 DOI: 10.3389/fphar.2023.1146280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Background: Immunotherapy has been a key option for the treatment of many types of cancer. A positive response to immunotherapy is heavily dependent on tumor microenvironment (TME) interaction. However, in pancreatic adenocarcinoma (PAAD), the association between TME mode of action and immune cell infiltration and immunotherapy, clinical outcome remained unknown.Methods: We systematically evaluated 29 TME genes in PAAD signature. Molecular subtypes of distinct TME signatures in PAAD were characterized by consensus clustering. After this, we comprehensively analyzed their clinical features, prognosis, and immunotherapy/chemotherapy response using correlation analysis, Kaplan-Meier curves analysis, ssGSEA analysis. 12 programmed cell death (PCD) patterns were acquired from previous study. Differentially expressed genes (DEGs) were acquired based on differential analysis. Key genes affecting overall survival (OS) of PAAD were screened by COX regression analysis and used to develop a RiskScore evaluation model. Finally, we assessed the value of RiskScore in predicting prognosis and treatment response in PAAD.Results: We identified 3 patterns of TME-associated molecular subtypes (C1, C2, C3), and observed that clinicopathological characteristics, prognosis, pathway features and immune features, immunotherapy/chemosensitivity of patients were correlated with the TME related subtypes. C1 subtype was more sensitive to the four chemotherapeutic drugs. PCD patterns were more likely to occur at C2 or C3. At the same time, we also detected 6 key genes that could affect the prognosis of PAAD, and 5 genes expressions were closely associated to methylation level. Low-risk patients with high immunocompetence had favorable prognostic results and high immunotherapy benefit. Patients in the high-risk group were more sensitive to chemotherapeutic drugs. RiskScore related to TME was an independent prognostic factor for PAAD.Conclusion: Collectively, we identified a prognostic signature of TME in PAAD patients, which could help elucidate the specific mechanism of action of TME in tumors and help to explore more effective immunotherapy strategies.
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Affiliation(s)
- Liang Yu
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Risheng He
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Yunfu Cui,
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