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You X, Wang M, Wang X, Wang X, Cheng Y, Zhang C, Miao Q, Feng Y. Gliomedin drives gastric cancer cell proliferation and migration, correlating with a poor prognosis. Heliyon 2024; 10:e38153. [PMID: 39347389 PMCID: PMC11437838 DOI: 10.1016/j.heliyon.2024.e38153] [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: 05/30/2024] [Revised: 09/18/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024] Open
Abstract
Gastric cancer (GC) is a prevalent global malignancy, often diagnosed at advanced stage due to a lack of early symptoms and reliable markers. Previous research has identified gliomedin (GLDN) as a potential predictive marker for poor prognosis in cancer patients. However, the specific relationship between GLDN expression and GC prognosis has been unclear. Using the Tumor-Immune System Interaction Database (TISIDB), we examined GLDN expression in GC tissues and found a positive correlation with advanced clinical stages. Kaplan-Meier Plotter analysis further demonstrated that elevated GLDN levels were closely associated with poor prognosis in GC patients. To explore the functional significance of GLDN in GC, we conducted experiments involving GLDN overexpression and knockdown in GC cell lines, as well as subcutaneous tumor formation in nude mice. Our findings provided compelling evidence that GLDN promotes GC cell proliferation, viability, and migration, significantly enhancing tumor growth in vivo. Mechanistically, RNA-sequencing (RNA-seq) combined with bioinformatics analysis revealed that GLDN influences genes enriched in the p53 signaling pathway. Our data suggest that GLDN likely regulates cell proliferation through the p53-p21-CyclinD/CDK4 signaling axis. In conclusion, our study underscores GLDN's critical role in regulating GC cell proliferation and migration, and proposes its potential as a prognostic marker for GC patients.
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Affiliation(s)
- Xue You
- Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, 133 Hehua Road, Jining, Shandong, 272067, PR China
| | - Minghe Wang
- College of Second Clinical Medical, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Xuejing Wang
- College of Second Clinical Medical, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Xiaotong Wang
- College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Yuting Cheng
- College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Chuan Zhang
- College of Second Clinical Medical, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Qingrun Miao
- College of Second Clinical Medical, Jining Medical University, Jining, Shandong, 272067, PR China
| | - Ying Feng
- Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, 133 Hehua Road, Jining, Shandong, 272067, PR China
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Gao Z, Liu S, Xiao H, Li M, Ren WG, Xu L, Peng ZM. IRF8 deficiency-induced myeloid-derived suppressor cell promote immune evasion in lung adenocarcinoma. J Transl Med 2024; 22:678. [PMID: 39049031 PMCID: PMC11270856 DOI: 10.1186/s12967-024-05519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Patients with lung adenocarcinoma (LUAD) have a low response rate to immune checkpoint blockade. It is highly important to explore the tumor immune escape mechanism of LUAD patients and expand the population of patients who may benefit from immunotherapy. METHODS Based on 954 bulk RNA-seq data of LUAD patients and 15 single-cell RNA-seq data, the relationships between tumor immune dysfunction and exclusion (TIDE) scores and survival prognosis in each patient were calculated and evaluated, and the immune escape mechanism affecting the independent prognosis of LUAD patients was identified. Functional enrichment analysis explored the antitumour immune response and biological behavior of tumor cells among different LUAD groups. Single-cell annotation and pseudotemporal analysis were used to explore the target molecules and immune escape mechanisms of LUAD. RESULTS Myeloid-derived suppressor cells (MDSCs) and IRF8 were identified as risk and protective factors for the independent prognosis of LUAD patients, respectively. In the tumor microenvironment of patients with high infiltration of MDSCs, the antitumor immune response is significantly suppressed, while tumor cell division, proliferation, and distant metastasis are significantly enhanced. Single-cell RNA-seq analysis revealed that IRF8 is an important regulator of MDSC differentiation in LUAD myeloid cells. In addition, IRF8 may regulate the differentiation of MDSCs through the IL6-JAK-STAT3 signalling pathway. CONCLUSIONS IRF8 deficiency impairs the normal development of LUAD myeloid cells and induces their differentiation into MDSCs, thereby accelerating the immune escape of LUAD cells. IRF8-targeted activation to inhibit the formation of MDSCs may be a new target for immunotherapy in LUAD.
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Affiliation(s)
- Zhen Gao
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Shang Liu
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Han Xiao
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Meng Li
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Wan-Gang Ren
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Lin Xu
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China.
| | - Zhong-Min Peng
- Department of Thoracic Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China.
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3
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Kraft T, Grützmann K, Meinhardt M, Meier F, Westphal D, Seifert M. Personalized identification and characterization of genome-wide gene expression differences between patient-matched intracranial and extracranial melanoma metastasis pairs. Acta Neuropathol Commun 2024; 12:67. [PMID: 38671536 PMCID: PMC11055243 DOI: 10.1186/s40478-024-01764-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Melanoma is the most serious type of skin cancer that frequently spreads to other organs of the human body. Especially melanoma metastases to the brain (intracranial metastases) are hard to treat and a major cause of death of melanoma patients. Little is known about molecular alterations and altered mechanisms that distinguish intra- from extracranial melanoma metastases. So far, almost all existing studies compared intracranial metastases from one set of patients to extracranial metastases of an another set of melanoma patients. This neglects the important facts that each melanoma is highly individual and that intra- and extracranial melanoma metastases from the same patient are more similar to each other than to melanoma metastases from other patients in the same organ. To overcome this, we compared the gene expression profiles of 16 intracranial metastases to their corresponding 21 patient-matched extracranial metastases in a personalized way using a three-state Hidden Markov Model (HMM) to identify altered genes for each individual metastasis pair. This enabled three major findings by considering the predicted gene expression alterations across all patients: (i) most frequently altered pathways include cytokine-receptor interaction, calcium signaling, ECM-receptor interaction, cAMP signaling, Jak-STAT and PI3K/Akt signaling, (ii) immune-relevant signaling pathway genes were downregulated in intracranial metastases, and (iii) intracranial metastases were associated with a brain-like phenotype gene expression program. Further, the integration of all differentially expressed genes across the patient-matched melanoma metastasis pairs led to a set of 103 genes that were consistently down- or up-regulated in at least 11 of the 16 of the patients. This set of genes contained many genes involved in the regulation of immune responses, cell growth, cellular signaling and transport processes. An analysis of these genes in the TCGA melanoma cohort showed that the expression behavior of 11 genes was significantly associated with survival. Moreover, a comparison of the 103 genes to three closely related melanoma metastasis studies revealed a core set of eight genes that were consistently down- or upregulated in intra- compared to extracranial metastases in at least two of the three related studies (down: CILP, DPT, FGF7, LAMP3, MEOX2, TMEM119; up: GLDN, PMP2) including FGF7 that was also significantly associated with survival. Our findings contribute to a better characterization of genes and pathways that distinguish intra- from extracranial melanoma metastasis and provide important hints for future experimental studies to identify potential targets for new therapeutic approaches.
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Affiliation(s)
- Theresa Kraft
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Konrad Grützmann
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Matthias Meinhardt
- Department of Pathology, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- Skin Cancer Center at the University Cancer Center (UCC) Dresden and the National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
- National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany.
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4
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Zhang Z, Wang X, Liu Y, Wu H, Zhu X, Ye C, Ren H, Chong W, Shang L, Li L. Phospholysine phosphohistidine inorganic pyrophosphate phosphatase suppresses insulin-like growth factor 1 receptor expression to inhibit cell adhesion and proliferation in gastric cancer. MedComm (Beijing) 2024; 5:e472. [PMID: 38292328 PMCID: PMC10827000 DOI: 10.1002/mco2.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/01/2024] Open
Abstract
Phospholysine phosphohistidine inorganic pyrophosphate phosphatase (LHPP) has recently emerged as a novel tumor suppressor. Researchers have observed that LHPP plays a crucial role in inhibiting proliferation, growth, migration, invasion, and cell metabolism across various cancers. Nevertheless, the specific functions and underlying mechanisms of LHPP as a tumor suppressor in gastric cancer (GC) require further exploration. The expression of LHPP was assessed in human GC specimens and cell lines. Various assays were employed to evaluate the impact of LHPP on GC cells. RNA sequencing and Gene Set Enrichment Analysis were conducted to unravel the mechanism through which LHPP regulates GC cell behavior. Additionally, xenograft nude mouse models were utilized to investigate the in vivo effects of LHPP. The findings indicate that LHPP, functioning as a tumor suppressor, is downregulated in both GC tissues and cells. LHPP emerges as an independent risk factor for GC patients, and its expression level exhibits a positive correlation with patient prognosis. LHPP exerts inhibitory effects on the adhesion and proliferation of GC cells by suppressing the expression of insulin-like growth factor 1 receptor (IGF1R) and modulating downstream signaling pathways. Consequently, LHPP holds potential as a biomarker for targeted therapy involving IGF1R inhibition in GC patients.
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Affiliation(s)
- Zihao Zhang
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of General SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Xu Wang
- Department of AnesthesiologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Yuan Liu
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Hao Wu
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Department of General SurgeryPeking Union Medical CollegePeking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Xingyu Zhu
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Chunshui Ye
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Huicheng Ren
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Wei Chong
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesShandongChina
- Key Laboratory of Engineering of Shandong ProvinceShandong Provincial HospitalJinanShandongChina
| | - Liang Shang
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesShandongChina
- Key Laboratory of Engineering of Shandong ProvinceShandong Provincial HospitalJinanShandongChina
| | - Leping Li
- Department of Gastrointestinal SurgeryShandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesShandongChina
- Key Laboratory of Engineering of Shandong ProvinceShandong Provincial HospitalJinanShandongChina
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5
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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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6
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Li L, Ye H, Chen Q, Wei L. COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells. Ren Fail 2023; 45:2187236. [PMID: 36883360 PMCID: PMC10013395 DOI: 10.1080/0886022x.2023.2187236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Type XXVIII collagen (COL28) is involved in cancer and lung fibrosis. COL28 polymorphisms and mutations might be involved in kidney fibrosis, but the exact role of COL28 in renal fibrosis is unknown. This study explored the function of COL28 in renal tubular cells by examining the expression of COL28 mRNA and the effects of COL28 overexpression in human tubular cells. COL28 mRNA expression and localization were observed in normal and fibrotic kidney tissues from humans and mice using real-time PCR, western blot, immunofluorescence, and immunohistochemistry. The consequences of COL28 overexpression on cell proliferation, migration, cell polarity, and epithelial-to-mesenchymal transition (EMT) induced by TGF-β1 were examined in human tubular HK-2 cells. COL28 expression was low in human normal renal tissues, mainly observed in the renal tubular epithelial cells and especially in proximal renal tubules. COL28 protein expression in human and mouse obstructive kidney disease was higher than in normal tissues (p < 0.05) and more significant in the UUO2-Week than the UUO1-Week group. The overexpression of COL28 promoted HK-2 cell proliferation and enhanced their migration ability (all p < 0.05). TGF-β1 (10 ng/ml) induced COL28 mRNA expression in HK-2 cells, decreased E-cadherin and increased α-SMA in the COL28-overexpression group compared with controls (p < 0.05). ZO-1 expression decreased while COL6 increased in the COL28-overexpression group compared with controls (p < 0.05). In conclusion, COL28 overexpression promotes the migration and proliferation of renal tubular epithelial cells. The EMT could also be involved. COL28 could be a therapeutic target against renal- fibrotic diseases.
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Affiliation(s)
- Linlin Li
- Department of nephrology, Fujian Medical University, Union Hospital, Fuzhou, Fujian, China
| | - Hong Ye
- Department of nephrology, Fujian Medical University, Union Hospital, Fuzhou, Fujian, China
| | - Qiaoling Chen
- Department of nephrology, Fujian Medical University, Union Hospital, Fuzhou, Fujian, China
| | - Lixin Wei
- Department of nephrology, Fujian Medical University, Union Hospital, Fuzhou, Fujian, China
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7
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Gui C, Wei J, Mo C, Liang Y, Cen J, Chen Y, Wang D, Luo J. Therapeutic implications for localized prostate cancer by multiomics analyses of the ageing microenvironment landscape. Int J Biol Sci 2023; 19:3951-3969. [PMID: 37564213 PMCID: PMC10411471 DOI: 10.7150/ijbs.85209] [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: 04/12/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
Background: Numerous studies have substantiated the association between aging and the progression of malignant tumors in humans, notably prostate cancer (PCa). Nevertheless, to the best of our knowledge, no studies have comprehensively elucidated the intricate characteristics of the aging microenvironment (AME) in PCa. Methods: AME regulatory patterns were determined using the NMF algorithm. Then an ageing microenvironment index (AMI) was constructed, with excellent prognostic and immunotherapy prediction ability, and its' clinical relevance was surveyed through spatial transcriptomics. Further, the drug response was analysed using the Genomics of Drug Sensitivity in Cancer (GDSC), the Connectivity Map (CMap) and CellMiner database for patients with PCa. Finally, the AME was studied using in vitro and vivo experiments. Results: Three different AME regulatory patterns were identified across 813 PCa patients, associated with distinct clinical prognosis and physiological pathways. Based on the AMI, patients with PCa were divided into the high-score and low-score subsets. Higher AMI score was significantly infiltrated with more immune cells, higher rate of biochemical recurrence (BCR) and worse response to immunotherapy, antiandrogen therapy and chemotherapy in PCa. In addition, we found that the combination of bicalutamide and embelin was capable of suppressing tumor growth of PCa. Besides, as the main components of AMI, COL1A1 and BGLAP act as oncogenes and were verified via in vivo and in vitro experiments. Conclusions: AME regulation is significantly associated with the diversity and complexity of TME. Quantitative evaluation of the AME regulatory patterns may provide promising novel molecular markers for individualised therapy in PCa.
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Affiliation(s)
- Chengpeng Gui
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jinhuan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chengqiang Mo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanping Liang
- Department of Laboratory Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junjie Cen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuhang Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Daohu Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junhang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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8
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Xu X, Ding C, Zhong H, Qin W, Shu D, Yu M, Abuduaini N, Zhang S, Yang X, Feng B. Integrative analysis revealed that distinct cuprotosis patterns reshaped tumor microenvironment and responses to immunotherapy of colorectal cancer. Front Immunol 2023; 14:1165101. [PMID: 37006250 PMCID: PMC10060625 DOI: 10.3389/fimmu.2023.1165101] [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: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundCuprotosis is a novel form of programmed cell death that involves direct targeting of key enzymes in the tricarboxylic acid (TCA) cycle by excess copper and may result in mitochondrial metabolic dysfunction. However, whether cuprotosis may mediate the tumor microenvironment (TME) and immune regulation in colorectal cancer (CRC) remains unclear.MethodsTen cuprotosis-related genes were selected and unsupervised consensus clustering was performed to identify the cuprotosis patterns and the correlated TME characteristics. Using principal component analysis, a COPsig score was established to quantify cuprotosis patterns in individual patients. The top 9 most important cuprotosis signature genes were analyzed using single-cell transcriptome data.ResultsThree distinct cuprotosis patterns were identified. The TME cell infiltration characteristics of three patterns were associated with immune-excluded, immune-desert, and immune-inflamed phenotype, respectively. Based on individual cuprotosis patterns, patients were assigned into high and low COPsig score groups. Patients with a higher COPsig score were characterized by longer overall survival time, lower immune cell as well as stromal infiltration, and greater tumor mutational burden. Moreover, further analysis demonstrated that CRC patients with a higher COPsig score were more likely to respond to immune checkpoint inhibitors and 5-fluorouracil chemotherapy. Single-cell transcriptome analysis indicated that cuprotosis signature genes recruited tumor-associated macrophages to TME through the regulation of TCA and the metabolism of glutamine and fatty acid, thus influencing the prognosis of CRC patients.ConclusionThis study indicated that distinct cuprotosis patterns laid a solid foundation to the explanation of heterogeneity and complexity of individual TME, thus guiding more effective immunotherapy as well as adjuvant chemotherapy strategies.
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Affiliation(s)
| | | | | | | | | | | | | | - Sen Zhang
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
| | - Xiao Yang
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
| | - Bo Feng
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
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9
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Wang Q, Zhang W, Guo Y, Shi F, Li Y, Kong Y, Lyu J, Wang S. A mutational signature and significantly mutated driver genes associated with immune checkpoint inhibitor response across multiple cancers. Int Immunopharmacol 2023; 116:109821. [PMID: 36753986 DOI: 10.1016/j.intimp.2023.109821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/08/2023]
Abstract
Immune checkpoint inhibitor (ICI) treatments dramatically prolong the survival outcomes of several advanced cancers. However, as multiple studies reported, only a subset of patients could benefit from the ICI treatment. In this study, we aim to uncover novel molecular biomarkers predictive of immunotherapy efficacy across multiple cancers. Pre-treatment somatic mutational profiles and immunotherapy clinical information were obtained from 1097 samples of multiple cancers, including melanoma, non-small cell lung cancer (NSCLC), clear cell renal cell carcinoma (ccRCC), bladder carcinoma (BLCA), and head and neck squamous cell carcinoma (HNSCC). Mutational signatures, molecular subtypes, and significantly mutated genes (SMGs) were determined, and their connections with ICI response and outcome were also evaluated. We extracted a total of six mutational signatures across all samples. Among, a mutational signature featured by T > C substitutions was identified to associate with an ICI resistance. A molecular subtype determined based on mutational activities was connected with a significantly improved ICI response rate and outcome. Totaling 50 SMGs were identified, and we observed that patients with COL11A1 or COL4A6 mutations exhibited a superior ICI treatment efficacy than those without such mutations. In this study, we uncovered several novel molecular determinants of cancer immunotherapy response under a multiple-cancer setting, which provides clues for enrolling patients to receive immunotherapy and customizing personalized treatment strategies.
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Affiliation(s)
- Qinghua Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China.
| | - Wenjing Zhang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuxian Guo
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Fuyan Shi
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuting Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yujia Kong
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Juncheng Lyu
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Suzhen Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
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10
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Tan H, Yu T, Liu C, Wang Y, Jing F, Ding Z, Liu J, Shi H. Identifying tumor antigens and immuno-subtyping in colon adenocarcinoma to facilitate the development of mRNA vaccine. Cancer Med 2022; 11:4656-4672. [PMID: 35593226 PMCID: PMC9741973 DOI: 10.1002/cam4.4846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
The mRNA vaccine has provided a promising approach for cancer immunotherapies. However, only a few mRNA vaccines have been developed against colon adenocarcinoma (COAD). Screening potential targets for mRNA vaccines from numerous candidates is a substantial challenge. Considering the tumor heterogeneity, only a subset of patients might respond to vaccinations. This study was conducted to identify potential candidates for mRNA vaccines, and distinguish appropriate subgroups of COAD patients for vaccination. A total of five tumor antigens with prognostic values were identified, including IGF2BP3, DPCR1, HOXD10, TRIM7, and ZIC5. The COAD patients were stratified into five immune subtypes (IS1-IS5), according to consensus clustering analysis. Higher tumor mutation burden (TMB) was observed in IS1 and IS5 subtypes. The IS1 and IS5 subtypes have shown the baseline of immune-hot tumor microenvironment, while other subtypes displayed immune desert phenotype. Distinct expressions of immune checkpoints (ICPs)-related genes and immunogenic cell death (ICD) modulators were observed among five immune subtypes. Finally, the immune landscape was conducted to narrow the immune components for better personalized mRNA-based vaccination. The IFIT3, PARP9, TAP1, STAT1, and OAS2 were confirmed as hub genes, and COAD patients with higher expressions of these genes might be more appropriate for mRNA vaccination. In conclusion, the IGF2BP3, DPCR1, HOXD10, TRIM7, and ZIC5 were identified as potential candidates for developing mRNA vaccines against COAD, and patients in IS1 and IS5 subtypes might respond better to mRNA vaccination.
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Affiliation(s)
- Huaicheng Tan
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Ting Yu
- Department of Pathology and Laboratory of Pathology, State Key Laboratory of Biotherapy, West China Hospital, West China School of Medicine, Sichuan UniversityChengduChina
| | - Chunhua Liu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Yang Wang
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Fangqi Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengduChina
| | - Zhenyu Ding
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Jiyan Liu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Huashan Shi
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan UniversityChengduChina
- Department of RadiotherapyCancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan UniversityChengduChina
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11
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Immune checkpoint blockade in melanoma: Advantages, shortcomings and emerging roles of the nanoparticles. Int Immunopharmacol 2022; 113:109300. [DOI: 10.1016/j.intimp.2022.109300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
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12
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Wang L, Hu X, Liu X, Feng Y, Zhang Y, Han J, Liu X, Meng F. m7G regulator-mediated methylation modification patterns define immune cell infiltration and patient survival. Front Immunol 2022; 13:1022720. [DOI: 10.3389/fimmu.2022.1022720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have demonstrated the important roles of epigenetic modifications in tumorigenesis, progression and prognosis. However, in hepatocellular carcinoma, the potential link between N7-methylguanosine (m7G) modification and molecular heterogeneity and tumor microenvironment (TME) remains unclear.MethodWe performed a comprehensive evaluation of m7G modification patterns in 816 hepatocellular carcinoma samples based on 24 m7G regulatory factors, identified different m7G modification patterns, and made a systematic correlation of these modification patterns with the infiltration characteristics of immunocytes. Then, we built and validated a scoring tool called m7G score.ResultsIn this study, we revealed the presence of three distinct m7G modification patterns in liver cancer, with remarkable differences in the immunocyte infiltration characteristics of these three subtypes. The m7G scoring system of this study could assess m7G modification patterns in individual hepatocellular carcinoma patients, could predict TME infiltration characteristics, genetic variants and patient prognosis. We also found that the m7G scoring system may be useful in guiding patients’ clinical use of medications.ConclusionsThis study revealed that m7G methylation modifications exerted a significant role in formation of TME in hepatocellular carcinoma. Assessing the m7G modification patterns of single patients would help enhance our perception of TME infiltration characteristics and give significant insights into immunotherapy efficacy.
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13
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Wang XX, Wu LH, Dou QY, Ai L, Lu Y, Deng SZ, Liu QQ, Ji H, Zhang HM. Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response. Front Mol Biosci 2022; 9:1034928. [PMID: 36339715 PMCID: PMC9634552 DOI: 10.3389/fmolb.2022.1034928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Increasing evidence illustrated that m6A regulator-mediated modification plays a crucial role in regulating tumor immune and angiogenesis microenvironment. And the combination of immune checkpoint inhibitor and anti-angiogenic therapy has been approved as new first-line therapy for advanced HCC. This study constructed a novel prognosis signature base on m6A-mediated modification and explored the related mechanism in predicting immune and anti-angiogenic responses. Methods: Gene expression profiles and clinical information were collected from TCGA and GEO. The ssGSEA, MCPCOUNT, and TIMER 2.0 algorithm was used to Estimation of immune cell infiltration. The IC50 of anti-angiogenic drugs in GDSC was calculated by the “pRRophetic” package. IMvigor210 cohort and Liu et al. cohort were used to validate the capability of immunotherapy response. Hepatocellular carcinoma single immune cells sequencing datasets GSE140228 were collected to present the expression landscapes of 5 hub genes in different sites and immune cell subpopulations of HCC patients. Results: Three m6A clusters with distinct immune and angiogenesis microenvironments were identified by consistent cluster analysis based on the expression of m6A regulators. We further constructed a 5-gene prognosis signature (termed as m6Asig-Score) which could predict both immune and anti-angiogenic responses. We illustrated that high m6Asig-Score is associated with poor prognosis, advanced TNM stage, and high TP53 mutation frequency. Besides, the m6Asig-Score was negatively associated with immune checkpoint inhibitors and anti-angiogenic drug response. We further found that two of the five m6Asig-Score inner genes, B2M and SMOX, were associated with immune cell infiltration, immune response, and the sensitivity to sorafenib, which were validated in two independent immunotherapy cohorts and the Genomics of Drug Sensitivity in Cancer (GDSC) database. Conclusion: We constructed a novel prognosis signature and identified B2M and SMOX for predicting immune and anti-angiogenic efficacy in HCC, which may guide the combined treatment strategies of immunotherapy and anti-angiogenic therapy in HCC.
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Affiliation(s)
- Xiang-Xu Wang
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Li-Hong Wu
- Xijing 986 Hospital Department, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qiong-Yi Dou
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Liping Ai
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yajie Lu
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Shi-Zhou Deng
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qing-Qing Liu
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Hongchen Ji
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Hong-Mei Zhang
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
- *Correspondence: Hong-Mei Zhang,
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14
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Luo H, Ye M, Hu Y, Wu M, Cheng M, Zhu X, Huang K. DNA methylation regulator-mediated modification patterns and tumor microenvironment characterization in glioma. Aging (Albany NY) 2022; 14:7824-7850. [PMID: 36152044 PMCID: PMC9596205 DOI: 10.18632/aging.204291] [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: 06/16/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Growing evidences indicate DNA methylation plays a crucial regulatory role in inflammation, innate immunity, and immunotherapy. However, the overall landscape of various DNA methylation regulatory genes and their relationship with the infiltration of immune cells into the tumor microenvironment (TME) as well as the response to immunotherapy in gliomas is still not clear. Therefore, we comprehensively analyzed the correlation between DNA methylation regulator patterns, infiltration of immune cell-types, and tumor immune response status in gather glioma cohorts. Furthermore, we calculated the DNA methylation score (DMS) for individual glioma samples, then evaluated the relationship between DMS, clinicopathological characteristics, and overall survival (OS) in patients with gliomas. Our results showed three distinct DNA methylation regulator patterns among the glioma patients which correlated with three distinct tumor immune response phenotypes, namely, immune-inflamed, immune-excluded, and immune desert. We then calculated DMS for individual glioma samples based on the expression of DNA methylation-related gene clusters. Furthermore, DMS, tumor mutation burden (TMB), programmed death 1 (PD-1) expression, immune cell infiltration status in the TME, and Tumor Immune Dysfunction and Exclusion (TIDE) scores were associated with survival outcomes and clinical responses to immune checkpoint blockade therapy. We also validated the predictive value of DMS in two independent immunotherapy cohorts. In conclusion, our results demonstrated that three DNA methylation regulator patterns that correlated with three tumor immune response phenotypes. Moreover, we demonstrated that DMS was an independent predictive biomarker that correlated with survival outcomes of glioma patients and their responses to immunotherapy therapeutic regimens.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Minhua Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Yan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi Province, China
| | - Miaojing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China
| | - Mengqi Cheng
- Department of Obstetrics and Gynecology, Suizhou Central Hospital, Hubei University of Medicine, Suizhou, Hubei Province, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
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15
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Xu L. Crosstalk of three novel types of programmed cell death defines distinct microenvironment characterization and pharmacogenomic landscape in breast cancer. Front Immunol 2022; 13:942765. [PMID: 36032140 PMCID: PMC9403178 DOI: 10.3389/fimmu.2022.942765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Prior studies have highlighted that novel programmed cell death (PCD) modalities, including ferroptosis, pyroptosis, and necroptosis, are correlated with tumor progression and antitumor immunity. Nonetheless, comprehensive analysis of tumor microenvironment (TME) profiles mediated by the crosstalk of distinct PCD forms has not been conducted in breast cancer (BC). Methods Here, we curated 34 identified PCD-associated genes (PCDAGs) and applied the consensus clustering algorithm to establish PCD-mediated tumor patterns in BC. Subsequently, based on prognostic differentially expressed genes extracted from distinct PCD-mediated patterns, we applied the LASSO algorithm to construct CD_Score. Furthermore, the correlation analysis between CD_Score and TME features, molecular subtypes, clinicopathological characteristics, drug response, and immunotherapeutic efficacy was performed. Results Three distinct PCD-clusters were determined among 2,038 BC samples, which did not only display different clinical outcomes but highly correlated to the established immunological tumor phenotypes: “desert,” “excluded,” and “inflamed” immune profiles. Based on the CD_Score derived from the PCD-related gene signature, BC patients could be stratified into CD_Score-low and -high group, of which the former displayed satisfactory survival outcome and enhanced immune infiltration. Further exploration identified that the CD_Score-high group significantly correlated with elevated neoantigen load and higher mutation frequency in SMGs (e.g., TP53 and MAP3K1) and reduced expression of immune checkpoint proteins. Conclusions This research is the first to emphasize the close relationship between distinct cell death modalities and the diversity and complexity of immune infiltration in TME. We established the CD_Score, which could help enhance our cognition of TME features and facilitate the clinical application of immunotherapy.
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16
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Tang TY, Huang X, Zhang G, Lu MH, Liang TB. mRNA vaccine development for cholangiocarcinoma: a precise pipeline. Mil Med Res 2022; 9:40. [PMID: 35821067 PMCID: PMC9277828 DOI: 10.1186/s40779-022-00399-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Cholangiocarcinoma (CHOL) is one of the most aggressive tumors worldwide and cannot be effectively treated by conventional and novel treatments, including immune checkpoint blockade therapy. The mRNA vaccine-based immunotherapeutic strategy has attracted much attention for various diseases, however, its application in CHOL is limited due to the thoughtlessness in the integration of vaccine design and patient selection. A recent study established an integrated path for identifying potent CHOL antigens for mRNA vaccine development and a precise stratification for identifying CHOL patients who can benefit from the mRNA vaccines. In spite of a promising prospect, further investigations should identify immunogenic antigens and onco-immunological characteristics of CHOL to guide the clinical application of CHOL mRNA vaccines in the future.
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Affiliation(s)
- Tian-Yu Tang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003 China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009 China
- Cancer Center, Zhejiang University, Hangzhou, 310058 China
| | - Xing Huang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003 China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009 China
- Cancer Center, Zhejiang University, Hangzhou, 310058 China
| | - Gang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003 China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009 China
- Cancer Center, Zhejiang University, Hangzhou, 310058 China
| | - Ming-Hao Lu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003 China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009 China
- Cancer Center, Zhejiang University, Hangzhou, 310058 China
| | - Ting-Bo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003 China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009 China
- Cancer Center, Zhejiang University, Hangzhou, 310058 China
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17
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Chen H, Zhang T, Zhang Y, Wu H, Fang Z, Liu Y, Chen Y, Wang Z, Jia S, Ji X, Shang L, Du F, Liu J, Lu M, Chong W. Deciphering the tumor cell-infiltrating landscapes reveal microenvironment subtypes and therapeutic potentials for nonsquamous NSCLC. JCI Insight 2022; 7:152815. [PMID: 35511432 DOI: 10.1172/jci.insight.152815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies highlighted the clinicopathologic importance of tumor microenvironment (TME) in delineating molecular attributes and therapeutic potentials. However, the overall TME cell-infiltration landscape in non-squamous NSCLC have not been comprehensively recognized. In this study, we employed consensus non-negative matrix factorization (NMF) molecular subtyping to determine the TME cell infiltration patterns and identified three TME clusters (TME-C1, -C2, -C3) characterized by distinct clinicopathologic features, infiltrating cells, and biological processes. Proteomics analyses revealed that cGAS-STING immune signaling mediated protein and phosphorylation level were significantly upregulated in inflamed-related TME-C2 clusters. The TMEsig-score extracted from the TME-related signature divided NSCLC patients into high- and low-score subgroups, where a high score was associated with favorable prognosis and immune infiltration. Genomic landscape revealed that patients with low TMEsig-score harbored greater somatic copy number alternations and higher mutation frequency of driver genes involving STK11, KEAP1 and SMARCA4 et al. Drug sensitivity analyses suggested that tumors with high TMEsig-score were responsible for favorable clinical response to immune check-point inhibitors (ICI) treatment. In summary, this study highlights that comprehensive recognizing of the TME cell infiltration landscape will contribute to enhance our understanding of TME immune regulation and promote effectiveness of precision biotherapy strategies.
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Affiliation(s)
- Hao Chen
- Clinical Research Center of Shandong University, Qilu Hospital of Shandong University, Jinan, China
| | - Tongchao Zhang
- Clinical Research Center of Shandong University, Qilu Hospital of Shandong University, Jinan, China
| | - Yuan Zhang
- Clinical Research Center of Shandong University, Qilu Hospital of Shandong University, Jinan, China
| | - Hao Wu
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Zhen Fang
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Yang Liu
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Yang Chen
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhe Wang
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Shengtao Jia
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xingzhao Ji
- Department of Pulmonary Medicine, Shandong Provincial Hospital, Jinan, China
| | - Liang Shang
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Fengying Du
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Jin Liu
- Research Center for Experimental Nuclear Medicine, Shandong University, Jinan, China
| | - Ming Lu
- Clinical Research Center of Shandong University, Qilu Hospital of Shandong University, Jinan, China
| | - Wei Chong
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
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18
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Fan Y, Zhou Y, Lou M, Li X, Zhu X, Yuan K. m6A Regulator-Mediated Methylation Modification Patterns and Characterisation of Tumour Microenvironment Infiltration in Non-Small Cell Lung Cancer. J Inflamm Res 2022; 15:1969-1989. [PMID: 35356071 PMCID: PMC8958726 DOI: 10.2147/jir.s356841] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yongfei Fan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
| | - Yong Zhou
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
| | - Ming Lou
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
| | - Xinwei Li
- Department of Gastroenterology, Affiliated Cancer Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Xudong Zhu
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
| | - Kai Yuan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, People’s Republic of China
- Correspondence: Kai Yuan, Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, No. 29 Xinglong Lane, Changzhou, 213003, Jiangsu Province, People’s Republic of China, Tel +86-13915890721, Email
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19
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Zhu M, Cui Y, Mo Q, Zhang J, Zhao T, Xu Y, Wu Z, Sun D, Zhang X, Li Y, You Q. Characterization of m 6A RNA Methylation Regulators Predicts Survival and Immunotherapy in Lung Adenocarcinoma. Front Immunol 2022; 12:782551. [PMID: 34975871 PMCID: PMC8718692 DOI: 10.3389/fimmu.2021.782551] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is a reversible mechanism that regulates eukaryotic gene expression. Growing evidence has demonstrated an association between m6A modification and tumorigenesis and response to immunotherapy. However, the overall influence of m6A regulators on the tumor microenvironment and their effect on the response to immunotherapy in lung adenocarcinoma remains to be explored. Here, we comprehensively analyzed the m6A modification patterns of 936 lung adenocarcinoma samples based on 24 m6A regulators. First, we described the features of genetic variation in these m6A regulators. Many m6A regulators were aberrantly expressed in tumors and negatively correlated with most tumor-infiltrating immune cell types. Furthermore, we identified three m6A modification patterns using a consensus clustering method. m6A cluster B was preferentially associated with a favorable prognosis and enriched in metabolism-associated pathways. In contrast, m6A cluster A was associated with the worst prognosis and was enriched in the process of DNA repair. m6A cluster C was characterized by activation of the immune system and a higher stromal cell score. Surprisingly, patients who received radiotherapy had a better prognosis than patients without radiotherapy only in the m6A cluster C group. Subsequently, we constructed an m6A score model that qualified the m6A modification level of individual samples by using principal component analysis algorithms. Patients with high m6A score were characterized by enhanced immune cell infiltration and prolonged survival time and were associated with lower tumor mutation burden and PD-1/CTLA4 expression. The combination of the m6A score and tumor mutation burden could accurately predict the prognosis of patients with lung adenocarcinoma. Furthermore, patients with high m6A score exhibited greater prognostic benefits from radiotherapy and immunotherapy. This study demonstrates that m6A modification is significantly associated with tumor microenvironment diversity and prognosis. A comprehensive evaluation of m6A modification patterns in single tumors will expand our understanding of the tumor immune landscape. In addition, our m6A score model demonstrated that the level of immune cell infiltration plays a significant role in cancer immunotherapy and provides a basis to increase the efficiency of current immune therapies and promote the clinical success of immunotherapy.
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Affiliation(s)
- Minggao Zhu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yachao Cui
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Qi Mo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Junwei Zhang
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Ting Zhao
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yujie Xu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Zhenpeng Wu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Donglin Sun
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Xiaoren Zhang
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yingchang Li
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Qiang You
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China.,Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
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Ji L, Peng P, Gui L, Yuan P, Qian W, Wang Y, Gao WQ, Ma B. CD24 Is a Superior Immunotherapeutic Target to PD-1 in a Mouse Model of Helicobacter-Induced Gastric Cancer. GASTRO HEP ADVANCES 2022; 1:79-82. [PMID: 39129936 PMCID: PMC11307929 DOI: 10.1016/j.gastha.2021.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/30/2021] [Indexed: 08/13/2024]
Affiliation(s)
- L. Ji
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - P. Peng
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - L. Gui
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - P. Yuan
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - W. Qian
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Y. Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - W.-Q. Gao
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
- Clinical Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - B. Ma
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
- Clinical Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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21
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Yi L, Huang P, Gu Y, Wu G, Zou X, Guo L, Wen C, Zhu J, Zhao D. Clinical Significance and Immune Landscape of Recurrence-Associated Ferroptosis Signature in Early-Stage Lung Adenocarcinoma. Front Oncol 2022; 12:794293. [PMID: 35155238 PMCID: PMC8828635 DOI: 10.3389/fonc.2022.794293] [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: 10/13/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The prevalence of patients newly diagnosed with early-stage lung adenocarcinoma (LUAD) is growing alongside significant advances in screening approaches. This study aimed to construct ferroptosis-related gene score (FRGscore) for predicting recurrence, explore immune-molecular characteristics, and determine the benefit of immunotherapy in distinct ferroptosis-based patterns and FRGscore-defined subgroups. METHODS A total of 1,085 early-stage LUAD patients from four independent cohorts were included. Consensus clustering analysis was performed using 217 co-expressed FRGs to explore different ferroptosis-mediated patterns. An FRG scoring system was established to predict relapse, quantify ferroptosis-mediated patterns, and evaluate the response to immunotherapy in individual patients based on Lasso-penalized and stepwise Cox regression analyses. Immune landscape involving multiple parameters was further evaluated, stratified by cluster subtypes and FRGscore subgroups. RESULTS Two ferroptosis-mediated patterns were identified and verified, which were characterized by significantly distinct prognosis and immune profiles. Analyses of immune characteristics showed that identified ferroptosis patterns were characterized as immune-inflamed phenotype and immune-exhausted phenotype. The FRG scoring model based on 11 FRG-derived signatures panel classified patients into the FRGscore-high and FRGscore-low subgroups. Significantly longer recurrence-free survival (RFS) and overall survival (OS) were observed in the FRGscore-low subgroup. FRGscore-low patients were characterized by higher tumor mutational burden (TMB), immunoscore, immunophenoscore, and PD-L1 expression level and were associated with lower Tumor Immune Dysfunction and Exclusion (TIDE) score, whereas the opposite was observed in FRGscore-high patients. Immune-active pathways were remarkably enriched in the FRGscore-low subgroup. This scoring model remained highly predictive of prognosis across different clinical, molecular, and immune subgroups. Further analysis indicated that FRGscore-low patients exhibited higher response to anti-PD-1/PD-L1 immunotherapy and better clinical benefits based on two independent immunotherapy cohorts. CONCLUSION The proposed FRGscore could highly distinguish the recurrence patterns and molecular and immune characteristics and could predict immunotherapy prognosis, potentially representing a powerful prognostic tool for further optimization of individuated treatment and management strategies in early-stage LUAD.
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Affiliation(s)
- Lilan Yi
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Ping Huang
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Yinfang Gu
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Guowu Wu
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Xiaofang Zou
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Longhua Guo
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Chunling Wen
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Junlin Zhu
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Dongdong Zhao
- Department of Oncology, Cancer Center, Meizhou People’s Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
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22
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The Hypoxia-Related Gene COL5A1 Is a Prognostic and Immunological Biomarker for Multiple Human Tumors. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6419695. [PMID: 35082969 PMCID: PMC8786464 DOI: 10.1155/2022/6419695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/15/2021] [Accepted: 12/14/2021] [Indexed: 01/19/2023]
Abstract
Background Collagen type V alpha 1 chain (COL5A1) is a hypoxia-related gene (a collagen family protein) and participates in the formation of the extracellular matrix. Although some evidence supports a significant role for COL5A1 in the progression of several cancers, a pan-cancer analysis of COL5A1 is not currently available. Herein, we aimed to assess the prognostic value of COL5A1 in 33 human cancers and to investigate its underlying immunological function. Methods Through multiple bioinformatics methods, we analyzed the data from Oncomine, TCGA, CCLE, HPA, DNMIVD, and cBioPortal database to explore the potential underlying carcinogenic effect of COL5A1, including the relevance of COL5A1 to the outcome, DNA methylation, tumor microenvironment, immune cells infiltration, and drug sensitivity in 33 human cancers. The effects of COL5A1 on glioma cell proliferation, migration, and invasion were verified in cellular experiments. Results Our findings indicated that COL5A1 was expressed at high levels in 13 cancers and was negatively related to the prognosis of 11 cancers. Additionally, COL5A1 was coexpressed with genes encoding the major histocompatibility complex, immune activators, immune suppressors, chemokines, chemokine receptors, mismatch repair genes, and immune checkpoints. We also identified different roles for COL5A1 in the immunocyte infiltration in different cancers. The correlation between COL5A1 and drug sensitivity was found in several cancers. COL5A1 potentially influenced the tumor progression through immune-related pathways, negative regulation of immune system processes, chemokine signaling pathways, JAK-STAT pathways, T cell receptor pathways, lymphocyte migration, and antigen processing and presentation, among other processes. Conclusions Based on our study, COL5A1 may be employed as a prognostic marker in different malignancies because of its impact on tumorigenesis and immune cell infiltration and have implications for cancer immune checkpoint inhibitors and chemotherapy.
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Du F, Li H, Li Y, Liu Y, Li X, Dang N, Chu Q, Yan J, Fang Z, Wu H, Zhang Z, Zhu X, Li X. Identification of m6A Regulator-Associated Methylation Modification Clusters and Immune Profiles in Melanoma. Front Cell Dev Biol 2021; 9:761134. [PMID: 34993195 PMCID: PMC8724425 DOI: 10.3389/fcell.2021.761134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
RNA N6-methyladenosine (m6A) modification in tumorigenesis and progression has been highlighted and discovered in recent years. However, the molecular and clinical implications of m6A modification in melanoma tumor microenvironment (TME) and immune infiltration remain largely unknown. Here, we utilized consensus molecular clustering with nonnegative matrix factorization based on the melanoma transcriptomic profiles of 23 m6A regulators to determine the m6A modification clusters and m6A-related gene signature. Three distinct m6A modification patterns (m6A-C1, C2, and C3), which are characterized by specific m6A regulator expression, survival outcomes, and biological pathways, were identified in more than 1,000 melanoma samples. The immune profile analyses showed that these three m6A modification subtypes were highly consistent with the three known immune phenotypes: immune-desert (C1), immune-excluded (C2), and immune-inflamed (C3). Tumor digital cytometry (CIBERSORT, ssGSEA) algorithm revealed an upregulated infiltration of CD8+ T cell and NK cell in m6A-C3 subtype. An m6A scoring scheme calculated by principal component of m6A signatures stratified melanoma patients into high- and low-m6sig score subgroups; a high score was significantly associated with prolonged survival and enhanced immune infiltration. Furthermore, fewer somatic copy number alternations (SCNA) and PD-L1 expression were found in patients with high m6Sig score. In addition, patients with high m6Sig score demonstrated marked immune responses and durable clinical benefits in two independent immunotherapy cohorts. Overall, this study indicated that m6A modification is involved in melanoma tumor microenvironment immune regulation and contributes to formation of tumor immunogenicity. Comprehensive evaluation of the m6A modification pattern of individual tumors will provide more insights into molecular mechanisms of TME characterization and promote more effective personalized biotherapy strategies.
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Affiliation(s)
- Fengying Du
- Department of Dermatology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Han Li
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Yan Li
- Department of Respiratory and Critical care, Shandong public health clinical center, Jinan, China
| | - Yang Liu
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xinyu Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ningning Dang
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qingqing Chu
- Outpatient of Podiatric Rehabilitation, Maternity and Child Health Care of Zaozhuang, Zaozhuang, China
| | - Jianjun Yan
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, China
| | - Zhen Fang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Zhang
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xingyu Zhu
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaokang Li
- Department of Dermatology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Xiaokang Li,
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Predictive Biomarkers for Outcomes of Immune Checkpoint Inhibitors (ICIs) in Melanoma: A Systematic Review. Cancers (Basel) 2021; 13:cancers13246366. [PMID: 34944986 PMCID: PMC8699321 DOI: 10.3390/cancers13246366] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have strongly improved the survival of melanoma patients. However, as durable response to ICIs are only seen in a minority, there is an unmet need to identify biomarkers that predict response. Therefore, we provide a systematic review that evaluates all biomarkers studied in association with outcomes of melanoma patients receiving ICIs. We searched Pubmed, COCHRANE Library, Embase, Emcare, and Web of Science for relevant articles that were published before June 2020 and studied blood, tumor, or fecal biomarkers that predicted response or survival in melanoma patients treated with ICIs. Of the 2536 identified reports, 177 were included in our review. Risk of bias was high in 40%, moderate in 50% and low in 10% of all studies. Biomarkers that correlated with response were myeloid-derived suppressor cells (MDSCs), circulating tumor cells (CTCs), CD8+ memory T-cells, T-cell receptor (TCR) diversity, tumor-infiltrating lymphocytes (TILs), gene expression profiling (GEP), and a favorable gut microbiome. This review shows that biomarkers for ICIs in melanoma patients are widely studied, but heterogeneity between studies is high, average sample sizes are low, and validation is often lacking. Future studies are needed to further investigate the predictive utility of some promising candidate biomarkers.
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Exploration of Redox-Related Molecular Patterns and the Redox Score for Prostate Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4548594. [PMID: 34804366 PMCID: PMC8601839 DOI: 10.1155/2021/4548594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/07/2021] [Accepted: 10/22/2021] [Indexed: 12/21/2022]
Abstract
Redox homeostasis is the key to cell survival, and its imbalance can promote the occurrence and progression of tumors. However, it remains unclear whether these redox-related genes (RRGs) have potential roles in the tumor microenvironment, immunotherapy, and drug sensitivity. Here, we performed a systematic and comprehensive analysis of 489 prostate cancer (PC) samples from The Cancer Genome Atlas database and 214 PC samples from 8 datasets in the Gene Expression Omnibus database to determine redox modification patterns and the redox scoring system for PC. We identified two modification patterns (Redox_A and Redox_B) in PC using unsupervised consensus clustering based on 1410 differential expression RRGs. We then compared the prognostic value, tumor microenvironment characteristics, immune cell infiltration, and molecular characteristics of the two patterns. The Redox_A pattern was significantly enriched in the carcinogenic activation signaling pathways and had a poor prognosis, while the Redox_B pattern was mainly enriched in a variety of metabolic and redox pathways and had a good prognosis. Next, redox-related characteristic genes were extracted from these two patterns, and a scoring system (Redox_score) was constructed to evaluate PC patients. Further analysis indicated that lower Redox_score patients had a better prognosis, while higher Redox_score patients had a higher tumor mutation burden, driver gene mutation rate, and immune checkpoint inhibitor gene expression. We also found that higher Redox_score patients were more responsive to anti-PD-1 immunotherapy. Moreover, Redox_score was determined to be significantly correlated with anticancer drug sensitivity and resistance. Our study provides a comprehensive analysis of redox modifications in PC and reveals new patterns of PC based on RRGs, which will provide insights into the complex mechanisms of PC and develop more effective individualized therapeutic strategies.
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Collagen Family Genes Associated with Risk of Recurrence after Radiation Therapy for Vestibular Schwannoma and Pan-Cancer Analysis. DISEASE MARKERS 2021; 2021:7897994. [PMID: 34691289 PMCID: PMC8528601 DOI: 10.1155/2021/7897994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Background The safety of radiotherapy techniques in the treatment of vestibular schwannoma (VS) shows a high rate of tumor control with few side effects. Neuropeptide Y (NPY) may have a potential relevance to the recurrence of VS. Further research is still needed on the key genes that determine the sensitivity of VS to radiation therapy. Materials and Methods Transcriptional microarray data and clinical information data from VS patients were downloaded from GSE141801, and vascular-related genes associated with recurrence after radiation therapy for VS were obtained by combining information from MSigDB. Logistics regression was applied to construct a column line graph prediction model for recurrence status after radiation therapy. Pan-cancer analysis was also performed to investigate the cooccurrence of these genes in tumorigenesis. Results We identified eight VS recurrence-related genes from the GSE141801 dataset. All of these genes were highly expressed in the VS recurrence samples. Four collagen family genes (COL5A1, COL3A1, COL4A1, and COL15A1) were further screened, and a model was constructed to predict the risk of recurrence of VS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these four collagen family genes play important roles in a variety of biological functions and cellular pathways. Pan-cancer analysis further revealed that the expression of these genes was significantly heterogeneous across immune phenotypes and significantly associated with immune infiltration. Finally, Neuropeptide Y (NPY) was found to be significantly and negatively correlated with the expression of COL5A1, COL3A1, and COL4A1. Conclusions Four collagen family genes have been identified as possible predictors of recurrence after radiation therapy for VS. Pan-cancer analysis reveals potential associations between the pathogenesis of VS and other tumorigenic factors. The relevance of NPY to VS was also revealed for the first time.
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He H, Qiao B, Guo S, Cui H, Li N, Liu H, Qin J, He J, Yang X, Xue W, Wang Y. Induction of T helper 17 cell response by interleukin-7 in patients with primary cutaneous melanoma. Melanoma Res 2021; 31:328-337. [PMID: 34054059 DOI: 10.1097/cmr.0000000000000751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Interleukin (IL)-7 plays a vital role in proliferation and activation of T cells, however, its signaling through CD127 is impaired in T cells in cancers and chronic infections. The mechanisms underlying T helper 17 (Th17) cell responses by IL-7 in melanoma remain not fully understood. The aim of this study was to assess the effect of IL-7 signaling on Th17 responses in patients with primary cutaneous melanoma. Healthy and primary cutaneous melanoma donors were selected for this study of Th17 cell function. IL-17+CD4+ Th17 cells and CD127 expression on Th17 cells were determined by flow cytometry. Cytokine level was measured by ELISA. Peripheral and tissue-infiltrating CD4+ T cells were isolated using magnetic beads, and then stimulated with IL-7 and/or signal transducer and activator of transcription 5 inhibitor. Activated signaling molecules were analyzed by flow cytometry. Peripheral and tumor-infiltrating Th17 cells percentage was decreased, while peripheral IL-7 level was also reduced in melanoma patients. There was no significant difference of CD127 expression on Th17 cells between melanoma patients and controls. Antiapoptotic protein Bcl-2 was downregulated, whereas proapoptotic protein-activated caspase-3 was upregulated in peripheral and tissue-infiltrating Th17 cells in melanoma patients. Higher concentration of IL-7 (10 ng/mL), but not lower IL-7 concentration (1 ng/mL), promoted Bcl-2 expression and decreased caspase-3 expression in Th17 cells in melanoma patients. Inhibition of signal transducer and activator of transcription 5 resulted in the downregulation of Bcl-2 while upregulation of caspase-3 in Th17 cells. The present data suggested that reduced IL-7 responsiveness might be insufficient for Th17 activation in patients with primary cutaneous melanoma.
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Affiliation(s)
| | | | | | | | - Ning Li
- Department of Pathology, The First Hospital of Shanxi Medical University
| | | | - Junxia Qin
- Department of Dermatology, The Affiliated Shanxi Provincial People's Hospital of Shanxi Medical University
| | - Jinghong He
- Department of Radiology, The First Hospital of Shanxi Medical University
| | | | | | - Yanzhen Wang
- Department of Rehabilitation, Children's Hospital of Shanxi Province, Taiyuan, Shanxi Province, China
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Jiang M, Ren L, Chen Y, Wang H, Wu H, Cheng S, Li G, Yu S. Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer. Front Mol Biosci 2021; 8:613359. [PMID: 34026819 PMCID: PMC8138130 DOI: 10.3389/fmolb.2021.613359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/22/2021] [Indexed: 01/19/2023] Open
Abstract
Accumulating evidence indicates that hypoxia is highly associated with bladder cancer genesis, progression, and immune microenvironment. Nevertheless, few studies have identified the role of hypoxia-related genes as a prognostic signature in bladder cancer. This study aimed to establish a hypoxia-related signature with high accuracy for prognosis and immune microenvironment prediction in bladder cancer. We obtained expression profiles and clinical information from Gene Expression Omnibus and The Cancer Genome Atlas. Then the univariate Cox regression, random survival forest algorithm, and multivariate Cox regression analysis were conducted to identify the core genes and four hypoxia-related genes (ANXA2, GALK1, COL5A1, and HS3ST1) were selected to construct the signature. Kaplan-Meier survival analysis demonstrated that patients with a low-risk score had a higher disease-specific survival rate (p < 0.0001). The areas under the curve of the signature were 0.829 at 1 year, 0.869 at 3 years, and 0.848 at 5 years, respectively. Additionally, we found this hypoxia-related signature was highly correlated with tumor immune microenvironment and had the potential to predict the efficacy of immunotherapy. In summary, our study developed a hypoxia-related signature, which had high accuracy for prognosis prediction and the potential to guide the immunotherapy for bladder cancer patients.
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Affiliation(s)
- Minxiao Jiang
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liangliang Ren
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanlei Chen
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huan Wang
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyang Wu
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Cheng
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gonghui Li
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shicheng Yu
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Thinking Small: Small Molecules as Potential Synergistic Adjuncts to Checkpoint Inhibition in Melanoma. Int J Mol Sci 2021; 22:ijms22063228. [PMID: 33810078 PMCID: PMC8005112 DOI: 10.3390/ijms22063228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Metastatic melanoma remains the deadliest form of skin cancer. Immune checkpoint inhibition (ICI) immunotherapy has defined a new age in melanoma treatment, but responses remain inconsistent and some patients develop treatment resistance. The myriad of newly developed small molecular (SM) inhibitors of specific effector targets now affords a plethora of opportunities to increase therapeutic responses, even in resistant melanoma. In this review, we will discuss the multitude of SM classes currently under investigation, current and prospective clinical combinations of ICI and SM therapies, and their potential for synergism in melanoma eradication based on established mechanisms of immunotherapy resistance.
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Shahmoradi M, Rezvani Z. Functional Prediction of Long Noncoding RNAs in Cutaneous Melanoma Using a Systems Biology Approach. Bioinform Biol Insights 2021; 15:1177932220988508. [PMID: 33613027 PMCID: PMC7868446 DOI: 10.1177/1177932220988508] [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: 09/08/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
Cutaneous melanoma is the most aggressive type of skin cancer which its incidence has significantly increased in recent years worldwide. Thus, more investigations are required to identify the underlying mechanisms of melanoma malignant transformation and metastasis. In this context, long noncoding RNAs (lncRNAs) are a new type of noncoding transcripts that their dysregulations are associated with almost all cancers including melanoma. However, the precise functional roles of most of the significantly altered lncRNAs in melanoma have not yet been fully inspected. In this study, a comprehensive list of lncRNAs was interrogated across cutaneous melanoma samples to identify the significantly altered/dysregulated lncRNAs. To this end, lncRNAs were filtered in several steps and the selected lncRNAs projected to a bioinformatic and systems biology analysis using several publicly available databases and tools such as GEPIA and cBioPortal. According to our results, 30 lncRNAs were notably altered/dysregulated in cutaneous melanoma most of which were co-expressed with each other. Also, co-expression/alteration and differential expression analyses led to the selection of 12 out of these 30 lncRNAs as cutaneous melanoma key lncRNAs. Furthermore, functional demonstrated that these 12 lncRNAs might be involved in melanoma-relevant biological processes and pathways. In addition, the end result of our analyses demonstrated that these lncRNAs are associated with the clinicopathological features of melanoma patients. These 12 lncRNAs need to be further investigated in future studies to characterize their exact roles in melanoma development and to identify their potential for being used as drug targets and/or biomarkers for cutaneous melanoma.
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Affiliation(s)
- Mozhdeh Shahmoradi
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Zahra Rezvani
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
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Advantages of targeting the tumor immune microenvironment over blocking immune checkpoint in cancer immunotherapy. Signal Transduct Target Ther 2021; 6:72. [PMID: 33608497 PMCID: PMC7896069 DOI: 10.1038/s41392-020-00449-4] [Citation(s) in RCA: 217] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/31/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
Despite great success in cancer immunotherapy, immune checkpoint-targeting drugs are not the most popular weapon in the armory of cancer therapy. Accumulating evidence suggests that the tumor immune microenvironment plays a critical role in anti-cancer immunity, which may result in immune checkpoint blockade therapy being ineffective, in addition to other novel immunotherapies in cancer patients. In the present review, we discuss the deficiencies of current cancer immunotherapies. More importantly, we highlight the critical role of tumor immune microenvironment regulators in tumor immune surveillance, immunological evasion, and the potential for their further translation into clinical practice. Based on their general targetability in clinical therapy, we believe that tumor immune microenvironment regulators are promising cancer immunotherapeutic targets. Targeting the tumor immune microenvironment, alone or in combination with immune checkpoint-targeting drugs, might benefit cancer patients in the future.
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Liu J, Lu J, Li W. A Comprehensive Prognostic and Immunological Analysis of a New Three-Gene Signature in Hepatocellular Carcinoma. Stem Cells Int 2021; 2021:5546032. [PMID: 34188686 PMCID: PMC8192212 DOI: 10.1155/2021/5546032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/07/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
There are few reports on the role of genes associated with the mRNA expression-based stemness index (mRNAsi) in the prognosis and immune regulation of hepatocellular carcinoma (HCC). This study is aimed at analyzing the expression profile and prognostic significance of a new mRNAsi-based three-gene signature in HCC. This three-gene signature was identified by analyzing mRNAsi data from the Cancer Genome Atlas (TCGA) HCC dataset. The prognostic value of the risk score based on the three-gene signature was evaluated by Cox regression and Kaplan-Meier analysis and then verified in the International Cancer Genome Consortium (ICGC) database. Meanwhile, the correlations between the risk score and immune cell infiltration patterns, microsatellite instability (MSI), tumor mutation burden (TMB), immune checkpoint molecules, hypoxia-related genes, immunotherapy response, and compounds targeting the gene signature were explored, respectively. The results showed that compared with normal liver tissues, the mRNAsi score of HCC tissues was significantly increased. PTDSS2, MRPL9, and SOCS were the genes most related to mRNAsi in HCC tissues. Survival analysis results suggested the risk score based on the three-gene signature was an independent predictor of the prognosis for patients with HCC. The nomogram combining the risk score and pathological stage showed a good predictive ability for the overall survival of patients with HCC patients. Meanwhile, the risk score was significantly related to immune cell infiltration patterns, MSI, TMB, several immune checkpoint molecules, and hypoxia-related genes. In addition, the risk score was associated with the immunotherapy response, and fifteen potential therapeutic drugs targeting the three-gene signature were identified. Therefore, we propose to use this three-gene signature including PTDSS2, MRPL9, and SOCS as a potential prognostic biomarker for HCC.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jianjun Lu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510080, China
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
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Chong W, Shang L, Liu J, Fang Z, Du F, Wu H, Liu Y, Wang Z, Chen Y, Jia S, Chen L, Li L, Chen H. m 6A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer. Am J Cancer Res 2021; 11:2201-2217. [PMID: 33500720 PMCID: PMC7797678 DOI: 10.7150/thno.52717] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/21/2020] [Indexed: 12/28/2022] Open
Abstract
Recent studies have highlighted the biological significance of RNA N6-methyladenosine (m6A) modification in tumorigenicity and progression. However, it remains unclear whether m6A modifications also have potential roles in immune regulation and tumor microenvironment (TME) formation. Methods: In this study, we curated 23 m6A regulators and performed consensus molecular subtyping with NMF algorithm to determine m6A modification patterns and the m6A-related gene signature in colon cancer (CC). The ssGSEA and CIBERSORT algorithms were employed to quantify the relative infiltration levels of various immune cell subsets. An PCA algorithm based m6Sig scoring scheme was used to evaluate the m6A modification patterns of individual tumors with an immune response. Results: Three distinct m6A modification patterns were identified among 1307 CC samples, which were also associated with different clinical outcomes and biological pathways. The TME characterization revealed that the identified m6A patterns were highly consistent with three known immune profiles: immune-inflamed, immune-excluded, and immune-desert, respectively. Based on the m6Sig score, which was extracted from the m6A-related signature genes, CC patients can be divided into high and low score subgroups. Patients with lower m6Sig score was characterized by prolonged survival time and enhanced immune infiltration. Further analysis indicated that lower m6Sig score also correlated with greater tumor mutation loads, PD-L1 expression, and higher mutation rates in SMGs (e.g., PIK3CA and SMAD4). In addition, patients with lower m6Sig scores showed a better immune responses and durable clinical benefits in three independent immunotherapy cohorts. Conclusions: This study highlights that m6A modification is significantly associated with TME diversity and complexity. Quantitatively evaluating the m6A modification patterns of individual tumors will strengthen our understanding of TME characteristics and promote more effective immunotherapy strategies.
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Chong W, Wang Z, Shang L, Jia S, Liu J, Fang Z, Du F, Wu H, Liu Y, Chen Y, Chen H. Association of clock-like mutational signature with immune checkpoint inhibitor outcome in patients with melanoma and NSCLC. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:89-100. [PMID: 33335795 PMCID: PMC7723771 DOI: 10.1016/j.omtn.2020.10.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Immune checkpoint inhibitor (ICI) therapy has achieved remarkable clinical benefit in melanoma and non-small cell lung cancer (NSCLC). Tumor mutational signatures are the fingerprints of endogenous and exogenous factors that have acted throughout tumorigenesis and heterogeneity; however, their association with immune response in ICI-treated samples remains unclear. Here, we leveraged whole-exome sequencing (WES)-based mutational profiles combined with clinicopathologic characteristics from melanoma and NSCLC datasets to examine whether tumor genomic features contribute to clinical benefit of ICI treatment. Mutational data acquired from targeted next-generation sequencing (NGS) assays (MSK-IMPACT panels) were also employed for further corroboration. A mutational signature (known as age-related clock-like processing) characterized by enrichment of C>T mutations at NpCpG trinucleotides were identified to be associated with a worse prognosis and lower tumor mutation load (TML) in both WES and targeted NGS immunotherapy cohorts. We also analyzed gene transcriptomic profiles and identified immune regulation-related gene pathways that were significantly altered in samples with different clock-like signature grouping. Leucocyte subset analysis further revealed that clock-like signature was associated with the reduction of cytotoxic cell infiltration and elevation of regulatory T cells. Overall, our work re-annotated that the age-related clock-like signature was associated with worse prognosis and lower immune activity, offering opportunities to stratify patients into optimal immunotherapy plans based on genomic subtyping.
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Affiliation(s)
- Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Zhe Wang
- Tianjin Sino-US Diagnostics Co., Ltd, Tianjin 300060, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Shengtao Jia
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Jin Liu
- Department of Gastroenterology, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Zhen Fang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Fengying Du
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Hao Wu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Yang Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong 250021, China
| | - Yang Chen
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong 250021, China
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Chen Y, Li ZY, Zhou GQ, Sun Y. An Immune-Related Gene Prognostic Index for Head and Neck Squamous Cell Carcinoma. Clin Cancer Res 2020; 27:330-341. [PMID: 33097495 DOI: 10.1158/1078-0432.ccr-20-2166] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/07/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To construct an immune-related gene prognostic index (IRGPI) for head and neck squamous cell carcinoma (HNSCC) and clarify the molecular and immune characteristics and the benefit of immune checkpoint inhibitor (ICI) therapy in IRGPI-defined subgroups of HNSCC. EXPERIMENTAL DESIGN On the basis of The Cancer Genome Atlas HNSCC immune dataset (n = 546), 22 immune-related hub genes were identified by weighted gene coexpression network analysis. Three genes were identified to construct an IRGPI by using the Cox regression method and validated with the Gene Expression Omnibus (GEO) dataset (n = 270). Afterward, the molecular and immune characteristics and the benefit of ICI therapy in IRGPI-defined subgroups were analyzed. RESULTS The IRGPI was constructed on the basis of SFRP4, CPXM1, and COL5A1 genes. IRGPI-high patients had a better overall survival than IRGPI-low patients, consistent with the results in the GEO cohort. The comprehensive results showed that a high IRGPI score was correlated with DNA repair-related pathways; low TP53 mutation rate; high infiltration of CD8 T cells, CD4 T cells, and M1 macrophages; active immunity and less aggressive phenotypes; and more benefit from ICI therapy. In contrast, a low IRGPI score was associated with cancer and metastasis-related pathways; high TP53 and PIK3CA mutation rate; high infiltration of B cells, M0 macrophages, and M2 macrophages; suppressive immunity and more aggressive phenotypes; and less benefit from ICI therapy. CONCLUSIONS IRGPI is a promising biomarker to distinguish the prognosis, the molecular and immune characteristics, and the immune benefit from ICI therapy in HNSCC.
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Affiliation(s)
- Yue Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - Zhi-Yong Li
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Guan-Qun Zhou
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China.
| | - Ying Sun
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China.
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36
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Li X, Wen D, Li X, Yao C, Chong W, Chen H. Identification of an Immune Signature Predicting Prognosis Risk and Lymphocyte Infiltration in Colon Cancer. Front Immunol 2020; 11:1678. [PMID: 33013820 PMCID: PMC7497441 DOI: 10.3389/fimmu.2020.01678] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/23/2020] [Indexed: 12/28/2022] Open
Abstract
Increasing studies have highlighted the effects of the tumor immune micro-environment (TIM) on colon cancer (CC) tumorigenesis, prognosis, and metastasis. However, there is no reliable molecular marker that can effectively estimate the immune infiltration and predict the CC relapse risk. Here, we leveraged the gene expression profile and clinical characteristics from 1430 samples, including four gene expression omnibus database (GEO) databases and the cancer genome atlas (TCGA) database, to construct an immune risk signature that could be used as a predictor of survival outcome and immune activity. A risk model consisting of 10 immune-related genes were screened out in the Lasso-Cox model and were then aggregated to generate the immune risk signature based on the regression coefficients. The signature demonstrated robust prognostic ability in discovery and validation datasets, and this association remained significant in the multivariate analysis after controlling for age, gender, clinical stage, or microsatellite instability status. Leukocyte subpopulation analysis indicated that the low-risk signature was enriched with cytotoxic cells (activated CD4/CD8+ T cell and NK cell) and depleted of myeloid-derived suppressor cells (MDSC) and regulatory T cells. Further analysis indicated patients with a low-risk signature harbored higher tumor mutation loads and lower mutational frequencies in significantly mutated genes of APC and FBXW7. Together, our constructed signature could predict prognosis and represent the TIM of CC, which promotes individualized treatment and provides a promising novel molecular marker for immunotherapy.
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Affiliation(s)
- Xinyu Li
- Department of Gastrointestinal Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Department of General, Visceral, and Transplant Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Dacheng Wen
- Department of Gastrointestinal Nutrition and Hernia Surgery, The 2nd Hospital of Jilin University, Changchun, China
| | - Xiaokang Li
- Department of General, Visceral, and Transplant Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany.,Department of Dermatology, Jinan Central Hospital, Cheelo College of Medicine, Shandong University, Jinan, China
| | - Chunli Yao
- Department of Dermatology, The 2nd Hospital of Jilin University, Changchun, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
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Aquaporin 1 promotes sensitivity of anthracycline chemotherapy in breast cancer by inhibiting β-catenin degradation to enhance TopoIIα activity. Cell Death Differ 2020; 28:382-400. [PMID: 32814878 PMCID: PMC7852611 DOI: 10.1038/s41418-020-00607-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Anthracyclines are a class of conventional and commonly used frontline chemotherapy drugs to treat breast cancer. However, the anthracycline-based regimens can only reduce breast cancer mortality by 20–30%. Furthermore, there is no appropriate biomarker for predicting responses to this kind of chemotherapy currently. Here we report our findings that may fill this gap by showing the AQP1 (Aquaporin1) protein as a potential response predictor in the anthracycline chemotherapy. We showed that breast cancer patients with a high level of AQP1 expression who underwent the anthracycline treatment had a better clinical outcome relative to those with a low level of AQP1 expression. In the exploration of the underlying mechanisms, we found that the AQP1 and glycogen synthase kinase-3β (GSK3β) competitively interacted with the 12 armadillo repeats of β-catenin, followed by the inhibition of the β-catenin degradation that led to β-catenin’s accumulation in the cytoplasm and nuclear translocation. The nuclear β-catenin interacted with TopoIIα and enhanced TopoIIα’s activity, which resulted in a high sensitivity of breast cancer cells to anthracyclines. We also found, the miR-320a-3p can attenuate the anthracycline’s chemosensitivity by inhibiting the AQP1 expression. Taken together, our findings suggest the efficacy of AQP1 as a response predictor in the anthracycline chemotherapy. The application of our study includes, but is not limited to, facilitating screening of the most appropriate breast cancer patients (who have a high AQP1 expression) for better anthracycline chemotherapy and improved prognosis purposes.
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Zhang Q, Wang J, Liu M, Zhu Q, Li Q, Xie C, Han C, Wang Y, Gao M, Liu J. Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma. Aging (Albany NY) 2020; 12:13502-13517. [PMID: 32644941 PMCID: PMC7377834 DOI: 10.18632/aging.103454] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022]
Abstract
In this study, we constructed a new survival model using mRNA expression-based stemness index (mRNAsi) for prognostic prediction in hepatocellular carcinoma (HCC). Weighted correlation network analysis (WGCNA) of HCC transcriptome data (374 HCC and 50 normal liver tissue samples) from the TCGA database revealed 7498 differentially expressed genes (DEGs) that clustered into seven gene modules. LASSO regression analysis of the top two gene modules identified ANGPT2, EMCN, GLDN, USHBP1 and ZNF532 as the top five mRNAsi-related genes. We constructed our survival model with these five genes and tested its performance using 243 HCC and 202 normal liver samples from the ICGC database. Kaplan-Meier survival curve and receive operating characteristic curve analyses showed that the survival model accurately predicted the prognosis and survival of high- and low-risk HCC patients with high sensitivity and specificity. The expression of these five genes was significantly higher in the HCC tissues from the TCGA, ICGC, and GEO datasets (GSE25097 and GSE14520) than in normal liver tissues. These findings demonstrate that a new survival model derived from five strongly correlating mRNAsi-related genes provides highly accurate prognoses for HCC patients.
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Affiliation(s)
- Qiujing Zhang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Jia Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.,Department of Oncology, Zibo Maternal and Child Health Hospital, Zibo 255000, Shandong, China
| | - Menghan Liu
- Basic Medicine College, Shandong First Medical University, Taian 271016, Shandong, China
| | - Qingqing Zhu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Qiang Li
- Department of Oncology, Mengyin County Hospital, Linyi 276299, Shandong, China
| | - Chao Xie
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Congcong Han
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yali Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Min Gao
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
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Jin J, Zhao Q. Emerging role of mTOR in tumor immune contexture: Impact on chemokine-related immune cells migration. Theranostics 2020; 10:6231-6244. [PMID: 32483450 PMCID: PMC7255024 DOI: 10.7150/thno.45219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/17/2020] [Indexed: 12/27/2022] Open
Abstract
During the last few decades, cell-based anti-tumor immunotherapy emerged and it has provided us with a large amount of knowledge. Upon chemokines recognition, immune cells undergo rapid trafficking and activation in disease milieu, with immune cells chemotaxis being accompanied by activation of diverse intercellular signal transduction pathways. The outcome of chemokines-mediated immune cells chemotaxis interacts with the cue of mammalian target of rapamycin (mTOR) in the tumor microenvironment (TME). Indeed, the mTOR cascade in immune cells involves migration and infiltration. In this review, we summarize the available mTOR-related chemokines, as well as the characterized upstream regulators and downstream targets in immune cells chemotaxis and assign potential underlying mechanisms in each evaluated chemokine. Specifically, we focus on the involvement of mTOR in chemokine-mediated immune related cells in the balance between tumor immunity and malignancy.
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Affiliation(s)
- Jing Jin
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qijie Zhao
- Laboratory of Molecular Pharmacology, Southwest Medical University, Luzhou, 646000, Sichuan, PR China
- Department of Pathophysiology, College of Basic Medical Science, Southwest Medical University, Luzhou, 646000, Sichuan, PR China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, PR China
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