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Ma B, Ren C, Yin Y, Zhao S, Li J, Yang H. Immune cell infiltration and prognostic index in cervical cancer: insights from metabolism-related differential genes. Front Immunol 2024; 15:1411132. [PMID: 38840928 PMCID: PMC11150690 DOI: 10.3389/fimmu.2024.1411132] [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: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
Background Cervical cancer remains a significant gynecologic malignancy in both China and the United States, posing a substantial threat to women's lives and health due to its high morbidity and mortality rates. Altered energy metabolism and dysregulated mitochondrial function play crucial roles in the development, growth, metastasis, and recurrence of malignant tumors. In this study, we aimed to predict prognosis and assess efficacy of anti-tumor therapy in cervical cancer patients based on differential genes associated with mitochondrial metabolism. Methods Transcriptomic data and clinical profiles of cervical cancer patients were retrieved from the TCGA and GEO databases. Differential gene-related cellular pathways were identified through GO, KEGG, and GSEA analyses. Prognostic indices were constructed using LASSO regression analysis. Immune cell infiltration was assessed using CIBERSORT and ssGSEA, and the correlation between immune checkpoint inhibitor genes and differential genes was examined. Tumor mutation load (TMB) and its association with prognostic indices were analyzed using nucleotide variant data from the TCGA database. Patient response to immunotherapy and sensitivity to antitumor drugs were determined using the TIDE algorithm and the oncoPredic algorithm, respectively. Results A prognostic index based on metabolism-related differential genes was developed to predict the clinical outcome of cervical cancer patients, enabling their classification into two distinct subtypes. The prognostic index emerged as an independent risk factor for unfavorable prognosis. The high-index group exhibited a significantly worse overall prognosis, along with elevated tumor mutation burden (TMB), increased immune cell infiltration, and lower TIDE scores, indicating a potential benefit from immunotherapy. Conversely, the low-index group demonstrated increased sensitivity to metabolism-related antitumor agents, specifically multikinase inhibitors. Conclusion The aim of this study was to develop a prognostic index based on differential genes associated with mitochondrial metabolism, which could be used to predict cervical cancer patients' prognoses. When combined with TIDE and TMB analyses, this prognostic index offers insights into the immune cell infiltration landscape, as well as the potential efficacy of immunotherapy and targeted therapy. Our analysis suggests that the Iron-Sulfur Cluster Assembly Enzyme (ISCU) gene holds promise as a biomarker for cervical cancer immunotherapy.
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Affiliation(s)
| | | | | | | | - Jia Li
- Department of Obstetrics and Gynecology, Xijing Hospital, Air Force Medical University, Shaanxi, Xi’an, China
| | - Hong Yang
- Department of Obstetrics and Gynecology, Xijing Hospital, Air Force Medical University, Shaanxi, Xi’an, China
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Awadasseid A, Wang R, Sun S, Zhang F, Wu Y, Zhang W. Small molecule and PROTAC molecule experiments in vitro and in vivo, focusing on mouse PD-L1 and human PD-L1 differences as targets. Biomed Pharmacother 2024; 172:116257. [PMID: 38350367 DOI: 10.1016/j.biopha.2024.116257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/20/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
In recent years, several monoclonal antibodies (mAbs) targeting PD-L1 have been licensed by the FDA for use in the treatment of cancer, demonstrating the effectiveness of blocking immune checkpoints, particularly the PD-1/PD-L1 pathway. Although mAb-based therapies have made great strides, they still have their limitations, and new small-molecule or PROTAC-molecule inhibitors that can block the PD-1/PD-L1 axis are desperately needed. Therefore, it is crucial to translate initial in vitro discoveries into appropriate in vivo animal models when creating PD-L1-blocking therapies. Due to their widespread availability and low experimental expenses, classical immunocompetent mice are appealing for research purposes. However, it is yet unclear whether the mouse (m) PD-L1 interaction with human (h) PD-1 in vivo would produce a functional immunological checkpoint. In this review, we summarize the in vitro and in vivo experimental studies of small molecules and PROTAC molecules, particularly the distinctions between mPD-L1 as a target and hPD-L1 as a target.
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Affiliation(s)
- Annoor Awadasseid
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Moganshan Institute ZJUT, Deqing 313202, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China; Department of Biochemistry & Food Sciences, University of Kordofan, El-Obeid 51111, Sudan
| | - Rui Wang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shishi Sun
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Feng Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China.
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China.
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Zhu J, Wang Y, Chang WY, Malewska A, Napolitano F, Gahan JC, Unni N, Zhao M, Yuan R, Wu F, Yue L, Guo L, Zhao Z, Chen DZ, Hannan R, Zhang S, Xiao G, Mu P, Hanker AB, Strand D, Arteaga CL, Desai N, Wang X, Xie Y, Wang T. Mapping Cellular Interactions from Spatially Resolved Transcriptomics Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558298. [PMID: 37781617 PMCID: PMC10541142 DOI: 10.1101/2023.09.18.558298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Cell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently, through the introduction of spatially resolved transcriptomics technologies (SRTs), especially those that achieve single cell resolution. However, significant challenges remain to analyze such highly complex data properly. Here, we introduce a Bayesian multi-instance learning framework, spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight spacia's power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates, and most importantly the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of spacia for all three commercialized single cell resolution ST technologies: MERSCOPE/Vizgen, CosMx/Nanostring, and Xenium/10X. Spacia unveiled how endothelial cells, fibroblasts and B cells in the tumor microenvironment contribute to Epithelial-Mesenchymal Transition and lineage plasticity in prostate cancer cells. We deployed spacia in a set of pan-cancer datasets and showed that B cells also participate in PDL1/PD1 signaling in tumors. We demonstrated that a CD8+ T cell/PDL1 effectiveness signature derived from spacia analyses is associated with patient survival and response to immune checkpoint inhibitor treatments in 3,354 patients. We revealed differential spatial interaction patterns between γδ T cells and liver hepatocytes in healthy and cancerous contexts. Overall, spacia represents a notable step in advancing quantitative theories of cellular communications.
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Affiliation(s)
- James Zhu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, OH, 45221, USA
| | - Woo Yong Chang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Alicia Malewska
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Fabiana Napolitano
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey C. Gahan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nisha Unni
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Min Zhao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rongqing Yuan
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Fangjiang Wu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Yue
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zhuo Zhao
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Danny Z. Chen
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Raquibul Hannan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Siyuan Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ariella B. Hanker
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Douglas Strand
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carlos L. Arteaga
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Neil Desai
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xinlei Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA
- Center for Data Science Research and Education, College of Science, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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Parvez A, Choudhary F, Mudgal P, Khan R, Qureshi KA, Farooqi H, Aspatwar A. PD-1 and PD-L1: architects of immune symphony and immunotherapy breakthroughs in cancer treatment. Front Immunol 2023; 14:1296341. [PMID: 38106415 PMCID: PMC10722272 DOI: 10.3389/fimmu.2023.1296341] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
PD-1 (Programmed Cell Death Protein-1) and PD-L1 (Programmed Cell Death Ligand-1) play a crucial role in regulating the immune system and preventing autoimmunity. Cancer cells can manipulate this system, allowing them to escape immune detection and promote tumor growth. Therapies targeting the PD-1/PD-L1 pathway have transformed cancer treatment and have demonstrated significant effectiveness against various cancer types. This study delves into the structure and signaling dynamics of PD-1 and its ligands PD-L1/PD-L2, the diverse PD-1/PD-L1 inhibitors and their efficacy, and the resistance observed in some patients. Furthermore, this study explored the challenges associated with the PD-1/PD-L1 inhibitor treatment approach. Recent advancements in the combination of immunotherapy with chemotherapy, radiation, and surgical procedures to enhance patient outcomes have also been highlighted. Overall, this study offers an in-depth overview of the significance of PD-1/PD-L1 in cancer immunotherapy and its future implications in oncology.
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Affiliation(s)
- Adil Parvez
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia, Hamdard, New Delhi, India
| | - Furqan Choudhary
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia, Hamdard, New Delhi, India
| | - Priyal Mudgal
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia, Hamdard, New Delhi, India
| | - Rahila Khan
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia, Hamdard, New Delhi, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, Saudi Arabia
| | - Humaira Farooqi
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia, Hamdard, New Delhi, India
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Chen M, Bie L, Ying J. Cancer cell-intrinsic PD-1: Its role in malignant progression and immunotherapy. Biomed Pharmacother 2023; 167:115514. [PMID: 37716115 DOI: 10.1016/j.biopha.2023.115514] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Programmed cell death protein-1 (PD-1), also called CD279, is coded by the PDCD1 gene and is constitutively expressed on the surface of immune cells. As a receptor and immune checkpoint, PD-1 can bind to programmed death ligand-1/programmed death ligand-2 (PD-L1/PD-L2) in tumor cells, leading to tumor immune evasion. Anti-PD-1 and anti-PD-L1 are important components in tumor immune therapy. PD-1 is also expressed as an intrinsic variant (iPD-1) in cancer cells where it plays important roles in malignant progression as proposed by recent studies. However, iPD-1 has received much less attention compared to PD-1 expressed on immune cells although there is an unmet medical need for fully elucidating the mechanisms of actions to achieve the best response in tumor immunotherapy. iPD-1 suppresses tumorigenesis in non-small cell lung cancer (NSCLC) and colon cancer, whereas it promotes tumorigenesis in melanoma, hepatocellular carcinoma (HCC), pancreatic ductal adenocarcinoma (PDAC), thyroid cancer (TC), glioblastoma (GBM), and triple-negative breast cancer (TNBC). In this review, we focus on the role of iPD-1 in tumorigenesis and development and its molecular mechanisms. We also deeply discuss nivolumab-based combined therapy in common tumor therapy. iPD-1 may explain the different therapeutic effects of anti-PD-1 treatment and provide critical information for use in combined anti-tumor approaches.
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Affiliation(s)
- Muhua Chen
- Department of Hepato-Pancreato-Biliary & Gastric Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Lei Bie
- Department of Thoracic Surgery, Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jieer Ying
- Department of Hepato-Pancreato-Biliary & Gastric Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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